Computational Analysis of Protein Stability and Allosteric Interaction Networks in Distinct Conformational Forms of the SARS-CoV-2 Spike D614G Mutant: Reconciling Functional Mechanisms through Allosteric Model of Spike Regulation

Abstract

Structural and biochemical studies SARS-CoV-2 spike mutants with the enhanced infectivity have attracted significant attention and offered several mechanisms to explain the experimental data. The development of a unified view and a working model which is consistent with the diverse experimental data is an important focal point of the current work. In this study, we used an integrative computational approach to examine molecular mechanisms underlying functional effects of the D614G mutation by exploring atomistic modeling of the SARS-CoV-2 spike proteins as allosteric regulatory machines. We combined coarse-grained simulations, protein stability and dynamic fluctuation communication analysis along with network-based community analysis to simulate structures of the native and mutant SARS-CoV-2 spike proteins in different functional states. The results demonstrated that the D614 position anchors a key regulatory cluster that dictates functional transitions between open and closed states. Using molecular simulations and mutational sensitivity analysis of the SARS-CoV-2 spike proteins we showed that the D614G mutation can improve stability of the spike protein in both closed and open forms, but shifting thermodynamic preferences towards the open mutant form. The results offer support to the reduced shedding mechanism of S1 domain as a driver of the increased infectivity triggered by the D614G mutation. Through distance fluctuations communication analysis, we probed stability and allosteric communication propensities of protein residues in the native and mutant SARS-CoV-2 spike proteins, providing evidence that the D614G mutation can enhance long-range signaling of the allosteric spike engine. By employing network community analysis of the SARS-CoV-2 spike proteins, our results revealed that the D614G mutation can promote the increased number of stable communities and allosteric hub centers in the open form by reorganizing and enhancing the stability of the S1-S2 inter-domain interactions and restricting mobility of the S1 regions. This study provides atomistic-based view of the allosteric interactions and communications in the SARS-CoV-2 spike proteins, suggesting that the D614G mutation can exert its primary effect through allosterically induced changes on stability and communications in the residue interaction networks.

Distant residues modulate conformational opening in SARS-CoV-2 spike protein

“…The D614G mutant prefers the one RBD “up” state 7 times more than the “three-down” configuration, while they are equally likely in the WT strain ( 54 ). The specific role of the D614G mutation was recently also established by coarse-grained MD study ( 72 ). Our model predicted the D614 residue as a key player in RBD dynamics from physics-based atomistic simulations without any prior knowledge of the mutation profile of the spike.…”

“…We also point out that our simulation of the WT spike can, by fiat, only identify the residue to be mutated, but not the amino acid to which the residue will be mutated. However, both experimental and computer simulation studies have already established that D614G, A570D, and a few other mutations transform the dynamics of the RBD and favor an “up” state ( 54 , 55 , 59 , 61 , 72 ). In the current work, we highlighted a set of residues which show high correlation with RBD opening motion.…”

Naturally-acquired immunity in Syrian Golden Hamsters provides protection from re-exposure to emerging heterosubtypic SARS-CoV-2 variants B.1.1.7 and B.1.351

“…The first may disrupt a salt bridge with D30 of ACE2. The second may disrupt the interaction of RBD with K31 of hACE2 and enhance ACE2 binding 1,4 . Recent data have shown that VOC, especially those like B.1.351 with aa.…”

Distant Residues Modulate Conformational Opening in SARS-CoV-2 Spike Protein

“…The D614G mutant prefers the one RBD "up" state ∼7 times more than the "3-down" configuration while they are equally likely in the wild type strain (52). The specific role of the D614G mutation was recently also established by coarse grained MD study (70) residues, but did not yet become as widespread as D614G, likely because it did not have substantial evolutionary advan-the RBD opening motion increases infectivity can only be resolved in vivo, given the complexity of the viral entry process. A number of experiments and computational studies indicated that binding to ACE2 is feasible only when the RBD is "up" (26)(27)(28)(29)(30).…”

“…While our study did not focus on actual mutants, the role of specific point mutations in the dynamics of RBD of the spike protein has been explored using MD simulation in the literature. (58,70) From the point of view of immediate therapeutic interventions, this study opens up the possibility of designing inhibitors that bind to the regions outside the RBD, thereby preventing infection by freezing RBD dynamics via steric restrictions on specific distant residues. Such treatments are less likely to be affected by the evolutionary adaptations in RBD sequence that the virus performs frequently to evade the immune response.…”