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1. A comparative analysis of machine learning classifiers for predicting protein-binding nucleotides in RNA sequences

Author:
Ankita Agarwal; Kunal Singh; Shri Kant; Ranjit Prasad Bahadur
Source:
Computational and Structural Biotechnology Journal 2022 v.20 pp. 3195-3207
ISSN:
2001-0370
Subject:
RNA; artificial intelligence; biotechnology; nucleotides; protein binding
Abstract:
... RNA-protein interactions play vital roles in driving the cellular machineries. Despite significant involvement in several biological processes, the underlying molecular mechanism of RNA-protein interactions is still elusive. This may be due to the experimental difficulties in solving co-crystallized RNA-protein complexes. Inherent flexibility of RNA molecules to adopt different conformations makes ...
DOI:
10.1016/j.csbj.2022.06.036

2. A phase 1/2 randomised placebo-controlled study of the COVID-19 vaccine mRNA-1273 in healthy Japanese adults: An interim report

Author:
Taisei Masuda; Kyoko Murakami; Kenkichi Sugiura; Sho Sakui; Ron Philip Schuring; Mitsuhiro Mori
Source:
Vaccine 2022 v.40 no.13 pp. 2044-2052
ISSN:
0264-410X
Subject:
COVID-19 infection; Japan; Severe acute respiratory syndrome coronavirus 2; biomedical research; confidence interval; immunogenicity; injection site; pain; pharmaceutical industry; placebos; protein binding; research and development; risk; seroconversion; vaccination; vaccines
Abstract:
... The mRNA vaccine, mRNA-1273/TAK-919, encodes the prefusion-stabilised spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We report interim results of the first study evaluating safety and immunogenicity of mRNA-1273 in healthy Japanese participants. This phase 1/2, randomised, observer-blind, placebo-controlled trial, conducted in Japan (two sites), enrolled healthy adu ...
DOI:
10.1016/j.vaccine.2022.02.030

3. Calcium ion can alleviate ammonia inhibition on anaerobic digestion via balanced-strengthening dehydrogenases and reinforcing protein-binding structure: Model evaluation and microbial characterization

Author:
Hangyu Sun; Ziyi Yang; Ling Zhou; Vagelis G. Papadakis; Maria A. Goula; Guangqing Liu; Yi Zhang; Wen Wang
Source:
Bioresource technology 2022 v.354 pp. 127165
ISSN:
0960-8524
Subject:
acetates; ammonia; anaerobic digestion; calcium; equations; methane; methane production; model validation; oxidation; oxidoreductases; protein binding; simulation models
Abstract:
... Experimental investigation and model simulation was combined to identify the effect of metal ions on mitigating ammonia inhibition during anaerobic digestion. Five metal ions (Ca, Mg, Cu, Zn, Fe) were tested in reactors with 1 g-glucose/L/d and 5 g-N/L under fed batch operation. Ca addition was considered the optimal approach with a 25% increment in methane production via balanced-strengthening de ...
DOI:
10.1016/j.biortech.2022.127165

4. Cdna Cloning and Expression Analysis of Chaperonin Containing T-Complex Polypeptide 1-Alpha in the Pearl Oyster Pinctada maxima Exposed to Cold Stress

Author:
Xiaochen Tang; Aitao Mao; Yu Ding; Zhigang Liu; Huazhong Liu
Source:
Journal of shellfish research 2022 v.40 no.3 pp. 505-510
ISSN:
0730-8000
Subject:
Aplysia californica; Danio rerio; Delia antiqua; Gallus gallus; Xenopus laevis; bioinformatics; chaperonins; cold shock response; cold stress; genes; heart; hepatopancreas; muscles; nucleotide sequences; oysters; polypeptides; protein binding; quantitative polymerase chain reaction; research; shellfish
Abstract:
... The complete cDNA sequence of chaperonin-containing T-complex polypeptide 1-alpha (CCT-alpha) gene of the pearl oyster Pinctada maxima was determined using rapid amplification of cDNA ends technique and characterized with bioinformatic analysis. Its expression profile in different organs and under cold stress was characterized using real-time quantitative polymerase chain reaction. Results reveale ...
DOI:
10.2983/035.040.0307

5. Complementarity of the residue-level protein function and structure predictions in human proteins

Author:
Bálint Biró; Bi Zhao; Lukasz Kurgan
Source:
Computational and Structural Biotechnology Journal 2022 v.20 pp. 2223-2234
ISSN:
2001-0370
Subject:
biotechnology; data collection; empirical research; humans; protein binding; solvents
Abstract:
... Sequence-based predictors of the residue-level protein function and structure cover a broad spectrum of characteristics including intrinsic disorder, secondary structure, solvent accessibility and binding to nucleic acids. They were catalogued and evaluated in numerous surveys and assessments. However, methods focusing on a given characteristic are studied separately from predictors of other chara ...
DOI:
10.1016/j.csbj.2022.05.003

6. Computational Identification of Potential Multitarget Inhibitors of Nipah Virus by Molecular Docking and Molecular Dynamics

Author:
Vinay Randhawa; Shivalika Pathania; Manoj Kumar
Source:
Microorganisms 2022 v.10 no.6 pp. -
ISSN:
2076-2607
Subject:
Nipah henipavirus; Respirovirus; drugs; encephalitis; glycoproteins; humans; molecular dynamics; nucleoproteins; pandemic; pathogenicity; pharmacokinetics; phytochemicals; protein binding; therapeutics; virus replication; viruses
Abstract:
... Nipah virus (NiV) is a recently emerged paramyxovirus that causes severe encephalitis and respiratory diseases in humans. Despite the severe pathogenicity of this virus and its pandemic potential, not even a single type of molecular therapeutics has been approved for human use. Considering the role of NiV attachment glycoprotein G (NiV-G), fusion glycoprotein (NiV-F), and nucleoprotein (NiV-N) in ...
DOI:
10.3390/microorganisms10061181

7. Design, synthesis and biological activity of novel triketone‐containing quinoxaline as HPPD inhibitor

Author:
Wei Hu; Shuang Gao; Li‐Xia Zhao; Ke‐Liang Guo; Jia‐Yu Wang; Ying‐Chao Gao; Xin‐Xin Shao; Ying Fu; Fei Ye
Source:
Pest management science 2022 v.78 no.3 pp. 938-946
ISSN:
1526-498X
Subject:
4-hydroxyphenylpyruvate dioxygenase; Arabidopsis thaliana; active ingredients; albino; aromatic compounds; carotenoids; death; herbicidal properties; hydrogen bonding; mass spectrometry; mesotrione; molecular dynamics; photosynthesis; postemergent weed control; protein binding; pyruvic acid
Abstract:
... BACKGROUND: 4‐Hydroxyphenyl pyruvate dioxygenase (EC 1.13.11.27, HPPD) is one of the important target enzymes used to address the issue of weed control. HPPD‐inhibiting herbicides can reduce the carotenoid content in plants and hinder photosynthesis, eventually causing albinism and death. Exploring novel HPPD‐inhibiting herbicides is a significant direction in pesticide research. In the process of ...
DOI:
10.1002/ps.6703

8. Genetic mapping of tolerance to iron deficiency chlorosis in peanut (Arachis hypogaea L.)

Author:
Ankur D. Tayade; Babu N. Motagi; Mangesh P. Jadhav; Anjum S. Nadaf; Rajshekar V. Koti; Sunil S. Gangurde; Vinay Sharma; Rajeev K. Varshney; Manish K. Pandey; Ramesh S. Bhat
Source:
Euphytica 2022 v.218 no.4 pp. 46
ISSN:
0014-2336
Subject:
Arachis hypogaea; abiotic stress; chlorophyll; chlorosis; chromosome mapping; chromosomes; genomics; inbred lines; introns; peanuts; phenotypic variation; prediction; protein binding
Abstract:
... Iron deficiency chlorosis (IDC) under calcareous and alkaline soils is a significant abiotic stress affecting the growth and yield of peanut. In this study, the genomic regions governing IDC tolerance were mapped using a recombinant inbred line (RIL) population derived from TMV 2 (susceptible to IDC) and TMV 2-NLM (tolerant to IDC), which was phenotyped during the rainy seasons of 2019 and 2020 in ...
DOI:
10.1007/s10681-022-02996-z

9. Insights into the Competitive Mechanisms of Per- and Polyfluoroalkyl Substances Partition in Liver and Blood

Author:
Yibo Jia; Yumin Zhu; Dashan Xu; Xuemin Feng; Xiaoyong Yu; Guoqiang Shan; Lingyan Zhu
Source:
Environmental science & technology 2022 v.56 no.10 pp. 6192-6200
ISSN:
1520-5851
Subject:
blood serum; environmental science; fatty acids; hepatotoxicity; humans; liver; males; technology
Abstract:
... Some per- and polyfluoroalkyl substances (PFASs) tend to be accumulated in liver and cause hepatotoxicity. However, the difficulty to directly measure liver concentrations of PFASs in humans hampers our understanding of their hepatotoxicity and mechanisms of action. We investigated the partitioning of 11 PFASs between liver and blood in male CD-1 mice. Although accumulation of the perfluoroalkanes ...
DOI:
10.1021/acs.est.1c08493

10. Mechanistic Insight on General Protein-Binding Ability of ATP and the Impacts of Arginine Residues

Author:
Guorong Hu; Xinwen Ou; Jingyuan Li
Source:
Journal of physical chemistry 2022 v.126 no.25 pp. 4647-4658
ISSN:
1520-5207
Subject:
adenosine triphosphate; arginine; molecular dynamics; protein binding; separation
Abstract:
... Recent experiments suggested that adenosine triphosphate (ATP) can regulate liquid–liquid phase separation (LLPS) of various proteins and inhibit protein aggregations at its physiological concentration, which is highly correlated with the nonspecific interactions of ATP to a wide variety of proteins. However, the mechanism underlying the general binding capability of ATP largely remains unclear. I ...
DOI:
10.1021/acs.jpcb.2c01478

11. Paper‐based open microfluidic platform for protein electrophoresis and immunoprobing

Author:
Stefan Hennig; Zhe Shu; Ludwig Gutzweiler; Peter Koltay; Felix von Stetten; Roland Zengerle; Susanna M. Früh
Source:
Electrophoresis 2022 v.43 no.4 pp. 621-631
ISSN:
0173-0835
Subject:
antibodies; automation; bacteria; cellulose acetate; electrophoresis; immunoassays; immunoblotting; molecular weight; protein binding
Abstract:
... Protein electrophoresis and immunoblotting are indispensable analytical tools for the characterization of proteins and posttranslational modifications in complex sample matrices. Owing to the lack of automation, commonly employed slab‐gel systems suffer from high time demand, significant sample/antibody consumption, and limited reproducibility. To overcome these limitations, we developed a paper‐b ...
DOI:
10.1002/elps.202100327

12. SARS-CoV-2 Nucleocapsid Protein Targets a Conserved Surface Groove of the NTF2-like Domain of G3BP1

Author:
Mahamaya Biswal; Jiuwei Lu; Jikui Song
Source:
Journal of molecular biology 2022 v.434 no.9 pp. 167516
ISSN:
0022-2836
Subject:
Severe acute respiratory syndrome coronavirus 2; crystal structure; hydrophobicity; molecular biology; mutation; nucleocapsid; nucleocapsid proteins; peptides; protein binding; therapeutics; virus replication
Abstract:
... Stress granule (SG) formation mediated by Ras GTPase-activating protein-binding protein 1 (G3BP1) constitutes a key obstacle for viral replication, which makes G3BP1 a frequent target for viruses. For instance, the SARS-CoV-2 nucleocapsid (N) protein interacts with G3BP1 directly to suppress SG assembly and promote viral production. However, the molecular basis for the SARS-CoV-2 N − G3BP1 interac ...
DOI:
10.1016/j.jmb.2022.167516

13. Screening of α-glucosidase inhibitors in large-leaf yellow tea by offline bioassay coupled with liquid chromatography tandem mass spectrometry

Author:
You Wu; Zisheng Han; Mingchun Wen; Chi-Tang Ho; Zongde Jiang; Yijun Wang; Na Xu; Zhongwen Xie; Jinsong Zhang; Liang Zhang; Xiaochun Wan
Source:
Food science and human wellness 2022 v.11 no.3 pp. 627-634
ISSN:
2213-4530
Subject:
alpha-amylase; bioassays; black tea; caffeine; ethyl acetate; flavanols; food science; high performance liquid chromatography; humans; protein binding; tandem mass spectrometry; China
Abstract:
... Larger-leaf yellow tea (LYT) is a characteristic type of Chinese tea produced in Huoshan County, Anhui Province, which is made by mature leaves with stems. According to recent report, LYT showed competitive effects in anti-hyperglycemia in comparison to other teas such as green or black tea. However, the bioactive compounds of LYT are still undiscovered so far. For this purpose, 5 fractions of LYT ...
DOI:
10.1016/j.fshw.2021.12.019

