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1. Contingency and entrenchment in protein evolution under purifying selection

Author:
Shah, Premal; McCandlish, David M.; Plotkin, Joshua B.
Source:
Proceedings of the National Academy of Sciences of the United States of America 2015 v.112 no.25 pp. E3226-E3235
ISSN:
0027-8424
Subject:
amino acid substitution,   etc   ; evolution; proteins;     Show all 3 Subjects
Abstract:
... Significance How large a role does history play in evolution? Do later events depend critically on specific earlier events, or do all events occur more or less independently? If a change occurs early in evolution, does it become easier or harder to revert the change as time proceeds? Here, we explore these ideas in the context of protein evolution, by simulating sequence evolution under purifying ...
DOI:
10.1073/pnas.1412933112

2. Multiple adaptive amino acid substitutions increase the virulence of a wild waterfowl-origin reassortant H5N8 avian influenza virus in mice

Author:
Yu, Zhijun; Cheng, Kaihui; Sun, Weiyang; Zhang, Xinghai; Xia, Xianzhu; Gao, Yuwei
Source:
Virus research 2018 v.244 pp. 13-20
ISSN:
0168-1702
Subject:
amino acid substitution,   etc   ; Influenza A virus; mice; mutants; poultry; proteins; sequence analysis; tissue tropism; virulence; viruses; Europe; North America; South Korea;     Show all 13 Subjects
Abstract:
... A novel H5N8 highly pathogenic avian influenza virus (HPAIV) caused poultry outbreaks in the Republic of Korea in 2014. The novel H5N8 HPAIV has spread to Asia, Europe, and North America and caused great public concern from then on. Here, we generated mouse-adapted variants of a wild waterfowl-origin H5N8 HPAIV to identify adaptive mutants that confer enhanced pathogenicity in mammals. The mouse l ...
DOI:
10.1016/j.virusres.2017.11.002

3. Emergence of norovirus GII.2 and its novel recombination during the gastroenteritis outbreak in Japanese children in mid-2016

Author:
Thongprachum, Aksara; Okitsu, Shoko; Khamrin, Pattara; Maneekarn, Niwat; Hayakawa, Satoshi; Ushijima, Hiroshi
Source:
Infection, Genetics and Evolution 2017 v.51 pp. 86-88
ISSN:
1567-1348
Subject:
amino acid substitution,   etc   ; Japanese people; Norovirus; children; gastroenteritis; genotype; immunoaffinity chromatography; Japan;     Show all 8 Subjects
Abstract:
... In mid-2016, norovirus GII.2 emerged as a major cause of gastroenteritis outbreak in Japan with overall detection rate of 56.3% of norovirus cases. The differences in ORF1 and ORF2 of some norovirus GII were observed. Inter-subtype recombinants GII.Pe/GII.2, GII.P16/GII.2 and GII.P17/GII.2 were detected. Three amino acid substitutions were noted at P2 antigenic site of GII.P16/GII.2 recombinants. ...
DOI:
10.1016/j.meegid.2017.03.020

4. Contrasting patterns of adaptive sequence convergence among echolocating mammals

Author:
Lambert, Matthew J.; Nevue, Alexander A.; Portfors, Christine V.
Source:
Gene 2017 v.605 pp. 1-4
ISSN:
0378-1119
Subject:
amino acid substitution,   etc   ; Chiroptera; cadherins; convergent evolution; dolphins; echolocation; genes; hearing; phylogeny;     Show all 9 Subjects
Abstract:
... Several recent studies have described genes demonstrating adaptive sequence convergence between echolocating bats and dolphin, suggesting that common selective pressures can induce common molecular changes, even in distantly related species. However, in the case of the auditory genes Otoferlin (Otof), Cadherin 23 (Cdh23) and Protocadherin 15 (Pcdh15), the reported sequence convergence was supporte ...
DOI:
10.1016/j.gene.2016.12.017

5. Improving special hydrolysis characterization into Talaromyces thermophilus F1208 xylanase by engineering of N-terminal extension and site-directed mutagenesis in C-terminal

