Modulation of biophysical properties of nucleocapsid protein in the mutant spectrum of SARS-CoV-2

• Published in: eLife Vol. 13
• Main Authors: Nguyen, Ai, Zhao, Huaying, Myagmarsuren, Dulguun, Srinivasan, Sanjana, Wu, Di, Chen, Jiji, Piszczek, Grzegorz, Schuck, Peter
• Format: Journal Article
• Language: English
• Published: England eLife Sciences Publications Ltd 28.06.2024
• Subjects: Amino acids; biophysical fitness landscape; Coronavirus Nucleocapsid Proteins - chemistry; Coronavirus Nucleocapsid Proteins - genetics; Coronavirus Nucleocapsid Proteins - metabolism; Coronaviruses; COVID-19 - genetics; COVID-19 - virology; Evolution; Functional plasticity; Genetic diversity; genotype-phenotype relationship; Humans; intrinsically disordered protein; Intrinsically Disordered Proteins - chemistry; Intrinsically Disordered Proteins - genetics; Intrinsically Disordered Proteins - metabolism; mutant spectrum; Mutation; Nucleocapsid Proteins - chemistry; Nucleocapsid Proteins - genetics; Nucleocapsid Proteins - metabolism; Nucleocapsids; Phenotypes; Phenotypic plasticity; Phenotypic variations; Phosphoproteins - chemistry; Phosphoproteins - genetics; Phosphoproteins - metabolism; Physicochemical properties; Point mutation; protein evolution; Protein interaction; Protein Stability; Protein structure; Proteins; RNA viruses; SARS-CoV-2; SARS-CoV-2 - chemistry; SARS-CoV-2 - genetics; SARS-CoV-2 - metabolism; Secondary structure; Severe acute respiratory syndrome coronavirus 2; Thermodynamics; mutant spectrum; SARS-CoV-2; viruses; intrinsically disordered protein; protein evolution; infectious disease; biophysical fitness landscape; microbiology; genotype-phenotype relationship; structural biology; molecular biophysics
• ISSN: 2050-084X; 2050-084X
• DOI: 10.7554/eLife.94836

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