14. Selenium-containing tea polysaccharides ameliorate DSS-induced ulcerative colitis via enhancing the intestinal barrier and regulating the gut microbiota

Author:
Yuning Zhao; Hong Chen; Wenting Li; Qian He; Jingyimei Liang; Xiaohai Yan; Yahong Yuan; Tianli Yue
Source:
International journal of biological macromolecules 2022 v.209 pp. 356-366
ISSN:
0141-8130
Subject:
antioxidant activity; arabinose; colon; cytokines; dextran; functional foods; galactose; glucose; glucuronic acid; histology; intestinal microorganisms; mannose; occludins; protein binding; remission; selenium; sodium sulfate; tea; ulcerative colitis; weight loss; xylose
Abstract:
... Both tea polysaccharides and selenium have certain remission potential for ulcerative colitis (UC), but few reports focused on natural selenium-containing tea polysaccharides. The purpose of this study was to isolate a selenium-containing tea polysaccharide (ASeTP) and determine its structure and effects on UC. Results showed that ASeTP was primarily composed of three purified, β-pyranoside-linked ...
DOI:
10.1016/j.ijbiomac.2022.04.028

15. Albumin-binding prodrugs via reversible iminoboronate forming nanoparticles for cancer drug delivery

Author:
Lingqiao Hao; Quan Zhou; Ying Piao; Zhuxian Zhou; Jianbin Tang; Youqing Shen
Source:
Journal of controlled release 2021 v.330 pp. 362-371
ISSN:
0168-3659
Subject:
antineoplastic agents; bovine serum albumin; chemical bonding; curcumin; cytosol; drug formulations; encapsulation; environment; glutathione; hydrophobicity; models; nanomedicine; nanoparticles; neoplasms; pharmacokinetics; protein binding
Abstract:
... Albumin-based nanomedicines are important nanoplatforms for cancer drug delivery. The drugs are either physically encapsulated or covalently conjugated to albumin or albumin-based nanosystems. Physical encapsulation is advantageous due to requiring no chemical modification of drug molecules, but many drugs, for instance, camptothecin (CPT) and curcumin (CCM), though very hydrophobic, can't be load ...
DOI:
10.1016/j.jconrel.2020.12.035

16. Allosteric coupling and biased agonism in G protein‐coupled receptors

Author:
Andreas Bock; Marcel Bermudez
Source:
FEBS journal 2021 v.288 no.8 pp. 2513-2528
ISSN:
1742-464X
Subject:
agonists; cell membranes; drugs; ligands; protein binding; therapeutics
Abstract:
... G protein‐coupled receptors (GPCRs) are essential cell membrane signaling molecules and represent the most important class of drug targets. Some signaling pathways downstream of a GPCR may be responsible for drug adverse effects, while others mediate therapeutic efficacy. Biased ligands preferentially activate only a subset of all GPCR signaling pathways. They hold great potential to become next‐g ...
DOI:
10.1111/febs.15783

17. An integrative approach uncovers transcriptome‐wide determinants of mRNA stability regulation in Saccharomyces cerevisiae

Author:
Rafal Tomecki; Karolina Drazkowska
Source:
FEBS journal 2021 v.288 no.11 pp. 3418-3423
ISSN:
1742-464X
Subject:
Saccharomyces cerevisiae; gene expression regulation; half life; protein binding; ribonucleases; ribonucleoproteins; yeasts
Abstract:
... mRNA degradation rate is one of the key stages of gene expression regulation in eukaryotic cells. To date, intertwined processes of post‐transcriptional control have been widely investigated, but focused rather on the examination of mechanisms controlling stability of particular protein‐coding transcripts. Currently, a wealth of information from structural, biochemical, and high‐throughput studies ...
DOI:
10.1111/febs.15742

18. Assessing multiple conformations of lanthanide binding tags for proteins using a sensitive ¹⁹F-reporter

Author:
Jia-Liang Chen; Ben-Guang Chen; Bin Li; Feng Yang; Xun-Cheng Su
Source:
Chemical communications 2021 v.57 no.35 pp. 4291-4294
ISSN:
1364-548X
Subject:
binding properties; binding proteins; chemical communication; lanthanides; protein binding; protein tagging; screening; solutions; species abundance
Abstract:
... Quantifying the isomeric species of metal complexes in solution is difficult. ¹⁹F NMR herein was used to determine the abundance of isomeric species and dynamic properties of lanthanide binding tags. The results suggest that ¹⁹F is an efficient reporter in assessing and screening paramagnetic tags suitable for protein NMR analysis. ...
DOI:
10.1039/d1cc00791b

19. Assessment of the orientation and conformation of pigments in protein binding sites from infrared difference spectra

Author:
Leyla Rohani; Gary Hastings
Source:
Biochimica et biophysica acta 2021 v.1862 no.4 pp. 148366
ISSN:
0005-2728
Subject:
binding sites; frequency; hydrogen bonding; naphthoquinones; photosystem I; phylloquinone; pigments; protein binding; spectroscopy; tail
Abstract:
... Time resolved FTIR difference spectroscopy (DS) has been used to study photosystem I (PSI) with the disubstituted 1,4-naphthoquinones acequinocyl (AcQ) and lapachol (Lpc) incorporated into the A₁ binding site. AcQ is a 2-acetoxy-3-dodecyl-1,4-naphthoquinone, Lpc is a 2-hydroxy-3-(3-methyl-2-butenyl)-1,4-naphthoquinone. To assess whether the experimental spectra are specific to different orientatio ...
DOI:
10.1016/j.bbabio.2020.148366

20. CADM1 promotes malignant features of small-cell lung cancer by recruiting 4.1R to the plasma membrane

Author:
Toko Funaki; Takeshi Ito; Zen-ichi Tanei; Akiteru Goto; Toshiro Niki; Daisuke Matsubara; Yoshinori Murakami
Source:
Biochemical and biophysical research communications 2021 v.534 pp. 172-178
ISSN:
0006-291X
Subject:
agar; cell adhesion; cell adhesion molecules; cell lines; epithelium; lung neoplasms; plasma membrane; protein binding; research
Abstract:
... Cell adhesion molecule 1 (CADM1), which mediates intercellular adhesion between epithelial cells, is shown to be highly expressed in small-cell lung cancer (SCLC) and to enhance tumorigenicity of SCLC cells in nude mice. Here, we investigated the molecular mechanism underlying the oncogenic role of CADM1 in SCLC. CADM1 promoted colony formation of SCLC cells in soft agar. Analysis of deletion and ...
DOI:
10.1016/j.bbrc.2020.11.121

21. Cefovecin protein binding as a predictor for extended duration of action: a review of current literature and in vitro analysis in multiple zoological species

Author:
Marc T. Valitutto; Jennifer H. Yu; Bonnie L. Raphael; Paul P. Calle; John M. Sykes; Jean Paré; Robert P. Moore; Mark G. Papich
Source:
Journal of zoo and wildlife medicine 2021 v.52 no.4 pp. 1185-1194
ISSN:
1937-2825
Subject:
Carnivora; Equidae; Rucervus duvaucelii; Tursiops truncatus; blood proteins; cefovecin; half life; medicine; pharmacokinetics; protein binding; wildlife; zoos
Abstract:
... Cefovecin is a third-generation cephalosporin antibiotic with an efficacy of 2 wk following a single injection in domestic dogs and cats. A high degree of plasma protein binding to cefovecin has been proposed as one of the mechanisms responsible for the long elimination half-life, but protein binding has not been evaluated extensively in nondomestic species. In this study, a review of the current ...
DOI:
10.1638/2021-0068

22. Cell surface heat shock protein-mediated entry of tumor cell-adapted rotavirus into U-937 cells

Author:
José Rico; Claudia Perez; Juan Hernandez; Carlos Guerrero; Orlando Acosta
Source:
Folia microbiologica 2021 v.66 no.4 pp. 623-638
ISSN:
0015-5632
Subject:
B-cell lymphoma; Rotavirus; carcinogenesis; cell proliferation; flow cytometry; gangliosides; heat stress; heat-shock protein 40; humans; immunochemistry; integrins; monocytes; protein binding; protein disulfide-isomerase; viruses
Abstract:
... Rotaviruses infect cells by binding to specific cell surface molecules including gangliosides, heat shock protein cognate protein 70 (Hsc70), and some integrins. The characterization of cell surface receptors defining viral tropism is crucial for inhibiting entry into the normal cells or the cancer cells. In the present work, several tumor cell-adapted rotavirus isolates were tested for their inte ...
DOI:
10.1007/s12223-020-00845-x

23. Comparison of two Turnip mosaic virus P1 proteins in their ability to co-localize with the Arabidopsis thaliana G3BP-2 protein

Author:
Hendrik Reuper; Björn Krenz
Source:
Virus genes 2021 v.57 no.2 pp. 233-237
ISSN:
0920-8569
Subject:
Arabidopsis thaliana; RNA; Turnip mosaic virus; abiotic stress; host range; mammals; polyproteins; protein binding; proteinases; viruses
Abstract:
... Turnip mosaic virus (TuMV), belonging to the genus Potyvirus (family Potyviridae), has a large host range and consists of a single-stranded positive sense RNA genome encoding 12 proteins, including the P1 protease. This protein which is separated from the polyprotein by cis cleavage at its respective C-terminus, has been attributed with different functions during potyviral infection of plants. P1 ...
DOI:
10.1007/s11262-021-01829-w

24. Comprehensive circRNA expression profile and function network in osteoblast-like cells under simulated microgravity

Author:
Zhen Cao; Yang Zhang; Shuping Wei; Xizheng Zhang; Yong Guo; Biao Han
Source:
Gene 2021 v.764 pp. 145106
ISSN:
0378-1119
Subject:
bone formation; circular RNA; focal adhesions; gene expression; gene expression regulation; gene ontology; microRNA; microfilaments; microgravity; morphogenesis; non-coding RNA; osteoblasts; pathogenesis; protein binding; quantitative polymerase chain reaction; regulator genes; research; sequence analysis; signal transduction; transcriptomics
Abstract:
... Circular RNAs (circRNAs) are a new class of non-coding RNA with a stable structure formed by special loop splicing. Research increasingly suggests that circRNAs play a vital role in the pathogenesis and progression of various diseases. However, the roles of circRNAs in osteoblast differentiation under microgravity remain largely unknown. Here, we investigated the roles and mechanobiological respon ...
DOI:
10.1016/j.gene.2020.145106

25. Crystal structure of the sugar acid‐binding protein CxaP from a TRAP transporter in Advenella mimigardefordensis strain DPN7T

Author:
Lukas Schäfer; Christina Meinert‐Berning; Stefanie Kobus; Astrid Höppner; Sander H. J. Smits; Alexander Steinbüchel
Source:
FEBS journal 2021 v.288 no.16 pp. 4905-4917
ISSN:
1742-464X
Subject:
acids; binding sites; crystal proteins; crystal structure; crystallization; journals; ligands; protein binding; strains; sugar acids; sugar crystals; transporters
Abstract:
... Recently, CxaP, a sugar acid substrate binding protein (SBP) from Advenella mimigardefordensis strain DPN7ᵀ, was identified as part of a novel sugar uptake strategy. In the present study, the protein was successfully crystallized. Although several SBP structures of tripartite ATP‐independent periplasmic transporters have already been solved, this is the first structure of an SBP accepting multiple ...
DOI:
10.1111/febs.15789

26. Cu(II)–Glycerol–N-Ethylmorpholine Complex Stability Revealed by X-ray Spectroscopy

Author:
Giovanni La Penna; Fabrizio Machetti; Olivier Proux; Giancarlo Rossi; Francesco Stellato; Silvia Morante
Source:
Journal of physical chemistry 2021 v.125 no.2 pp. 1483-1492
ISSN:
1932-7455
Subject:
X-radiation; X-ray absorption spectroscopy; aqueous solutions; cryoprotectants; glycerol; ice; molecular dynamics; pH; protein binding
Abstract:
... We report on a detailed X-ray absorption spectroscopy study of the Cu(II) coordination mode in aqueous solution in the presence of glycerol cryoprotectant and N-ethylmorpholine buffer. The first additive is often used when working at very low temperatures with the purpose of avoiding unwanted ice diffraction, the second is added to allow adjusting the pH at the desired value. Additives of this kin ...
DOI:
10.1021/acs.jpcc.0c08676

