Subject: "protein secondary structure" / Subject: amino acid sequences

1. Inactivation mechanisms of electron beam irradiation on Listeria innocua through the integrity of cell membrane, genomic DNA and protein structures

Author:: Shi, Feifei; Zhao, Hongwei; Wang, Li; Cui, Xiaorui; Guo, Weiling; Zhang, Weidong; Song, Hongbo; Li, Shurong
Source:: International journal of food science & technology 2019 v.54 no.5 pp. 1804-1815
ISSN:: 0950-5423
Subject:: protein secondary structure, etc ; DNA; Listeria innocua; amino acid sequences; cell membranes; electron microscopy; food preservation; genome; irradiation; membrane permeability; physiological state; staining; Show all 12 Subjects
Abstract:: ... As a non‐thermal sterilisation technology, electron beam irradiation (EBI) has attracted great interest for microbial inactivation in food preservation. This study aims to investigate the effects of EBI on membrane permeability, physiological status, morphological structure, genome integrity and protein structures of Listeria innocua irradiated at doses of 0.75, 1.50, 2.25, 3.00, 3.75 and 5.00 kGy ...
DOI:: 10.1111/ijfs.14081
: http://dx.doi.org/10.1111/ijfs.14081

2. Transition of Metastable Cross-α Crystals into Cross-β Fibrils by β-Turn Flipping

Author:: Mondal, Sudipta; Jacoby, Guy; Sawaya, Michael R.; Arnon, Zohar A.; Adler-Abramovich, Lihi; Rehak, Pavel; Vuković, Lela; Shimon, Linda J. W.; Král, Petr; Beck, Roy; Gazit, Ehud
Source:: Journal of the American Chemical Society 2018 v.141 no.1 pp. 363-369
ISSN:: 1520-5126
Subject:: protein secondary structure, etc ; amino acid sequences; amyloid; crystals; energy; peptides; thermodynamics; Show all 7 Subjects
Abstract:: ... The ensemble of native, folded state was once considered to represent the global energy minimum of a given protein sequence. More recently, the discovery of the cross-β amyloid state revealed that deeper energy minima exist, often associated with pathogenic, fibrillar deposits, when the concentration of proteins reaches a critical value. Fortunately, a sizable energy barrier impedes the conversion ...
DOI:: 10.1021/jacs.8b10289
: http://dx.doi.org/10.1021/jacs.8b10289

3. PATSIM: Prediction and analysis of protein sequences using hybrid Knuth-Morris Pratt (KMP) and Boyer-Moore (BM) algorithm

Author:: Manikandan, P.; Ramyachitra, D.
Source:: Gene 2018 v.657 pp. 50-59
ISSN:: 0378-1119
Subject:: protein secondary structure, etc ; algorithms; amino acid sequences; amino acids; databases; genome; genomics; hydrophilicity; hydrophobicity; prediction; proteins; Show all 11 Subjects
Abstract:: ... In phylogenomic profiling, the genomic context based methods are based on the observation that two or more proteins having the same pattern of presence or absence in many diverse genomes most likely have a functional link. In this research work, a tool (PATSIM) has been developed to predict the protein patterns based on the SOPM tool. In this tool, the secondary structure for CATH database protein ...
DOI:: 10.1016/j.gene.2018.02.069
: http://dx.doi.org/10.1016/j.gene.2018.02.069

4. Groups of coevolving positions provide drug resistance to Mycobacterium tuberculosis: A study using targets of first-line antituberculosis drugs

Author:: Vats, Sharad; Shanker, Asheesh
Source:: International journal of antimicrobial agents 2019 v.53 no.3 pp. 197-202
ISSN:: 0924-8579
Subject:: protein secondary structure, etc ; Mycobacterium tuberculosis; active sites; amino acid sequences; amino acids; bioinformatics; coevolution; drugs; isoniazid; multiple drug resistance; pathogens; point mutation; proteins; resistance genes; rifampicin; single nucleotide polymorphism; tuberculosis; Show all 17 Subjects
Abstract:: ... Drug resistance has been associated with point mutations in coding regions leading to an altered protein sequence and structure. Such changes have been seen as isolated events occurring at various positions in a sequence. However, we hypothesise that it is not a single mutation at a specific position but a group of positions that coevolve in a correlated fashion to increase the fitness of a target ...
DOI:: 10.1016/j.ijantimicag.2018.10.027
: https://dx.doi.org/10.1016/j.ijantimicag.2018.10.027

5. Identification of variants and therapeutic epitopes in HPV-33/HPV-58 E6 and E7 in Southwest China

Author:: He, Jiaoyu; Yang, Yasi; Chen, Zuyi; Liu, Yang; Bao, Shanfei; Zhao, Yun; Ding, Xianping
Source:: Virology journal 2019 v.16 no.1 pp. 72
ISSN:: 1743-422X
Subject:: protein secondary structure, etc ; B-lymphocytes; Chinese people; DNA; HLA antigens; Papillomaviridae; T-lymphocytes; amino acid sequences; amino acids; bioinformatics; computer software; databases; epitopes; genetic polymorphism; immune response; nucleotide sequences; oncogene proteins; physicochemical properties; therapeutics; translation (genetics); uterine cervical neoplasms; vaccine development; vaccines; women; China; Show all 25 Subjects
Abstract:: ... BACKGROUND: Human papillomavirus (HPV) E6 and E7 oncoproteins play a crucial role in HPV-related diseases, such as cervical cancer, and can be used as ideal targets for therapeutic vaccines. Human leukocyte antigen (HLA) participates in the immune response to block HPV infection and invasion by its target/recognition function. HPV-33 and HPV-58 are highly prevalent among Chinese women. Therefore, ...
DOI:: 10.1186/s12985-019-1168-y
: https://dx.doi.org/10.1186/s12985-019-1168-y

6. Photoactivation Mechanism, Timing of Protein Secondary Structure Dynamics and Carotenoid Translocation in the Orange Carotenoid Protein

Author:: Konold, Patrick E.; van Stokkum, Ivo H. M.; Muzzopappa, Fernando; Wilson, Adjélé; Groot, Marie-Louise; Kirilovsky, Diana; Kennis, John T. M.
Source:: Journal of the American Chemical Society 2018 v.141 no.1 pp. 520-530
ISSN:: 1520-5126
Subject:: protein secondary structure, etc ; Cyanobacteria; absorption; amino acid sequences; amino acids; blue light; carotenoids; dissociation; hydrogen bonding; lighting; models; photons; photostability; spectroscopy; Show all 14 Subjects
Abstract:: ... The orange carotenoid protein (OCP) is a two-domain photoactive protein that noncovalently binds an echinenone (ECN) carotenoid and mediates photoprotection in cyanobacteria. In the dark, OCP assumes an orange, inactive state known as OCPᴼ; blue light illumination results in the red active state, known as OCPᴿ. The OCPᴿ state is characterized by large-scale structural changes that involve dissocia ...
DOI:: 10.1021/jacs.8b11373
: http://dx.doi.org/10.1021/jacs.8b11373

7. A new hybrid coding for protein secondary structure prediction based on primary structure similarity

Author:: Li, Zhong; Wang, Jing; Zhang, Shunpu; Zhang, Qifeng; Wu, Wuming
Source:: Gene 2017 v.618 pp. 8-13
ISSN:: 0378-1119
Subject:: protein secondary structure, etc ; amino acid sequences; amino acids; hybrids; physicochemical properties; prediction; principal component analysis; support vector machines; Show all 8 Subjects
Abstract:: ... The coding pattern of protein can greatly affect the prediction accuracy of protein secondary structure. In this paper, a novel hybrid coding method based on the physicochemical properties of amino acids and tendency factors is proposed for the prediction of protein secondary structure. The principal component analysis (PCA) is first applied to the physicochemical properties of amino acids to cons ...
DOI:: 10.1016/j.gene.2017.03.011
: https://dx.doi.org/10.1016/j.gene.2017.03.011

8. Sixty-five years of the long march in protein secondary structure prediction: the final stretch?

Author:: Yang, Yuedong; Gao, Jianzhao; Wang, Jihua; Heffernan, Rhys; Hanson, Jack; Paliwal, Kuldip; Zhou, Yaoqi
Source:: Briefings in bioinformatics 2016 v.19 no.3 pp. 482-494
ISSN:: 1477-4054
Subject:: protein secondary structure, etc ; amino acid sequences; databases; methodology; polypeptides; prediction; proteins; Show all 7 Subjects
Abstract:: ... Protein secondary structure prediction began in 1951 when Pauling and Corey predicted helical and sheet conformations for protein polypeptide backbone even before the first protein structure was determined. Sixty-five years later, powerful new methods breathe new life into this field. The highest three-state accuracy without relying on structure templates is now at 82–84%, a number unthinkable jus ...
DOI:: 10.1093/bib/bbw129
: https://dx.doi.org/10.1093/bib/bbw129

9. Effect of Helical Flanking Sequences on the Morphology of Polyglutamine-Containing Fibrils

Author:: Kokona, Bashkim; Johnson, Karl A.; Fairman, Robert
Source:: Biochemistry 2014 v.53 no.43 pp. 6747-6753
ISSN:: 1520-4995
Subject:: protein secondary structure, etc ; amino acid sequences; peptides; protein aggregates; transmission electron microscopy; Show all 5 Subjects
Abstract:: ... A peptide model system has been developed to study the effects of helical flanking sequences on polyglutamine aggregation. In a companion manuscript, the kinetics of aggregation are described, comparing the influence of a well-defined heterotetrameric coiled coil to that of the helix-rich structure found in Httᴺᵀ, a 17-residue flanking sequence found in the huntingtin protein, on polyglutamine agg ...
DOI:: 10.1021/bi501066q
: http://dx.doi.org/10.1021%2Fbi501066q

10. PEG–Peptide Conjugates

Author:: Hamley, Ian W.
Source:: Biomacromolecules 2014 v.15 no.5 pp. 1543-1559
ISSN:: 1526-4602
Subject:: protein secondary structure, etc ; amino acid sequences; biochemical compounds; chemical bonding; materials science; nanotechnology; synthetic products; Show all 7 Subjects
Abstract:: ... The remarkable diversity of the self-assembly behavior of PEG–peptides is reviewed, including self-assemblies formed by PEG–peptides with β-sheet and α-helical (coiled-coil) peptide sequences. The modes of self-assembly in solution and in the solid state are discussed. Additionally, applications in bionanotechnology and synthetic materials science are summarized. ...
DOI:: 10.1021/bm500246w
: http://dx.doi.org/10.1021%2Fbm500246w

11. Molecular phylogenetic and sequence variation analysis of dimeric α-amylase inhibitor genes in wheat and its wild relative species

Author:: Pandey, Bharati; Saini, Manoj; Sharma, Pradeep
Source:: Plant gene 2016 v.6 pp. 48-58
ISSN:: 2352-4073
Subject:: protein secondary structure, etc ; Aegilops tauschii; Triticum; alpha-amylase; amino acid sequences; breads; chloroplasts; conserved sequences; cysteine; durum wheat; energy; genes; genetic databases; genotype; insects; mitochondria; phylogeny; proteins; sequence alignment; sequence diversity; single nucleotide polymorphism; starch; Show all 22 Subjects
Abstract:: ... Dimeric alpha-amylase inhibitors serve protection against insects that are highly dependent on starch for their energy. In order to study the molecular evolution and sequence variation, we have sequenced dimeric α-amylase inhibitors gene from different genomes in Triticeae including Indian bread and durum wheat genotypes. Using BLAST, obtained sequences show very high homology with other inhibitor ...
DOI:: 10.1016/j.plgene.2016.03.004
: https://dx.doi.org/10.1016/j.plgene.2016.03.004

12. Human and Tree Shrew Alpha-synuclein: Comparative cDNA Sequence and Protein Structure Analysis

Author:: Wu, Zheng -Cun; Huang, Zhang-Qiong; Jiang, Qin-Fang; Dai, Jie-jie; Zhang, Ying; Gao, Jia-Hong; Sun, Xiao-Mei; Chen, Nai-Hong; Yuan, Yu-He; Li, Cong; Han, Yuan-Yuan; Li, Yun; Ma, Kai-Li
Source:: Applied biochemistry and biotechnology 2015 v.177 no.4 pp. 957-966
ISSN:: 0273-2289
Subject:: protein secondary structure, etc ; Scandentia; amino acid sequences; animal models; complementary DNA; humans; neurodegenerative diseases; nucleotide sequences; pathogenesis; phosphorylation; reverse transcriptase polymerase chain reaction; sequence analysis; Show all 12 Subjects
Abstract:: ... The synaptic protein alpha-synuclein (α-syn) is associated with a number of neurodegenerative diseases, and homology analyses among many species have been reported. Nevertheless, little is known about the cDNA sequence and protein structure of α-syn in tree shrews, and this information might contribute to our understanding of its role in both health and disease. We designed primers to the human α- ...
DOI:: 10.1007/s12010-015-1789-6
: http://dx.doi.org/10.1007/s12010-015-1789-6

13. Spontaneous C-cleavage of a mini-intein without its conserved N-terminal motif A

Author:: Qi, Xingmei; Meng, Qing; Liu, Xiang-Qin
Source:: FEBS letters 2011 v.585 no.15 pp. 2513-2518
ISSN:: 0014-5793
Subject:: protein secondary structure, etc ; RNA splicing; amino acid sequences; mutation; Show all 4 Subjects
Abstract:: ... Previously, the C-terminal fragment of a split intein was known to undergo controllable C-cleavage at its C-terminus only when the N-terminal fragment of the intein was added. Here we constructed a similar split intein from the Ssp DnaX intein, but we unexpectedly observed that its C-terminal 136-aa fragment could undergo spontaneous C-cleavage without the N-terminal fragment that was up to 15 aa ...
DOI:: 10.1016/j.febslet.2011.06.035
: http://dx.doi.org/10.1016/j.febslet.2011.06.035

