Comparative Analysis of Ramachandran Plot Conformations in Spike Protein Sequences of SARS-CoV-2, SARS-CoV, and MERS-CoV

Abstract

Introduction: The spike protein of coronaviruses is crucial for host cell recognition and viral entry, making it a key target for therapeutic interventions and vaccine development. Understanding the structural dynamics and evolutionary relationships of spike proteins across different coronaviruses is crucial for elucidating their functional diversity and potential vulnerabilities.

Objectives: The objective of this study is to present a comprehensive analysis of spike protein sequences from three prominent coronaviruses: SARS-CoV-2, SARS-CoV and MERS-CoV, using the Ramachandran plot to assess protein backbone conformational quality. The study aims to identify the conformational space occupied by these spike proteins and highlight regions of structural stability and flexibility.

Methods: The spike protein sequences of SARS-CoV, MERS-CoV, and SARS-CoV-2 were retrieved from UniProt. The sequences were aligned using BLASTP and verified with ClustalW to identify conserved and variable regions. Ramachandran plots for each protein were generated through PDBsum to analyze backbone torsion angles and compare structural conformations.

Results: The analysis revealed distinct distribution of phi (ϕ) and psi (ψ) torsion angles across the spike proteins, elucidated the conformational space occupied by each spike proteins. The study identifies regions of structural stability and flexibility, contributing to the understanding of functional and evolutionary differences among the spike proteins.

Conclusions: The outcomes of this investigation provide valuable insights into the structural dynamics and evolutionary constraints shaping spike protein diversity across coronaviruses, offering new opportunities for the rational design of antiviral treatments and vaccines.