Allosteric communication in class A β-lactamases occurs via cooperative coupling of loop dynamics

Abstract

Understanding allostery in enzymes and tools to identify it, offer promising alternative strategies to inhibitor development. Through a combination of equilibrium and nonequilibrium molecular dynamics simulations, we identify allosteric effects and communication pathways in two prototypical class A β-lactamases, TEM-1 and KPC-2, which are important determinants of antibiotic resistance. The nonequilibrium simulations reveal pathways of communication operating over distances of 30 Å or more. Propagation of the signal occurs through cooperative coupling of loop dynamics. Notably, 50% or more of clinically relevant amino acid substitutions map onto the identified signal transduction pathways. This suggests that clinically important variation may affect, or be driven by, differences in allosteric behavior, providing a mechanism by which amino acid substitutions may affect the relationship between spectrum of activity, catalytic turnover and potential allosteric behavior in this clinically important enzyme family. Simulations of the type presented here will help in identifying and analyzing such differences.

The Role of Hydrophobic Nodes in the Dynamics of Class A β-Lactamases

“…Although the novel bicyclic-boronate derivatives, including taniborbactam (which is currently undergoing phase III trials), are predicted to be highly effective in the short term, there is no certainty that resistance to these novel active site inhibitors will not emerge after several years in circulation. To work towards addressing such a risk, which history is teaching us to anticipate, this study provides supporting evidence in line with the alternative allosteric approach for inhibition of class A enzymes; a strategy which has already been receiving steady interest in TEM-1 and KPC-2 ( Horn and Shoichet, 2004 ; Meneksedag et al, 2013 ; Bowman et al, 2015 ; Avcı et al, 2016 ; Hart et al, 2016 ; Grigorenko et al, 2017 ; Galdadas et al, 2018 , 2021 ).…”

The fatty acid site is coupled to functional motifs in the SARS-CoV-2 spike protein and modulates spike allosteric behaviour

“…The results here further highlight the potential of dynamical-nonequilibrium simulations for identifying pathways of allosteric communication (32)(33)(34) and suggest that this approach may be useful in analysing mutations and differences in functionally important dynamical behaviour, and possibly different effects of linoleic acid, between SARS-CoV-2 spike variants of clinical relevance.…”

“…Running multiple (in this case, 90) dynamical-nonequilibrium simulations reduces the noise associated with the structural response of the protein and allows for the determination of the statistical significance of the observed response. Nonequilibrium simulations of this type are emerging as an effective tool to study signal transmission and identify communication networks within proteins (32)(33)(34)(35)(36). Here, the direct comparison between the equilibrium LAbound and nonequilibrium apo spike simulations using the Kubo-Onsager approach (29-31) (bottom panel in Figure S2), and the average of the results over all the 90 replicates, allows for identification of the temporal sequence of conformational changes associated with the response of the spike to LA removal (Figures 2 and S4), and also the determination of their statistical significance (Figure S5).…”

“…We have shown this approach to be effective in identifying structural communication pathways in a variety of proteins, e.g. in identifying a general mechanism of interdomain signal propagation in nicotinic acetylcholine receptors (32,33) and mapping the networks connecting the allosteric and catalytic sites in two clinically relevant β-lactamase enzymes (34). This approach is based on, first of all, equilibrium simulations of the system in question, which generate configurations for multiple dynamical-nonequilibrium simulations where the effect of a perturbation can be studied.…”

Activation mechanism of Drosophila cryptochrome through an allosteric switch

“…Elucidation of the structural determinants and the details of conformational activation mechanism of CRY signaling could facilitate CRY engineering as a promising candidate for optogenetics (43,44). The identification of allosteric networks in signaling proteins and enzymes on the basis of equilibrium and nonequilibrium MD simulations can provide further insights into the functional dynamics of biological systems as illustrated in recent studies (28,45).…”