14. Spherical Micelles Assembled from Variants of Recombinant Oleosin

Author:: Vargo, Kevin B.; Sood, Nimil; Moeller, Tyler D.; Heiney, Paul A.; Hammer, Daniel A.
Source:: Langmuir 2014 v.30 no.38 pp. 11292-11300
ISSN:: 1520-5827
Subject:: protein secondary structure, etc ; X-radiation; amino acid sequences; biocompatible materials; biotechnology; engineering; genetic engineering; hydrophobicity; ionic surfactants; light scattering; micelles; molecular biology; molecular weight; oleosin; transmission electron microscopy; Show all 15 Subjects
Abstract:: ... An emerging field in biomaterials is the creation and engineering of protein surfactants made by recombinant biotechnology. Protein surfactants made by recombinant biotechnology allow for complete control of the molecular weight and chemical sequence of the surfactant. The proteins are monodisperse in molecular weight, and functionalization with bioactive amino acid sequences is straightforwardly ...
DOI:: 10.1021/la502664e
: http://dx.doi.org/10.1021%2Fla502664e

15. Goose Toll-like receptor 7 (TLR7), myeloid differentiation factor 88 (MyD88) and antiviral molecules involved in anti-H5N1 highly pathogenic avian influenza virus response

Author:: Wei, Liangmeng; Jiao, Peirong; Yuan, Runyu; Song, Yafen; Cui, Pengfei; Guo, Xuchen; Zheng, Bofang; Jia, Weixin; Qi, Wenbao; Ren, Tao; Liao, Ming
Source:: Veterinary immunology and immunopathology 2013 v.153 no.1-2 pp. 99-106
ISSN:: 0165-2427
Subject:: protein secondary structure, etc ; messenger RNA; ducks; hosts; Influenza A virus; polymerase chain reaction; amino acid sequences; geese; viruses; immune response; lungs; mammals; receptors; mortality; Show all 14 Subjects
Abstract:: ... In mammals, Toll-like receptor 7 (TLR7) is an important membrane-bound receptor triggered by antiviral compounds and single-stranded RNA. It is implicated in the immune response to viruses such as influenza virus. It was not known whether geese, a natural host for avian influenza viruses, possess a homologue of mammalian TLR7 for recognizing avian influenza virus. In this study, we cloned the full ...
DOI:: 10.1016/j.vetimm.2013.02.012
PubMed:: 23481654
: https://dx.doi.org/10.1016/j.vetimm.2013.02.012

16. Use of the Burrows-Wheeler similarity distribution to the comparison of the proteins

Author:: Yang, Lianping; Chang, Guisong; Zhang, Xiangde; Wang, Tianming
Source:: Amino acids 2010 v.39 no.3 pp. 887-898
ISSN:: 0939-4451
Subject:: protein secondary structure, etc ; amino acid sequences; hydrophobicity; physical properties; proteins; topology; Show all 6 Subjects
Abstract:: ... In this paper, we present an approach based on Burrows-Wheeler transform to compare the protein sequences. The strings representing amino acid sequences do not reflect the chemical physical properties better, and it is very hard to extract any key features by reading these long character strings directly. The use of the Burrows-Wheeler similarity distribution needs a suitable representation which ...
DOI:: 10.1007/s00726-010-0547-x
PubMed:: 20300789
: http://dx.doi.org/10.1007/s00726-010-0547-x

17. Purification of Parvalbumin from Carp: A Protocol that Avoids Heat-Treatment

Author:: Koppelman, Stef J.; Romijn, Roland A.; de Jongh, Harmen H.J.; Nordlee, Julie A.; Piersma, Sander; Hessing, Martin; Taylor, Steve L.
Source:: Journal of food science 2010 v.75 no.3 pp. T49
ISSN:: 0022-1147
Subject:: protein secondary structure, etc ; albumins; food analysis; carp; allergens; amino acid sequences; yields; molecular weight; detection; Show all 9 Subjects
Abstract:: ... Parvalbumin from carp, a major allergen, was purified to homogeneity using ion exchange chromatography and size exclusion chromatography (estimated purity >95% to 98% based on SDS-PAGE and native PAGE) with a yield of 318 mg, and a number of basic biochemical characteristics were determined. The identity was confirmed by peptide-mass fingerprinting, and IgE-binding was demonstrated. The UV/Vis abs ...
DOI:: 10.1111/j.1750-3841.2010.01513.x
PubMed:: 20492314
: http://dx.doi.org/10.1111/j.1750-3841.2010.01513.x

18. Linear antimicrobial peptides from Ectatomma quadridens ant venom

Author:: Pluzhnikov, Kirill A.; Kozlov, Sergey A.; Vassilevski, Alexander A.; Vorontsova, Olga V.; Feofanov, Alexei V.; Grishin, Eugene V.
Source:: Biochimie 2014 v.107 pp. 211-215
ISSN:: 0300-9084
Subject:: protein secondary structure, etc ; Gram-negative bacteria; Paraponera clavata; Sarcophagidae; amino acid sequences; antibacterial properties; antimicrobial peptides; erythrocytes; growth retardation; humans; insect larvae; lethal dose 50; leukemia; mass spectrometry; reversed-phase liquid chromatography; venoms; Show all 16 Subjects
Abstract:: ... Venoms from three poneromorph ant species (Paraponera clavata, Ectatomma quadridens and Ectatomma tuberculatum) were investigated for the growth inhibition of Gram-positive and Gram-negative bacteria. It was shown that the venom of E. quadridens and its peptide fraction in particular possess marked antibacterial action. Three linear antimicrobial peptides sharing low similarity to the well-known p ...
DOI:: 10.1016/j.biochi.2014.09.012
: http://dx.doi.org/10.1016/j.biochi.2014.09.012

19. Umbelliferone induces changes in the structure and pharmacological activities of Bn IV, a phospholipase A₂ isoform isolated from Bothrops neuwiedi

Author:: Toyama, Daniela de Oliveira; Diz Filho, Eduardo Britto dos Santos; Cavada, Benildo Sousa; da Rocha, Bruno Anderson Matias; de Oliveira, Simone Cristina Buzzo; Cotrim, Camila Aparecida; Soares, Veronica Cristina Gomes; Delatorre, Plínio; Marangoni, Sérgio; Toyama, Marcos Hikari
Source:: Toxicon 2011 v.57 no.6 pp. 851-860
ISSN:: 0041-0101
Subject:: protein secondary structure, etc ; Bothrops; amino acid sequences; edema; fluorescence; lysine; phospholipase A2; platelet aggregation; snakes; spectral analysis; synergism; umbelliferones; venoms; Show all 13 Subjects
Abstract:: ... In this paper was demonstrated that umbelliferone induces changes in structure and pharmacological activities of Bn IV, a lysine 49 secretory phospholipase A₂ (sPLA2) from Bothrops neuwiedi. Incubation of Bn IV with umbelliferone virtually abolished platelet aggregation, edema, and myotoxicity induced by native Bn IV. The amino acid sequence of Bn IV showed high sequence similarities with other Ly ...
DOI:: 10.1016/j.toxicon.2011.02.024
: http://dx.doi.org/10.1016/j.toxicon.2011.02.024

20. A novel biomarker for marine environmental pollution of pi-class glutathione S-transferase from Mytilus coruscus

Author:: Liu, Huihui; He, Jianyu; Zhao, Rongtao; Chi, Changfeng; Bao, Yongbo
Source:: Ecotoxicology and environmental safety 2015 v.118 pp. 47-54
ISSN:: 0147-6513
Subject:: protein secondary structure, etc ; Mytilus; Vibrio alginolyticus; Vibrio harveyi; amino acid sequences; bacteria; bacterial infections; biomarkers; cadmium; complementary DNA; copper; exposure duration; gene expression; glutathione transferase; heavy metals; hemocytes; hepatopancreas; innate immunity; messenger RNA; metabolic detoxification; muscles; nucleotide sequences; phylogeny; pollution; prediction; quantitative polymerase chain reaction; reverse transcriptase polymerase chain reaction; Show all 27 Subjects
Abstract:: ... Glutathione S-transferases (GSTs) are the superfamily of phase II detoxification enzymes that play crucial roles in innate immunity. In this study, a pi-class GST homolog was identified from Mytilus coruscus (named as McGST1, KC525103). The full-length cDNA sequence of McGST1 was 621bp with a 5ʹ untranslated region (UTR) of 70bp and a 3ʹ-UTR of 201bp. The deduced amino acid sequence was 206 residu ...
DOI:: 10.1016/j.ecoenv.2015.04.012
: http://dx.doi.org/10.1016/j.ecoenv.2015.04.012

21. Non-covalent binding of proteins to polyphenols correlates with their amino acid sequence

Author:: Nagy, Kornél; Courtet-Compondu, Marie-Claude; Williamson, Gary; Rezzi, Serge; Kussmann, Martin; Rytz, Andreas
Source:: Food chemistry 2012 v.132 no.3 pp. 1333-1339
ISSN:: 0308-8146
Subject:: protein secondary structure, etc ; albumins; amino acid sequences; binding proteins; casein; denaturation; mass spectrometry; models; multivariate analysis; pH; polyphenols; prediction; proline; quercitrin; ultrafiltration; Show all 15 Subjects
Abstract:: ... The present paper describes the assessment of non-covalent binding (NCB) between milk proteins and polyphenols and its correlation with the physicochemical parameters of proteins. A method based on ultrafiltration and liquid chromatography–tandem mass spectrometry was used to analyse free and non-covalently bound polyphenols (ligands) in mixtures with major milk proteins. Binding strength values o ...
DOI:: 10.1016/j.foodchem.2011.11.113
: http://dx.doi.org/10.1016/j.foodchem.2011.11.113

22. NetCSSP: web application for predicting chameleon sequences and amyloid fibril formation

Author:: Kim, Changsik; Choi, Jiwon; Lee, Seong Joon; Welsh, William J.; Yoon, Sukjoon
Source:: Nucleic acids research 2009 v.37 no.suppl_2 pp. W469
ISSN:: 0305-1048
Subject:: protein secondary structure, etc ; Internet; algorithms; amino acid sequences; amyloid; nucleic acids; prediction; Show all 7 Subjects
Abstract:: ... The calculation of contact-dependent secondary structure propensity (CSSP) is a unique and sensitive method that detects non-native secondary structure propensities in protein sequences. This method has applications in predicting local conformational change, which typically is observed in core sequences of protein aggregation and amyloid fibril formation. NetCSSP implements the latest version of t ...

23. Influence of cation-π interactions to the structural stability of prokaryotic and eukaryotic translation elongation factors

Author:: Prasad, Vibhu Ranjan; Sathpathy, Shankha
Source:: Protoplasma 2009 v.238 no.1-4 pp. 11-20
ISSN:: 0033-183X
Subject:: protein secondary structure, etc ; amino acid sequences; binding proteins; probability; translation (genetics); Show all 5 Subjects
Abstract:: ... We have investigated the role of cation-π interactions on translation elongation factors. In our investigation, an average of four significant cation-π interactions were found, that is, an average of one cation-π interaction per 44 residues in the ten elongation factors were observed. The analysis on the influence of short (<±4), medium (>±4 to <±20) and long (>20) range contacts showed that catio ...
DOI:: 10.1007/s00709-009-0066-3
: http://dx.doi.org/10.1007/s00709-009-0066-3

24. Divergence in structure and function of tau class glutathione transferase from Pinus tabulaeformis, P. yunnanensis and P. densata

Author:: Zeng, Q.Y.; Wang, X.R.
Source:: Biochemical systematics and ecology 2006 v.34 no.9 pp. 678-690
ISSN:: 0305-1978
Subject:: protein secondary structure, etc ; glutathione transferase; amino acid sequences; sequence alignment; Show all 4 Subjects
Abstract:: ... Glutathione transferases (GSTs) are a family of enzymes that play important roles in stress tolerance and detoxification in plants. The plant GSTs are divided into four classes (phi, tau, zeta and theta), among which tau is the most numerously represented. To date, studies on GSTs in plants have focused largely on crop species. There is extremely little information on the molecular characteristics ...
DOI:: 10.1016/j.bse.2006.04.004
: http://dx.doi.org/10.1016/j.bse.2006.04.004

25. Expression of the sucrose binding protein from soybean: Renaturation and stability of the recombinant protein

Author:: Rocha, C.S.; Luz, D.F.; Oliveira, M.L.; Baracat-Pereira, M.C.; Medrano, F.J.; Fontes, E.P.B.
Source:: Phytochemistry 2007 v.68 no.6 pp. 802-810
ISSN:: 0031-9422
Subject:: protein secondary structure, etc ; Glycine max; soybeans; plant proteins; protein isoforms; recombinant fusion proteins; amino acid sequences; Show all 7 Subjects
Abstract:: ... The sucrose binding protein (SBP) belongs to the cupin family of proteins and is structurally related to vicilin-like storage proteins. In this investigation, a SBP isoform (GmSBP2/S64) was expressed in E. coli and large amounts of the protein accumulated in the insoluble fraction as inclusion bodies. The renatured protein was studied by circular dichroism (CD), intrinsic fluorescence, and binding ...
DOI:: 10.1016/j.phytochem.2006.11.036
PubMed:: 17222874
: http://dx.doi.org/10.1016/j.phytochem.2006.11.036

26. Probing protein structural requirements for activation of membrane-bound NAC transcription factors in Arabidopsis and rice

Author:: Kim, Sang-Gyu; Lee, Sangmin; Ryu, Jaeyong; Park, Chung-Mo
Source:: Plant science 2010 v.178 no.3 pp. 239-244
ISSN:: 0168-9452
Subject:: protein secondary structure, etc ; Oryza sativa; Arabidopsis thaliana; amino acid sequences; structure-activity relationships; hydrophilic interactions; transcription factors; membrane proteins; amino acid motifs; proteolysis; transcriptional activation; Show all 11 Subjects
Abstract:: ... Many transcription factors are stored in a dormant state through association with the cellular membranes in plants. Upon stimulation by internal and environmental signals, they are activated through proteolytic cleavage events either by membrane-associated proteases or by ubiquitination-dependent proteasome activities. Controlled proteolytic activation of the dormant, membrane-bound transcription ...
DOI:: 10.1016/j.plantsci.2009.12.007
: http://dx.doi.org/10.1016/j.plantsci.2009.12.007

27. Structural aspects of the Mucor bacilliformis proteinase, a new member of the aspartyl-proteinase family

Author:: Machalinski, C.; Pirpignani, M.L.; Marino, C.; Mantegazza, A.; Biscoglio de Jimenez Bonino, M.
Source:: Journal of biotechnology 2006 v.123 no.4 pp. 443-452
ISSN:: 0168-1656
Subject:: protein secondary structure, etc ; milk clotting; sequence alignment; cattle; amino acid sequences; Rhizomucor pusillus; chymosin; Show all 7 Subjects
DOI:: 10.1016/j.jbiotec.2005.12.035
: http://dx.doi.org/10.1016/j.jbiotec.2005.12.035

28. Molecular cloning and characterization of SoNCED, a novel gene encoding 9-cis-epoxycarotenoid dioxygenase from sugarcane (Saccharum officinarum L.)

