Abstract
SARS-CoV-2 infects cells by attachment to its receptor – the angiotensin converting enzyme 2 (ACE2). Regardless of the wealth of structural data, little is known about the physicochemical mechanism of interactions of the viral spike (S) protein with ACE2 and how this mechanism has evolved during the pandemic. Here, we applied experimental and computational approaches to characterize the molecular interaction of S proteins from SARS-CoV-2 variants of concern (VOC). Data on kinetics, activation- and equilibrium thermodynamics of binding of the receptor binding domain (RBD) from VOC with ACE2 as well as data from computational protein electrostatics revealed a profound remodeling of the physicochemical characteristics of the interaction during the evolution. Thus, as compared to RBDs from Wuhan strain and other VOC, Omicron RBD presented as a unique protein in terms of conformational dynamics and types of non-covalent forces driving the complex formation with ACE2. Viral evolution resulted in a restriction of the RBD structural dynamics, and a shift to a major role of electrostatic forces for ACE2 binding. Further, we investigated how the reshaping of the physicochemical qualities affect the functional properties of S proteins. Data from various binding assays revealed that SARS-CoV-2 Wuhan and Omicron RBDs manifest capacity for off-target (promiscuous) recognition of multiple unrelated proteins, but they harbor distinct reactivity patterns. This study provides mechanistic explanations for changes in the viral tropism, infectivity, and capacity to evade immune responses during evolution.
Significance Since the beginning of COVID-19 pandemic SARS-CoV-2 has constantly mutated. Certain variants of the virus have manifested increased infectivity. The mutations often localized in the receptor binding domain (RBD). However, a little is known about the consequences of these mutations on mechanism of receptor binding. By using interdisciplinary approach, we depicted the evolution trajectory of the interactions of RBD with its receptor and with off-targets (unrelated proteins). The viral evolution resulted in a reduction of the structural dynamics of RBD and a shift to a major role of charge interactions for receptor binding. Strikingly, RBD Omicron manifested qualities of a completely different protein as compared to other viral variants in term of its receptor binding and repertoire of recognized off-target molecules.
Competing Interest Statement
The authors have declared no competing interest.
