Conformational variability of loops in the SARS‐CoV‐2 spike protein

• Published in: Proteins, structure, function, and bioinformatics structure, function, and bioinformatics, 2022-03, Vol.90 (3), p.691-703
• Main Authors: Wong, Samuel W. K., Liu, Zongjun
• Format: Article
• Language: English
• Subjects: Cluster Analysis; conformational ensembles; COVID-19 - virology; COVID‐19; decoy selection; Humans; loop modeling; Models, Molecular; Protein Conformation; protein structure prediction; Proteins; SARS-CoV-2 - chemistry; sequence variants; Severe acute respiratory syndrome; Severe acute respiratory syndrome coronavirus 2; Spike Glycoprotein, Coronavirus - chemistry; Spike protein; Variability; Viral diseases
• ISSN: 0887-3585; 1097-0134
• DOI: 10.1002/prot.26266

The SARS‐CoV‐2 spike (S) protein facilitates viral infection, and has been the focus of many structure determination efforts. Its flexible loop regions are known to be involved in protein binding and may adopt multiple conformations. This article identifies the S protein loops and studies their conformational variability based on the available Protein Data Bank structures. While most loops had essentially one stable conformation, 17 of 44 loop regions were observed to be structurally variable with multiple substantively distinct conformations based on a cluster analysis. Loop modeling methods were then applied to the S protein loop targets, and the prediction accuracies discussed in relation to the characteristics of the conformational clusters identified. Loops with multiple conformations were found to be challenging to model based on a single structural template.