Author:: Li, Chang-Ning; Srivastava, Manoj-Kumar; Nong, Qian; Yang, Li-Tao; Li, Yang-Rui
Source:: Genes & genomics 2013 v.35 no.1 pp. 101-109
ISSN:: 1976-9571
Subject:: protein secondary structure, etc ; Saccharum officinarum; abscisic acid; amino acid sequences; amino acids; complementary DNA; drought tolerance; gas production (biological); gene expression; genes; isoelectric point; leaves; messenger RNA; molecular cloning; molecular weight; open reading frames; oxygen; oxygenases; phylogeny; quantitative polymerase chain reaction; roots; sequence alignment; sugarcane; water stress; Show all 24 Subjects
Abstract:: ... Abscisic acid (ABA) plays important roles in adaptive responses to various environmental stresses. The rate-limiting step in ABA biosynthesis is the oxidative cleavage of cis-epoxycarotenoids, which is catalyzed by 9-cis-epoxycarotenoid dioxygenase (NCED). In this experiment, a full-length cDNA encoding NCED gene was cloned by RT-PCR and RACE from sugarcane (Saccharum officinarum L.). The full-len ...
DOI:: 10.1007/s13258-013-0065-9
: http://dx.doi.org/10.1007/s13258-013-0065-9

29. Multiple Pro197 Substitutions in the Acetolactate Synthase of Corn Poppy (Papaver rhoeas) Confer Resistance to Tribenuron

Author:: Kaloumenos, Nikolaos S.; Dordas, Christos A.; Diamantidis, Grigorios C.; Eleftherohorinos, Ilias G.
Source:: Weed science 2009 v.57 no.4 pp. 362-368
ISSN:: 0043-1745
Subject:: protein secondary structure, etc ; alleles; proline; broadleaf weeds; mutation; herbicide-resistant weeds; acetolactate synthase; amino acid sequences; codons; heterozygosity; genetic variation; tribenuron; Papaver rhoeas; Show all 13 Subjects
Abstract:: ... Variations in the acetolactate synthase (ALS) gene sequence were determined from 28 populations of corn poppy resistant (R) to tribenuron and from 6 populations susceptible (S) to this herbicide. The ALS gene fragment (634 bp) sequence revealed in R populations five point mutations at the codon Pro₁₉₇, and among them the substitution of Pro₁₉₇ by Ala was the most common. The sequencing chromatogra ...
DOI:: 10.1614/WS-08-166.1
: http://dx.doi.org/10.1614%2FWS-08-166.1

30. Purification and characterization of mosquitocidal Bacillus sphaericus BinA protein

Author:: Hire, Ramesh S.; Hadapad, Ashok B.; Dongre, Tanaji K.; Kumar, Vinay
Source:: Journal of invertebrate pathology 2009 v.101 no.2 pp. 106-111
ISSN:: 0022-2011
Subject:: protein secondary structure, etc ; Culex quinquefasciatus; lethal dose 50; recombinant proteins; mosquito control; amino acid sequences; Bacillus sphaericus; bacterial insecticides; genes; bacterial proteins; molecular cloning; nucleotide sequences; bacterial toxins; Show all 13 Subjects
Abstract:: ... Certain strains of Bacillus sphaericus produce a highly toxic mosquito-larvicidal binary toxin during sporulation. The binary toxin is composed of toxic BinA (41.9 kDa) and receptor binding BinB (51.4 kDa) polypeptides and is active against vectors of filariasis, encephalitis and malaria. The toxin has been tested with limited use for the control of vector mosquitoes for more than two decades. The ...
DOI:: 10.1016/j.jip.2009.03.005
PubMed:: 19348810
: http://dx.doi.org/10.1016/j.jip.2009.03.005

31. A Secreted SPRY Domain-Containing Protein (SPRYSEC) from the Plant-Parasitic Nematode Globodera rostochiensis Interacts with a CC-NB-LRR Protein from a Susceptible Tomato

Author:: Rehman, Sajid; Postma, Wiebe; Tytgat, Tom; Prins, Pjotr; Qin, Ling; Overmars, Hein; Vossen, Jack; Spiridon, Laurentiu-N.; Petrescu, Andrei-J.; Goverse, Aska; Bakker, Jaap; Smant, Geert
Source:: Molecular plant-microbe interactions 2009 v.22 no.3 pp. 330-340
ISSN:: 0894-0282
Subject:: protein secondary structure, etc ; tomatoes; Solanum lycopersicum var. lycopersicum; animal proteins; plant parasitic nematodes; host plants; plant pests; amino acid sequences; resistance mechanisms; protein secretion; pest resistance; Globodera rostochiensis; Show all 12 Subjects
Abstract:: ... Esophageal gland secretions from nematodes are believed to include effectors that play important roles in plant parasitism. We have identified a novel gene family encoding secreted proteins specifically expressed in the dorsal esophageal gland of Globodera rostochiensis early in the parasitic cycle, and which contain the B30.2/SPRY domain. The secondary structure of these proteins, named the secre ...
DOI:: 10.1094/MPMI-22-3-0330
PubMed:: 19245327
: http://dx.doi.org/10.1094/MPMI-22-3-0330

32. Modèle topologique de la structure d'un antiport vacuolaire de type NHX chez la vigne cultivée (Vitis vinifera)

Author:: Hanana, Mohsen; Cagnac, Olivier; Mliki, Ahmed; Blumwald, Eduardo
Source:: Botany 2009 v.87 no.3 pp. 339-347
ISSN:: 1916-2804
Subject:: protein secondary structure, etc ; transport proteins; transmembrane proteins; grapes; bioinformatics; protein tertiary structure; vacuoles; isoelectric point; amino acid sequences; genomics; hydrophobicity; Vitis vinifera; molecular weight; exons; Show all 14 Subjects
DOI:: 10.1139/B08-141
: http://dx.doi.org/10.1139/B08-141

33. Molecular cloning, heterologous expression, and phylogenetic analysis of a novel y-type HMW glutenin subunit gene from the G genome of Triticum timopheevi

Author:: Li, Xiaohui; Zhang, Yanzhen; Gao, Liyan; Wang, Aili; Ji, Kangmin; He, Zhonghu; Appels, Rudi; Ma, Wujun; Yan, Yueming
Source:: Genome = 2007 v.50 no.12 pp. 1130–1140
ISSN:: 0831-2796
Subject:: protein secondary structure, etc ; glutenins; open reading frames; Triticum timopheevii; protein tertiary structure; amino acid sequences; genes; molecular cloning; molecular weight; Show all 9 Subjects
Abstract:: ... A novel y-type high molecular weight (HMW) glutenin subunit gene from the G genome of Triticum timopheevi (2n = 4x = 28, AAGG) was isolated and characterized. Genomic DNA from accession CWI17006 was amplified and a 2200 bp fragment was obtained. Sequence analysis revealed a complete open reading frame including N- and C-terminal ends and a central repetitive domain encoding 565 amino acid residues ...
DOI:: 10.1139/G07-089
: http://dx.doi.org/10.1139/G07-089

34. A Continent of Plant Defense Peptide Diversity: Cyclotides in Australian Hybanthus (Violaceae)

Author:: Simonsen, Shane M.; Sando, Lillian; Ireland, David C.; Colgrave, Michelle L.; Bharathi, Rekha; Göransson, Ulf; Craik, David J.
Source:: plant cell 2005 v.17 no.11 pp. 3176-3189
ISSN:: 1040-4651
Subject:: protein secondary structure, etc ; Hybanthus; resistance mechanisms; plant proteins; peptides; amino acid sequences; geographical variation; Australia; Show all 8 Subjects
Abstract:: ... Cyclotides are plant-derived miniproteins that have the unusual features of a head-to-tail cyclized peptide backbone and a knotted arrangement of disulfide bonds. It had been postulated that they might be an especially large family of host defense agents, but this had not yet been tested by field data on cyclotide variation in wild plant populations. In this study, we sampled Australian Hybanthus ...
DOI:: 10.1105/tpc.105.034678
PubMed:: 16199617
PubMed Central:: PMC1276036
: http://dx.doi.org/10.1105/tpc.105.034678

35. A cluster of diagnostic Hsp68 amino acid sites that are identified in Drosophila from the melanogaster species group are concentrated around β-sheet residues involved with substrate binding

Author:: Kellett, M.; McKechnie, S.W.
Source:: Genome = 2005 v.48 no.2 pp. 226-233
ISSN:: 0831-2796
Subject:: protein secondary structure, etc ; heat shock proteins; amino acid sequences; binding sites; genes; nucleotide sequences; Drosophila; adenosinetriphosphatase; Show all 8 Subjects
Abstract:: ... The coding region of the hsp68 gene has been amplified, cloned, and sequenced from 10 Drosophila species, 5 from the melanogaster subgroup and 5 from the montium subgroup. When the predicted amino acid sequences are compared with available Hsp70 sequences, patterns of conservation suggest that the C-terminal region should be subdivided according to predominant secondary structure. Conservation lev ...
DOI:: 10.1139/g04-113
: http://dx.doi.org/10.1139/g04-113

36. Functional characterization of KIHEM13, a hypoxic gene of Kluyveromyces lactis. [Erratum: 2005 May, v. 51, no. 5, p. 431.]

Author:: Blanco, M.; Becerra, M.; Gonzalez-Siso, M.I.; Cerdan, M.E.
Source:: Canadian journal of microbiology 2005 v.51 no.3 pp. 241-249
ISSN:: 0008-4166
Subject:: protein secondary structure, etc ; Kluyveromyces marxianus var. lactis; amino acid sequences; oxidoreductases; genes; promoter regions; Show all 6 Subjects
DOI:: 10.1139/w04-133
: http://dx.doi.org/10.1139/w04-133

37. Solution Structure of an Arabidopsis WRKY DNA Binding Domain

Author:: Yamasaki, Kazuhiko; Kigawa, Takanori; Inoue, Makoto; Tateno, Masaru; Yamasaki, Tomoko; Yabuki, Takashi; Aoki, Masaaki; Seki, Eiko; Matsuda, Takayoshi; Tomo, Yasuko; Hayami, Nobuhiro; Terada, Takaho; Shirouzu, Mikako; Tanaka, Akiko; Seki, Motoaki; Shinozaki, Kazuo; Yokoyama, Shigeyuki
Source:: plant cell 2005 v.17 no.3 pp. 944-956
ISSN:: 1040-4651
Subject:: protein secondary structure, etc ; Arabidopsis thaliana; transcription factors; DNA-binding domains; amino acid sequences; Show all 5 Subjects
Abstract:: ... The WRKY proteins comprise a major family of transcription factors that are essential in pathogen and salicylic acid responses of higher plants as well as a variety of plant-specific reactions. They share a DNA binding domain, designated as the WRKY domain, which contains an invariant WRKYGQK sequence and a CX₄₋₅CX₂₂₋₂₃HXH zinc binding motif. Herein, we report the NMR solution structure of the C-t ...
DOI:: 10.1105/tpc.104.026435
PubMed:: 15705956
PubMed Central:: PMC1069710
: http://dx.doi.org/10.1105/tpc.104.026435

38. Complete amino acid sequence of the lentil trypsin-chymotrypsin inhibitor LCI-1.7 and a discussion of atypical binding sites of Bowman-Birk inhibitors

Author:: Weder, J.K.P.; Hinkers, S.C.
Source:: Journal of agricultural and food chemistry 2004 v.52 no.13 pp. 4219-4226
ISSN:: 0021-8561
Subject:: protein secondary structure, etc ; trypsin inhibitors; chymotrypsin; amino acid sequences; antinutritional factors; binding sites; Lens culinaris; lentils; Show all 8 Subjects
Abstract:: ... The complete primary structure of the lentil (Lens culinaris) trypsin-chymotrypsin inhibitor LCI-1.7 was determined by conventional methods in order to find relationships between partial sequences and the difference in action against human and bovine chymotrypsin. As other Bowman-Birk type inhibitors, LCI-1.7 contained 68 amino acid residues, seven disulfide bridges, and two reactive sites, Arg16- ...
DOI:: 10.1021/jf030768d
: http://dx.doi.org/10.1021/jf030768d

39. Defining subdomains of the K domain important for protein-protein interactions of plant MADS proteins

Author:: Yang, Y.; Jack, T.
Source:: Plant molecular biology 2004 v.55 no.1 pp. 45-59
ISSN:: 0167-4412
Subject:: protein secondary structure, etc ; Arabidopsis thaliana; transcription factors; protein-protein interactions; binding sites; amino acid sequences; mutants; Show all 7 Subjects
Abstract:: ... The MADS proteins APETALA3 (AP3), PISTILLATA (PI), SEPALLATA1 (SEP1), SEP2, SEP3, AGAMOUS, and APETALA1 are required for proper floral organ identity in Arabidopsis flowers. All of these floral MADS proteins conserve two domains: the MADS domain that mediates DNA binding and dimerization, and the K domain that mediates protein-protein interaction. The K domain is postulated to form a several amphi ...
PubMed:: 15604664

40. Isolation and temporal endospermal expression of γ-kafirin gene of grain sorghum (Sorghum bicolor L. Moench) var. M 35-1 for introgression analysis of transgene

Author:: Bansal, Sangita; Mishra, Avinash; Tomar, Akash; Sharma, Shailendra; Khanna, Vijay Kumar; Garg, Govind Krishan
Source:: Journal of cereal science 2008 v.48 no.3 pp. 808-815
ISSN:: 0733-5210
Subject:: protein secondary structure, etc ; Sorghum bicolor; grain sorghum; endosperm; gene expression; kafirins; molecular cloning; genes; nucleotide sequences; amino acid sequences; messenger RNA; seed development; Show all 12 Subjects
Abstract:: ... A gamma-kafirin gene of Sorghum bicolor L var. M35-1 was isolated using a PCR based approach by designing specific primers. The primers gave highly reproducible amplification. The amplicons were then cloned and sequenced. Nucleotide sequences were subjected to the homology search and a comparative analysis was done with other prolamins. Amplified γ-kafirin gene (accession no. AY566298 and AY566299 ...
DOI:: 10.1016/j.jcs.2008.06.004
: http://dx.doi.org/10.1016/j.jcs.2008.06.004