Author:
Li, Qin; Sun, Baoguo; Xiong, Ke; Teng, Chao; Xu, Youqiang; Li, Liangjun; Li, Xiuting
Source:
International journal of biological macromolecules 2017 v.96 pp. 451-458
ISSN:
0141-8130
Subject:
amino acid substitution,   etc   ; Talaromyces; engineering; hydrolysis; pH; site-directed mutagenesis; xylan; xylanases; xylooligosaccharides; xylose;     Show all 10 Subjects
Abstract:
... The purpose of this study was to gain insights into the hydrolysis characteristics of xylanase in producing xylo-oligosaccharides and to improve these by protein engineering. In this study, a hybrid enzyme (T-XynFM) was created from Talaromyces thermophilus F1208 xylanase (T-Xyn) by replacement of the N-terminal extension Phe1-Pro16 with Ala1-Gln8 and substitution of amino acid Phe193 (185) with S ...
DOI:
10.1016/j.ijbiomac.2016.12.050

6. Direct Observation of Nanosecond Water Exchange Dynamics at a Protein Metal Site

Author:
Stachura, Monika; Chakraborty, Saumen; Gottberg, Alexander; Ruckthong, Leela; Pecoraro, Vincent L.; Hemmingsen, Lars
Source:
Journal of the American Chemical Society 2017 v.139 no.1 pp. 79-82
ISSN:
1520-5126
Subject:
amino acid substitution,   etc   ; binding sites; cadmium; catalytic activity; gamma radiation; ligands; metalloproteins; nuclear magnetic resonance spectroscopy;     Show all 8 Subjects
Abstract:
... Nanosecond ligand exchange dynamics at metal sites within proteins is essential in catalysis, metal ion transport, and regulatory metallobiochemistry. Herein we present direct observation of the exchange dynamics of water at a Cd²⁺ binding site within two de novo designed metalloprotein constructs using ¹¹¹ᵐCd perturbed angular correlation (PAC) of γ-rays and ¹¹³Cd NMR spectroscopy. The residence ...
DOI:
10.1021/jacs.6b11525

7. Transposition of the bamboo Mariner-like element Ppmar1 in yeast

Author:
Ming-Bing, Zhou; Hui, Hu; Miskey, Csaba; Lazarow, Katina; Ivics, Zoltan; Kunze, Reinhard; Guojun, Yang; Izsvák, Zsuzsanna; Ding-Qin, Tang
Source:
Molecular phylogenetics and evolution 2017
ISSN:
1055-7903
Subject:
amino acid substitution,   etc   ; Phyllostachys edulis; Saccharomyces cerevisiae; bamboos; chromosomes; genes; insertional mutagenesis; plasmids; transposons; yeasts;     Show all 10 Subjects
Abstract:
... The moso bamboo genome contains the two structurally intact and thus potentially functional mariner-like elements Ppmar1 and Ppmar2. Both elements contain perfect terminal inverted repeats (TIRs) and a full-length intact transposase gene. Here we investigated whether Ppmar1 is functional in yeast (Saccharomyces cerevisiae). We have designed a two-component system consisting of a transposase expres ...
DOI:
10.1016/j.ympev.2017.02.005

8. Substitutions of Amino Acids with Large Number of Contacts in the Native State Have no Effect on the Rates of Protein Folding

Author:
Melnik, Bogdan S.; Nagibina, Galina S.; Glukhov, Anatoly S.; Melnik, Tatiana N.; Uversky, Vladimir N.
Source:
BBA - Proteins and Proteomics 2016 v.1864 pp. 1809-1817
ISSN:
1570-9639
Subject:
amino acid substitution,   etc   ; amino acids; hydrophobicity; mutants; protein folding; proteins;     Show all 6 Subjects
Abstract:
... Various effects of amino acid substitutions on properties of globular proteins have been described in a large number of research papers. Nevertheless, no definite “rule” has been formulated as of yet that could be used by experimentalists to introduce desirable changes in the properties of proteins. Herein we attempt to establish such a “rule”. To this end, a hypothesis is proposed on the effects ...
DOI:
10.1016/j.bbapap.2016.09.006

