scholarly journals Spike Protein of SARS-CoV-2: Impact of Single Amino Acid Mutation and Effect of Drug Binding to the Variant-in Silico Analysis

2020 ◽  
Author(s):  
Pratibha Manickavasagam
Keyword(s):  
Amino Acid ◽  
Host Cell ◽  
Drug Binding ◽  
Spike Protein ◽  
Single Amino Acid ◽  
Wild Type ◽  
Amino Acid Mutation ◽  
S Protein ◽  
The Impact ◽  
Single Amino Acid Mutation

Novel SARS-CoV-2, a bat based virus originated in Wuhan, China that caused a global pandemic in December, 2019 belongs to the Betacorona virus family and contains single stranded genome of ~29Kbp. The host cell invasion of SARS-CoV-2 is facilitated by interaction of C-Terminal Domain (CTD) of Spike (S) protein of virus and host ACE2 receptor in the presence of TMPRSS seine protease secreted by the host cell. In this study the mutation hotspots of S-protein will be identified and the impact of such mutation in the binding affinity will be studied. Additionally, the lead molecule which can bind to the mutated protein also will be identified. Multiple sequence alignment of the spike protein sequence of SARS-CoV-2 shows the number of single amino acid mutation hotspots such as L5F, R214L, R408I, G476S, V483A, H519Q, A520S, T572I, D614G and H655Y. Among these mutations D614G has 57.5% occurrence and G476S, V483A has 7.5% occurrence. The mutated proteins were modelled based on wild type homolog and docked to ACE2 receptor. When the mutated S protein is docked, the ∆G (binding free energy) value is very minimal in mutated protein showed the stability of variants. By the drug repurposing method, 1000 FDA approved drugs were virtually screened for its binding to RBD of S1 domain. Among these drugs Digitoxin, Gliquidone and Zorubicin Hcl binds to spike proteins with higher docking score (lesser than -8.5 Kcal/mol) to both wild type and mutants.

scholarly journals Loss of Function in Zeaxanthin Epoxidase of Dunaliella tertiolecta Caused by a Single Amino Acid Mutation within the Substrate-Binding Site

Marine Drugs ◽  
2018 ◽  
Vol 16 (11) ◽  
pp. 418 ◽  
Author(s):  
Minjae Kim ◽  
Jisu Kang ◽  
Yongsoo Kang ◽  
Beom Kang ◽  
EonSeon Jin
Keyword(s):  
Amino Acid ◽  
Binding Site ◽  
Conformational Change ◽  
Substrate Binding ◽  
Single Amino Acid ◽  
Wild Type ◽  
Amino Acid Mutation ◽  
Zeaxanthin Epoxidase ◽  
Substrate Binding Site ◽  
Single Amino Acid Mutation

The zea1 mutant of marine microalga Dunaliella tertiolecta accumulates zeaxanthin under normal growth conditions, and its phenotype has been speculated to be related to zeaxanthin epoxidase (ZEP). In this study, we isolated the ZEP gene from both wild-type D. tertiolecta and the mutant. We found that the zea1 mutant has a point mutation of the 1337th nucleotide of the ZEP sequence (a change from guanine to adenine), resulting in a change of glycine to aspartate in a highly conserved region in the catalytic domain. Similar expression levels of ZEP mRNA and protein in both wild-type and zea1 were confirmed by using qRT-PCR and western blot analysis, respectively. Additionally, the enzyme activity analysis of ZEPs in the presence of cofactors showed that the inactivation of ZEP in zea1 was not caused by deficiency in the levels of cofactors. From the predicted three-dimensional ZEP structure of zea1, we observed a conformational change on the substrate-binding site in the ZEP. A comparative analysis of the ZEP structures suggested that the conformational change induced by a single amino acid mutation might impact the interaction between the substrate and substrate-binding site, resulting in loss of zeaxanthin epoxidase function.

scholarly journals Prospective mapping of viral mutations that escape antibodies used to treat COVID-19

Science ◽  
2021 ◽  
Vol 371 (6531) ◽  
pp. 850-854 ◽  
Author(s):  
Tyler N. Starr ◽  
Allison J. Greaney ◽  
Amin Addetia ◽  
William W. Hannon ◽  
Manish C. Choudhary ◽  
...  
Keyword(s):  
Amino Acid ◽  
Infected Patient ◽  
Viral Escape ◽  
Single Amino Acid ◽  
Receptor Binding Domain ◽  
Amino Acid Mutation ◽  
The Individual ◽  
Viral Surveillance ◽  
Single Amino Acid Mutation

Antibodies are a potential therapy for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), but the risk of the virus evolving to escape them remains unclear. Here we map how all mutations to the receptor binding domain (RBD) of SARS-CoV-2 affect binding by the antibodies in the REGN-COV2 cocktail and the antibody LY-CoV016. These complete maps uncover a single amino acid mutation that fully escapes the REGN-COV2 cocktail, which consists of two antibodies, REGN10933 and REGN10987, targeting distinct structural epitopes. The maps also identify viral mutations that are selected in a persistently infected patient treated with REGN-COV2 and during in vitro viral escape selections. Finally, the maps reveal that mutations escaping the individual antibodies are already present in circulating SARS-CoV-2 strains. These complete escape maps enable interpretation of the consequences of mutations observed during viral surveillance.

Single amino acid mutation in alpha-helical peptide affect second harmonic generation hyperpolarizability

2013 ◽  
Vol 556 ◽  
pp. 260-265 ◽  
Author(s):  
Jing Wei ◽  
Jin-Yun Wang ◽  
Min-Yi Zhang ◽  
Guo-Liang Chai ◽  
Chen-Sheng Lin ◽  
...  
Keyword(s):  
Amino Acid ◽  
Second Harmonic Generation ◽  
Harmonic Generation ◽  
Second Harmonic ◽  
Single Amino Acid ◽  
Amino Acid Mutation ◽  
Helical Peptide ◽  
Single Amino Acid Mutation ◽  
Alpha Helical Peptide

Tetramer formation of Bacillus subtilis YabJ protein that belongs to YjgF/YER057c/UK114 family

2021 ◽  
Vol 85 (2) ◽  
pp. 297-306
Author(s):  
Zui Fujimoto ◽  
Le Thi Thu Hong ◽  
Naomi Kishine ◽  
Nobuhiro Suzuki ◽  
Keitarou Kimura
Keyword(s):  
Bacillus Subtilis ◽  
Quaternary Structure ◽  
Single Amino Acid ◽  
Wild Type ◽  
Amino Acid Mutation ◽  
X Ray Crystallography ◽  
Ligand Binding Sites ◽  
Potential Ligand ◽  
Single Amino Acid Mutation

ABSTRACT Bacillus subtilis YabJ protein belongs to the highly conserved YjgF/YER057c/UK114 family, which has a homotrimeric quaternary structure. The dominant allele of yabJ gene that is caused by a single amino acid mutation of Ser103Phe enables poly-γ-glutamic acid (γPGA) production of B. subtilis under conditions where the cell-density signal transduction was disturbed by the loss of DegQ function. X-ray crystallography of recombinant proteins revealed that unlike the homotrimeric wild-type YabJ, the mutant YabJ(Ser103Phe) had a homotetrameric quaternary structure, and the structural change appeared to be triggered by an inversion of the fifth β-strand. The YabJ homotetramer has a hole that is highly accessible, penetrating through the tetramer, and 2 surface concaves as potential ligand-binding sites. Western blot analyses revealed that the conformational change was also induced in vivo by the Ser103Phe mutation.

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