Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability.

Gennady Verkhivker

doi:10.3390/ijms23031646

Abstract

Structural and functional studies of the SARS-CoV-2 spike proteins have recently determined distinct functional states of the B.1.1.7 and B.1.351 spike variants, providing a molecular framework for understanding the mechanisms that link the effect of mutations with the enhanced virus infectivity and transmissibility. A detailed dynamic and energetic analysis of these variants was undertaken in the present work to quantify the effects of different mutations on functional conformational changes and stability of the SARS-CoV-2 spike protein. We employed the efficient and accurate coarse-grained (CG) simulations of multiple functional states of the D614G mutant, B.1.1.7 and B.1.351 spike variants to characterize conformational dynamics of the SARS-CoV-2 spike proteins and identify dynamic signatures of the functional regions that regulate transitions between the closed and open forms. By combining molecular simulations with full atomistic reconstruction of the trajectories and the ensemble-based mutational frustration analysis, we characterized how the intrinsic flexibility of specific spike regions can control functional conformational changes required for binding with the host-cell receptor. Using the residue-based mutational scanning of protein stability, we determined protein stability hotspots and identified potential energetic drivers favoring the receptor-accessible open spike states for the B.1.1.7 and B.1.351 spike variants. The results suggested that modulation of the energetic frustration at the inter-protomer interfaces can serve as a mechanism for allosteric couplings between mutational sites and the inter-protomer hinges of functional motions. The proposed mechanism of mutation-induced energetic frustration may result in greater adaptability and the emergence of multiple conformational states in the open form. This study suggested that SARS-CoV-2 B.1.1.7 and B.1.351 variants may leverage the intrinsic plasticity of functional regions in the spike protein for mutation-induced modulation of protein dynamics and allosteric regulation to control binding with the host cell receptor.

Highlights

The coronavirus SARS-CoV-2 infection is transmitted when the viral spike (S) glycoprotein binds to the angiotensin-converting enzyme 2 (ACE2) host receptor, leading to the entry of S protein into host cells and membrane fusion [1,2]
A strong preference of the mutational sites towards neutrally frustrated environment may allow for suboptimal inter-protomer interactions and regulatory control of SARS-CoV-2 S binding with the ACE2 host cell receptor
We found that K417N, E484K and N501Y sites are relatively tolerant to modifications in the S-B.1.351 closed and open conformations

Summary

Introduction

The coronavirus SARS-CoV-2 infection is transmitted when the viral spike (S) glycoprotein binds to the angiotensin-converting enzyme 2 (ACE2) host receptor, leading to the entry of S protein into host cells and membrane fusion [1,2]. Structural and biochemical studies established that the mechanism of virus infection may involve conformational transitions between distinct functional forms of the SARS-CoV-2 S protein in which the RBDs continuously switch between “down” and “up” positions [3,4,5,6,7,8,9,10]. Protein engineering and structural studies showed that specific disulfide bonds and proline mutations can modulate stability of the SARS-CoV-2 S trimer [6] and lead to the thermodynamic shifts between the closed and open forms [7,8,9]. Dynamic structural changes that accompany SARS-CoV-2 S binding with the ACE2 host receptor were described in cryo-EM experiments, showing a cascade of conformational transitions from a compact closed form, weakened after furin cleavage, to the partially open states, and, subsequently, the ACE2-bound open form priming the S protein for fusion [10]. The cryo-EM studies and biophysical studies of SARS-CoV-2 S trimer examined conformational flexibility and distribution of S trimers in situ on the virion surface, showing that spontaneous conformational changes and population shifts between different functional states are maintained in different biological environments and can coexist with receptor-induced structural adaptation, reflecting the intrinsic conformational landscapes of the SARS-CoV-2 S proteins [11,12]

Methods

Results

Conclusion