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


Arangasamy Yazhini, Das Swayam Prakash Sidhanta & Narayanaswamy Srinivasan*



Molecular Biophysics Unit; Indian Institute of Science; Bangalore, Karnataka, 560012, India



N Srinivasan - Email: ns@iisc.ac.in; AY - yazhini@iisc.ac.in ; DSPS - sidhantap@iisc.ac.in


Article Type

Research Article



Received March 28, 2021; Revised March 30, 2021; Accepted March 30, 2021, Published March 31, 2021



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.



SARS-CoV-2, COVID-19, spike protein, D614G variant, mutation, normal mode analysis, residue contacts, frustration index, protein stability



Yazhini et al. Bioinformation 17(3): 439-445 (2021)


Supplementary Material



Edited by

P Kangueane






Biomedical Informatics



This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.