27. G3BPs tether the TSC complex to lysosomes and suppress mTORC1 signaling

Author:
Mirja Tamara Prentzell; Ulrike Rehbein; Marti Cadena Sandoval; Ann-Sofie De Meulemeester; Ralf Baumeister; Laura Brohée; Bianca Berdel; Mathias Bockwoldt; Bernadette Carroll; Suvagata Roy Chowdhury; Andreas von Deimling; Constantinos Demetriades; Gianluca Figlia; Mariana Eca Guimaraes de Araujo; Alexander M. Heberle; Ines Heiland; Birgit Holzwarth; Lukas A. Huber; Jacek Jaworski; Magdalena Kedra; Katharina Kern; Andrii Kopach; Viktor I. Korolchuk; Ineke van 't Land-Kuper; Matylda Macias; Mark Nellist; Wilhelm Palm; Stefan Pusch; Jose Miguel Ramos Pittol; Michèle Reil; Anja Reintjes; Friederike Reuter; Julian R. Sampson; Chloë Scheldeman; Aleksandra Siekierska; Eduard Stefan; Aurelio A. Teleman; Laura E. Thomas; Omar Torres-Quesada; Saskia Trump; Hannah D. West; Peter de Witte; Sandra Woltering; Teodor E. Yordanov; Justyna Zmorzynska; Christiane A. Opitz; Kathrin Thedieck; Genomics England Research Consortium
Source:
Cell 2021 v.184 no.3 pp. 655-674.e27
ISSN:
0092-8674
Subject:
Danio rerio; breast neoplasms; cell movement; insulin; lysosomes; neoplasm cells; neurons; protein binding; rapamycin; sclerosis
Abstract:
... Ras GTPase-activating protein-binding proteins 1 and 2 (G3BP1 and G3BP2, respectively) are widely recognized as core components of stress granules (SGs). We report that G3BPs reside at the cytoplasmic surface of lysosomes. They act in a non-redundant manner to anchor the tuberous sclerosis complex (TSC) protein complex to lysosomes and suppress activation of the metabolic master regulator mechanis ...
DOI:
10.1016/j.cell.2020.12.024

28. G4-PROTAC: targeted degradation of a G-quadruplex binding protein

Author:
Kiran M. Patil; Danielle Chin; Hui Ling Seah; Qi Shi; Kah Wai Lim; Anh Tuân Phan
Source:
Chemical communications 2021 v.57 no.95 pp. 12816-12819
ISSN:
1364-548X
Subject:
binding proteins; chemical communication; chimerism; protein binding; protein degradation; therapeutics
Abstract:
... G-quadruplex (G4) binding proteins regulate important biological processes, but their interaction networks are poorly understood. We report the first use of G4 as a warhead of a proteolysis-targeting chimera (G4-PROTAC) for targeted degradation of a G4-binding protein (RHAU/DHX36). G4-PROTAC provides a new way to explore G4-protein networks and to develop potential therapeutics. ...
DOI:
10.1039/d1cc05025g

29. Growth and transcriptome analysis of tomato under seawater stress

Author:
Xiaolu Mu; Lili Zhang; Hongyun Wang; Shoujun Cao; Jiangang Yao; Tao Li; Xiubo Xia
Source:
South African journal of botany 2021 v.137 pp. 463-474
ISSN:
0254-6299
Subject:
biochemical pathways; branches; functional properties; gene expression regulation; gene ontology; genetic variation; high-throughput nucleotide sequencing; industry; information; nutrient solutions; protein binding; research; salt tolerance; sampling; seawater; soil salinization; tomatoes; transcription factors; transcriptome; transcriptomics; unigenes; volume
Abstract:
... The tomato industry has been seriously affected by continuous soil salinization and seawater irritation. This study analyzed the salt tolerance mechanism of tomato from physiological and molecular aspects and screened out the salt tolerance genes; this information provides a foundation for future research on tomato salt tolerance and environmental adaptability. In this study, tomato was used as th ...
DOI:
10.1016/j.sajb.2020.11.016

30. Host assisted molecular recognition by human serum albumin: Study of molecular recognition controlled protein/drug mimic binding in a microfluidic channel

Author:
Dipanjan Mukherjee; Priya Singh; Soumendra Singh; Debanjona Singh Roy; Subhankar Singha; Uttam Pal; Jhimli Sengupta; Rami J. Obaid; Saleh A. Ahmed; Tanusri Saha Dasgupta; Ranjan Das; Samir Kumar Pal
Source:
International journal of biological macromolecules 2021 v.176 pp. 137-144
ISSN:
0141-8130
Subject:
binding proteins; cyclodextrins; drugs; encapsulation; hosts; human serum albumin; journals; protein binding
Abstract:
... Human serum albumin (HSA) plays a pivotal role in drug release from its delivery vehicles such as cyclodextrins (CDs) by binding to the drugs. Here molecular recognition and binding of a drug mimic (CD1) to HSA have been explored in a microfluidic channel when CD1 is encapsulated in β-cyclodextrin (βCD) and heptakis(2,3,6-tri-O-methyl)-β-cyclodextrin (TRIMEB), respectively, to investigate whether ...
DOI:
10.1016/j.ijbiomac.2021.02.002

31. Hotspot Coevolution Is a Key Identifier of Near-Native Protein Complexes

Author:
Sambit K. Mishra; Connor J. Cooper; Jerry M. Parks; Julie C. Mitchell
Source:
Journal of physical chemistry 2021 v.125 no.23 pp. 6058-6067
ISSN:
1520-5207
Subject:
Gibbs free energy; binding proteins; coevolution; journals; protein binding; protein subunits; protein-protein interactions; testing
Abstract:
... Protein–protein interactions play a key role in mediating numerous biological functions, with more than half the proteins in living organisms existing as either homo- or hetero-oligomeric assemblies. Protein subunits that form oligomers minimize the free energy of the complex, but exhaustive computational search-based docking methods have not comprehensively addressed the challenge of distinguishi ...
DOI:
10.1021/acs.jpcb.0c11525

32. ISRIB Blunts the Integrated Stress Response by Allosterically Antagonising the Inhibitory Effect of Phosphorylated eIF2 on eIF2B

Author:
Alisa F. Zyryanova; Kazuhiro Kashiwagi; Claudia Rato; Heather P. Harding; Ana Crespillo-Casado; Luke A. Perera; Ayako Sakamoto; Madoka Nishimoto; Mayumi Yonemochi; Mikako Shirouzu; Takuhiro Ito; David Ron
Source:
Molecular cell 2021 v.81 no.1 pp. 88-103.e6
ISSN:
1097-2765
Subject:
cryo-electron microscopy; guanine nucleotide exchange factors; stress response
Abstract:
... The small molecule ISRIB antagonizes the activation of the integrated stress response (ISR) by phosphorylated translation initiation factor 2, eIF2(αP). ISRIB and eIF2(αP) bind distinct sites in their common target, eIF2B, a guanine nucleotide exchange factor for eIF2. We have found that ISRIB-mediated acceleration of eIF2B’s nucleotide exchange activity in vitro is observed preferentially in the ...
DOI:
10.1016/j.molcel.2020.10.031

33. Identification of aberrantly expressed circular RNAs in hyperlipidemia-induced retinal vascular dysfunction in mice

Author:
Ya-Nan Sun; Ban Liu; Jia-Jian Wang; Xiu-Miao Li; Jun-Ya Zhu; Chang Liu; Jin Yao; Yu-ling Zhong; Qin Jiang; Biao Yan
Source:
Genomics 2021 v.113 no.1 pp. 593-600
ISSN:
0888-7543
Subject:
animal models; apoptosis; blood serum; cell differentiation; cell viability; circular RNA; coronary artery disease; cytoplasm; disease progression; endothelial cells; focal adhesions; gene expression regulation; genes; hyperlipidemia; macular degeneration; mice; microarray technology; patients; prediction; protein binding; retina
Abstract:
... Hyperlipidemia-induced retinal vascular dysfunction is a complex pathological process. circRNAs are important regulators of biological processes and disease progression. However, the expression pattern of circRNAs in hyperlipidemia-induced retinal vascular dysfunction remains unclear. Herein, we used a murine model of hyperlipidemia and identified 317 differentially expressed circRNAs between hype ...
DOI:
10.1016/j.ygeno.2020.09.055

34. Interaction of Differently Sized, Shaped, and Functionalized Silver and Gold Nanoparticles with Glycosylated versus Nonglycosylated Transferrin

Author:
Rinea Barbir; Rafael Ramírez Jiménez; Rafael Martín-Rapún; Vida Strasser; Darija Domazet Jurašin; Sanja Dabelić; Jesus M. de la Fuente; Ivana Vinković Vrček
Source:
ACS applied materials & interfaces 2021 v.13 no.23 pp. 27533-27547
ISSN:
1944-8252
Subject:
blood serum; bovine serum albumin; circular dichroism spectroscopy; fluorescence; gel electrophoresis; glycosylation; gold; humans; nanogold; protein corona; protein secondary structure; safety assessment; silver; transferrin; transmission electron microscopy
Abstract:
... Exposure of nanomaterials (NMs) to biological medium results in their direct interaction with biomolecules and the formation of a dynamic biomolecular layer known as the biomolecular corona. Despite numerous published data on nano-biointeractions, the role of protein glycosylation in the formation, characteristics, and fate of such nano-biocomplexes has been almost completely neglected, although m ...
DOI:
10.1021/acsami.1c04063

35. Intestinal proteases profiling from Anticarsia gemmatalis and their binding to inhibitors

Author:
Neilier R. Silva‐Júnior; Yaremis M. Cabrera; Samuel L. Barbosa; Rafael de A. Barros; Edvaldo Barros; Camilo E. Vital; Humberto J. O. Ramos; Maria Goreti A. Oliveira
Source:
Archives of insect biochemistry and physiology 2021 v.107 no.3 pp. e21792
ISSN:
0739-4462
Subject:
Anticarsia gemmatalis; active sites; binding sites; computer simulation; insect larvae; intestines; protein binding; protein isoforms; protein-protein interactions; proteolysis; proteome; proteomics; soybeans; trypsin; trypsin inhibitors
Abstract:
... Although the importance of intestinal hydrolases is recognized, there is little information on the intestinal proteome of lepidopterans such as Anticarsia gemmatalis. Thus, we carried out the proteomic analysis of the A. gemmatalis intestine to characterize the proteases by LC/MS. We examined the interactions of proteins identified with protease inhibitors (PI) using molecular docking. We found 54 ...
DOI:
10.1002/arch.21792

36. Light-stabilized FHA2 suppresses miRNA biogenesis through interactions with DCL1 and HYL1

Author:
Seung Jun Park; Suk Won Choi; Gu Min Kim; Christian Møller; Hyun-Sook Pai; Seong Wook Yang
Source:
Molecular plant 2021 v.14 no.4 pp. 647-663
ISSN:
1674-2052
Subject:
DNA-binding domains; RNA-binding proteins; biogenesis; endoribonucleases; etiolation; gene expression; gene expression regulation; light intensity; messenger RNA; microRNA; plant proteins; protein binding; scotophase; seedlings; survival rate
Abstract:
... The precise regulation of microRNA (miRNA) biogenesis is crucial for plant development, which requires core microprocessors and many fine tuners to coordinate their miRNA processing activity/specificity in fluctuating cellular environments. During de-etiolation, light triggers a dramatic accumulation of core microprocessors and primary miRNAs (pri-miRNAs) but decreases pri-miRNA processing activit ...
DOI:
10.1016/j.molp.2021.01.020

37. Modulation of Stem Cell Progeny by Probiotics during Regeneration of Gastric Mucosal Erosions

Author:
Farah Al-Yassir; Ghalia Khoder; Subi Sugathan; Prashanth Saseedharan; Asma Al Menhali; Sherif M. Karam
Source:
Biology 2021 v.10 no.7 pp. -
ISSN:
2079-7737
Subject:
H+/K+-exchanging ATPase; animal disease models; aspirin; cell proliferation; digestive system diseases; gastric mucosa; ghrelin; immunohistochemistry; lectins; mice; mucus; pepsinogen; probiotics; protein binding; stem cells; tissue repair
Abstract:
... Patients with gastric mucosal erosions are predisposed to chronic gastritis, ulcer or even cancer. The repair of mucosal erosions involves several events including proliferation of gastric epithelial stem cells. The aim of this study was to investigate the effects of the probiotic mixture of De Simone Formulation on gastric epithelial stem cell lineages in mouse models of gastric mucosal erosions. ...
DOI:
10.3390/biology10070596