9. Hereditary angioedema in a Jordanian family with a novel missense mutation in the C1-inhibitor N-terminal domain

Author:
Jaradat, Saied A; Caccia, Sonia; Rawashdeh, Rifaat; Melhem, Motasem; Al-Hawamdeh, Ali; Carzaniga, Thomas; Haddad, Hazem
Source:
Molecular Immunology 2016 v.71 pp. 123-130
ISSN:
0161-5890
Subject:
amino acid substitution,   etc   ; DNA; alleles; heterozygosity; missense mutation; parents; phenotype;     Show all 7 Subjects
Abstract:
... Hereditary angioedema due to C1-inhibitor deficiency (C1-INH-HAE) is an autosomal dominant disease caused by mutations in the SERPING1 gene. A Jordanian family, including 14 individuals with C1-INH-HAE clinical symptoms, was studied. In the propositus and his parents, SERPING1 had four mutations leading to amino acid substitutions. Two are known polymorphic variants (c.167T>C; p.Val34Ala and c.143 ...
DOI:
10.1016/j.molimm.2016.02.001

10. Epidemiology and molecular characterization of protoparvoviruses infecting wild raccoons (Procyon lotor) in British Columbia, Canada

Author:
Canuti, Marta; Britton, Ann P.; Graham, Stephanie M.; Lang, Andrew S.
Source:
Virus research 2017 v.242 pp. 85-89
ISSN:
0168-1702
Subject:
amino acid substitution,   etc   ; Carnivore protoparvovirus 1; Procyon lotor; cats; dogs; enteritis; epidemiology; viruses; wild animals; wildlife; British Columbia; United States;     Show all 12 Subjects
Abstract:
... Feline panleukopenia virus (FPV) and canine parvovirus 2 (CPV-2) belong to the species Carnivore protoparvovirus 1. While FPV has been endemic in cats for many years, CPV-2 emerged at the end of the 1970s and 3 antigenic variants (CPV-2a, b and c) are currently circulating in domestic and wild animals. Although raccoons played a fundamental role in the emergence of CPV-2a in dogs, knowledge about ...
DOI:
10.1016/j.virusres.2017.09.015

11. Substitutions in Spodoptera exigua topoisomerase I modulate its relaxation activity and camptothecin sensitivity

Author:
Zhang, Pei; Zhang, Lan; Zhang, Yanning; Mao, Liangang; Jiang, Hongyun
Source:
Pest management science 2017 v.73 no.6 pp. 1179-1186
ISSN:
1526-498X
Subject:
amino acid substitution,   etc   ; DNA topoisomerase; Spodoptera exigua; bioactive properties; insect control; insect pests; mutants; pesticides; plasmids; potassium chloride; salt concentration;     Show all 11 Subjects
Abstract:
... BACKGROUND: Topoisomerase I (Top I) is referred as the cellular target of the camptothecins (CPTs) which are now being explored as potential pesticides for insect control. Three amino acid substitutions, including L530P, A653T and S729T, in Top Is of insects were found in our previous studies. In order to investigate the effect of these three substitutions, a comparative analysis was conducted bet ...
DOI:
10.1002/ps.4440

12. Antigenic and genetic characterization of influenza viruses circulating in Bulgaria during the 2015/2016 season

Author:
Korsun, Neli; Angelova, Svetla; Gregory, Viki; Daniels, Rodney; Georgieva, Irina; McCauley, John
Source:
Infection, Genetics and Evolution 2017 v.49 pp. 241-250
ISSN:
1567-1348
Subject:
amino acid substitution,   etc   ; Influenza A virus; amino acids; genetic variation; hemagglutinins; influenza; monitoring; sialidase; vaccines; viruses; Bulgaria;     Show all 11 Subjects
Abstract:
... Influenza virological surveillance is an essential tool for early detection of novel genetic variants of epidemiologic and clinical significance. The aim of this study was to determine the antigenic and molecular characteristics of influenza viruses circulating in Bulgaria during the 2015/2016 season. The season was characterized by dominant circulation of A(H1N1)pdm09 viruses, accounting for 66% ...
DOI:
10.1016/j.meegid.2017.01.027

