Many Roles of Carbohydrates: A Computational Spotlight on the Coronavirus S Protein Binding

ACS Applied Bio Materials, Journal Year: 2023, Volume and Issue: 7(2), P. 646 - 656

Published: March 22, 2023

Glycosylation is one of the post-translational modifications with more than 50% human proteins being glycosylated. The exact nature and chemical composition glycans are inaccessible to X-ray or cryo-electron microscopy imaging techniques. Therefore, computational modeling studies molecular dynamics must be used as a "computational microscope". spike (S) protein SARS-CoV-2 heavily glycosylated, few play functional role "beyond shielding". In this mini-review, we discuss investigations roles specific S-protein ACE2 in overall ACE2-S binding. We highlight different functions demonstrated myriad models simulations context virus binding receptor. also interactions between glycocalyx S protein, which may utilized design prophylactic polysaccharide-based therapeutics targeting protein. addition, underline recent emergence coronavirus variants their impact on its glycans.

Language: Английский

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An evolutionary theory on virus mutation in COVID-19

Virus Research, Journal Year: 2024, Volume and Issue: 344, P. 199358 - 199358

Published: March 22, 2024

With the rapid evolution of SARS-CoV-2, emergence new strains is an intriguing question. This paper presents evolutionary theory to analyze mutations virus and identify conditions that lead generation strains. We represent variants using a 4-letter sequence based on amino acid spike protein employ n-distance algorithm derive variant phylogenetic tree. show theoretically-derived tree aligns with experimental data evolution. Additionally, we propose A-X model, utilizing set existing mutation sites (A) randomly generated (X), calculate Our findings demonstrate sufficient number random iterations can predict macro-lineages when in X large enough. These results provide crucial theoretical basis for understanding SARS-CoV-2.

Language: Английский

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Signature genomic traits of the core and accessory genome of Vibrio Cholerae O1 drive lineage transmission and disease severity

Research Square (Research Square), Journal Year: 2024, Volume and Issue: unknown

Published: April 5, 2024

Abstract In Bangladesh, Vibrio cholerae lineages are undergoing genomic evolution, causing pandemics and outbreaks with increased virulence, resistance, spreading ability disease severity. However, our understanding of the determinants influencing transmission severity patterns, as well their interplay, remains incomplete. Here, we developed a computational framework based on machine-learning, genome scale metabolic modelling (GSSM) 3D structural analysis, to identify V. signatures traits linked lineage dynamics We analysed isolates collected from in-patients across six regions in Bangladesh 2015 2021, uncovered core set accessory genes, coding, intergenic SNPs uniquely present most recent dominant underlying transmission, motility, colonization, biofilm formation, acid tolerance bacteriophage resistance functions. Furthermore, existence strong correlation between patterns (diarrhoeal duration, number stools, abdominal pain, vomit, dehydration). A subset these overlapped those driving dynamics. Through GSMM structure inferred mechanistic bases selection unveiled complex interplay transcription regulation, protein interactions stability, networks leading severe symptoms. These connections influence lifestyle adaptation, intestinal oxidative stress through modulation ribosome, fatty peptide biosynthesis, bacterial efflux systems, resistant genes. Our allows uncover signature which can provide insights for advancing therapeutics developing targeted interventions mitigate cholera spread.

Language: Английский

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Semi-Covariance Coefficient Analysis of Spike Proteins from SARS-CoV-2 and Its Variants Omicron, BA.5, EG.5, and JN.1 for Viral Infectivity, Virulence and Immune Escape

Viruses, Journal Year: 2024, Volume and Issue: 16(8), P. 1192 - 1192

Published: July 25, 2024

Semi-covariance has attracted significant attention in recent years and is increasingly employed to elucidate statistical phenomena exhibiting fluctuations, such as the similarity or difference charge patterns of spike proteins among coronaviruses. In this study, by examining values above below average/mean based on positive negative amino acid residues SARS-CoV-2 its current circulating variants, proposed methods offer profound insights into nonlinear evolving trends those viral proteins. Our study indicates that span value can predict infectivity virus density estimate virulence virus, both predicated appear be associated with capability immune escape. This semi-covariance coefficient analysis may used not only infectivity, escape for coronaviruses but also analyze functionality other improves our understanding trend evolution terms escape, which remains further validated more future studies data.