41. Purification and characterization of a trypsin inhibitor from Putranjiva roxburghii seeds

Author:: Chaudhary, N.S.; Shee, C.; Islam, A.; Ahmad, F.; Yernool, D.; Kumar, P.; Sharma, A.K.
Source:: Phytochemistry 2008 v.69 no.11 pp. 2120-2126
ISSN:: 0031-9422
Subject:: protein secondary structure, etc ; trypsin; Drypetes; seeds; Euphorbiaceae; chymotrypsin; amino acid sequences; ornamental trees; enzyme inhibition; Kunitz-type proteinase inhibitor; plant proteins; Show all 11 Subjects
Abstract:: ... A highly stable and potent trypsin inhibitor was purified to homogeneity from the seeds of Putranjiva roxburghii belonging to Euphorbiaceae family by acid precipitation, cation-exchange and anion-exchange chromatography. SDS-PAGE analysis, under reducing condition, showed that protein consists of a single polypeptide chain with molecular mass of approximately 34 kDa. The purified inhibitor inhibit ...
DOI:: 10.1016/j.phytochem.2008.05.002
PubMed:: 18561964
: http://dx.doi.org/10.1016/j.phytochem.2008.05.002

42. Characterization of the endo-β-1,3-glucanase activity of S. cerevisiae Eng2 and other members of the GH81 family

Author:: Martín-Cuadrado, A.B.; Fontaine, T.; Esteban, P.F.; Encinar del Dedo, J.; Medina-Redondo, M. de; Rey, F. del; Latgé, J.P.; Vázquez de Aldana, C.R.
Source:: Fungal genetics and biology 2008 v.45 no.4 pp. 542-553
ISSN:: 1087-1845
Subject:: protein secondary structure, etc ; interspecific variation; glucose; Schizosaccharomyces pombe; Saccharomyces cerevisiae; beta-glucanase; amino acid sequences; enzymatic hydrolysis; fungal proteins; oligosaccharides; enzyme substrates; enzyme activity; beta-glucans; Show all 13 Subjects
DOI:: 10.1016/j.fgb.2007.09.001
: http://dx.doi.org/10.1016/j.fgb.2007.09.001

43. Keratin 26, a novel member of the goat type I keratin gene family

Author:: Jin, Mei; Xing, Mengxin; Li, Shuang
Source:: Small ruminant research 2010 v.93 no.1 pp. 24-30
ISSN:: 0921-4488
Subject:: protein secondary structure, etc ; Cashmere (goat breed); DNA libraries; complementary DNA; goats; expressed sequence tags; reverse transcriptase polymerase chain reaction; keratin; amino acid sequences; hair follicles; multigene family; amino acid composition; cashmere wool; sequence homology; Show all 14 Subjects
Abstract:: ... Keratins and keratin-associated proteins make up the main structural components of the cashmere fiber. In this study, we constructed a skin cDNA library of Liaoning new-breeding cashmere goat during follicle anagen. A total of 1986 ESTs were sequenced from the skin library and the 1126 unisequences were homologous to functionally characterized or hypothetical proteins, including 14 unisequences th ...
DOI:: 10.1016/j.smallrumres.2010.04.026
: http://dx.doi.org/10.1016/j.smallrumres.2010.04.026

44. Purification and characterization of a new alkali-thermostable lipase from Staphylococcus aureus isolated from Arachis hypogaea rhizosphere

Author:: Sarkar, Prodipta; Yamasaki, Shinji; Basak, Soumen; Bera, Amit; Bag, Prasanta K.
Source:: Process biochemistry 2012 v.47 no.5 pp. 858-866
ISSN:: 1359-5113
Subject:: protein secondary structure, etc ; Arachis hypogaea; Staphylococcus aureus; acetonitrile; active sites; agarose; amino acid sequences; beta-mercaptoethanol; biotransformation; calcium; copper; detergents; dimethyl sulfoxide; ethylene glycol; gel chromatography; genes; heat inactivation; hydrophobic bonding; industry; iron; isopropyl alcohol; magnesium; medicine; mercury; metal ions; methanol; molecular weight; octoxynol; pH; phospholipids; polysorbates; rhizosphere; sodium; solvents; substrate specificity; temperature; toluene; triacylglycerol lipase; triacylglycerols; Show all 39 Subjects
Abstract:: ... An extracellular lipase (EC 3.1.1.3), SAL-PP1, from Staphylococcus aureus isolated from Arachis hypogaea rhizosphere was purified and characterized. The enzyme was purified using PALL'S Microsep centrifugal device (10kD cut off), hydrophobic interaction (phenyl sepharose CL-4B column) and Superose-12 gel filtration chromatography and found to have a molecular mass of around 49kDa. The gene fragmen ...
DOI:: 10.1016/j.procbio.2012.02.023
: http://dx.doi.org/10.1016/j.procbio.2012.02.023

45. Plus and minus sexual agglutinins from Chlamydomonas reinhardtii

Author:: Ferris, P.J.; Waffenschmidt, S.; Umen, J.G.; Lin, H.; Lee, J.H.; Ishida, K.; Kubo, T.; Lau, J.; Goodenough, U.W.
Source:: plant cell 2005 v.17 no.2 pp. 597-615
ISSN:: 1040-4651
Subject:: protein secondary structure, etc ; agglutinins; glycoproteins; complementary DNA; amino acid sequences; sexual reproduction; exons; Chlamydomonas reinhardtii; introns; cell adhesion; Show all 10 Subjects
Abstract:: ... Gametes of the unicellular green alga Chlamydomonas reinhardtii undergo sexual adhesion via enormous chimeric Hyp-rich glycoproteins (HRGPs), the plus and minus sexual agglutinins, that are displayed on their flagellar membrane surfaces. We have previously purified the agglutinins and analyzed their structural organization using electron microscopy. We report here the cloning and sequencing of the ...
DOI:: 10.1105/tpc.104.028035
PubMed:: 15659633
PubMed Central:: PMC548829
: http://dx.doi.org/10.1105/tpc.104.028035

46. Prion protein NMR structures of cats, dogs, pigs, and sheep

Author:: Lysek, D.A.; Schorn, C.; Nivon, L.G.; Esteve-Moya, V.; Christen, B.; Calzolai, L.; Schroetter, C. von.; Fiorito, F.; Herrmann, T.; Guntert, P.
Source:: Proceedings of the National Academy of Sciences of the United States of America 2005 v.102 no.3 pp. 640-645
ISSN:: 0027-8424
Subject:: protein secondary structure, etc ; prions; nuclear magnetic resonance spectroscopy; cats; dogs; swine; sheep; protein isoforms; amino acid sequences; sequence alignment; Show all 10 Subjects
Abstract:: ... The NMR structures of the recombinant cellular form of the prion proteins (PrP(C)) of the cat (Felis catus), dog (Canis familiaris), and pig (Sus scrofa), and of two polymorphic forms of the prion protein from sheep (Ovis aries) are presented. In all of these species, PrP(C) consists of an N-terminal flexibly extended tail with approximately 100 amino acid residues and a C-terminal globular domain ...
DOI:: 10.1073/pnas.0408937102
PubMed:: 15647367
PubMed Central:: PMC545531
: http://dx.doi.org/10.1073/pnas.0408937102

47. Prion protein NMR structures of chickens, turtles, and frogs

Author:: Calzolai, L.; Lysek, D.A.; Perez, D.R.; Guntert, P.; Wuthrich, K.
Source:: Proceedings of the National Academy of Sciences of the United States of America 2005 v.102 no.3 pp. 651-655
ISSN:: 0027-8424
Subject:: protein secondary structure, etc ; prions; nuclear magnetic resonance spectroscopy; chickens; Trachemys scripta; turtles; Xenopus laevis; amino acid sequences; Show all 8 Subjects
Abstract:: ... The NMR structures of the recombinant prion proteins from chicken (Gallus gallus; chPrP), the red-eared slider turtle (Trachemys scripta; tPrP), and the African clawed frog (Xenopus laevis; xlPrP) are presented. The amino acid sequences of these prion proteins show approximately 30% identity with mammalian prion proteins. All three species form the same molecular architecture as mammalian PrP(C), ...
DOI:: 10.1073/pnas.0408939102
PubMed:: 15647366
PubMed Central:: PMC545536
: http://dx.doi.org/10.1073/pnas.0408939102

48. Taenia solium: Identification and preliminary characterization of a lipid binding protein with homology to the SEC14 catalytic domain

Author:: Montero, E.; Gonzalez, L.M.; Bonay, P.; Rosas, G.; Hernandez, B.; Sciutto, E.; Parkhouse, R.M.E.; Harrison, L.J.S.; Angel Morales, M.; Garate, T.
Source:: Experimental parasitology 2007 v.116 no.3 pp. 191-200
ISSN:: 0014-4894
Subject:: protein secondary structure, etc ; Taenia solium; binding proteins; lipids; molecular cloning; nucleotide sequences; amino acid sequences; sequence homology; binding properties; gene expression; recombinant proteins; Golgi apparatus; metacestodes; Show all 13 Subjects
Abstract:: ... The objective of this work is to identify proteins of the human and porcine parasite, Taenia solium, which may be exploited for control of the parasite. Through screening a cDNA library of T. solium metacestodes, we have identified a novel Sec-14-like Taenia lipid-binding protein that may play an important role in membrane trafficking. The Sec14-like sequence is a single copy gene, encoding a puta ...
DOI:: 10.1016/j.exppara.2006.12.015
PubMed:: 17324397
: http://dx.doi.org/10.1016/j.exppara.2006.12.015

49. Effect of Solvent and Temperature on Secondary and Tertiary Structure of Zein by Circular Dichroism

Author:: Selling, G.W.; Hamaker, S.A.H.; Sessa, D.J.
Source:: Cereal chemistry 2007 v.84 no.3 pp. 265
ISSN:: 0009-0352
Subject:: protein secondary structure, etc ; zein; protein tertiary structure; solvents; ambient temperature; circular dichroism spectroscopy; pH; denaturation; acetic acid; dimethylformamide; sodium hydroxide; amino acid sequences; Show all 12 Subjects
Abstract:: ... Circular dichroism studies were performed on zein to determine how the secondary and tertiary structure changes with different solvents, temperatures, or pH. Alcoholic solvent type and common denaturants such as SDS and low amounts of urea had little effect on the secondary structure of zein. Utilization of dimethylformamide or acetic acid as solvent gave changes in tertiary structure. Solutions o ...
Handle:: 10113/12837
DOI:: 10.1094/CCHEM-84-3-0265
: http://dx.doi.org/10.1094/CCHEM-84-3-0265

50. Cloning and characterization of full-length coding sequence (CDS) of the ovine 37/67-kDa laminin receptor (RPSA)

Author:: Qiao, Junwen; Su, Xiaoou; Wang, Yiqin; Yang, Jianmin; Kouadir, Mohammed; Zhou, Xiangmei; Yin, Xiaomin; Zhao, Deming
Source:: Molecular biology reports 2009 v.36 no.8 pp. 2131-2137
ISSN:: 0301-4851
Subject:: protein secondary structure, etc ; chickens; messenger RNA; open reading frames; sequence alignment; sheep; cattle; reverse transcriptase polymerase chain reaction; single nucleotide polymorphism; amino acid sequences; mice; amino acids; swine; laminin; exons; prions; Show all 16 Subjects
Abstract:: ... The 37-kDa Laminin Receptor Precursor (LRP)/67-kDa Laminin Receptor (LR), also known as ribosomal protein SA (RPSA), had been identified as a putative cell surface receptor for prions. Herein, we isolated the full-length coding sequence (CDS) of the ovine 37/67-kDa LRP/LR gene and submitted it to the GenBank under accession number EF649775. The open reading frame (ORF) of the 37/67-kDa LRP/LR CDS ...
DOI:: 10.1007/s11033-008-9426-x
PubMed:: 19105045
: http://dx.doi.org/10.1007/s11033-008-9426-x

51. Comparative assessment of Th1 and Th2 cytokines of swamp type buffalo and other bubaline breeds by molecular cloning, sequencing and phylogenetics

Author:: Mingala, C.N.; Odbileg, R.; Konnai, S.; Ohashi, K.; Onuma, M.
Source:: Veterinary immunology and immunopathology 2006 v.113 no.3-4 pp. 348-356
ISSN:: 0165-2427
Subject:: protein secondary structure, etc ; breed differences; messenger RNA; buffaloes; alternative splicing; interleukins; phylogeny; amino acid sequences; genotype; nucleotide sequences; genetic variation; interferons; Show all 12 Subjects
Abstract:: ... Comparative assessment of Th1 and Th2 cytokines of three bubaline breeds namely swamp buffalo, its crossbreed with riverine buffalo (CB), and the improved breed of Bulgarian Murrah buffalo (BMB), was done by molecular cloning, sequencing and phylogenetic analysis. The Th1 cytokines analyzed included IL-2, IL-12p35, IL-12p40, and IFN-γ while Th2 cytokines included IL-4 and IL-10. Both groups showed ...
DOI:: 10.1016/j.vetimm.2006.06.005
: http://dx.doi.org/10.1016/j.vetimm.2006.06.005

52. Extensive analysis of different allelelic structures of the chicken BF2 and β2m proteins

Author:: Li, X.S.; Fang, Q.M.; Yan, R.Q.; Gao, F.S.; Hao, H.F.; Jia, Z.H.; Lin, C.Y.; Xia, C.
Source:: Veterinary immunology and immunopathology 2006 v.113 no.1-2 pp. 215-223
ISSN:: 0165-2427
Subject:: protein secondary structure, etc ; chickens; mathematical models; alleles; antigens; food animals; animal proteins; amino acid sequences; major histocompatibility complex; gene expression; binding sites; genetic polymorphism; Show all 12 Subjects
Abstract:: ... No information is available to date on the different allelelic structures of the chicken MHC class I (BF2) and β2m proteins. To elucidate the structure, new allelic β2m and five different BF2 genes were expressed solubly and purified in a pMAL-p2X/E. coli TB1 system. The 2D structure was detected by circular dichroism (CD) spectroscopy, and the 3D structures of their peptide-binding domain (PBD) w ...
DOI:: 10.1016/j.vetimm.2006.03.023
: http://dx.doi.org/10.1016/j.vetimm.2006.03.023