38. OmpC, a novel factor H-binding surface protein, is dispensable for the adherence and virulence of Salmonella enterica serovar Typhimurium

Author:
Quan Li; Yuhan Hu; Xia Fei; Yuanzhao Du; Weiwei Guo; Dianfeng Chu; Xiaobo Wang; Shifeng Wang; Huoying Shi
Source:
Veterinary microbiology 2021 v.259 pp. 109157
ISSN:
0378-1135
Subject:
Salmonella Typhimurium; amino acid deletion; animal disease models; antibacterial properties; bacterial adhesion; bacterial proteins; binding proteins; blood serum; complement; human cell lines; humans; immune evasion; innate immunity; lesions (animal); mice; outer membrane proteins; pathogen survival; protein binding; salmonellosis; surface proteins; virulence
Abstract:
... Salmonella enterica serovar Typhimurium utilizes a series of strategies to evade host innate immune defenses, including the serum complement system. Many microbial pathogens have evolved the ability to bind the complement regulatory protein factor H (FH) through their surface factor H-binding proteins (FHBPs) to circumvent the complement-mediated bactericidal effect. However, the roles of FHBPs in ...
DOI:
10.1016/j.vetmic.2021.109157

39. Origins and evolving functionalities of tRNA-derived small RNAs

Author:
Qi Chen; Xudong Zhang; Junchao Shi; Menghong Yan; Tong Zhou
Source:
Trends in biochemical sciences 2021 v.46 no.10 pp. 790-804
ISSN:
0968-0004
Subject:
biogenesis; epigenetics; genes; germplasm conservation; precision medicine; protein binding; ribosomes; transfer RNA
Abstract:
... Transfer RNA (tRNA)-derived small RNAs (tsRNAs) are among the most ancient small RNAs in all domains of life and are generated by the cleavage of tRNAs. Emerging studies have begun to reveal the versatile roles of tsRNAs in fundamental biological processes, including gene silencing, ribosome biogenesis, retrotransposition, and epigenetic inheritance, which are rooted in tsRNA sequence conservation ...
DOI:
10.1016/j.tibs.2021.05.001

40. Rapid Characterization of Human Serum Albumin Binding for Per- and Polyfluoroalkyl Substances Using Differential Scanning Fluorimetry

Author:
Thomas W. Jackson; Chris M. Scheibly; M. E. Polera; Scott M. Belcher
Source:
Environmental science & technology 2021 v.55 no.18 pp. 12291-12301
ISSN:
1520-5851
Subject:
blood serum; decanoic acid; denaturation; dissociation; dose response; environmental science; fluorometry; hexadecenoic acid; human serum albumin; humans; ibuprofen; ligands; octanoic acid; perfluorocarbons; pharmacokinetics; protein binding; regression analysis; technology; temperature; thermal stability; transport proteins; warfarin
Abstract:
... Per- and polyfluoroalkyl substances (PFAS) are a diverse class of synthetic chemicals that accumulate in the environment. Many proteins, including the primary human serum transport protein albumin (HSA), bind PFAS. The predictive power of physiologically based pharmacokinetic modeling approaches is currently limited by a lack of experimental data defining albumin-binding properties for most PFAS. ...
DOI:
10.1021/acs.est.1c01200

41. Regulation of RNA Interference Pathways in the Insect Vector Laodelphax striatellus by Viral Proteins of Rice Stripe Virus

Author:
Yan Xiao; Qiong Li; Wei Wang; Yumei Fu; Feng Cui
Source:
Viruses 2021 v.13 no.8 pp. -
ISSN:
1999-4915
Subject:
Laodelphax striatellus; RNA interference; RNA-directed RNA polymerase; Rice stripe tenuivirus; coevolution; insect vectors; microRNA; protein binding; virus replication
Abstract:
... RNA interference (RNAi), especially the small interfering RNA (siRNA) and microRNA (miRNA) pathways, plays an important role in defending against viruses in plants and insects. However, how insect-transmitted phytoviruses regulate the RNAi-mediated antiviral response in vector insects has barely been uncovered. In this study, we explored the interaction between rice stripe virus (RSV) and the miRN ...
DOI:
10.3390/v13081591

42. Rice protein-binding microarrays: a tool to detect cis-acting elements near promoter regions in rice

Author:
Joung Sug Kim; SongHwa Chae; Kyong Mi Jun; Gang-Seob Lee; Jong-Seong Jeon; Kyung Do Kim; Yeon-Ki Kim
Source:
Planta 2021 v.253 no.2 pp. 40
ISSN:
0032-0935
Subject:
Oryza sativa; gene expression; genes; microarray technology; protein binding; rice; transcription (genetics)
Abstract:
... MAIN CONCLUSION: The present study showed that a rice (Oryza sativa)-specific protein-binding microarray (RPBM) can be applied to analyze DNA-binding motifs with a TF where binding is evaluated in extended natural promoter regions. The analysis may facilitate identifying TFs and their downstream genes and constructing gene networks through cis-elements. Transcription factors (TFs) regulate gene ex ...
DOI:
10.1007/s00425-021-03572-w

43. Serum Levels of Vitamin D and Dental Caries in 7-Year-Old Children in Porto Metropolitan Area

Author:
Cátia Carvalho Silva; Sandra Gavinha; Maria Conceição Manso; Rita Rodrigues; Sandra Martins; João Tiago Guimarães; Ana Cristina Santos; Paulo Melo
Source:
Nutrients 2021 v.13 no.1 pp. -
ISSN:
2072-6643
Subject:
bivariate analysis; blood serum; childhood; dental caries; dental health; electrochemiluminescence; enamel; gastrointestinal system; health status; immunoassays; metropolitan areas; protein binding; regression analysis; teeth; Portugal
Abstract:
... Vitamin D deficiency has been associated with significant changes in dental structures. In children, it can induce enamel and dentin defects, which have been identified as risk factors for caries. This study aimed to assess the association between low serum 25-hydroxyvitamin D (25(OH) D) levels (<30 ng/mL) and the prevalence of caries in the permanent teeth and mixed dentition of 7-year-old childr ...
DOI:
10.3390/nu13010166

44. Signaling at the endosome: cryo‐EM structure of a GPCR–G protein–beta‐arrestin megacomplex

Author:
Anthony H. Nguyen; Robert J. Lefkowitz
Source:
FEBS journal 2021 v.288 no.8 pp. 2562-2569
ISSN:
1742-464X
Subject:
G-protein coupled receptors; binding proteins; cell communication; cryo-electron microscopy; journals; protein binding; therapeutics
Abstract:
... G protein‐coupled receptors (GPCRs) are a large class of cell‐surface receptor involved in cellular signaling that are currently the target of over one third of all clinically approved therapeutics. Classically, an agonist‐bound, active GPCR couples to and activates G proteins through the receptor intracellular core. To attenuate G protein signaling, the GPCR is phosphorylated at its C‐terminal ta ...
DOI:
10.1111/febs.15773

45. Single-stranded and double-stranded DNA-binding protein prediction using HMM profiles

Author:
Ronesh Sharma; Shiu Kumar; Tatsuhiko Tsunoda; Thirumananseri Kumarevel; Alok Sharma
Source:
Analytical biochemistry 2021 v.612 pp. 113954
ISSN:
0003-2697
Subject:
DNA; DNA-binding proteins; Markov chain; accuracy; bioactive properties; data collection; extraction; information; literature; prediction; protein binding
Abstract:
... DNA-binding proteins perform important roles in cellular processes and are involved in many biological activities. These proteins include crucial protein-DNA binding domains and can interact with single-stranded or double-stranded DNA, and accordingly classified as single-stranded DNA-binding proteins (SSBs) or double-stranded DNA-binding proteins (DSBs). Computational prediction of SSBs and DSBs ...
DOI:
10.1016/j.ab.2020.113954

46. Structural characterization of NORAD reveals a stabilizing role of spacers and two new repeat units

Author:
Uciel Chorostecki; Ester Saus; Toni Gabaldón
Source:
Computational and Structural Biotechnology Journal 2021 v.19 pp. 3245-3254
ISSN:
2001-0370
Subject:
DNA damage; biotechnology; evolution; genomics; germplasm conservation; microRNA; non-coding RNA; protein binding
Abstract:
... Long non-coding RNAs (lncRNAs) can perform a variety of key cellular functions by interacting with proteins and other RNAs. Recent studies have shown that the functions of lncRNAS are largely mediated by their structures. However, our structural knowledge for most lncRNAS is limited to sequence-based computational predictions. Non-coding RNA activated by DNA damage (NORAD) is an atypical lncRNA du ...
DOI:
10.1016/j.csbj.2021.05.045

47. TaVrt2, an SVP‐like gene, cooperates with TaVrn1 to regulate vernalization‐induced flowering in wheat

Author:
Li Xie; Yong Zhang; Ke Wang; Xumei Luo; Dengan Xu; Xiuling Tian; Lingli Li; Xingguo Ye; Xianchun Xia; Wenxue Li; Liuling Yan; Shuanghe Cao
Source:
The new phytologist 2021 v.231 no.2 pp. 834-848
ISSN:
0028-646X
Subject:
chromatin immunoprecipitation; epistasis; genes; genetic analysis; genetically modified organisms; population genetics; protein binding; transcription factors; transcriptomics; vernalization; wheat
Abstract:
... TaVrn1, encoding a MADS‐box transcription factor (TF), is the central regulator of wheat vernalization‐induced flowering. Considering that the MADS‐box TF usually works by forming hetero‐ or homodimers, we conducted yeast‐two‐hybrid screening and identified an SVP‐like MADS‐box protein TaVrt2 interacting with TaVrn1. However, the specific function of TaVrt2 and the biological implication of its in ...
DOI:
10.1111/nph.16339

48. Towards the mechanism(s) of YB-3 synthesis regulation by YB-1

Author:
D.N. Lyabin; E.A. Smolin; K.S. Budkina; I.A. Eliseeva; L.P. Ovchinnikov
Source:
RNA biology 2021 v.18 no.11 pp. 1630-1641
ISSN:
1555-8584
Subject:
DNA repair; RNA; RNA packaging; binding proteins; cold stress; protein binding; transcription (genetics)
Abstract:
... Y-box binding proteins are members of the family of proteins containing the evolutionarily conserved cold shock domain. Their cellular functions are quite diverse, including transcription and translation regulation, participation in pre-mRNA splicing, mRNA stabilization and packaging into mRNPs, involvement in DNA repair, and some others. To date, we know little about the plausible functional inte ...
DOI:
10.1080/15476286.2020.1859243

49. Water mobility in cheese by means of Nuclear Magnetic Resonance relaxometry

Author:
Danuta Kruk; Malgorzata Florek – Wojciechowska; Elzbieta Masiewicz; Mecit Oztop; Anna Ploch-Jankowska; Piotr Duda; Slawomir Wilczynski
Source:
Journal of food engineering 2021 v.298 pp. 110483
ISSN:
0260-8774
Subject:
binding proteins; cheeses; food technology; journals; nuclear magnetic resonance spectroscopy; protein binding
Abstract:
... ¹H NMR relaxometry studies have been performed for different kinds of cheese in order to enquire into mechanisms of water mobility in the cheese structures. The exploited frequency range, from 4 kHz to 40 MHz, allowed probing water dynamics on a broad range of time scales. Two fractions of water of much different dynamical properties, referred to as confined-water and free-water, have been reveale ...
DOI:
10.1016/j.jfoodeng.2021.110483

50. A Computational Protocol for Regulating Protein Binding Reactions with a Light-Sensitive Protein Dimer

Author:
Frank D. Teets; Takashi Watanabe; Klaus M. Hahn; Brian Kuhlman
Source:
Journal of molecular biology 2020 v.432 no.4 pp. 805-814
ISSN:
0022-2836
Subject:
animals; blue light; guanosinetriphosphatase; irradiation; molecular models; optogenetics; protein binding; proteins
Abstract:
... Light-sensitive proteins can be used to perturb signaling networks in living cells and animals with high spatiotemporal resolution. We recently engineered a protein heterodimer that dissociates when irradiated with blue light and demonstrated that by fusing each half of the dimer to termini of a protein that it is possible to selectively block binding surfaces on the protein when in the dark. On a ...
DOI:
10.1016/j.jmb.2019.12.033
PubMed:
31887287
PubMed Central:
PMC7054171

