Diversity of Short Linear Interaction Motifs in SARS-CoV-2 Nucleocapsid Protein

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

Published: Aug. 1, 2023

Molecular mimicry of short linear interaction motifs has emerged as a key mechanism for viral proteins binding host domains and hijacking cell processes. Here, we examine the role RNA-virus sequence diversity in dynamics virus-host interface, by analyzing uniquely vast record viable SARS-CoV-2 species with focus on multi-functional nucleocapsid protein. We observe abundant presentation encoding several essential protein interactions, alongside majority possibly non-functional randomly occurring motif sequences absent subsets virus species. A large number emerge

Language: Английский

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Current Progress in Genomic and Genetic Research on Human Viral Diseases

Frontiers research topics, Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 1, 2024

it is a pioneering approach to the world of academia, radically improving way scholarly research managed.The grand vision Frontiers where all people have an equal opportunity seek, share and generate knowledge.Frontiers provides immediate permanent online open access its publications, but this alone not enough realize our goals. journal seriesThe series multi-tier interdisciplinary set openaccess, journals, promising paradigm shift from current review, selection dissemination processes in academic publishing.All journals are driven by researchers for researchers; therefore, they constitute service community.At same time, operates on revolutionary invention, tiered publishing system, initially addressing specific communities scholars, gradually climbing up broader public understanding, thus serving interests lay society, too. Dedication qualityEach article landmark highest quality, thanks genuinely collaborative interactions between authors review editors, who include some world's best academicians.Research must be certified peers before entering stream knowledge that may eventually reach -and shape society; only applies most rigorous unbiased reviews.Frontiers revolutionizes freely delivering outstanding research, evaluated with no bias both social point view.By applying advanced information technologies, catapulting into new generation.

Language: Английский

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Refining SARS-CoV-2 Intra-host Variation by Leveraging Large-Scale Sequencing Data

Published: April 29, 2024

Abstract Understanding the evolution of viral genomes is essential for elucidating how viruses adapt and change over time. Analyzing intra-host single nucleotide variants (iSNVs) provides key insights into mechanisms driving emergence new lineages, which are crucial predicting mitigating future threats. Despite potential next-generation sequencing (NGS) to capture these iSNVs, process fraught with challenges, particularly risk capturing artifacts that may result in false iSNVs. To tackle this issue, we developed a workflow designed enhance reliability iSNV detection large heterogeneous collections NGS libraries. We use 130,000 publicly available SARS-CoV-2 libraries show our comprehensive effectively distinguishes emerging mutations from errors. This approach incorporates rigorous bioinformatics protocols, stringent quality control metrics, innovative usage dimensionality reduction methods generate representations high-dimensional dataset. identified mitigated batch effects linked specific centers around world introduced metrics consider strand coverage imbalance, enhancing reliability. Additionally, pioneer application PHATE visualization genomic data introduce methodology quantifies related groups points within two-dimensional space, ability explain clustering patterns based on their shared genetic characteristics. Our sheds light complexities analysis state-of-the-art technologies advances accurate mutations, opening door an enhanced understanding adaptation mechanisms.

Language: Английский

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Modulation of Biophysical Properties of Nucleocapsid Protein in the Mutant Spectrum of SARS-CoV-2

Published: May 10, 2024

Genetic diversity is a hallmark of RNA viruses and the basis for their evolutionary success. Taking advantage uniquely large genomic database SARS-CoV-2, we examine impact mutations across spectrum viable amino acid sequences on biophysical phenotypes highly expressed multifunctional nucleocapsid protein. We find variation in physicochemical parameters its extended intrinsically disordered regions (IDRs) sufficient to allow local plasticity, but also exhibiting functional constraints that similarly occur related coronaviruses. In experiments with several N-protein species carrying associated major variants, point IDRs can have nonlocal modulate thermodynamic stability, secondary structure, protein oligomeric state, particle formation, liquid-liquid phase separation. Omicron variant, distant different compensatory effects shifting delicate balance interactions controlling assembly properties, include creation new protein-protein interaction interface N-terminal IDR through defining P13L mutation. A picture emerges where genetic accompanied by significant characteristics species, particular IDRs.

Language: Английский

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Dynamic expedition of leading mutations in SARS-CoV-2 spike glycoproteins

Computational and Structural Biotechnology Journal, Journal Year: 2024, Volume and Issue: 23, P. 2407 - 2417

Published: May 24, 2024

The continuous evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which caused the recent pandemic, has generated countless new variants with varying fitness. Mutations spike glycoprotein play a particularly vital role in shaping its evolutionary trajectory, as they have capability to alter infectivity and antigenicity. We present time-resolved statistical method, Dynamic Expedition Leading (deLemus), analyze dynamics SARS-CoV-2 glycoprotein. proposed

Language: Английский

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