53. Evolution of spider silks: conservation and diversification of the C-terminus

Author:: Challis, R.J.; Goodacre, S.L.; Hewitt, G.M.
Source:: Insect molecular biology 2006 v.15 no.1 pp. 45-56
ISSN:: 0962-1075
Subject:: protein secondary structure, etc ; physical properties; sequence analysis; silk; fibroins; silk proteins; conserved sequences; phylogeny; amino acid sequences; genes; Araneae; nucleotide sequences; Show all 12 Subjects
Abstract:: ... Analysis of DNA sequences coding for the C-terminus of spider silk proteins from a range of spiders suggests that many silk C-termini share a common origin, and that their physical properties have been highly conserved over several hundred million years. These physical properties are compatible with roles in protein synthesis, silk function and in recruiting accessory proteins. Phylogenetic relati ...
DOI:: 10.1111/j.1365-2583.2005.00606.x
PubMed:: 16469067
: http://dx.doi.org/10.1111/j.1365-2583.2005.00606.x

54. Amino acid sequences and solution structures of manganese stabilizing protein that affect reconstitution of Photosystem II activity

Author:: Popelkova, H.; Wyman, A.; Yocum, C.
Source:: Photosynthesis research 2003 v.77 no.1 pp. 21-34
ISSN:: 0166-8595
Subject:: protein secondary structure, etc ; manganese; protein folding; protein tertiary structure; binding proteins; amino acid sequences; photosystem II; mutants; plant proteins; Show all 9 Subjects

55. Generation of deviation parameters for amino acid singlets, doublets and triplets from three-dimensional structures of proteins and its implications for secondary structure prediction from amino acid sequences

Author:: Mugilan, S. A.; Veluraja, K.
Source:: Journal of biosciences 2000 v.25 no.1 pp. 81-90
ISSN:: 0250-5991
Subject:: protein secondary structure, etc ; amino acid sequences; amino acids; data collection; prediction; proteins; Show all 6 Subjects
Abstract:: ... We present a new method, secondary structure prediction by deviation parameter (SSPDP) for predicting the secondary structure of proteins from amino acid sequence. Deviation parameters (DP) for amino acid singlets, doublets and triplets were computed with respect to secondary structural elements of proteins based on the dictionary of secondary structure prediction (DSSP)-generated secondary struct ...
DOI:: 10.1007/BF02985185
: http://dx.doi.org/10.1007/BF02985185

56. Common physical-chemical properties correlate with similar structure of the IgE epitopes of peanut allergens

Author:: Schein, C.H.; Ovanciuc, O.; Braun, W.
Source:: Journal of agricultural and food chemistry 2005 v.53 no.22 pp. 8752-8759
ISSN:: 0021-8561
Subject:: protein secondary structure, etc ; peanuts; allergens; epitopes; immunoglobulin E; antigen-antibody reactions; bioinformatics; databases; protein tertiary structure; amino acid sequences; physicochemical properties; plant proteins; allergenicity; Show all 13 Subjects
Abstract:: ... Although many sequences and linear IgE epitopes of allergenic proteins have been identified and archived in databases, structural and physicochemical discriminators that define their specific properties are lacking. Current bioinformatics tools for predicting the potential allergenicity of a novel protein use methods that were not designed to compare peptides. Novel tools to determine the quantita ...
DOI:: 10.1021/jf051148a
: http://dx.doi.org/10.1021/jf051148a

57. Topological and transcriptional analysis of pssL gene product: a putative Wzx-like exopolysaccharide translocase in Rhizobium leguminosarum bv. trifolii TA1

Author:: Mazur, Andrzej; Marczak, Małgorzata; Król, Jarosław E.; Skorupska, Anna
Source:: Archives of microbiology 2005 v.184 no.1 pp. 1-10
ISSN:: 0302-8933
Subject:: protein secondary structure, etc ; Rhizobium leguminosarum; amino acid sequences; cytoplasm; exopolysaccharides; genes; messenger RNA; polymerization; reverse transcriptase polymerase chain reaction; sequence homology; topology; transcription (genetics); translation (genetics); transporters; Show all 14 Subjects
Abstract:: ... An identified pssL gene is yet another one, besides the pssT, pssN and pssP genes, encoding for a protein engaged in polysaccharide polymerization and export in Rhizobium leguminosarum bv. trifolii strain TA1 (RtTA1). Amino acid sequence similarity and hypothetical protein secondary structure placed the PssL protein within Wzx (RfbX) translocases with putative flippase function that belong to the ...
DOI:: 10.1007/s00203-005-0018-z
PubMed:: 16044265
: http://dx.doi.org/10.1007/s00203-005-0018-z

58. Characterization of bullet tuna myoglobin with reference to the thermostability-structure relationship

Author:: Ueki, N.; Chow, C.J.; Ochiai, Y.
Source:: Journal of agricultural and food chemistry 2005 v.53 no.12 pp. 4968-4975
ISSN:: 0021-8561
Subject:: protein secondary structure, etc ; tuna; Scombridae; myoglobin; differential scanning calorimetry; complementary DNA; nucleotide sequences; amino acid sequences; heat stability; amino acid substitution; Show all 10 Subjects
Abstract:: ... Myoglobin (Mb) was isolated from bullet tuna (Auxis rochei) skeletal muscle and characterized from the viewpoint of the thermostability-structure relationship. Differential scanning calorimetry (DSC) measurement showed that the thermostability of bullet tuna Mb was the lowest among all the scombridae fish Mbs so far examined. The highest value (72.8 degrees C) of melting temperature (T(m)) was obt ...
DOI:: 10.1021/jf050261y
: http://dx.doi.org/10.1021/jf050261y

59. Molecular cloning of a new cDNA and expression of 3-hydroxy-3-methylglutaryl-CoA synthase gene from Hevea brasiliensis

Author:: Sirinupong, N.; Suwanmanee, P.; Doolittle, R.F.; Suvachitanont, W.
Source:: Planta 2005 v.221 no.4 pp. 502-512
ISSN:: 0032-0935
Subject:: protein secondary structure, etc ; Hevea brasiliensis; plant genetics; plant biochemistry; oxo-acid-lyases; complementary DNA; sequence alignment; amino acid sequences; gene expression; nucleotide sequences; enzyme activity; plant proteins; Show all 12 Subjects
Abstract:: ... 3-Hydroxy-3-methylglutaryl-CoA synthase (HMGS), EC 4.1.3.5, is an essential enzyme in rubber biosynthesis in Hevea brasiliensis. We have isolated a new cDNA encoding HMGS in H. brasiliensis. The full-length hmgs2 consists of 1,916-bp and encodes a protein of 464 amino acids with a predicted molecular mass of 51.27 kDa and an isoelectric point of 6.02. In comparison, HMGS1 and HMGS2 show 92% and 94 ...
DOI:: 10.1007/s00425-004-1463-7
PubMed:: 15744497
: http://dx.doi.org/10.1007/s00425-004-1463-7

60. Effects of turn residues on beta-hairpin folding--a molecular dynamics study

Author:: Wang, H.; Sung, S.S.
Source:: Biopolymers 1999 v.50 no.7 pp. 763-776
ISSN:: 0006-3525
Subject:: protein secondary structure, etc ; protein folding; energy; amino acid sequences; solvents; temperature; molecular conformation; synthetic peptides; Show all 8 Subjects
DOI:: 10.1002/(SICI)1097-0282(199912)50:7<763::AID-BIP9>3.0.CO;2-W
PubMed:: 10547531
: http://dx.doi.org/10.1002/(SICI)1097-0282(199912)50:7<763::AID-BIP9>3.0.CO;2-W

61. Interleukin-10 expression by real-time PCR and homology modelling analysis in the European sea bass (Dicentrarchus Labrax L.)

Author:: Buonocore, F.; Randelli, E.; Bird, S.; Secombes, C.J.; Facchiano, A.; Costantini, S.; Scapigliati, G.
Source:: Aquaculture 2007 v.270 no.1-4 pp. 512-522
ISSN:: 0044-8486
Subject:: protein secondary structure, etc ; Dicentrarchus labrax; marine fish; interleukin-10; molecular cloning; complementary DNA; sequence analysis; conserved sequences; gene expression regulation; tissue distribution; anti-inflammatory activity; polymerase chain reaction; molecular models; fish culture; amino acid sequences; Show all 15 Subjects
Abstract:: ... In this paper we investigate the interleukin-10 (IL-10) expression and 3D modelling of the European sea bass (Dicentrarchus labrax L.). IL-10 is a regulatory cytokine that has been intensively studied in mammals and has been found mainly involved in the suppression or deactivation of activated immune responses. The full-length sea bass IL-10 cDNA consists of 1015 bp and is translated in a predicte ...
DOI:: 10.1016/j.aquaculture.2007.05.040
: http://dx.doi.org/10.1016/j.aquaculture.2007.05.040

62. ASP53, a thermostable protein from Acacia erioloba seeds that protects target proteins against thermal denaturation

Author:: Mtwisha, L.; Farrant, J.M.; Brandt, W.; Hlongwane, C.; Lindsey, G.G.
Source:: Functional plant biology 2007 v.34 no.2 pp. 139-149
ISSN:: 1445-4408
Subject:: protein secondary structure, etc ; messenger RNA; Acacia; air temperature; plant proteins; vacuoles; cotyledons; heat stress; trees; amino acid sequences; xerophytes; nucleotide sequences; cell wall components; protein degradation; immunocytochemistry; desiccation (plant physiology); pods; Show all 17 Subjects
DOI:: 10.1071/FP06135
: http://dx.doi.org/10.1071/FP06135

63. Gene cloning and characterization of a soybean (Glycine max L.) LEA protein, GmPM16

Author:: Shih, M.D.; Lin, S.C.; Hsieh, J.S.; Tsou, C.H.; Chow, T.Y.; Lin, T.P.; Hsing, Y.I.C.
Source:: Plant molecular biology 2004 v.56 no.5 pp. 689-703
ISSN:: 0167-4412
Subject:: protein secondary structure, etc ; messenger RNA; Glycine max; complementary DNA; soybeans; seed development; isoelectric point; cotyledons; gene expression; amino acid sequences; genes; nucleotide sequences; molecular weight; plant proteins; Show all 14 Subjects
Abstract:: ... Late embryogenesis abundant (LEA) proteins, present in abundance in seeds during the late stages of development, are associated with desiccation tolerance. In the present work, we characterize a soybean LEA protein, GmPM16, with low molecular weight, high pI value, and an unusual amino acid residue distribution along the protein. The transcripts were detected in cotyledon mesophyll cells but not i ...
PubMed:: 15803408

64. Structure-function analysis of the presumptive Arabidopsis auxin permease AUX1

Author:: Swarup, R.; Kargul, J.; Marchant, A.; Zadik, D.; Rahman, A.; Mills, R.; Yemm, A.; May, S.; Williams, L.; Millner, P.
Source:: plant cell 2004 v.16 no.11 pp. 3069-3083
ISSN:: 1040-4651
Subject:: protein secondary structure, etc ; Arabidopsis thaliana; membrane proteins; plasma membrane; auxins; active transport; cytochemistry; mutants; missense mutation; amino acid substitution; amino acid sequences; Show all 11 Subjects
Abstract:: ... We have investigated the subcellular localization, the domain topology, and the amino acid residues that are critical for the function of the presumptive Arabidopsis thaliana auxin influx carrier AUX1. Biochemical fractionation experiments and confocal studies using an N-terminal yellow fluorescent protein (YFP) fusion observed that AUX1 colocalized with plasma membrane (PM) markers. Because of it ...
DOI:: 10.1105/tpc.104.024737
PubMed:: 15486104
PubMed Central:: PMC527199
: http://dx.doi.org/10.1105/tpc.104.024737

65. Synergistic antifungal activity of two chitin-binding proteins from spindle tree (Euonymus europaeus L.)

Author:: Bergh, K.P.B. van den; Rouge, P.; Proost, P.; Coosemans, J.; Krouglova, T.; Engelborghs, Y.; Peumans, W.J.; Damme, E.J.M. van
Source:: Planta 2004 v.219 no.2 pp. 221-232
ISSN:: 0032-0935
Subject:: protein secondary structure, etc ; N-acetylglucosamine; Euonymus europaeus; molecular models; complementary DNA; sequence alignment; confocal laser scanning microscopy; antifungal properties; amino acid sequences; hevein; nucleotide sequences; chitin; chitinase; Show all 13 Subjects
Abstract:: ... Two structurally different chitin-binding proteins were isolated from bark and leaves of the spindle tree (Euonymus europaeus L.). Both the small hevein-like chitin-binding protein (Ee-CBP) and the classical class-I chitinase (Ee-chitinase) possess antifungal properties, Ee-CBP being far more potent than Ee-chitinase. In addition, Ee-CBP and Ee-chitinase display a pronounced synergistic effect whe ...
DOI:: 10.1007/s00425-004-1238-1
PubMed:: 15048569
: http://dx.doi.org/10.1007/s00425-004-1238-1

66. Crystal structure of the regulatory subunit H of the V-type ATPase of Saccharomyces cerevisiae

Author:: Sagermann, M.; Stevens, T.H.; Matthews, B.W.
Source:: Proceedings of the National Academy of Sciences of the United States of America 2001 v.98 no.13 pp. 7134-7139
ISSN:: 0027-8424
Subject:: protein secondary structure, etc ; X-ray diffraction; Saccharomyces cerevisiae; adenosinetriphosphatase; vacuoles; tonoplast; crystals; molecular conformation; amino acid sequences; Show all 9 Subjects
Abstract:: ... In contrast to the F-type ATPases, which use a proton gradient to generate ATP, the V-type enzymes use ATP to actively transport protons into organelles and extracellular compartments. We describe here the structure of the H-subunit (also called Vma13p) of the yeast enzyme. This is the first structure of any component of a V-type ATPase. The H-subunit is not required for assembly but plays an esse ...
DOI:: 10.1073/pnas.131192798
PubMed:: 11416198
PubMed Central:: PMC34635
: http://dx.doi.org/10.1073/pnas.131192798

