scholarly journals Whole Genome Identification of Potential G-Quadruplexes and Analysis of the G-Quadruplex Binding Domain for SARS-CoV-2

2020 ◽  
Vol 11 ◽  
Author(s):  
Rongxin Zhang ◽  
Ke Xiao ◽  
Yu Gu ◽  
Hongde Liu ◽  
Xiao Sun
Keyword(s):  
Amino Acid ◽  
Public Health Emergency ◽  
Whole Genome ◽  
Amino Acid Residues ◽  
Global Public Health ◽  
Potential Value ◽  
G Quadruplex ◽  
Fundamental Research ◽  
Unique Domain ◽  
Negative Sense

The coronavirus disease 2019 (COVID-19) pandemic caused by SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) has become a global public health emergency. G-quadruplex, one of the non-canonical secondary structures, has shown potential antiviral values. However, little is known about the G-quadruplexes of the emerging SARS-CoV-2. Herein, we characterized the potential G-quadruplexes in both positive and negative-sense viral strands. The identified potential G-quadruplexes exhibited similar features to the G-quadruplexes detected in the human transcriptome. Within some bat- and pangolin-related betacoronaviruses, the G-tracts rather than the loops were under heightened selective constraints. We also found that the amino acid sequence similar to SUD (SARS-unique domain) was retained in SARS-CoV-2 but depleted in some other coronaviruses that can infect humans. Further analysis revealed that the amino acid residues related to the binding affinity of G-quadruplexes were conserved among 16,466 SARS-CoV-2 samples. Moreover, the dimer of the SUD-homology structure in SARS-CoV-2 displayed similar electrostatic potential patterns to the SUD dimer from SARS. Considering the potential value of G-quadruplexes to serve as targets in antiviral strategy, our fundamental research could provide new insights for the SARS-CoV-2 drug discovery.

scholarly journals Whole genome identification of potential G-quadruplexes and analysis of the G-quadruplex binding domain for SARS-CoV-2

2020 ◽  
Author(s):  
Rongxin Zhang ◽  
Xiao Ke ◽  
Yu Gu ◽  
Hongde Liu ◽  
Xiao Sun
Keyword(s):  
Public Health ◽  
Drug Discovery ◽  
Severe Acute Respiratory Syndrome ◽  
Public Health Emergency ◽  
Whole Genome ◽  
Global Public Health ◽  
Potential Value ◽  
G Quadruplex ◽  
Fundamental Research ◽  
Negative Sense

AbstractThe Coronavirus Disease 2019 (COVID-19) pandemic caused by SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) quickly become a global public health emergency. G-quadruplex, one of the non-canonical secondary structures, has shown potential antiviral values. However, little is known about G-quadruplexes on the emerging SARS-CoV-2. Herein, we characterized the potential G-quadruplexes both in the positive and negative-sense viral stands. The identified potential G-quadruplexes exhibits similar features to the G-quadruplexes detected in the human transcriptome. Within some bat and pangolin related beta coronaviruses, the G-quartets rather than the loops are under heightened selective constraints. We also found that the SUD-like sequence is retained in the SARS-CoV-2 genome, while some other coronaviruses that can infect humans are depleted. Further analysis revealed that the SARS-CoV-2 SUD-like sequence is almost conserved among 16,466 SARS-CoV-2 samples. And the SARS-CoV-2 SUDcore-like dimer displayed similar electrostatic potential pattern to the SUD dimer. Considering the potential value of G-quadruplexes to serve as targets in antiviral strategy, we hope our fundamental research could provide new insights for the SARS-CoV-2 drug discovery.

scholarly journals Evidence of the Recombinant Origin and Ongoing Mutations in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)

2020 ◽  
Author(s):  
Jiao-Mei Huang ◽  
Syed Sajid Jan ◽  
Xiaobin Wei ◽  
Yi Wan ◽  
Songying Ouyang
Keyword(s):  
Public Health ◽  
Amino Acid ◽  
Recombinant Virus ◽  
Spike Protein ◽  
Whole Genome ◽  
Amino Acid Residues ◽  
Global Public Health ◽  
Whole Genome Analysis ◽  
Coding Regions ◽  
Genomic Similarity

SUMMARYThe recent global outbreak of viral pneumonia designated as Coronavirus Disease 2019 (COVID-19) by coronavirus (SARS-CoV-2) has threatened global public health and urged to investigate its source. Whole genome analysis of SARS-CoV-2 revealed ~96% genomic similarity with bat CoV (RaTG13) and clustered together in phylogenetic tree. Furthermore, RaTGl3 also showed 97.43% spike protein similarity with SARS-CoV-2 suggesting that RaTGl3 is the closest strain. However, RBD and key amino acid residues supposed to be crucial for human-to-human and cross-species transmission are homologues between SARS-CoV-2 and pangolin CoVs. These results from our analysis suggest that SARS-CoV-2 is a recombinant virus of bat and pangolin CoVs. Moreover, this study also reports mutations in coding regions of 125 SARS-CoV-2 genomes signifying its aptitude for evolution. In short, our findings propose that homologous recombination has been occurred between bat and pangolin CoVs that triggered cross-species transmission and emergence of SARS-CoV-2, and, during the ongoing outbreak, SARS-CoV-2 is still evolving for its adaptability.