51. A biostable, anti-fouling zwitterionic polyurethane-urea based on PDMS for use in blood-contacting medical devices

Author:
Seungil Kim; Sang-ho Ye; Arianna Adamo; Ryan A. Orizondo; Jaehyuk Jo; Sung Kwon Cho; William R. Wagner
Source:
Journal of materials chemistry B 2020 v.8 no.36 pp. 8305-8314
ISSN:
2050-7518
Subject:
adsorption; antifouling agents; biocompatibility; biocompatible materials; blood platelets; carboxylic ester hydrolases; chemical structure; coatings; cytotoxicity; fibrinogen; hemolysis; hydrogen peroxide; medical equipment; myocytes; physical properties; polydimethylsiloxane; polypropylenes; polyurethanes; protein binding; rats; sheep; smooth muscle; sulfobetaine; urea; zwitterions
Abstract:
... Polydimethylsiloxane (PDMS) is commonly used in medical devices because it is non-toxic and stable against oxidative stress. Relatively high blood platelet adhesion and the need for chemical crosslinking through curing, however, limit its utility. In this research, a biostable PDMS-based polyurethane-urea bearing zwitterion sulfobetaine (PDMS-SB-UU) was synthesized for potential use in the fabrica ...
DOI:
10.1039/d0tb01220c

52. A carbon nanoparticle and DNase I-Assisted amplified fluorescent biosensor for miRNA analysis

Author:
Hongfeng Li; Yang Li; Wenqin Li; Liang Cui; Guohua Huang; Jiahao Huang
Source:
Talanta 2020 v.213 pp. 120816
ISSN:
0039-9140
Subject:
DNA probes; biosensors; breast neoplasms; carbon nanoparticles; deoxyribonucleases; detection limit; disease diagnosis; environmental monitoring; fluorescence; food safety; microRNA; neoplasm cells; protein binding
Abstract:
... Nucleic acid-based biosensors have become powerful tools in biomedical applications. But the stability issue seriously limits their wide applications. Fortunately, the emergence of carbon nanoparticles (CNPs), which can effectively protect DNA probes from enzymatic digestion and unspecific protein binding, provides a good solution. In this work, a DNase I-aided cyclic enzymatic amplification metho ...
DOI:
10.1016/j.talanta.2020.120816

53. A new dendrimer series: synthesis, free radical scavenging and protein binding studies

Author:
Dhaval Makawana; Man Singh
Source:
RSC advances 2020 v.10 no.37 pp. 21914-21932
ISSN:
2046-2069
Subject:
acetone; ascorbic acid; bovine serum albumin; carbon; dendrimers; fluorides; free radical scavengers; free radicals; hydrophobicity; lysozyme; mass spectrometry; methanol; moieties; nuclear magnetic resonance spectroscopy; optical properties; organochlorine compounds; protein binding; protons; stable isotopes; trimesoyl chloride; ultraviolet-visible spectroscopy
Abstract:
... Tri-o-tolyl benzene-1,3,5-tricarboxylate (TOBT (T0)), tri-4-hydroxyphenyl benzene-1,3,5-tricarboxylate (THBT (T1)), and tri-3,5-dihydroxyphenyl benzene-1,3,5-tricarboxylate (TDBT (T2)), a series of 1ˢᵗ tier dendrimers with a common 1,3,5-benzenetricarbonyl trichloride/trimesoyl chloride (TMC) core, are reported. T0 does not have any replaceable H⁺ on its terminal phenyl group, acting as a branch. ...
DOI:
10.1039/d0ra04102e

54. A new insight into protein-protein interactions and the effect of conformational alterations in PCNA

Author:
Vijay Kumar Bhardwaj; Rituraj Purohit
Source:
International journal of biological macromolecules 2020 v.148 pp. 999-1009
ISSN:
0141-8130
Subject:
amino acids; hydrophobicity; molecular dynamics; mutants; mutation; peptides; proliferating cell nuclear antigen; protein binding; protein-protein interactions
Abstract:
... The sliding clamp proteins are present in almost all forms of life and participate in various fundamental processes. Many of these proteins accommodate a conserved sequence that interacts with the hydrophobic groove on sliding clamps. The conserved sequence on proteins is known as the PCNA-interacting protein box, and the hydrophobic groove of PCNA contains regions of the inter-domain connecting l ...
DOI:
10.1016/j.ijbiomac.2020.01.212

55. Accelerating Post-SELEX Aptamer Engineering Using Exonuclease Digestion

Author:
Juan Canoura; Haixiang Yu; Obtin Alkhamis; Daniel Roncancio; Rifat Farhana; Yi Xiao
Source:
Journal of the American Chemical Society 2020 v.143 no.2 pp. 805-816
ISSN:
1520-5126
Subject:
DNA; adenosine; automation; blood serum; detection limit; digestion; electrochemistry; ligands; nucleotide aptamers; protein binding; systematic evolution of ligands by exponential enrichment
Abstract:
... The systematic evolution of ligands by exponential enrichment (SELEX) process enables the isolation of aptamers from random oligonucleotide libraries. However, it is generally difficult to identify the best aptamer from the resulting sequences, and the selected aptamers often exhibit suboptimal affinity and specificity. Post-SELEX aptamer engineering can improve aptamer performance, but current me ...
DOI:
10.1021/jacs.0c09559

56. Amphiphilic dendrimers control protein binding and corona formation on liposome nanocarriers

Author:
Jessica Wagner; Marcel Dillenburger; Johanna Simon; Jennifer Oberländer; Katharina Landfester; Volker Mailänder; David Y. W. Ng; Klaus Müllen; Tanja Weil
Source:
Chemical communications 2020 v.56 no.61 pp. 8663-8666
ISSN:
1364-548X
Subject:
adsorption; blood plasma; chemical reactions; dendrimers; lipophilicity; nanocarriers; opsonins; protein binding; proteins
Abstract:
... Amphiphilic polyphenylene dendrimers (PPDs) with distinct lipophilic and positively or negatively charged surface groups were adsorbed onto liposomes and their impact on protein adsorption in blood plasma was studied. The PPD corona reduced binding of specific opsonins and increased the adsorption of proteins controlling cellular uptake based on their surface patches. ...
DOI:
10.1039/d0cc02486d

57. An adapted LC-MS/MS method for the determination of free plasma concentration of cefoperazone in children: Age-dependent protein binding

Author:
Min Kan; Yue-E Wu; Xue Li; Yi-Ning Dong; Bin Du; Zi-Xuan Guo; Hai-Yan Shi; Xin Huang; Le-Qun Su; Wen-Qi Wang; Yi Zheng; Wei Zhao
Source:
Journal of chromatography 2020 v.1144 pp. 122081
ISSN:
1570-0232
Subject:
acetonitrile; albumins; antibiotic residues; antimicrobial properties; cefoperazone; ceftiofur; children; drug therapy; electrospray ionization mass spectrometry; formic acid; liquid chromatography; monitoring; patients; protein binding; quality control; tandem mass spectrometry
Abstract:
... Antimicrobial activity of cefoperazone, a high protein bound cephalosporin, depends on its unbound concentration. However, the protein binding data of cefoperazone in children is limited, making it challenging to optimize antimicrobial therapy in pediatric clinical practice. Furthermore, a validated method to measure the free part in children is unavailable with the small volume of samples that ca ...
DOI:
10.1016/j.jchromb.2020.122081

58. Application of an in vitro digestion model to study the metabolic profile changes of an herbal extract combination by UHPLC–HRMS

Author:
Timo A. Thumann; Eva-Maria Pferschy-Wenzig; Heba Aziz-Kalbhenn; Ramy M. Ammar; Sabine Rabini; Christine Moissl-Eichinger; Rudolf Bauer
Source:
Phytomedicine 2020 v.71 pp. 153221
ISSN:
0944-7113
Subject:
Angelica archangelica; Melissa officinalis; Mentha piperita nothosubsp. piperita; Silybum marianum; bioavailability; caffeic acid; caraway; chamomile; colon; digestion; fruits; in vitro digestion; in vitro studies; indigestion; intestinal microorganisms; isomerization; licorice; medicinal plants; metabolites; models; protein binding; roots
Abstract:
... STW 5 is a fixed herbal combination containing extracts from nine medicinal plants: bitter candytuft, greater celandine, garden angelica roots, lemon balm leaves, peppermint leaves, caraway fruits, licorice roots, chamomile flowers, and milk thistle fruit. STW 5 is a clinically proven treatment for functional dyspepsia and irritable bowel syndrome.Using a static in vitro method, we simulated oral, ...
DOI:
10.1016/j.phymed.2020.153221

59. AtWRKY21 negatively regulates tolerance to osmotic stress in Arabidopsis

Author:
Kai Xuan Zhao; Shan Shan Chu; Xian Duo Zhang; Li Ping Wang; Justice Kipkoir Rono; Zhi Min Yang
Source:
Environmental and experimental botany 2020 v.169 pp. 103920
ISSN:
0098-8472
Subject:
Arabidopsis; chlorophyll; drought; drought tolerance; electrolyte leakage; gene expression regulation; gene overexpression; genetic lines; mutants; osmotic stress; peroxides; phenotype; phytomass; plant response; protein binding; rice; salinity; sequence analysis; stress response; survival rate; transcription factors; water stress
Abstract:
... WRKY transcription factors play crucial roles in plant response to environmental stresses. This study aimed to investigate an uncharacterized gene (At2g30590) encoding AtWRKY21 in mediating an adaptive response to osmotic stress in Arabidopsis. AtWRKY21expressed at various development stages and was substantially induced by drought stress but not salinity. Confocal scanning detection shows that At ...
DOI:
10.1016/j.envexpbot.2019.103920

60. Biopartitioning micellar chromatography under different conditions: Insight into the retention mechanism and the potential to model biological processes

Author:
Fotios Tsopelas; Panagiotis Danias; Athina Pappa; Anna Tsantili-Kakoulidou
Source:
Journal of chromatography 2020 v.1621 pp. 461027
ISSN:
0021-9673
Subject:
Gibbs free energy; absorption; albumins; blood proteins; chromatography; drugs; electrostatic interactions; human cell lines; humans; ionization; lipophilicity; membrane permeability; micelles; models; protein binding; sodium chloride; surface area; surfactants; temperature; topology
Abstract:
... In the present study, 88 structurally- diverse drugs were investigated by biopartitioning micellar chromatography (BMC) using Brij-35 as surfactant under different chromatographic conditions. It was found that temperature and presence of NaCl have only a minor effect in BMC retention. Correlation of BMC retention factors with octanol-water partitioning required the inclusion of fractions of ionize ...
DOI:
10.1016/j.chroma.2020.461027

61. Boronic acid functionalized fibrous cellulose for the selective enrichment of glycopeptides

Author:
Muhammad Salman Sajid; Fahmida Jabeen; Dilshad Hussain; Qurra‐tul‐Ann Afza Gardner; Muhammad Naeem Ashiq; Muhammad Najam‐ul‐Haq
Source:
Journal of separation science 2020 v.43 no.7 pp. 1348-1355
ISSN:
1615-9306
Subject:
Fourier transform infrared spectroscopy; binding capacity; blood serum; boronic acids; bovine serum albumin; cellulose; computer software; glycopeptides; glycoproteins; glycosylation; humans; hydrazides; immunoglobulins; lectins; oxidation; particle size; peroxidase; protein binding; scanning electron microscopy
Abstract:
... Enrichment of glycoproteins has been important because of their dynamicity and role in biological systems. Study of glycoproteins is complex because of the simultaneous glycosylation and deglycosylation inside the body. Often employed affinities for glycopeptides are hydrazide, boronic acid, or physiosorbed lectin on support materials. Cellulose, a natural polysaccharide, has rich surface chemistr ...
DOI:
10.1002/jssc.201900983

62. CRISPR–Cas9 Genome Interrogation: A Facilitated Subdiffusive Target Search Strategy

Author:
Diljith Thonnekottu; Debarati Chatterjee
Source:
Journal of physical chemistry 2020 v.124 no.16 pp. 3271-3282
ISSN:
1520-5207
Subject:
CRISPR-Cas systems; CRISPR-associated endonuclease 9; DNA; chromatin; fluorescence; gene editing; genome; mammals; models; prediction; probability; protein binding; spectroscopy
Abstract:
... The functional application of RNA-guided CRISPR-associated Cas9 protein, a bacterial immune system-based protein complex, via which in vivo, highly specific, and well-regulated, gene-editing processes are being monitored at an unprecedented level, has led to remarkable progress in genetic engineering and technology. The complicated in vivo process of genome interrogation followed by gene editing b ...
DOI:
10.1021/acs.jpcb.0c00086