67. Biological activities and structural properties of the atypical bacteriocins mesenterocin 52B and leucocin B-TA33a

Author:: Corbier, C.; Krier, F.; Mulliert, G.; Vitoux, B.; Revol-Junelles, A.M.
Source:: Applied and environmental microbiology 2001 v.67 no.4 pp. 1418-1422
ISSN:: 0099-2240
Subject:: protein secondary structure, etc ; bacteriocins; amino acid sequences; synthetic peptides; molecular conformation; antibacterial properties; Leuconostoc; lactic acid bacteria; spectroscopy; Weissella; Show all 10 Subjects
Abstract:: ... The antibacterial spectra and modes of action of synthetic peptides corresponding to mesenterocin 52B and leucocin B-TA33a greatly differ despite their high sequence homology. Circular dichroism experiments establish the capacity of each of these two peptides to partly fold into an amphiphilic helix that might be crucial for their adsorption at lipophilic-hydrophilic interfaces. ...
DOI:: 10.1128/AEM.67.4.1418-1422.2001
PubMed:: 11282585
PubMed Central:: PMC92749
: http://dx.doi.org/10.1128/AEM.67.4.1418-1422.2001

68. Reconstruction of a swine SLA-I protein complex and determination of binding nonameric peptides derived from the foot-and-mouth disease virus

Author:: Gao, F.S.; Fang, Q.M.; Li, Y.G.; Li, X.S.; Hao, H.F.; Xia, C.
Source:: Veterinary immunology and immunopathology 2006 v.113 no.3-4 pp. 328-338
ISSN:: 0165-2427
Subject:: protein secondary structure, etc ; T-lymphocytes; recombinant fusion proteins; polymerase chain reaction; peptides; amino acid sequences; binding proteins; swine; viral proteins; Foot-and-mouth disease virus; mass spectrometry; molecular weight; viral antigens; Show all 13 Subjects
Abstract:: ... No experimental system to date is available to identify viral T-cell epitopes in swine. In order to reconstruct the system for identification of short antigenic peptides, the swine SLA-2 gene was linked to the β2m gene via (G4S)3, a linker encoding a 15-amino acid glycine-rich sequence (G4S)3, using splicing overlap extension-PCR (SOE-PCR). The maltose binding protein (MBP)-SLA-2-(G4S)3-β2m fusion ...
DOI:: 10.1016/j.vetimm.2006.06.002
: http://dx.doi.org/10.1016/j.vetimm.2006.06.002

69. Structure and function of antimicrobial peptide penaeidin-5 from the black tiger shrimp Penaeus monodon

Author:: Hu, S.Y.; Huang, J.H.; Huang, W.T.; Yeh, Y.H.; Chen, M.H.C.; Gong, H.Y.; Chiou, T.T.; Yang, T.H.; Chen, T.T.; Lu, J.K.
Source:: Aquaculture 2006 v.260 no.1-4 pp. 61-68
ISSN:: 0044-8486
Subject:: protein secondary structure, etc ; messenger RNA; animal proteins; Fusarium oxysporum; Vibrio alginolyticus; tissue distribution; Penaeus monodon; amino acid sequences; antimicrobial peptides; Aerococcus viridans; animal pathogenic bacteria; antifungal properties; plant pathogenic fungi; shrimp; shrimp culture; circular dichroism spectroscopy; antibacterial properties; Show all 17 Subjects
Abstract:: ... The gene for penaeidin-5, an antimicrobial peptide comprising 55 amino acids, was isolated from the hemocyte of black tiger shrimp (Penaeus monodon). RT-PCR expression tests revealed that penaeidin-5 was produced in hemocytes, gills, the intestine and muscle. Western blot analysis confirmed the panaeidin-5 was aboundantin hemocytes, the intestine and hemolymph. Immunohistochemistry revealedpenaeid ...
DOI:: 10.1016/j.aquaculture.2006.06.017
: http://dx.doi.org/10.1016/j.aquaculture.2006.06.017

70. cDNA sequences, MALDI-TOF analyses, and molecular modelling of barley PR-5 proteins

Author:: Reiss, E.; Schlesier, B.; Brandt, W.
Source:: Phytochemistry 2006 v.67 no.17 pp. 1856-1864
ISSN:: 0031-9422
Subject:: protein secondary structure, etc ; sequence analysis; post-translational modification; barley; molecular models; plant biochemistry; complementary DNA; Hordeum vulgare; two-dimensional gel electrophoresis; protein isoforms; amino acid sequences; spectral analysis; pathogenesis-related proteins; Show all 13 Subjects
Abstract:: ... Barley plants are known to produce various PR-5 proteins. Transcripts encoding eight different barley PR-5 proteins (TLPs 1-8, TLP for thaumatin-like protein) were identified and cloned - seven from infected leaves and one from developing grains. Here, we describe the cDNA sequences of four of these TLP isoforms. Moreover, the TLPs from the infected leaves (TLPs 1, 2, and TLPs 4-8) were subjected ...
DOI:: 10.1016/j.phytochem.2006.06.014
PubMed:: 16876835
: http://dx.doi.org/10.1016/j.phytochem.2006.06.014

71. Purification and characterization of brochocin A and brochocin B(10-43), a functional fragment generated by heterologous expression in Carnobacterium piscicola

Author:: Garneau, S.; Ference, C.A.; Van Belkum, M.J.; Stiles, M.E.; Vederas, J.C.
Source:: Applied and environmental microbiology 2003 v.69 no.3 pp. 1352-1358
ISSN:: 0099-2240
Subject:: protein secondary structure, etc ; gene transfer; structural genes; Brochothrix campestris; bacteriocins; amino acid sequences; gene expression; nucleotide sequences; Carnobacterium piscicola; food preservatives; antibacterial properties; Show all 11 Subjects
Abstract:: ... Brochothrix campestris ATCC 43754 produces a heat-stable, two-component, nonlantibiotic, class IIb bacteriocin, brochocin C (BrcC), that is active against a broad range of gram-positive bacteria, including spores of Clostridium botulinum. An improved purification method was developed for BrcC, in which n-butanol and chloroform extraction are used. Mass spectral characterization of the two componen ...
DOI:: 10.1128/AEM.69.3.1352-1358.2003
PubMed:: 12620816
PubMed Central:: PMC150086
: http://dx.doi.org/10.1128/AEM.69.3.1352-1358.2003

72. The clot gene of Drosophila melanogaster encodes a conserved member of the Thioredoxin-like protein superfamily

Author:: Giordano, E.; Peluso, I.; Rendina, R.; Digilio, A.; Furia, M.
Source:: Molecular genetics and genomics 2003 v.268 no.5 pp. 692-697
ISSN:: 1617-4615
Subject:: protein secondary structure, etc ; proteins; messenger RNA; alleles; complementary DNA; amino acid sequences; oxidoreductases; gene expression; nucleotide sequences; molecular conformation; Drosophila melanogaster; Show all 11 Subjects
PubMed:: 12589444

73. Cloning and expression of a cDNA coding for catalase from zebrafish (Danio rerio)

Author:: Ken, C.F.; Lin, C.T.; Wu, J.L.; Shaw, J.F.
Source:: Journal of agricultural and food chemistry 2000 v.48 no.6 pp. 2092-2096
ISSN:: 0021-8561
Subject:: protein secondary structure, etc ; interspecific variation; complementary DNA; open reading frames; amino acid sequences; Danio rerio; enzyme activity; molecular conformation; Show all 8 Subjects
DOI:: 10.1021/jf990838+
PubMed:: 10888504
: http://dx.doi.org/10.1021/jf990838+

74. Light stress-regulated two-helix proteins in Arabidopsis thaliana related to the chlorophyll a/b-binding gene family

Author:: Heddad, M.; Adamska, I.
Source:: Proceedings of the National Academy of Sciences of the United States of America 2000 v.97 no.7 pp. 3741-3746
ISSN:: 0027-8424
Subject:: protein secondary structure, etc ; Arabidopsis thaliana; nucleotide sequences; amino acid sequences; molecular conformation; gene expression; light intensity; messenger RNA; cytochemistry; thylakoids; Show all 10 Subjects
Abstract:: ... The chlorophyll a/b, chlorophyll a/c, and chlorophyll a/a light-harvesting proteins are part of an extended gene family that also includes the transiently expressed stress proteins, the Elips (early light-induced proteins). Four Elip homologue proteins, encoded by single-copy nuclear genes, have been identified in the Arabidopsis thaliana database. These proteins were divided into two groups accor ...
DOI:: 10.1073/pnas.97.7.3741
PubMed:: 10725357
PubMed Central:: PMC16310
: http://dx.doi.org/10.1073/pnas.97.7.3741

75. Evidence that a plant virus switched hosts to infect a vertebrate and then recombined with a vertebrate-infecting virus

Author:: Gibbs, M.J.; Weiller, G.F.
Source:: Proceedings of the National Academy of Sciences of the United States of America 1999 v.96 no.14 pp. 8022-8027
ISSN:: 0027-8424
Subject:: protein secondary structure, etc ; plant viruses; Caliciviridae; replication origin; phylogeny; amino acid sequences; viral proteins; Porcine circovirus; molecular conformation; genetic recombination; Show all 10 Subjects
Abstract:: ... There are several similarities between the small, circular, single-stranded-DNA genomes of circoviruses that infect vertebrates and the nanoviruses that infect plants. We analyzed circovirus and nanovirus replication initiator protein (Rep) sequences and confirmed that an N-terminal region in circovirus Reps is similar to an equivalent region in nanovirus Reps. However, we found that the remaining ...
DOI:: 10.1073/pnas.96.14.8022
PubMed:: 10393941
PubMed Central:: PMC22181
: http://dx.doi.org/10.1073/pnas.96.14.8022

76. Protein structures of common bean (Phaseolus vulgaris) alpha-amylase inhibitors

Author:: Lee, S.C.; Gepts, P.L.; Whitaker, J.R.
Source:: Journal of agricultural and food chemistry 2002 v.50 no.22 pp. 6618-6627
ISSN:: 0021-8561
Subject:: protein secondary structure, etc ; beans; plant proteins; enzyme inhibitors; alpha-amylase; nucleotide sequences; amino acid sequences; molecular weight; molecular conformation; protein tertiary structure; Show all 10 Subjects
Abstract:: ... Two nucleotide sequences for genes that encode alpha-amylase inhibitor 4 (alphaAI-4) from white kidney bean (WKB) cv. 858, designated gene alphaAI-4 (Accession No. U84390), and alpha-amylase inhibitor 5 (alphaAI-5) from black bean (BB), designated gene alphaAI-5 (Accession No. U84391), were determined. Genes alphaAI-4 and alphaAI-5 encode 244 amino acid prepro-alphaAI-4 and prepro-alphaAI-5 polype ...
DOI:: 10.1021/jf020189t
PubMed:: 12381161
: http://dx.doi.org/10.1021/jf020189t

77. Sequence evolution and sex-specific expression patterns of the C class floral identity gene, SpAGAMOUS, in dioecious Spinacia oleracea L

Author:: Sather, D.N.; York, A.; Pobursky, K.J.; Golenberg, E.M.
Source:: Planta 2005 v.222 no.2 pp. 284-292
ISSN:: 0032-0935
Subject:: protein secondary structure, etc ; sequence analysis; plant genetics; flowering; Silene latifolia; complementary DNA; homeotic genes; spinach; evolution; vegetable crops; conserved sequences; Spinacia oleracea; amino acid sequences; nucleotide sequences; gene expression regulation; Show all 15 Subjects
Abstract:: ... Development in dioecious cultivated spinach, Spinacia oleracea, is distinguished by the absence of alternative reproductive organ primordia in male and female flowers. Given the highly derived floral developmental program in spinach, we wished to characterize a spinach C class floral identity gene and to determine the patterns of sequence evolution as well as compare the spatial and temporal expre ...
DOI:: 10.1007/s00425-005-1544-2
PubMed:: 15940462
: http://dx.doi.org/10.1007/s00425-005-1544-2

78. Cloning, characterization and structural model of a FatA-type thioesterase from sunflower seeds (Helianthus annuus L.)

