D614G substitution at the hinge region enhances the stability of trimeric SARS-CoV-2 spike protein

Abstract

Mutations in the spike protein of SARS-CoV-2 are the major causes for the modulation of ongoing COVID-19 infection. Currently, the D614G substitution in the spike protein has become dominant worldwide. It is associated with higher infectivity than the ancestral (D614) variant. We demonstrate using Gaussian network model-based normal mode analysis that the D614G substitution occurs at the hinge region that facilitates domain-domain motions between receptor binding domain and S2 region of the spike protein. Computer-aided mutagenesis and inter-residue energy calculations reveal that contacts involving D614 are energetically frustrated. However, contacts involving G614 are energetically favourable, implying the substitution strengthens residue contacts that are formed within as well as between protomers. We also find that the free energy difference (ΔΔG) between two variants is -2.6 kcal/mol for closed and -2.0 kcal/mol for 1-RBD up conformation. Thus, the hermodynamic stability has increased upon D614G substitution. Whereas the reverse mutation in spike protein structures having G614 substitution has resulted in the free energy differences of 6.6 kcal/mol and 6.3 kcal/mol for closed and 1-RBD up conformations, respectively, indicating that the overall thermodynamic stability has decreased. These results suggest that the D614G substitution modulates the flexibility of spike protein and confers enhanced thermodynamic stability irrespective of conformational states. This data concurs with the known information demonstrating increased availability of the functional form of spike protein trimer upon D614G substitution.

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

“…Computer simulations and protein modeling played an important role in shaping up our understanding of the dynamics and function of SARS-CoV-2 glycoproteins [46][47][48][49][50][51][52][53][54][55][56]. The latest extensive molecular dynamics (MD) simulations and free-energy landscape mapping studies of the SARS-CoV-2 S proteins and mutants detailed conformational changes and diversity of ensembles, further supporting the notion of enhanced functional and structural plasticity of S proteins [57][58][59][60][61][62][63]. Our recent studies offered evidence that the SARS-CoV-2 spike protein can function as an allosterically regulated machine that exploits plasticity of allosteric hotspots to fine-tune response to antibody binding [64][65][66][67][68][69].…”

“…The free-energy landscapes of the S protein derived from MD simulations, together with nudged elastic pathway optimization mapping of the RBD opening, revealed a specific transient allosteric pocket at the hinge region, which is located near D614 position, influences RBD dynamics [60]. The energy analysis of the S-D614 and S-G614 proteins showed that local interactions near D614 position may be energetically frustrated and become stabilized in the S-G614 mutant through strengthening the inter-protomer association between S1 and S2 regions [63].…”

Structural and Computational Studies of the SARS-CoV-2 Spike Protein Binding Mechanisms with Nanobodies: From Structure and Dynamics to Avidity-Driven Nanobody Engineering

“…Markov modeling characterized the dynamics of the S protein and mutational variants, predicting the increase in the open state occupancy for the D614G mutation due to the increased flexibility of the closed state and the enhanced stabilization of the open form [ 129 ]. The energy analysis of the S-D614 and S-G614 proteins in the closed and partially open conformations showed that local interactions near D614 position may be energetically frustrated and become stabilized in the S-G614 mutant through strengthening of the inter-protomer association between S1 and S2 regions [ 130 ].…”

Physicochemical effect of the N501Y, E484K/Q, K417N/T, L452R and T478K mutations on the SARS-CoV-2 spike protein RBD and its influence on agent fitness and on attributes developed by emerging variants of concern

“…The G614 mutation has implications for the spike protein structure, as it eliminates hydrogen bonds between the protein's S1 unit and S2 units naturally present in D614. This physicochemical change increased the protein chain flexibility ( Korber et al, 2020 ), confering enhanced thermodynamic stability irrespective of conformational states and most optimal for binding host ACE-2 ( Yazhini et al, 2021 ). Therefore, it is assumed that this mutation has improved the transmission efficiency of SARS-CoV-2 ( Yazhini et al, 2021 ; Volz et al, 2021 ) by up to approximately 50%, according to Pearson et al (2021) ( Pearson et al, 2021 ), and contributed to the increase in the variants' infectivity ( Giovanetti et al, 2021 ).…”

“…This physicochemical change increased the protein chain flexibility ( Korber et al, 2020 ), confering enhanced thermodynamic stability irrespective of conformational states and most optimal for binding host ACE-2 ( Yazhini et al, 2021 ). Therefore, it is assumed that this mutation has improved the transmission efficiency of SARS-CoV-2 ( Yazhini et al, 2021 ; Volz et al, 2021 ) by up to approximately 50%, according to Pearson et al (2021) ( Pearson et al, 2021 ), and contributed to the increase in the variants' infectivity ( Giovanetti et al, 2021 ). Additionally, it has been suggested that this mutation would be associated with an increase in the fatal cases rate ( Becerra-Flores and Cardozo, 2020 ), a phenomenon clearly observed after the VOCs emerging, so far.…”