Language: Английский

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Core and accessory genomic traits of Vibrio cholerae O1 drive lineage transmission and disease severity

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Sept. 23, 2024

Language: Английский

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Sulfated Cellulose Nanofiber Hydrogel with Mucus-Like Activities for Virus Inhibition

ACS Applied Materials & Interfaces, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 24, 2024

Mucus is the first defense barrier against viruses in human immune system. Inspired by mucus structure, we designed a highly sulfated hydrogel to bind and prevent infection of underlying cells. The was formed gelation cellulose nanofiber (SCNF) with Ca

Language: Английский

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An Evolutionary Theory on Virus Mutation in COVID-19

Published: Dec. 26, 2023

With the rapid evolution of SARS-CoV-2, emergence new strains is an intriguing question. This paper presents evolutionary theory to analyze mutations virus and identify conditions that lead generation strains. We represent variants using a 4-letter sequence based on amino acid spike protein employ n-distance algorithm derive variant phylogenetic tree. show theoretically-derived tree aligns with experimental data evolution. Additionally, we propose A-X model, utilizing set existing mutation sites (A) randomly generated (X), calculate Our findings demonstrate sufficient number random iterations can predict macro-lineages when in X large enough. These results provide crucial theoretical basis for understanding SARS-CoV-2.

Language: Английский

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An Evolutionary Theory on Virus Mutation in COVID-19

Published: March 26, 2024

With the rapid evolution of SARS-CoV-2, emergence new strains is an intriguing question. This paper presents evolutionary theory to analyze mutations virus and identify conditions that lead generation strains. We represent variants using a 4-letter sequence based on amino acid spike protein employ n-distance algorithm derive variant phylogenetic tree. show theoretically-derived tree aligns with experimental data evolution. Additionally, we propose A-X model, utilizing set existing mutation sites (A) randomly generated (X), calculate Our findings demonstrate sufficient number random iterations can predict macro-lineages when in X large enough. These results provide crucial theoretical basis for understanding SARS-CoV-2.

Language: Английский

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Evolutionary changes in the number of dissociable amino acids on spike proteins and nucleoproteins of SARS-CoV-2 variants

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: March 13, 2023

The spike protein of SARS-CoV-2 is responsible for target recognition, cellular entry, and endosomal escape the virus. At same time, it part virus which exhibits greatest sequence variation across many variants have emerged during its evolution. Recent studies indicated that with progressive lineage emergence, positive charge on has been increasing, certain positively charged amino acids improving binding to cell receptors. We performed a detailed analysis dissociable more than 1400 different lineages confirms these observations while suggesting this progression reached plateau omicron subvariants not increasing further. Analysis nucleocapsid shows no similar increase novel variants, further indicates being evolutionarily selected for. Furthermore, comparison proteins known coronaviruses already wild-type carries an unusually large amount when compared most other betacoronaviruses. Our study sheds light evolutionary changes in number SARS-CoV-2, complementing existing providing stepping stone towards better understanding relationship between viral infectivity transmissibility.

Language: Английский

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Changes in total charge on spike protein of SARS-CoV-2 in emerging lineages

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Oct. 23, 2023

Motivation: Charged amino acid residues on the spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been shown to influence its binding different cell surface receptors, non-specific electrostatic interactions with environment, and structural stability conformation. It is therefore important obtain a good understanding mutations that affect total charge which arisen across SARS-CoV-2 lineages during course virus' evolution. Results: We analyse change in number ionizable acids corresponding proteins almost 2200 emerged over span pandemic. Our results show previously observed trend toward an increase positive variants concern has essentially stopped emergence early omicron variants. Furthermore, recently greater diversity terms their composition acids. also demonstrate patterns are characteristic related within broader clade division phylogenetic tree. Due ubiquity biological our findings relevant for broad range studies dealing environment. Availability: The data underlying article available online Supplementary Material.

Language: Английский

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