Author:: Serrano-Vega, M.J.; Garces, R.; Martinez-Force, E.
Source:: Planta 2005 v.221 no.6 pp. 868-880
ISSN:: 0032-0935
Subject:: protein secondary structure, etc ; Helianthus annuus; oilseeds; thiolester hydrolases; complementary DNA; sequence analysis; gene expression; Escherichia coli; recombinant fusion proteins; enzyme activity; substrate specificity; enzyme kinetics; molecular models; site-directed mutagenesis; plant biochemistry; plant genetics; nucleotide sequences; amino acid sequences; Show all 18 Subjects
Abstract:: ... The substrate specificity of acyl-acyl carrier protein (ACP) thioesterases (EC 3.1.2.14) determines the fatty acids available for the biosynthesis of storage and membrane lipids in seeds. In order to determine the mechanisms involved in the biosynthesis of fatty acids in sunflower seeds (Helianthus annuus L.), we isolated, cloned and sequenced a cDNA clone of acyl-ACP thioesterase from developing ...
DOI:: 10.1007/s00425-005-1502-z
PubMed:: 15841386
: http://dx.doi.org/10.1007/s00425-005-1502-z

79. Folding of the squash trypsin inhibitor EETI II. Evidence of native and non-native local structural preferences in a linear analogue

Author:: Heitz, A.; Chiche, L.; Le-Nguyen, D.; Castro, B.
Source:: European journal of biochemistry 1995 v.233 no.3 pp. 837-846
ISSN:: 0014-2956
Subject:: protein secondary structure, etc ; protein folding; trypsin inhibitors; amino acid sequences; spectral analysis; molecular conformation; synthetic peptides; Show all 7 Subjects
Abstract:: ... A peptide, corresponding to the entire sequence of the squash trypsin inhibitor EETI II (Ecballium elaterium trypsin inhibitor) in which the six cysteines, engaged in three disulphide bridges in native EETI II, have been replaced by six serines, has been synthesised. CD, Fourier-transform infrared spectroscopy (FTIR) and 1H-NMR studies of this peptide revealed that some secondary structures presen ...
DOI:: 10.1111/j.1432-1033.1995.837_3.x
PubMed:: 8521849
: http://dx.doi.org/10.1111/j.1432-1033.1995.837_3.x

80. Prediction of protein folding class using global description of amino acid sequence

Author:: Dubchak, I.; Muchnik, I.; Holbrook, S.R.; Kim, S.H.
Source:: Proceedings of the National Academy of Sciences of the United States of America 1995 v.92 no.19 pp. 8700-8704
ISSN:: 0027-8424
Subject:: protein secondary structure, etc ; proteins; molecular conformation; amino acid sequences; prediction; computer analysis; hydrophobicity; solvents; neural networks; Show all 9 Subjects
Abstract:: ... We present a method for predicting protein folding class based on global protein chain description and a voting process. Selection of the best descriptors was achieved by a computer-simulated neural network trained on a data base consisting of 83 folding classes. Protein-chain descriptors include overall composition, transition, and distribution of amino acid attributes, such as relative hydrophob ...
DOI:: 10.1073/pnas.92.19.8700
PubMed:: 7568000
PubMed Central:: PMC41034
: http://dx.doi.org/10.1073/pnas.92.19.8700

81. On the existence and implications of an inverse folding code in proteins

Author:: Rackovsky, S.
Source:: Proceedings of the National Academy of Sciences of the United States of America 1995 v.92 no.15 pp. 6861-6863
ISSN:: 0027-8424
Subject:: protein secondary structure, etc ; proteins; amino acid sequences; molecular conformation; protein folding; Show all 5 Subjects
Abstract:: ... The existence of a code relating the set of possible sequences at a given position in a protein backbone to the local structure at that location is investigated. It is shown that only 73% of 4-C alpha structure fragments in a sample of 114 protein structures exhibit a preference for a particular set of sequences. The remaining structures can accommodate essentially any sequence. The structures tha ...
DOI:: 10.1073/pnas.92.15.6861
PubMed:: 7624332
PubMed Central:: PMC41429
: http://dx.doi.org/10.1073/pnas.92.15.6861

82. Structural and functional differences in two cyclic bacteriocins with the same sequences produced by lactobacilli

Author:: Kawai, Y.; Ishii, Y.; Arakawa, K.; Uemura, K.; Saitoh, B.; Nishimura, J.; Kitazawa, H.; Yamazaki, Y.; Tateno, Y.; Itoh, T.
Source:: Applied and environmental microbiology 2004 v.70 no.5 pp. 2906-2911
ISSN:: 0099-2240
Subject:: protein secondary structure, etc ; mechanism of action; intestinal microorganisms; membrane permeability; food biopreservatives; alanine; bacteriocins; amino acid sequences; potassium; amino acid composition; plasma membrane; Lactobacillus reuteri; Lactobacillus gasseri; circular dichroism spectroscopy; antibacterial properties; Show all 15 Subjects
Abstract:: ... Lactobacillus gasseri LA39 and L. reuteri LA6 isolated from feces of the same human infant were found to produce similar cyclic bacteriocins (named gassericin A and reutericin 6, respectively) that cannot be distinguished by molecular weights or primary amino acid sequences. However, reutericin 6 has a narrower spectrum than gassericin A. In this study, gassericin A inhibited the growth of L. reut ...
DOI:: 10.1128/AEM.70.5.2906-2911.2004
PubMed:: 15128550
PubMed Central:: PMC404377
: http://dx.doi.org/10.1128/AEM.70.5.2906-2911.2004

83. Evolutionary dynamics of the DNA-binding domains in putative R2R3-MYB genes identified from rice subspecies indica and japonica genomes

Author:: Jia, L.; Clegg, M.T.; Jiang, T.
Source:: Plant physiology 2004 v.134 no.2 pp. 575-585
ISSN:: 0032-0889
Subject:: protein secondary structure, etc ; Arabidopsis thaliana; transcription factors; protein binding; rice; plant genetics; grain crops; Oryza sativa; conserved sequences; phylogeny; amino acid sequences; binding sites; DNA-binding proteins; natural selection; plant proteins; Show all 15 Subjects
Abstract:: ... The molecular evolution of the R2R3-MYB gene family is of great interest because it is one of the most important transcription factor gene families in the plant kingdom. Comparative analyses of a gene family may reveal important adaptive changes at the protein level and thereby provide insights that relate structure to function. We have performed a range of comparative and bioinformatics analyses ...
DOI:: 10.1104/pp.103.027201
PubMed:: 14966247
PubMed Central:: PMC344534
: http://dx.doi.org/10.1104/pp.103.027201

84. Phylogenetic relationship of organisms obtained by ribosomal protein comparison

Author:: Muller, E.C.; Wittmann-Liebold, B.
Source:: Cellular and molecular life sciences 1997 v.53 no.1 pp. 34-50
ISSN:: 1420-682X
Subject:: protein secondary structure, etc ; proteins; chloroplasts; interspecific variation; phylogeny; eukaryotic cells; amino acid sequences; ribosomes; mitochondria; molecular conformation; bacteria; fungi; Show all 12 Subjects
PubMed:: 9117996

85. The apocytochrome-b gene in Chlorogonium elongatum (Chlamydomonadaceae): an intronic GIY-YIG ORF in green algal mitochondria

Author:: Kroymann, J.; Zetsche, K.
Source:: Current genetics 1997 v.31 no.5 pp. 414-418
ISSN:: 0172-8083
Subject:: protein secondary structure, etc ; apoproteins; structural genes; mitochondrial DNA; Chlorophyta; amino acid sequences; exons; cytochrome b; introns; molecular conformation; Show all 10 Subjects
Abstract:: ... The mitochondrial cob gene from the green alga Chlorogonium elongatum (Chlamydomonadaceae) is interrupted by two group-I introns each containing an open reading frame in-phase with the upstream exon. One of these ORFs belongs to the LAGLI-DADG family, the other to the GIY-YIG family. The latter has not yet been identified in any mitochondrial genome except those from fungi. The Chlorogonium ORFs a ...
DOI:: 10.1007/s002940050224
PubMed:: 9162113
: http://dx.doi.org/10.1007/s002940050224

86. Fat body expressed yolk protein genes in Hyphantria cunea are related to the YP4 follicular epithelium yolk protein subunit gene of pyralid moths

Author:: Cheon, H.M.; Kim, H.J.; Yun, C.Y.; Lee, H.J.; Lee, I.H.; Shirk, P.D.; Seo, S.J.
Source:: Insect molecular biology 2003 v.12 no.4 pp. 383
ISSN:: 0962-1075
Subject:: protein secondary structure, etc ; Hyphantria cunea; yolk proteins; structural genes; complementary DNA; nucleotide sequences; amino acid sequences; sequence alignment; sequence homology; vitellogenin; protein subunits; Pyralidae; moths; gene expression; messenger RNA; fat body; developmental stages; insect pests; Show all 18 Subjects
Abstract:: ... cDNA clones for two of the yolk proteins, YP1 and YP2, produced by the fat body of the moth, Hyphantria cunea, were sequenced and found to be homologous to the follicular epithelium yolk proteins of pyralid moths. Both cDNA clones coded for polypeptides of 290 residues and the deduced amino acid sequence identity between YP1 and YP2 was very high (79.0%). Analysis of the secondary structure of the ...
Handle:: 10113/2526
DOI:: 10.1046/j.1365-2583.2003.00422.x
PubMed:: 12864918
: http://dx.doi.org/10.1046/j.1365-2583.2003.00422.x

87. Identification of a high-affinity phosphate transporter gene in a prasinophyte alga, Tetraselmis chui, and its expression under nutrient limitation

Author:: Chung, C.C.; Hwang, S.P.L.; Chang, J.
Source:: Applied and environmental microbiology 2003 v.69 no.2 pp. 754-759
ISSN:: 0099-2240
Subject:: protein secondary structure, etc ; microalgae; phytoplankton; complementary DNA; structural genes; nucleotide sequences; amino acid sequences; transporters; phosphates; transcription (genetics); messenger RNA; gene expression regulation; nutrient deficiencies; hydrophobicity; nutrient availability; alkaline phosphatase; enzyme activity; Show all 17 Subjects
Abstract:: ... A high-affinity phosphate transporter gene, TcPHO, was isolated from a growth-dependent subtracted cDNA library of the marine unicellular alga Tetraselmis chui. The full-length cDNA of TcPHO obtained by 5' and 3' rapid amplification of cDNA ends was 1,993 bp long and encoded an open reading frame consisting of 610 amino acids. The deduced amino acid sequence of TcPHO exhibited 51.6 and 49.8% simil ...
DOI:: 10.1128/AEM.69.2.754-759.2003
PubMed:: 12570992
PubMed Central:: PMC143611
: http://dx.doi.org/10.1128/AEM.69.2.754-759.2003

88. Complex group-I introns in nuclear SSU rDNA of red and green algae: evidence of homing-endonuclease pseudogenes in the Bangiophyceae

Author:: Haugen, P.; Huss, V.A.R.; Nielsen, H.; Johansen, S.
Source:: Current genetics 1999 v.36 no.6 pp. 345-353
ISSN:: 0172-8083
Subject:: protein secondary structure, etc ; pseudogenes; ribosomal RNA; open reading frames; catalytic activity; ribosomal DNA; Scenedesmus; amino acid sequences; ribosomal proteins; nucleases; introns; molecular conformation; Rhodophyta; Show all 13 Subjects
DOI:: 10.1007/s002940050509
PubMed:: 10654088
: http://dx.doi.org/10.1007/s002940050509

89. A group-I intron in the mitochondrial small subunit ribosomal RNA gene of Sclerotinia sclerotiorum

Author:: Carbone, I.; Anderson, J.B.; Kohn, L.M.
Source:: Current genetics 1995 v.27 no.2 pp. 166-176
ISSN:: 0172-8083
Subject:: protein secondary structure, etc ; Sclerotinia sclerotiorum; ribosomal RNA; open reading frames; mitochondrial DNA; ribosomal DNA; amino acid sequences; introns; molecular conformation; Show all 9 Subjects
Abstract:: ... A 1 380-bp intervening sequence within the mitochondrial small subunit ribosomal RNA (mt SSU rRNA) gene of the fungus Sclerotinia sclerotiorum has been sequenced and identified as a group-1 intron. This is the first report of an intron in the mt SSU rRNA gene. The intron shows close similarity in secondary structure to the subgroup-IC2 introns from Podospora (ND3i1, ND5i2, and COIi5) and Neurospor ...
DOI:: 10.1007/BF00313431
PubMed:: 7788720
: http://dx.doi.org/10.1007/BF00313431

90. The cox2 locus of the primitive angiosperm plant Acorus calamus: molecular structure, transcript processing and RNA editing

Author:: Albertazzi, F.J.; Kudla, J.; Bock, R.
Source:: MGG 1998 v.259 no.6 pp. 591-600
ISSN:: 0026-8925
Subject:: protein secondary structure, etc ; messenger RNA; alternative splicing; loci; mitochondrial DNA; phylogeny; amino acid sequences; gene expression; cytochrome-c oxidase; RNA editing; Acorus calamus; molecular conformation; introns; Show all 13 Subjects
DOI:: 10.1007/s004380050852
PubMed:: 9819051
: http://dx.doi.org/10.1007/s004380050852

91. SIRE-1, a copia/Ty1-like retroelement from soybean, encodes a retroviral envelope-like protein

Author:: Laten, H.M.; Majumdar, A.; Gaucher, E.A.
Source:: Proceedings of the National Academy of Sciences of the United States of America 1998 v.95 no.12 pp. 6897-6902
ISSN:: 0027-8424
Subject:: protein secondary structure, etc ; RNA-directed DNA polymerase; retrotransposons; Glycine max; Retroviridae; transmembrane proteins; open reading frames; amino acid sequences; molecular conformation; Show all 9 Subjects
Abstract:: ... The soybean genome hosts a family of several hundred, relatively homogeneous copies of a large, copia/Ty1-like retroelement designated SIRE-1. A copy of this element has been recovered from a Glycine max genomic library. DNA sequence analysis of two SIRE-1 subclones revealed that SIRE-1 contains a long, uninterrupted, ORF between the 3' end of the pol ORF and the 3' long terminal repeat (LTR), a r ...
DOI:: 10.1073/pnas.95.12.6897
PubMed:: 9618510
PubMed Central:: PMC22677
: http://dx.doi.org/10.1073/pnas.95.12.6897

92. Two-dimensional 1H-NMR studies of maize lipid-transfer protein. Sequence-specific assignment and secondary structure

Author:: Petit, M.C.; Sodano, P.; Marion, D.; Ptak, M.
Source:: European journal of biochemistry 1994 v.222 no.3 pp. 1047-1054
ISSN:: 0014-2956
Subject:: protein secondary structure, etc ; Zea mays; seeds; lipids; binding proteins; amino acid sequences; binding sites; structure-activity relationships; spectral analysis; Show all 9 Subjects
Abstract:: ... Correlation spectroscopy (COSY), total correlation spectroscopy (TOCSY) and NOE spectroscopy (NOESY) experiments have been used to assign sequentially the 1H 500-MHz NMR spectra of a non-specific (ns) lipid-transfer protein extracted from maize seeds. The spin-system identification and sequential assignment were combined with secondary-structure determination to identify most of the proton resonan ...
DOI:: 10.1111/j.1432-1033.1994.tb18957.x
PubMed:: 8026483
: http://dx.doi.org/10.1111/j.1432-1033.1994.tb18957.x

93. Polymorphism of the thrombostasin gene in the horn fly (Haematobia irritans) revealed in a cDNA library and in genomic DNA

Author:: Zhang, D.; Cupp, M.S.; Cupp, E.W.
Source:: Molecular genetics and genomics 2001 v.266 no.2 pp. 296-302
ISSN:: 1617-4615
Subject:: protein secondary structure, etc ; DNA libraries; alleles; complementary DNA; molecular weight; mutation; heterozygosity; amino acid sequences; isoelectric point; Haematobia irritans; proteinase inhibitors; nucleotide sequences; genetic variation; thrombin; molecular conformation; saliva; Show all 16 Subjects
DOI:: 10.1007/s004380100556
PubMed:: 11683272
: http://dx.doi.org/10.1007/s004380100556

94. Cloning and characterization of a pollen-specific cDNA encoding a glutamic-acid-rich protein (GARP) from potato Solanum berthaultii