scholarly journals Pangolin homology associated with 2019-nCoV

2020 ◽  
Author(s):  
Tao Zhang ◽  
Qunfu Wu ◽  
Zhigang Zhang
Keyword(s):  
Amino Acid ◽  
Intermediate Host ◽  
Common Ancestor ◽  
Whole Genome ◽  
Amino Acid Residues ◽  
Pathogenic Potential ◽  
Lowest Common Ancestor ◽  
Amino Acid Mutations ◽  
Genome Level ◽  
Novel Coronavirus

AbstractTo explore potential intermediate host of a novel coronavirus is vital to rapidly control continuous COVID-19 spread. We found genomic and evolutionary evidences of the occurrence of 2019-nCoV-like coronavirus (named as Pangolin-CoV) from dead Malayan Pangolins. Pangolin-CoV is 91.02% and 90.55% identical at the whole genome level to 2019-nCoV and BatCoV RaTG13, respectively. Pangolin-CoV is the lowest common ancestor of 2019-nCoV and RaTG13. The S1 protein of Pangolin-CoV is much more closely related to 2019-nCoV than RaTG13. Five key amino-acid residues involved in the interaction with human ACE2 are completely consistent between Pangolin-CoV and 2019-nCoV but four amino-acid mutations occur in RaTG13. It indicates Pangolin-CoV has similar pathogenic potential to 2019-nCoV, and would be helpful to trace the origin and probable intermediate host of 2019-nCoV.

Substrate Recognition by Vitamin K-Dependent Carboxylase

1987 ◽  
Vol 57 (01) ◽  
pp. 017-019 ◽  
Author(s):  
Magda M W Ulrich ◽  
Berry A M Soute ◽  
L Johan M van Haarlem ◽  
Cees Vermeer
Keyword(s):  
Amino Acid ◽  
Vitamin K ◽  
Substrate Recognition ◽  
Bovine Liver ◽  
Amino Acid Residues

SummaryDecarboxylated osteocalcins were prepared and purified from bovine, chicken, human and monkey bones and assayed for their ability to serve as a substrate for vitamin K-dependent carboxylase from bovine liver. Substantial differences were observed, especially between bovine and monkey d-osteocalcin. Since these substrates differ only in their amino acid residues 3 and 4, it seems that these residues play a role in the recognition of a substrate by hepatic carboxylase.

Statistical Force-Field for Structural Modeling Using Chemical Cross-Linking/mass Spectrometry Distance Constraints

2018 ◽  
Author(s):  
Allan J. R. Ferrari ◽  
Fabio C. Gozzo ◽  
Leandro Martinez
Keyword(s):  
Mass Spectrometry ◽  
Amino Acid ◽  
Force Field ◽  
Protein Structures ◽  
Protein Structure Determination ◽  
Structural Modeling ◽  
Cross Linking ◽  
Amino Acid Residues ◽  
Distance Constraints ◽  
Chemical Cross Linking

<div><p>Chemical cross-linking/Mass Spectrometry (XLMS) is an experimental method to obtain distance constraints between amino acid residues, which can be applied to structural modeling of tertiary and quaternary biomolecular structures. These constraints provide, in principle, only upper limits to the distance between amino acid residues along the surface of the biomolecule. In practice, attempts to use of XLMS constraints for tertiary protein structure determination have not been widely successful. This indicates the need of specifically designed strategies for the representation of these constraints within modeling algorithms. Here, a force-field designed to represent XLMS-derived constraints is proposed. The potential energy functions are obtained by computing, in the database of known protein structures, the probability of satisfaction of a topological cross-linking distance as a function of the Euclidean distance between amino acid residues. The force-field can be easily incorporated into current modeling methods and software. In this work, the force-field was implemented within the Rosetta ab initio relax protocol. We show a significant improvement in the quality of the models obtained relative to current strategies for constraint representation. This force-field contributes to the long-desired goal of obtaining the tertiary structures of proteins using XLMS data. Force-field parameters and usage instructions are freely available at http://m3g.iqm.unicamp.br/topolink/xlff <br></p></div><p></p><p></p>

Life Lessons of the Pandemic ”Covid - 19”

2020 ◽  
Vol 11 (SPL1) ◽  
pp. 469-471 ◽  
Author(s):  
Bhagyashri Vijay Chaudhari ◽  
Priya P. Chawle
Keyword(s):  
Public Health ◽  
Review Article ◽  
Public Health Emergency ◽  
The Novel ◽  
Global Public Health ◽  
Strange Situation ◽  
Republic Of China ◽  
Lifetime History ◽  
The People ◽  
Life Lessons

“A lesson learned the hard way is a lesson learned for a lifetime.” Every bad situation hurts; however, it sure does teach us something a lesson. In the same manner of a new lesson for Human lifetime, history is observing 'The Novel COVID-19 ’, a very horrible and strange situation created due to fighting with a microscopic enemy. WHO on 11 February 2020 has announced a name for new disease as - 19 and has declared as a global public health emergency and subsequently as pandemic because of its widespread. This began as an outbreak in December 2019, with its in Wuhan, the People Republic of China has emerged as a public health emergency of international concern. is the group of a virus with non-segmented, single-stranded and positive RNA genome. This bad situation of pandemic creates new scenes in the life of people in a different manner, which will be going to be life lessons for them. Such lessons should be kept in mind for the safety of living beings and many more things. In this narrative review article, reference was taken from a different article published in various databases which include the view of different authors and writers on the &quot;Lessons to be from Corona&quot;.

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