63. Characteristics of the first H16N3 subtype influenza A viruses isolated in western China

Author:
Yulei Li; Minghui Li; Jingman Tian; Yaping Zhang; Xiaoli Bai; Xiaoliang Wang; Jianzhong Shi; Yumei Wang; Long Ma; Cen Yang; Yanbing Li
Source:
Transboundary and emerging diseases 2020 v.67 no.4 pp. 1677-1687
ISSN:
1865-1674
Subject:
Influenza A virus; avian influenza; disease surveillance; host specificity; human cell lines; interspecific variation; mice; phylogeny; protein binding; virulence; virus receptors; wild birds; zoonoses; China
Abstract:
... The first documented avian influenza virus subtype H16N3 was isolated in 1975 and is currently detectable in many countries worldwide. However, the prevalence, biological characteristics and threat to humans of the avian influenza virus H16N3 subtype in China remain poorly understood. We performed avian influenza surveillance in major wild bird gatherings across the country from 2017 to 2019, resu ...
DOI:
10.1111/tbed.13511

64. Comparative renal disposition of creatine, and technetium diagnostic contrast agents in the pigeon (columba livia)

Author:
Jeffrey Wimsatt; Roger Pearce; Phillip F. Steyn; Linda Vap; David K. Glover
Source:
Journal of zoo and wildlife medicine 2020 v.50 no.4 pp. 891-896
ISSN:
1937-2825
Subject:
Columba livia; animal models; blood plasma; blood proteins; creatine; creatinine; filtration; glomerular filtration rate; inulin; pigeons; protein binding; technetium; urea nitrogen; uric acid
Abstract:
... Clinical assessment of renal function in avian species often involves the measurement of plasma uric acid and blood urea nitrogen, relatively insensitive markers of renal dysfunction and dehydration. In mammals, endogenous creatinine is widely used as an indicator of renal glomerular dysfunction. However, avian species produce primarily creatine. Here, renal creatine, ⁹⁹ᵐTc99-DTPA (diethylenepenta ...
DOI:
10.1638/2018-0214

65. Comparative whole corona fingerprinting and protein adsorption thermodynamics of PLGA and PCL nanoparticles in human serum

Author:
Myolisi Ndumiso; Nela Buchtová; Lizex Husselmann; Gadija Mohamed; Ashwil Klein; Marique Aucamp; David Canevet; Sarah D’Souza; Retsepile E. Maphasa; Frank Boury; Admire Dube
Source:
Colloids and surfaces 2020 v.188 pp. 110816
ISSN:
0927-7765
Subject:
adsorption; biodegradability; blood serum; calorimetry; drug delivery systems; drugs; evaporation; fluorescence; gel electrophoresis; human serum albumin; humans; hydrophobicity; lactones; mass spectrometry; nanoparticles; polymers; protein binding; proteome; thermodynamics; titration; zeta potential
Abstract:
... Nanoparticles (NPs) based on biocompatible and biodegradable polymers such as poly(lactic-co-glycolic acid) (PLGA) and polycaprolactone (PCL) represent effective systems for systemic drug delivery. Upon injection into the blood circuit, the NP surface is rapidly modified due to adsorption of proteins that form a ‘protein corona’ (PC). The PC plays an important role in cellular targeting, uptake an ...
DOI:
10.1016/j.colsurfb.2020.110816
PubMed:
31991290
PubMed Central:
PMC7061085

66. Completing the ENCODE3 compendium yields accurate imputations across a variety of assays and human biosamples

Author:
Jacob Schreiber; Jeffrey Bilmes; William Stafford Noble
Source:
Genome biology 2020 v.21 no.1 pp. 82
ISSN:
1474-760X
Subject:
avocados; chromatin; epigenome; histone code; humans; models; protein binding; transcriptomics
Abstract:
... Recent efforts to describe the human epigenome have yielded thousands of epigenomic and transcriptomic datasets. However, due primarily to cost, the total number of such assays that can be performed is limited. Accordingly, we applied an imputation approach, Avocado, to a dataset of 3814 tracks of data derived from the ENCODE compendium, including measurements of chromatin accessibility, histone m ...
DOI:
10.1186/s13059-020-01978-5
PubMed:
32228713
PubMed Central:
PMC7104481

67. Comprehensive toxicokinetic analysis reveals major interspecies differences in absorption, distribution and elimination of citrinin in pigs and broiler chickens

Author:
Celine Meerpoel; Arnau Vidal; Bart Huybrechts; Emmanuel K. Tangni; Sarah De Saeger; Siska Croubels; Mathias Devreese
Source:
Food and chemical toxicology 2020 v.141 pp. 111365
ISSN:
0278-6915
Subject:
bioavailability; biotransformation; blood proteins; broiler chickens; citrinin; humans; intravenous injection; pharmacokinetics; protein binding; swine; toxicology
Abstract:
... A comprehensive toxicokinetic analysis of citrinin (CIT) revealed interspecies differences for all toxicokinetic parameters and in absolute oral bioavailability. Oral bioavailability for CIT was complete for broilers (113–131%), while ranging from 37 to 44% in pigs. CIT was more rapidly absorbed in pigs (Tₘₐₓ = 0.92 h) compared to broiler chickens (Tₘₐₓ = 7.33 h). The elimination of CIT was slower ...
DOI:
10.1016/j.fct.2020.111365

68. DEPICTER: Intrinsic Disorder and Disorder Function Prediction Server

Author:
Amita Barik; Akila Katuwawala; Jack Hanson; Kuldip Paliwal; Yaoqi Zhou; Lukasz Kurgan
Source:
Journal of molecular biology 2020 v.432 no.11 pp. 3379-3387
ISSN:
0022-2836
Subject:
data collection; nucleic acids; prediction; protein binding; proteins; sequence alignment
Abstract:
... Computational predictions of the intrinsic disorder and its functions are instrumental to facilitate annotation for the millions of unannotated proteins. However, access to these predictors is fragmented and requires substantial effort to find them and to collect and combine their results. The DEPICTER (DisorderEd PredictIon CenTER) server provides first-of-its-kind centralized access to 10 popula ...
DOI:
10.1016/j.jmb.2019.12.030

69. Deep learning model predicts water interaction sites on the surface of proteins using limited-resolution data

Author:
Jan Zaucha; Charlotte A. Softley; Michael Sattler; Dmitrij Frishman; Grzegorz M. Popowicz
Source:
Chemical communications 2020 v.56 no.98 pp. 15454-15457
ISSN:
1364-548X
Subject:
binding proteins; binding sites; chemical communication; crystal structure; drug design; models; prediction; protein binding; surface interactions; surface proteins; testing
Abstract:
... We develop a residual deep learning model, hotWater (https://pypi.org/project/hotWater/), to identify key water interaction sites on proteins for binding models and drug discovery. This is tested on new crystal structures, as well as cryo-EM and NMR structures from the PDB and in crystallographic refinement with promising results. ...
DOI:
10.1039/d0cc04383d

70. Demonstration that Small Molecules can Bind and Stabilize Low-abundance Short-lived RNA Excited Conformational States

Author:
Laura R. Ganser; Megan L. Kelly; Neeraj N. Patwardhan; Amanda E. Hargrove; Hashim M. Al-Hashimi
Source:
Journal of molecular biology 2020 v.432 no.4 pp. 1297-1304
ISSN:
0022-2836
Subject:
Human immunodeficiency virus 1; RNA; aminoglycosides; conformational isomerization; ligands; mutants; nuclear magnetic resonance spectroscopy; protein binding; transcriptional activation
Abstract:
... Many promising RNA drug targets have functions that require the formation of RNA-protein complexes, but inhibiting RNA-protein interactions can prove difficult using small molecules. Regulatory RNAs have been shown to transiently form excited conformational states (ESs) that remodel local aspects of secondary structure. In some cases, the ES conformation has been shown to be inactive and to be poo ...
DOI:
10.1016/j.jmb.2019.12.009
PubMed:
31863746
PubMed Central:
PMC7054137

71. Detailed cellular assessment of albumin-bound oligonucleotides: Increased stability and lower non-specific cell uptake

Author:
Aurélie Lacroix; Hassan H. Fakih; Hanadi F. Sleiman
Source:
Journal of controlled release 2020 v.324 pp. 34-46
ISSN:
0168-3659
Subject:
DNA; albumins; blood proteins; blood serum; cell membranes; drugs; immunogenicity; lipids; macrophages; moieties; nucleases; oligonucleotides; protein binding; therapeutics
Abstract:
... Conjugation of lipid moieties to nucleic-acid therapeutics increases their interaction with cellular membranes, enhances their uptake and influences in vivo distribution. Once injected in biological fluids, such modifications trigger the binding of various serum proteins, which in turn play a major role in determining the fate of oligonucleotides. Yet, the role played by each of these proteins, mo ...
DOI:
10.1016/j.jconrel.2020.04.020

72. Detection of biotin with zeptomole sensitivity using recombinant spores and a competition assay

Author:
Wen-Zhi Lin; Wan-Chun Liao; Fang-Hsi Chen; I-Cheng Ma; Shao-Yi Hou
Source:
Analytical and bioanalytical chemistry 2020 v.412 no.26 pp. 7219-7226
ISSN:
1618-2642
Subject:
analytical chemistry; biotin; chemical species; detection limit; endospores; equipment; magnetism; protein binding; streptavidin; toxicity
Abstract:
... Detection of protein-binding analytes is important for many applications. Currently, various instrument-based techniques are used for detecting protein-binding analytes. However, such techniques have several limitations including high cost and time-consuming sample processing. In order to overcome these limitations, we developed a sensitive competition assay for the detection of protein-binding an ...
DOI:
10.1007/s00216-020-02854-8

73. Development of a Linker-Mediated Immunoassay Using Chemically Transitioned Nanosensors

Author:
Lucas D. Smith; Michael C. Willard; Jordan P. Smith; Brian T. Cunningham
Source:
Analytical chemistry 2020 v.92 no.5 pp. 3627-3635
ISSN:
1520-6882
Subject:
DNA; additives; antibodies; antigens; biomarkers; blood serum; detection limit; diagnostic techniques; drug development; humans; immunoassays; melting point; myocardial infarction; patients; protein binding; sensors (equipment); troponin I
Abstract:
... Sensitive and specific quantification of protein biomarkers is important in medical diagnostics, academic research, and pharmaceutical development. However, multiple binding steps in conventional sandwich immunoassay protocols result in high assay hands-on-time and delayed results. This is particularly relevant for medical diagnostics, where assay turn-around-time can have an immense impact on pat ...
DOI:
10.1021/acs.analchem.9b04518

74. Diversity and genome mapping assessment of disordered and functional domains in trypanosomatids

Author:
Grace Santos Tavares Avelar; Leilane Oliveira Gonçalves; Frederico Gonçalves Guimarães; Paul Anderson Souza Guimarães; Luiz Gustavo do Nascimento Rocha; Maria Gabriela Reis Carvalho; Daniela de Melo Resende; Jeronimo Conceição Ruiz
Source:
Journal of proteomics 2020 v.227 pp. 103919
ISSN:
1874-3919
Subject:
Chagas disease; Leishmania braziliensis; Leishmania infantum; Trypanosoma cruzi; binding sites; chromosome mapping; drug therapy; etiological agents; gene expression; humans; leishmaniasis; loci; multigene family; parasites; post-translational modification; prediction; protein binding; protein folding; protein transport; proteins; proteome; structural biology; vaccines; virulence
Abstract:
... The proteins that have structural disorder exemplify a class of proteins which is part of a new frontier in structural biology that demands a new understanding of the paradigm of structure/function correlations. In order to address the location, relative distances and the functional/structural correlation between disordered and conserved domains, consensus disordered predictions were mapped togeth ...
DOI:
10.1016/j.jprot.2020.103919

75. Does cotton bollworm show cross-resistance to the Bacillus thuringiensis toxins Cry1Ac and Cry2Ab? A mini review

Author:
Jihong Ma; Changyan Tian; Guanghui Lyu; Wenxuan Mai
Source:
Journal of Arid Land 2020 v.12 no.2 pp. 349-356
ISSN:
1674-6767
Subject:
Bacillus thuringiensis; Helicoverpa armigera; arid lands; binding sites; cotton; insect pests; mutation; pest resistance; planting; protein binding; resistance genes; risk; toxins; transgenic plants
Abstract:
... Since 1996, transgenic Bacillus thuringiensis (Bt) cotton has been commercially grown in numerous countries in an effort to stem the losses caused by key lepidopteran pests. However, the development of pest resistance to Bt toxins has jeopardized the continued utilization of Bt cotton. As a strategy designed to circumvent the development of resistance, Bt cotton varieties expressing two or more to ...
DOI:
10.1007/s40333-020-0063-0