Author:: Liu, Jun-qi; Seul, Ursula; Thompson, Richard
Source:: Plant molecular biology 1997 v.33 no.2 pp. 291-300
ISSN:: 0167-4412
Subject:: protein secondary structure, etc ; 5' untranslated regions; Solanum berthaultii; amino acid sequences; amino acids; cDNA libraries; clones; complementary DNA; immunoblotting; molecular weight; plant proteins; pollen; pollen tubes; potatoes; Show all 14 Subjects
Abstract:: ... A pollen-specific cDNA was isolated from a cDNA library of in vitro germinated pollen of the diploid potato species Solanum berthaultii. The cDNA clone, designated SB401, hybridizes to a messenger RNA of 1.2 kb length in mature and germinated pollen. SB401 messenger RNA is absent from other parts of the plant, including other flower tissues. SB401 cDNA, which possesses a long stretch of AT-rich 5â ...
DOI:: 10.1023/A:1005746713759
: http://dx.doi.org/10.1023/A:1005746713759

95. Equine infectious anemia virus Tat is a predominantly helica protein

Author:: Sticht, H.; Willbold, D.; Bayer, P.; Ejchart, A.; Rosin-Arbesfeld, R.; Gazit, A.; Yaniv, A.; Frank, R.; Rosch, P.
Source:: European journal of biochemistry 1993 v.218 no.3 pp. 973-976
ISSN:: 0014-2956
Subject:: protein secondary structure, etc ; Equine infectious anemia virus; amino acid sequences; viral proteins; structure-activity relationships; spectral analysis; Show all 6 Subjects
Abstract:: ... Nuclear magnetic resonance (NMR) spectroscopy revealed features of the secondary structure of the equine infectious anemia virus (EIAV) Tat protein in solution. We could show that this protein, which is required in the replication cycle of lentiviruses, forms a predominantly helical structure in trifluoroethanol/water (40% by vol.) solution. In particular, the basic RNA-binding region and the adja ...
DOI:: 10.1111/j.1432-1033.1993.tb18455.x
: http://dx.doi.org/10.1111/j.1432-1033.1993.tb18455.x

96. Conformational preference functions for predicting helices in membrane proteins

Author:: Juretic, D.; Lee, B.; Trinajstic, N.; Williams, R.W.
Source:: Biopolymers 1993 v.33 no.2 pp. 255-273
ISSN:: 0006-3525
Subject:: protein secondary structure, etc ; proteins; cell membranes; molecular conformation; prediction; computer software; computer analysis; amino acid sequences; algorithms; Show all 9 Subjects
Abstract:: ... A suite of FORTRAN programs, PREF, is described for calculating preference functions from the data base of known protein structures and for comparing smoothed profiles of sequence-dependent preferences in proteins of unknown structure. Amino acid preferences for a secondary structure are considered as functions of a sequence environment. Sequence environment of amino acid residue in a protein is d ...
DOI:: 10.1002/bip.360330208
PubMed:: 8485300
: http://dx.doi.org/10.1002/bip.360330208

97. Predicting polypeptide and protein structures from amino acid sequence: antlion method applied to melittin

Author:: Head-Gordon, T.; Stillinger, F.H.
Source:: Biopolymers 1993 v.33 no.2 pp. 293-303
ISSN:: 0006-3525
Subject:: protein secondary structure, etc ; melittin; proteins; polypeptides; molecular conformation; prediction; amino acid sequences; algorithms; computer analysis; computer software; neural networks; Show all 11 Subjects
Abstract:: ... This report continues to explore the use of a strategy known as the antlion method for predicting polypeptide and protein structure. The method involves deformation of a biopolymer's potential energy hypersurface in order to retain only a single minimum, near to the native structure. The vexing multiple minimum problem thus is relieved, and the deformed hypersurface constitutes a key element in th ...
DOI:: 10.1002/bip.360330211
: http://dx.doi.org/10.1002/bip.360330211

98. Correlation of exons with functional domains and folding regions in a cellulase from Agaricus bisporus

Author:: Yague, E.; Chow, C.M.; Challen, M.P.; Thurston, C.F.
Source:: Current genetics 1996 v.30 no.1 pp. 56-61
ISSN:: 0172-8083
Subject:: protein secondary structure, etc ; promoter regions; messenger RNA; structural genes; Agaricus bisporus; cellulases; amino acid sequences; cellulose; binding sites; exons; molecular conformation; introns; Show all 12 Subjects
Abstract:: ... The cellulase gene cel3 has been isolated from Agaricus bisporus and sequenced. The 5'-end of the cel3 transcript was determined by primer extension and S1 nuclease protection. Putative regulatory elements have been identified in the cel3 promoter and 3'-untranslated regions. The cel3 coding region is interrupted by six short introns, two of which separate the coding regions for the three modules ...
DOI:: 10.1007/s002940050100
PubMed:: 8662210
: http://dx.doi.org/10.1007/s002940050100

99. Presence of a hypervariable region within the hr2 domain of the host range determining sequences of the envelope protein gp85 (SU) of subgroup-A avian sarcoma-leukosis viruses

Author:: Hara, H.; Tanaka, A.; Kaji, A.
Source:: Virus genes 1996 v.12 no.1 pp. 37-46
ISSN:: 0920-8569
Subject:: protein secondary structure, etc ; Rous sarcoma virus; Avian myeloblastosis virus; structural genes; nucleotide sequences; amino acid sequences; phylogeny; molecular conformation; biochemical polymorphism; Show all 9 Subjects
DOI:: 10.1007/BF00369999
PubMed:: 8879119
: http://dx.doi.org/10.1007/BF00369999

100. Purification and molecular cloning of chemosensory proteins from Bombyx mori

Author:: Picimbon, J.F.; Dietrich, K.; Angeli, S.; Scaloni, A.; Krieger, J.; Breer, H.; Pelosi, P.
Source:: Archives of insect biochemistry and physiology 2000 v.44 no.3 pp. 120-129
ISSN:: 0739-4462
Subject:: protein secondary structure, etc ; Bombyx mori; antennae; complementary DNA; binding proteins; nucleotide sequences; amino acid sequences; molecular conformation; molecular weight; isoelectric point; gene expression; messenger RNA; legs; abdomen; thorax; head; Show all 16 Subjects
DOI:: 10.1002/1520-6327(200007)44:3<120::AID-ARCH3>3.0.CO;2-H
PubMed:: 10897093
: http://dx.doi.org/10.1002/1520-6327(200007)44:3<120::AID-ARCH3>3.0.CO;2-H

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1. Inactivation mechanisms of electron beam irradiation on Listeria innocua through the integrity of cell membrane, genomic DNA and protein structures

2. Transition of Metastable Cross-α Crystals into Cross-β Fibrils by β-Turn Flipping

3. PATSIM: Prediction and analysis of protein sequences using hybrid Knuth-Morris Pratt (KMP) and Boyer-Moore (BM) algorithm

4. Groups of coevolving positions provide drug resistance to Mycobacterium tuberculosis: A study using targets of first-line antituberculosis drugs

5. Identification of variants and therapeutic epitopes in HPV-33/HPV-58 E6 and E7 in Southwest China

6. Photoactivation Mechanism, Timing of Protein Secondary Structure Dynamics and Carotenoid Translocation in the Orange Carotenoid Protein

7. A new hybrid coding for protein secondary structure prediction based on primary structure similarity

8. Sixty-five years of the long march in protein secondary structure prediction: the final stretch?

9. Effect of Helical Flanking Sequences on the Morphology of Polyglutamine-Containing Fibrils

10. PEG–Peptide Conjugates

11. Molecular phylogenetic and sequence variation analysis of dimeric α-amylase inhibitor genes in wheat and its wild relative species

12. Human and Tree Shrew Alpha-synuclein: Comparative cDNA Sequence and Protein Structure Analysis

13. Spontaneous C-cleavage of a mini-intein without its conserved N-terminal motif A

14. Spherical Micelles Assembled from Variants of Recombinant Oleosin

15. Goose Toll-like receptor 7 (TLR7), myeloid differentiation factor 88 (MyD88) and antiviral molecules involved in anti-H5N1 highly pathogenic avian influenza virus response

16. Use of the Burrows-Wheeler similarity distribution to the comparison of the proteins

17. Purification of Parvalbumin from Carp: A Protocol that Avoids Heat-Treatment

18. Linear antimicrobial peptides from Ectatomma quadridens ant venom

19. Umbelliferone induces changes in the structure and pharmacological activities of Bn IV, a phospholipase A₂ isoform isolated from Bothrops neuwiedi

20. A novel biomarker for marine environmental pollution of pi-class glutathione S-transferase from Mytilus coruscus

21. Non-covalent binding of proteins to polyphenols correlates with their amino acid sequence

22. NetCSSP: web application for predicting chameleon sequences and amyloid fibril formation

23. Influence of cation-π interactions to the structural stability of prokaryotic and eukaryotic translation elongation factors

24. Divergence in structure and function of tau class glutathione transferase from Pinus tabulaeformis, P. yunnanensis and P. densata

25. Expression of the sucrose binding protein from soybean: Renaturation and stability of the recombinant protein

26. Probing protein structural requirements for activation of membrane-bound NAC transcription factors in Arabidopsis and rice

27. Structural aspects of the Mucor bacilliformis proteinase, a new member of the aspartyl-proteinase family

28. Molecular cloning and characterization of SoNCED, a novel gene encoding 9-cis-epoxycarotenoid dioxygenase from sugarcane (Saccharum officinarum L.)

29. Multiple Pro197 Substitutions in the Acetolactate Synthase of Corn Poppy (Papaver rhoeas) Confer Resistance to Tribenuron

30. Purification and characterization of mosquitocidal Bacillus sphaericus BinA protein

31. A Secreted SPRY Domain-Containing Protein (SPRYSEC) from the Plant-Parasitic Nematode Globodera rostochiensis Interacts with a CC-NB-LRR Protein from a Susceptible Tomato

32. Modèle topologique de la structure d'un antiport vacuolaire de type NHX chez la vigne cultivée (Vitis vinifera)

33. Molecular cloning, heterologous expression, and phylogenetic analysis of a novel y-type HMW glutenin subunit gene from the G genome of Triticum timopheevi

34. A Continent of Plant Defense Peptide Diversity: Cyclotides in Australian Hybanthus (Violaceae)

35. A cluster of diagnostic Hsp68 amino acid sites that are identified in Drosophila from the melanogaster species group are concentrated around β-sheet residues involved with substrate binding

36. Functional characterization of KIHEM13, a hypoxic gene of Kluyveromyces lactis. [Erratum: 2005 May, v. 51, no. 5, p. 431.]

37. Solution Structure of an Arabidopsis WRKY DNA Binding Domain

38. Complete amino acid sequence of the lentil trypsin-chymotrypsin inhibitor LCI-1.7 and a discussion of atypical binding sites of Bowman-Birk inhibitors

39. Defining subdomains of the K domain important for protein-protein interactions of plant MADS proteins

40. Isolation and temporal endospermal expression of γ-kafirin gene of grain sorghum (Sorghum bicolor L. Moench) var. M 35-1 for introgression analysis of transgene

41. Purification and characterization of a trypsin inhibitor from Putranjiva roxburghii seeds

42. Characterization of the endo-β-1,3-glucanase activity of S. cerevisiae Eng2 and other members of the GH81 family

43. Keratin 26, a novel member of the goat type I keratin gene family

44. Purification and characterization of a new alkali-thermostable lipase from Staphylococcus aureus isolated from Arachis hypogaea rhizosphere

45. Plus and minus sexual agglutinins from Chlamydomonas reinhardtii

46. Prion protein NMR structures of cats, dogs, pigs, and sheep

47. Prion protein NMR structures of chickens, turtles, and frogs

48. Taenia solium: Identification and preliminary characterization of a lipid binding protein with homology to the SEC14 catalytic domain

49. Effect of Solvent and Temperature on Secondary and Tertiary Structure of Zein by Circular Dichroism

50. Cloning and characterization of full-length coding sequence (CDS) of the ovine 37/67-kDa laminin receptor (RPSA)

51. Comparative assessment of Th1 and Th2 cytokines of swamp type buffalo and other bubaline breeds by molecular cloning, sequencing and phylogenetics

52. Extensive analysis of different allelelic structures of the chicken BF2 and β2m proteins

53. Evolution of spider silks: conservation and diversification of the C-terminus

54. Amino acid sequences and solution structures of manganese stabilizing protein that affect reconstitution of Photosystem II activity

55. Generation of deviation parameters for amino acid singlets, doublets and triplets from three-dimensional structures of proteins and its implications for secondary structure prediction from amino acid sequences

56. Common physical-chemical properties correlate with similar structure of the IgE epitopes of peanut allergens

57. Topological and transcriptional analysis of pssL gene product: a putative Wzx-like exopolysaccharide translocase in Rhizobium leguminosarum bv. trifolii TA1

58. Characterization of bullet tuna myoglobin with reference to the thermostability-structure relationship

59. Molecular cloning of a new cDNA and expression of 3-hydroxy-3-methylglutaryl-CoA synthase gene from Hevea brasiliensis

60. Effects of turn residues on beta-hairpin folding--a molecular dynamics study

61. Interleukin-10 expression by real-time PCR and homology modelling analysis in the European sea bass (Dicentrarchus Labrax L.)

62. ASP53, a thermostable protein from Acacia erioloba seeds that protects target proteins against thermal denaturation

63. Gene cloning and characterization of a soybean (Glycine max L.) LEA protein, GmPM16

64. Structure-function analysis of the presumptive Arabidopsis auxin permease AUX1

65. Synergistic antifungal activity of two chitin-binding proteins from spindle tree (Euonymus europaeus L.)

66. Crystal structure of the regulatory subunit H of the V-type ATPase of Saccharomyces cerevisiae

67. Biological activities and structural properties of the atypical bacteriocins mesenterocin 52B and leucocin B-TA33a

68. Reconstruction of a swine SLA-I protein complex and determination of binding nonameric peptides derived from the foot-and-mouth disease virus

69. Structure and function of antimicrobial peptide penaeidin-5 from the black tiger shrimp Penaeus monodon

70. cDNA sequences, MALDI-TOF analyses, and molecular modelling of barley PR-5 proteins