Molecular Dynamics Analysis of a Flexible Loop at the Binding Interface of the SARS-CoV-2 Spike Protein Receptor-Binding Domain

Abstract

Since the identification of the SARS-CoV-2 virus as the causative agent of the current COVID-19 pandemic, considerable effort has been spent characterizing the interaction between the Spike protein receptor-binding domain (RBD) and the human angiotensin converting enzyme 2 (ACE2) receptor. This has provided a detailed picture of the end point structure of the RBD-ACE2 binding event, but what remains to be elucidated is the conformation and dynamics of the RBD prior to its interaction with ACE2. In this work we utilize molecular dynamics simulations to probe the flexibility and conformational ensemble of the unbound state of the receptor-binding domain from SARS-CoV-2 and SARS-CoV. We have found that the unbound RBD has a localized region of dynamic flexibility in Loop 3 and that mutations identified during the COVID-19 pandemic in Loop 3 do not affect this flexibility. We use a loop-modeling protocol to generate and simulate novel conformations of the CoV2-RBD Loop 3 region that sample conformational space beyond the ACE2 bound crystal structure. This has allowed for the identification of interesting substates of the unbound RBD that are lower energy than the ACE2-bound conformation, and that block key residues along the ACE2 binding interface. These novel unbound substates may represent new targets for therapeutic design.

Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency

“…[ 24 , 26 ]. Several structural and dynamic studies at the molecular level show that SARS-CoV-2 RBDs have to adapt open conformation (also known as “up” or “standing”) to effectively bind to ACE2 receptors [ 8 , 16 , 61 , 62 ]. So far, mutations in non-RBD residues, such as the D614G variant, can populate RBD open conformation rather than closed conformations [ 63 ].…”

“…The mutation of alanine instead of tyrosine at 501 (i.e., N501A) shows an increase in loop Y473–C489 flexibility and conformational compactness according to a related study [ 61 ]. Moreover, the same loop Y473–C489 in SARS-CoV RBD showed a higher flexibility in comparison to SARS-CoV-2 RBD [ 61 , 62 ]. This suggests that the higher infectivity of the N501Y variant might be attributed to an improvement in the N501Y RBD conformation and therefore a higher affinity to ACE2 receptor.…”

Molecular Dynamics Simulations Studies On The Effects Of Mutations On The Binding Affinities Between SARS-CoV-2 Spike RBD And Human ACE2

“…Previously, study revealed that the loop 3 and 4 regions are more flexible domains at the RBD (Williams et al, 2021). Upon the closer observation, the residue flexibility trajectories also reflected to have higher flexibility at the region of 470 -490.…”

Molecular dynamics simulations reveal the importance of conformational changes, glycosylation, mutations, and drug repurposing for the Sars-Cov-2 spike protein

“…This large shift was enhanced by five glycan residues bound to Asn53, Asn90, Asn103, Asn322, and Asn546 of ACE2, with Asn53 involved in both intramolecular homodimer and heterodimer contacts. [27,28] Williams and coworkers [29] suggested that in the RBD:ACE2 interaction pattern, residues Phe486, Asn487, and Tyr489 are responsible for the adaptive flexibility of RBD in establishing strong interactions with ACE2. At the same time, this study demonstrated how mutations in that RBD sub-region are crucial in the selective pressure of the virus, altering the flexibility of RBD and interfering in intra-monomer interactions within the RBD.…”

“…At the same time, this study demonstrated how mutations in that RBD sub-region are crucial in the selective pressure of the virus, altering the flexibility of RBD and interfering in intra-monomer interactions within the RBD. [29]!From a geometric perspective, effective interaction between SARS-CoV-2-spike and ACE2 would occur at an angle of inclination between the apical portion of RBD "up" and ACE2 of at least 52°. [30] Such MD results indicated that RBD "up" conformations have a large degree of manoeuvre to achieve sufficient residue exposure for ACE2 binding.…”