76. Down-regulation of Tet2 is associated with Foxp3 TSDR hypermethylation in regulatory T cell of allergic rhinitis

Author:
Lu Tan; Ting Qiu; Rong Xiang; Cheng Cao; Yuqin Deng; Zezhang Tao; Yu Xu
Source:
Life sciences 2020 v.241 pp. 117101
ISSN:
0024-3205
Subject:
DNA; DNA methylation; T-lymphocytes; allergic rhinitis; chromatin; flow cytometry; gene expression regulation; genes; messenger RNA; patients; precipitin tests; protein binding; quantitative polymerase chain reaction; sequence analysis; spleen
Abstract:
... Ten-eleven-translocation (Tet) proteins are 5-methylcytosine oxidases and have profound impact on DNA methylation and genes expression. This study aimed to investigate the role of Tet2 and its association with Foxp3 DNA methylation in regulatory T (Treg) cell of allergic rhinitis (AR). CD4⁺CD25⁺Treg cells were sorted from peripheral blood lymphocytes drawn from AR patients and spleen lymphocytes d ...
DOI:
10.1016/j.lfs.2019.117101

77. Doxorubicin inhibits PD-L1 expression by enhancing TTP-mediated decay of PD-L1 mRNA in cancer cells

Author:
Dong Jun Kim; Ji Hun Jang; Soo-Youn Ham; Seong Hee Choi; Sung Soon Park; So Yeon Jeong; Beom Chang Kim; Do Yong Jeon; Byung Ju Lee; Byung Kyun Ko; Jeong Woo Park; Wha Ja Cho
Source:
Biochemical and biophysical research communications 2020 v.522 no.2 pp. 402-407
ISSN:
0006-291X
Subject:
binding proteins; doxorubicin; neoplasm cells; protein binding; research
Abstract:
... Recent research revealed that doxorubicin (DOX) decreased expression of programmed death-ligand 1 (PD-L1) in cancer cells. However, the detailed mechanisms underlying this effect are not well established. Here, we demonstrate that doxorubicin down-regulates PD-L1 expression through induction of AU-rich element (ARE) binding protein tristetraprolin (TTP) in cancer cells. PD-L1 mRNA contain three AR ...
DOI:
10.1016/j.bbrc.2019.11.106

78. Effects of organic acids and common household products on the occurrence of false positive test results using immunochromatographic assays

Author:
Megan M. Foley; Catherine O. Brown; Christian G. Westring; Phillip B. Danielson; Heather E. McKiernan
Source:
Forensic science international 2020 v.308 pp. 110165
ISSN:
0379-0738
Subject:
body fluids; false positive results; forensic sciences; household products; immunoaffinity chromatography; immunologic techniques; lactic acid; protein binding; proteins
Abstract:
... Forensic serological analyses often rely on lateral flow immunochromatographic assays to detect proteins that are characteristic of forensically relevant body fluids. In this study, we demonstrate that a positive result, however, is not limited to target protein binding. Citric and lactic acids at various pH levels were tested using 9 different commercial immunochromatographic assays. Varying rate ...
DOI:
10.1016/j.forsciint.2020.110165

79. Enabling Molecular Gapping and Bridging on a Biosensing Surface via Electrochemical Cross-Linking and Cleavage

Author:
Lei Zhou; Jinglong Li; Kai Zhang; Lei Shi; Shaojiao Qin; Hao Li
Source:
Analytical chemistry 2020 v.92 no.3 pp. 2635-2641
ISSN:
1520-6882
Subject:
agitation; catalysts; cross-coupling reactions; crosslinking; electrochemistry; peptides; protein binding; proteins
Abstract:
... Protein detection in complicated biological samples requires robust design and a rigorous rinsing process. Many recently developed artificial targeting probes, however, often do not possess antibody-like binding strength that enables them to endure harsh biosensing conditions, and the classic 2-to-1 sandwich binding pattern is unavailable for many targets, often necessitating a complicated indirec ...
DOI:
10.1021/acs.analchem.9b04538

80. Epigenetic biosensors for bacteriophage detection and phage receptor discrimination

Author:
David R. Olivenza; Josep Casadesús; Mireille Ansaldi
Source:
Environmental microbiology 2020 v.22 no.8 pp. 3126-3142
ISSN:
1462-2912
Subject:
O-antigens; Salmonella enterica; biosensors; coliphages; epigenetics; operon; protein binding; virus receptors
Abstract:
... Environmental monitoring of bacteria using phage‐based biosensors has been widely developed for many different species. However, there are only a few available methods to detect specific bacteriophages in raw environmental samples. In this work, we developed a simple and efficient assay to rapidly monitor the phage content of a given sample. The assay is based on the bistable expression of the Sal ...
DOI:
10.1111/1462-2920.15050

81. Evaluation of inflammatory biomarkers in goats naturally infected with Babesia ovis

Author:
Bijan Esmaeilnejad; Sepideh Rajabi; Mousa Tavassoli; Mahmoud Rashnavadi; Farhad Seif; Armin Aligolzadeh; Ali Khoshnejad
Source:
Parasitology research 2020 v.119 no.12 pp. 4151-4158
ISSN:
0932-0113
Subject:
Babesia ovis; albumins; amyloid; biomarkers; blood serum; erythrocyte count; ferroxidase; fibrinogen; haptoglobins; hemoglobin; leukocyte count; microscopy; necrosis; neoplasms; parasitology; pathophysiology; protein binding; research; Iran
Abstract:
... This study was designed to evaluate the effects of Babesia ovis infection on concentrations of some essential acute phase proteins (APPs) including albumin, fibrinogen, serum amyloid A, haptoglobin, and ceruloplasmin as well as total, protein-binding, and lipid-binding sialic acids (TSA, PBSA, and LBSA) and two crucial cytokines including interferon-γ (IFN-γ) and tumor necrosis factor-α (TNF-α). S ...
DOI:
10.1007/s00436-020-06829-7

82. Examining Uncertainty in In Vitro–In Vivo Extrapolation Applied in Fish Bioconcentration Models

Author:
Heike Laue; Lu Hostettler; Remo P. Badertscher; Karen J. Jenner; Gordon Sanders; Jon A. Arnot; Andreas Natsch
Source:
Environmental science & technology 2020 v.54 no.15 pp. 9483-9494
ISSN:
1520-5851
Subject:
bioaccumulation; biotransformation; gills; in vitro to in vivo extrapolation; interspecific variation; liver; model uncertainty; odor compounds; protein binding; trout
Abstract:
... In vitro biotransformation rates were determined for 30 chemicals, mostly fragrance ingredients, using trout liver S9 fractions (RT-S9) and incorporated into in vitro–in vivo extrapolation (IVIVE) models to predict bioconcentration factors (BCFs). Predicted BCFs were compared against empirical BCFs to explore potential major uncertainties involved in the in vitro methods and IVIVE models: (i) in v ...
DOI:
10.1021/acs.est.0c01492

83. Formation of glyco-functionalized interfaces for protein binding using polyphenolic glycoside

Author:
Hirokazu Seto; Mao Harada; Hidenori Nagaura; Honoka Taniguchi; Tatsuya Murakami; Ichiro Kimura; Yumiko Hirohashi; Hiroyuki Shinto
Source:
Carbohydrate research 2020 v.492 pp. 108002
ISSN:
0008-6215
Subject:
Bauhinia purpurea; adsorption; agglutinins; air; aqueous solutions; binding capacity; binding sites; concanavalin A; glycosides; gold; peanuts; polyethylene; polystyrenes; polytetrafluoroethylene; protein binding; rutin; silica
Abstract:
... In this study, a polyphenolic glycoside (α-glucosyl rutin) was used to form glyco-functionalized interfaces for protein binding. α-Glucosyl rutin was coated onto precious metals, metal oxides, and synthetic polymers, including polyethylene and polytetrafluoroethylene with poor surface modifiability. The glyco-functionalized interfaces bound strongly and specifically to concanavalin A and Bauhinia ...
DOI:
10.1016/j.carres.2020.108002

84. Gain-Scanning for Protein Microarray Assays

Author:
Feng Feng; Sila Toksoz Ataca; Mingxuan Ran; Yumei Wang; Michael Breen; Thomas B. Kepler
Source:
Journal of proteome research 2020 v.19 no.7 pp. 2664-2675
ISSN:
1535-3907
Subject:
antibody specificity; biomarkers; blood serum; data collection; humans; immune response; information processing; microbial detection; models; monoclonal antibodies; protein binding; protein microarrays; proteins; proteome
Abstract:
... Protein microarrays consist of known proteins spotted onto solid substrates and are used to perform highly multivariate assessments of protein-binding interactions. Human protein arrays are routinely applied to pathogen detection, immune response biomarker profiling, and antibody specificity profiling. Here, we describe and demonstrate a new data processing procedure, gain-scan, in which data were ...
DOI:
10.1021/acs.jproteome.9b00892

85. Generation of mWasabi fluorescent protein-binding nanobodies

Author:
Shufeng Li; Haitao Shan; Ting Wang; Xiaojuan Zheng; Minke Shi; Baojun Chen; Haiqin Lu; Ying Zhang; Sheng Zhao; Zichun Hua
Source:
Analytical biochemistry 2020 v.608 pp. 113875
ISSN:
0003-2697
Subject:
antibodies; binding properties; design; fields; fluorescence; green fluorescent protein; protein binding; research
Abstract:
... mWasabi is a bright monomeric green fluorescent protein. It can be used as a fusion tag to monitor various biological events, e.g. protein localization. Here we report the selection of camelid-derived single-domain antibody fragments (nanobodies) against mWasabi. In this work, phage-display approach was employed to select the high affinity mWasabi-specific Nb (nanobodies). These nanobodies were ab ...
DOI:
10.1016/j.ab.2020.113875

86. Heat Induced Grafting of Poly(glycidyl methacrylate) on Polybutylene Terephthalate Nonwovens for Bioseparations

Author:
Michael Heller; Qian Li; Kellie Esinhart; Behnam Pourdeyhimi; Cristiana Boi; Ruben G. Carbonell
Source:
Industrial & engineering chemistry process design and development 2020 v.59 no.12 pp. 5371-5380
ISSN:
1520-5045
Subject:
adenosine triphosphate; adsorption; binding capacity; heat; ion exchange; lysozyme; molecular weight; nonwoven fabrics; polymers; process design; protein binding; sorption isotherms; weight gain
Abstract:
... Polybutylene terephthalate (PBT) nonwovens were successfully grafted with poly(glycidyl methacrylate) (polyGMA) using a heat induced grafting approach with the thermal initiator benzoyl peroxide (Bz₂O₂). This grafting method resulted in complete, uniform, and conformal grafted layers around the PBT fibers that could be further functionalized as ion exchangers for protein capture. Protein binding c ...
DOI:
10.1021/acs.iecr.9b04936

87. Highly Efficient and Sustainable Synthesis of Neoglycoproteins Using Galactosidases

Author:
P. Hoyos; T. Bavaro; A. Perona; A. Rumbero; S. Tengattini; M. Terreni; María J. Hernáiz
Source:
ACS sustainable chemistry & engineering 2020 v.8 no.16 pp. 6282-6292
ISSN:
2168-0485
Subject:
Bacillus circulans; Escherichia coli; N-acetylglucosamine; beta-galactosidase; catalytic activity; disaccharides; enzyme activity; enzyme substrates; glycoconjugates; glycosylation; models; moieties; protein binding; regioselectivity; ribonucleases; solvents; vaccines
Abstract:
... Oligosaccharides are a key component on glycoconjugates with biomedical applications. However, the investigation of more efficient and environmental protocols for their preparation carrying defined oligosaccharides remains a big challenge due to lack of access to structurally well-defined and functionalized oligosaccharides. In this work a highly sustainable and efficient chemoenzymatic synthesis ...
DOI:
10.1021/acssuschemeng.9b07785

88. Identification of the COMM-domain containing protein 1 as specific binding partner for the guanine-rich RNA sequence binding factor 1

Author:
Bernhard Dumoulin; Christoph Ufer; Sabine Stehling; Dagmar Heydeck; Hartmut Kuhn; Sajad Sofi
Source:
Biochimica et biophysica acta 2020 v.1864 no.11 pp. 129678
ISSN:
0304-4165
Subject:
RNA; RNA-binding proteins; brain; cDNA libraries; cell senescence; complementary DNA; erythropoiesis; homeostasis; humans; mitochondria; nucleotide sequences; precipitin tests; protein binding; protein-protein interactions; two hybrid system techniques
Abstract:
... The guanine-rich RNA sequence binding factor 1 (GRSF1) is an RNA-binding protein of the hnRNP H/F family, which has been implicated in erythropoiesis, regulation of the redox homeostasis, embryonic brain development, mitochondrial function and cellular senescence. The molecular basis for GRSF1-RNA interaction has extensively been studied in the past but for the time being GRSF1 binding proteins ha ...
DOI:
10.1016/j.bbagen.2020.129678

