Entropic overcompensation of the N501Y mutation on SARS-CoV-2 S binding to ACE2

Abstract

Recent experimental work has shown that the N501Y mutation in the SARS-CoV-2 S glycoprotein's receptor binding domain (RBD) increases binding affinity to the angiotensin-converting enzyme 2 (ACE2), primarily by overcompensating for a less favorable enthalpy of binding by a greatly reducing the entropic penalty for complex formation, but the basis for this entropic overcompensation is not clear [Pr'evost et al., J. Biol. Chem. (2021) 297;10115]. We use all-atom molecular dynamics simulations and free-energy calculations to qualitatively assess the impact of the N501Y mutation on enthalpy and entropy of binding of RBD to ACE2. Our calculations correctly predict that N501Y causes a less favorable enthalpy of binding to ACE2 relative to the original strain. Further, we show that this is overcompensated for by a more entropically favorable increase in large-scale quaternary flexibility and intra-protein root-mean squared fluctuations of residue positions upon binding in both RBD and ACE2. The enhanced quaternary flexibility stems from N501Y's ability to remodel the interresidue interactions between the two proteins away from interactions central to the epitope and toward more peripheral interactions. These findings suggest that an important factor in determining protein-protein binding affinity is the degree to which fluctuations are distributed throughout the complex, and that residue mutations that may seem to result in weaker interactions than their wild-type counterparts may yet result increased binding affinity thanks to their ability to suppress unfavorable entropy changes upon binding.

Making sense of chaos: uncovering the mechanisms of conformational entropy

“…The alpha variant mutation, N501Y, which leads to enhanced infection and transmission 66 through increasing the affinity of the RBD to angiotensin-converting enzyme 2 (ACE2). This mutant does not optimze packing at the interface, but increases flexibility of the complex in a way that favors binding entropically 67,68 . In agreement with more traditional concepts of affinity maturation, nanobodies selected to neutralize spike exhibit decreases in flexibility and more optimal interfaces as affinity increases 69 .…”