13. Single-nucleotide polymorphisms, mapping and association analysis of 1-FFT-A1 gene in wheat

Author:
YUE, Ai-qin; LI, Ang; MAO, Xin-guo; CHANG, Xiao-ping; LI, Run-zhi; JING, Rui-lian
Source:
Journal of integrative agriculture 2017 v.16 pp. 789-799
ISSN:
2095-3119
Subject:
amino acid substitution,   etc   ; Triticum aestivum; agronomic traits; biosynthesis; chromosomes; filling period; fructans; genes; haplotypes; inflorescences; peduncle; single nucleotide polymorphism; wheat;     Show all 13 Subjects
Abstract:
... Fructans are major nonstructural carbohydrates in wheat (Triticum aestivum L.). Fructan 1-fructosyltransferase (1-FFT) is the key enzyme in fructan biosynthesis. In the present study, 96 sequence variants were detected in the 1-FFT-A1 gene among 26 wheat accessions including UR208, and 15 of them result in amino acid substitutions, forming four haplotypes. Two markers M39 and M2164 were developed ...
DOI:
10.1016/S2095-3119(16)61471-5

14. Characterization of human monoclonal antibodies that neutralize multiple poliovirus serotypes

Author:
Puligedda, Rama Devudu; Kouiavskaia, Diana; Al-Saleem, Fetweh H.; Kattala, Chandana Devi; Nabi, Usman; Yaqoob, Hamid; Bhagavathula, V. Sandeep; Sharma, Rashmi; Chumakov, Konstantin; Dessain, Scott K.
Source:
Vaccine 2017
ISSN:
0264-410X
Subject:
amino acid substitution,   etc   ; Enterovirus C; Pan troglodytes; chemical elements; epitopes; humans; live vaccines; monoclonal antibodies; mutants; neutralization; serotypes; therapeutics;     Show all 12 Subjects
Abstract:
... Following the eradication of wild poliovirus (PV), achieving and maintaining a polio-free status will require eliminating potentially pathogenic PV strains derived from the oral attenuated vaccine. For this purpose, a combination of non-cross-resistant drugs, such as small molecules and neutralizing monoclonal antibodies (mAbs), may be ideal. We previously isolated chimpanzee and human mAbs capabl ...
DOI:
10.1016/j.vaccine.2017.03.038

15. Overgrowth (Della) mutants of wheat: development, growth and yield of intragenic suppressors of the Rht-B1c dwarfing gene

Author:
Derkx, Adinda P.; Harding, Carol A.; Miraghazadeh, Asemeh; Chandler, Peter M.
Source:
Functional plant biology 2017 v.44 no.5 pp. 525-537
ISSN:
1445-4408
Subject:
amino acid substitution,   etc   ; Triticum aestivum; agronomic traits; alleles; coleoptiles; dormancy; dwarfing; grain yield; leaves; mutants; phenology; stop codon; tillering; wheat;     Show all 14 Subjects
Abstract:
... A suppressor screen using the dwarf Rht-B1c Della mutant of wheat (Triticum aestivum L.) led to the isolation of overgrowth mutants, which retained the original dwarfing gene but grew at a faster rate because of a new mutation elsewhere in that gene. Forty-six alleles were identified, which included amino acid substitutions, premature stop codons, and splice site alterations. The sites of amino ac ...
DOI:
10.1071/FP16262

16. Structural basis for the transglycosylase activity of a GH57-type glycogen branching enzyme from Pyrococcus horikoshii

Author:
Na, Soohui; Park, Minjeong; Jo, Inseong; Cha, Jaeho; Ha, Nam-Chul
Source:
Biochemical and biophysical research communications 2017
ISSN:
0006-291X
Subject:
amino acid substitution,   etc   ; 1,4-alpha-glucan branching enzyme; Pyrococcus horikoshii; active sites; crystal structure; enzyme activity; glycogenesis; glycosides;     Show all 8 Subjects
Abstract:
... Glycogen branching enzyme (GBE) catalyzes the formation of α-1,6-branching points during glycogenesis by cleaving α-1,4 bonds and making new α-1,6 bonds. Most GBEs belong to the glycoside hydrolase 13 family (GH13), but new GBEs in the GH57 family have been isolated from Archaea. Here, we determined the crystal structure of a GH57 GBE from the hyperthermophilic archaeon Pyrococcus horikoshii (PhGB ...
DOI:
10.1016/j.bbrc.2017.02.002