89. Impact of Holder pasteurization on essential elements from human donor milk: Total contents and protein-binding profiles

Author:
Rafaella R. Alves Peixoto; Sonia Fernández-Menéndez; Belén Fernández-Colomer; Ana I. Pérez Vaquero; Solange Cadore; Alfredo Sanz-Medel; María L. Fernández-Sánchez
Source:
Journal of food composition and analysis 2020 v.87 pp. 103395
ISSN:
0889-1575
Subject:
atomic absorption spectrometry; breast milk; chemical speciation; copper; gel chromatography; heat; iron; milk; milk banks; milk composition; pasteurization; protein binding; protein composition; proteins; temperature; zinc
Abstract:
... Holder pasteurization is a thermal treatment commonly applied to milk in human milk banks. However, the application of heating processes can affect the actual composition of milk. In this work, the effect of Holder pasteurization on essential elements in donor human breast milk was studied, including total contents and protein-binding profile of Cu, Fe, Se and Zn. The total contents were determine ...
DOI:
10.1016/j.jfca.2019.103395

90. Improved recovery of galloyl metabolites from mango (Mangifera indica L.) in human plasma using protein precipitation with sodium dodecyl sulfate and methanol

Author:
Ryan C. Barnes; Hyemee Kim; Susanne U. Mertens-Talcott; Stephen T. Talcott
Source:
Food research international 2020 v.129 pp. 108812
ISSN:
0963-9969
Subject:
Mangifera indica; absorption; bioavailability; blood plasma; chemical species; chemical structure; ethyl gallate; females; foods; high performance liquid chromatography; males; mango pulp; mangoes; mass spectrometry; metabolites; methanol; pharmacokinetics; protein binding; pyrogallol; sodium dodecyl sulfate; solid phase extraction; solvents
Abstract:
... Extraction of polyphenolic metabolites from blood fractions can be challenging since compound recovery can be limited by chemical structure, polarity, and protein-binding affinity of analytes. Gallic acid and its metabolites exhibit particularly low recoveries from plasma and can lead to an underestimation of their bioavailability from foods. A modified method to extract free gallic acid and its m ...
DOI:
10.1016/j.foodres.2019.108812

91. In Situ Cascade Derivation toward a Hierarchical Layered Double Hydroxide Magnetic Absorbent for High-Performance Protein Separation

Author:
Shuo Shi; Wentao Zhang; Haofen Wu; Yuchen Li; Xinyi Ren; Min Li; Jie Liu; Jing Sun; Tianli Yue; Jianlong Wang
Source:
ACS sustainable chemistry & engineering 2020 v.8 no.12 pp. 4966-4974
ISSN:
2168-0485
Subject:
absorbents; adsorbents; adsorption; binding capacity; blood sampling; coordination compounds; hemoglobin; histidine; ions; iron; iron oxides; magnetism; models; nickel; protein binding; proteomics
Abstract:
... Selective enrichment and purification of histidine (His)-rich protein from complex mixtures is vital to satisfy the requirements of proteomic and diagnostic applications, but it still remain a challenge. Herein, a high-performance layered double hydroxide (LDH)-based adsorbent is designed and prepared, via a metal–organic framework (MOF)-mediated in situ cascade derivation strategy, for enhanced H ...
DOI:
10.1021/acssuschemeng.0c00934

92. In Vivo Imaging of Hypoxia Associated with Inflammatory Bowel Disease by a Cytoplasmic Protein-Powered Fluorescence Cascade Amplifier

Author:
Yibo Zhou; Sheng Yang; Jingru Guo; Hao Dong; Keyi Yin; Wei Tao Huang; Ronghua Yang
Source:
Analytical chemistry 2020 v.92 no.8 pp. 5787-5794
ISSN:
1520-6882
Subject:
benzoic acids; beta-cyclodextrin; fluorescence; fluorescent dyes; hypoxia; image analysis; inflammatory bowel disease; nanoparticles; oxygen; polymers; porous media; protein binding; silica
Abstract:
... Accurate and sensitive imaging of hypoxia associated with inflammatory bowel disease (IBD) is significant for the precise diagnosis and treatment of this disease, but it remains a challenge for traditional hypoxia-activatable fluorescence probes because of a more moderate hypoxic state during IBD than under other pathological conditions. To address this issue, herein, we designed a hypoxia-activat ...
DOI:
10.1021/acs.analchem.9b05278

93. Interaction of antitubercular drug candidates with α1-acid glycoprotein produced in pulmonary granulomas

Author:
Ferenc Zsila; Szilvia Bősze; Tamás Beke-Somfai
Source:
International journal of biological macromolecules 2020 v.147 pp. 1318-1327
ISSN:
0141-8130
Subject:
Mycobacterium tuberculosis; antibiotics; binding properties; binding sites; bioavailability; blood serum; circular dichroism spectroscopy; computer simulation; drugs; extracellular matrix; glycoproteins; granuloma; macrophages; multiple drug resistance; organic matter; pathogens; protein binding; spectral analysis; tuberculosis
Abstract:
... The intracellular pathogen Mycobacterium tuberculosis can survive and replicate within host macrophages. Among various immunomodulatory substances, macrophages also produce α1-acid glycoprotein (AAG) which is secreted into the extracellular matrix of tuberculosis granulomas that represents a specific binding environment. Employing circular dichroism (CD) and UV/VIS absorption spectroscopic methods ...
DOI:
10.1016/j.ijbiomac.2019.10.096

94. Interactions of zearalanone, α-zearalanol, β-zearalanol, zearalenone-14-sulfate, and zearalenone-14-glucoside with serum albumin

Author:
Zelma Faisal; Virág Vörös; Eszter Fliszár-Nyúl; Beáta Lemli; Sándor Kunsági-Máté; Miklós Poór
Source:
Mycotoxin research 2020 v.36 no.4 pp. 389-397
ISSN:
0178-7888
Subject:
Fusarium; affinity chromatography; fluorescence emission spectroscopy; interspecific variation; metabolites; mycotoxicosis; protein binding; serum albumin; zearalenol; zearalenone
Abstract:
... The xenoestrogenic mycotoxin zearalenone is a Fusarium-derived food and feed contaminant. In mammals, the reduced (e.g., zearalanone, α-zearalanol, and β-zearalanol) and conjugated (e.g., zearalenone-14-sulfate) metabolites of zearalenone are formed. Furthermore, filamentous fungi and plants are also able to convert zearalenone to conjugated derivatives, including zearalenone-14-sulfate and zearal ...
DOI:
10.1007/s12550-020-00404-w

95. Intrinsically Disordered Bacterial Polar Organizing Protein Z, PopZ, Interacts with Protein Binding Partners Through an N-terminal Molecular Recognition Feature

Author:
Christopher T. Nordyke; Yasin M. Ahmed; Ryan Z. Puterbaugh; Grant R. Bowman; Krisztina Varga
Source:
Journal of molecular biology 2020 v.432 no.23 pp. 6092-6107
ISSN:
0022-2836
Subject:
Caulobacter crescentus; amino acids; cytoplasm; nuclear magnetic resonance spectroscopy; point mutation; protein binding; regulatory proteins; surfactants
Abstract:
... The polar organizing protein Z (PopZ) is necessary for the formation of three-dimensional microdomains at the cell poles in Caulobacter crescentus, where it functions as a hub protein that recruits multiple regulatory proteins from the cytoplasm. Although a large portion of the protein is predicted to be natively unstructured, in reconstituted systems PopZ can self-assemble into a macromolecular s ...
DOI:
10.1016/j.jmb.2020.09.020

96. Label-Free Analysis of Multivalent Protein Binding Using Bioresponsive Nanogels and Surface Plasmon Resonance (SPR)

Author:
Hae Min Yang; Jie Ying Teoh; Guk Hee Yim; Yongdoo Park; Young Gyu Kim; Jongseong Kim; Dongwon Yoo
Source:
ACS applied materials & interfaces 2020 v.12 no.5 pp. 5413-5419
ISSN:
1944-8252
Subject:
antibodies; antigens; biochemical pathways; calcium; cations; immunotherapy; iron; ligands; medicine; moieties; nanoparticles; neoplasms; physiology; potassium; protein binding; protein-protein interactions; receptors; sodium; surface plasmon resonance
Abstract:
... Precise identification of protein–protein interactions is required to improve our understanding of biochemical pathways for biology and medicine. In physiology, how proteins interact with other proteins or small molecules is crucial for maintaining biological functions. For instance, multivalent protein binding (MPB), in which a ligand concurrently interacts with two or more receptors, plays a key ...
DOI:
10.1021/acsami.9b17328

97. Leaflet-Dependent Distribution of PtdIns[4,5]P₂ in Supported Model Membranes

Author:
Jonas Schäfer; Jessica Nehls; Markus Schön; Ingo Mey; Claudia Steinem
Source:
Langmuir 2020 v.36 no.5 pp. 1320-1328
ISSN:
1520-5827
Subject:
adsorption; atomic force microscopy; binding proteins; hydrophilicity; lipid bilayers; lipids; models; organosilicon compounds; plasma membrane; protein binding; reflectometry; silica; spectroscopy
Abstract:
... Supported planar lipid bilayers (SLBs) prepared by spreading of unilamellar vesicles on hydrophilic substrates such as silicon dioxide are frequently used to investigate lipid–protein interactions by means of surface-sensitive methods. In recent years, the receptor lipid phosphatidylinositol-4,5-bisphosphate (PtdIns[4,5]P₂) became particularly important as a significant number of proteins bind to ...
DOI:
10.1021/acs.langmuir.9b03793

98. Mapping DNA Topoisomerase Binding and Cleavage Genome Wide Using Next-Generation Sequencing Techniques

Author:
Shannon J. McKie; Anthony Maxwell; Keir C. Neuman
Source:
Genes 2020 v.11 no.1 pp. -
ISSN:
2073-4425
Subject:
DNA; DNA damage; DNA topoisomerase; chromatin immunoprecipitation; genome; high-throughput nucleotide sequencing; metabolism; protein binding; topology; transcription (genetics)
Abstract:
... Next-generation sequencing (NGS) platforms have been adapted to generate genome-wide maps and sequence context of binding and cleavage of DNA topoisomerases (topos). Continuous refinements of these techniques have resulted in the acquisition of data with unprecedented depth and resolution, which has shed new light on in vivo topo behavior. Topos regulate DNA topology through the formation of rever ...
DOI:
10.3390/genes11010092

99. Meat color is determined not only by chromatic heme pigments but also by the physical structure and achromatic light scattering properties of the muscle

Author:
Joanne M. Hughes; Frank M. Clarke; Peter P. Purslow; Robyn D. Warner
Source:
Comprehensive reviews in food science and food safety 2020 v.19 no.1 pp. 44-63
ISSN:
1541-4337
Subject:
cell adhesion; color; consumer acceptance; cytoskeleton; denaturation; economic impact; extracellular space; heme; light scattering; livestock and meat industry; meat; microstructure; muscles; myofibrillar proteins; myosin; pH; pigments; protein binding; protein composition; protein solubility; sarcomeres; shrinkage; water holding capacity
Abstract:
... Meat color is important for consumer acceptability, with excessively dark meat often associated with consumer rejection. It is determined chromatically by pigment content (measured by hue and chroma) and achromatically by scattering of light by the microstructure (measured by lightness), the latter of which has received minimal research focus. This review discusses the individual components of the ...
DOI:
10.1111/1541-4337.12509

100. Membrane Shape and the Regulation of Biological Processes

Author:
José Carlos Bozelli; Richard M. Epand
Source:
Journal of molecular biology 2020 v.432 no.18 pp. 5124-5136
ISSN:
0022-2836
Subject:
bending strength; enzyme activity; lipid bilayers; organelles; protein binding; proteins
Abstract:
... Biological membranes define and determine the architecture, i.e., shape, of cells and organelles. While most membranes present a planar morphology on the nanometer length scale, their shape could change in a wide range of length and time scales, leading to more intricate shapes that could be (transient) short- or long-lived. The change in membrane shape from the energetically more stable planar on ...
DOI:
10.1016/j.jmb.2020.03.028