17. Characterization of the mechanism of action of the fungicide fenpicoxamid and its metabolite UK‐2A

Author:
Young, David H; Wang, Nick X; Meyer, Stacy T; Avila‐Adame, Cruz
Source:
Pest management science 2018 v.74 no.2 pp. 10-498
ISSN:
1526-498X
Subject:
amino acid substitution,   etc   ; Botrytis cinerea; Mycosphaerella graminicola; NADH dehydrogenase; Saccharomyces cerevisiae; antimycin A; benzimidazole fungicides; binding sites; cross resistance; cytochrome b; mechanism of action; membrane potential; metabolism; metabolites; mitochondrial membrane; models; spores;     Show all 17 Subjects
Abstract:
... BACKGROUND: Fenpicoxamid is a new fungicide for control of Zymoseptoria tritici, and is a derivative of the natural product UK‐2A. Its mode of action and target site interactions have been investigated. RESULTS: UK‐2A strongly inhibited cytochrome c reductase, whereas fenpicoxamid was much less active, consistent with UK‐2A being the fungicidally active species generated from fenpicoxamid by metab ...
DOI:
10.1002/ps.4743

18. PAAS: Fast Retrieval of Plant Amino Acid Substitutions and Their Effects on Comparative Phenomics

Author:
Yue, Junyang; Wang, Wenjie; Ban, Rongjun; Zhu, Yunye; Liu, Jia; Liu, Yongsheng
Source:
Plant molecular biology reporter 2015 v.33 no.3 pp. 748-750
ISSN:
0735-9640
Subject:
amino acid substitution,   etc   ; Internet; databases; genes; phenotype; plant proteins;     Show all 6 Subjects
Abstract:
... PAAS (Plant Amino Acid Substitutions) is a web database that provides a comprehensive collection of single amino acid substitutions and plant phenotype effects. It gives direct access to the query for comparative phenotype among different species. From here, users can obtain detailed annotation of each variants, substitution combination, and corresponding protein effects. Currently, PAAS covers 4, ...
DOI:
10.1007/s11105-014-0777-2

19. Amino acid substitutions involved in the adaptation of a novel highly pathogenic H5N2 avian influenza virus in mice

Author:
Wu, Haibo; Peng, Xiuming; Peng, Xiaorong; Wu, Nanping
Source:
Virology journal 2016 v.13 no.1 pp. 159-159
ISSN:
1743-422X
Subject:
amino acid substitution,   etc   ; Influenza A virus; amino acids; ducks; histology; mice; monitoring; proteins; virulence; viruses; China;     Show all 11 Subjects
Abstract:
... BACKGROUND: H5N2 avian influenza viruses (AIVs) can infect individuals that are in frequent contact with infected birds. In 2013, we isolated a novel reassortant highly pathogenic H5N2 AIV strain [A/duck/Zhejiang/6DK19/2013(H5N2) (6DK19)] from a duck in Eastern China. This study was undertaken to understand the adaptive processes that led enhanced replication and increased virulence of 6DK19 in ma ...
DOI:
10.1186/s12985-016-0612-5

20. Platform for determining the inhibition profile of neuraminidase inhibitors in an influenza virus N1 background

Author:
Hoffmann, Anja; Schade, Dennis; Kirchmair, Johannes; Clement, Bernd; Sauerbrei, Andreas; Schmidtke, Michaela
Source:
Journal of virological methods 2016 v.237 pp. 192-199
ISSN:
0166-0934
Subject:
amino acid substitution,   etc   ; Influenza A virus; binding capacity; genetic background; influenza; oseltamivir; pandemic; sialidase; viruses;     Show all 9 Subjects
Abstract:
... Efforts to develop novel neuraminidase inhibitors (NAIs) for the treatment of influenza are ongoing. Novel NAIs should in particular be also effective against seasonal and/or pandemic N1 that carry a H274Y or N294S substitution (N2 numbering), which are most commonly linked to oseltamivir resistance. Here we report a platform for profiling the efficacy of novel NAIs in the N1 genetic background of ...
DOI:
10.1016/j.jviromet.2016.09.014