Some like it hot, others not: Enzymes strike a delicate balance between features that enhance chemical reactivity and those that contribute to stable structure. Both features are important and can be unrelated or antagonistic. Pinneyet al.combined rich experimental work on thermophilic and mesophilic variants of the enzyme ketosteroid isomerase (KSI) with bioinformatic data from a diverse set of bacterial enzymes to reveal the molecular determinants of thermal adaptation in enzymes. For KSI, they observed a trade-off between activity and thermal stability that comes down to a single active-site residue. With their larger dataset, they identified patterns of individual amino acid substitutions that are favored at higher temperatures, and also consider how networks of stabilizing interactions develop.Science, this issue p.eaay2784

The Meyer-Miller (MM) classical vibronic (electronic + nuclear) Hamiltonian for electronically non-adiabatic dynamics—as used, for example, with the recently developed symmetrical quasiclassical (SQC) windowing model—can be written in either a diabatic or an adiabatic representation of the electronic degrees of freedom, the two being a canonical transformation of each other, thus giving the same dynamics. Although most recent applications of this SQC/MM approach have been carried out in the diabatic representation—because most of the benchmark model problems that have exact quantum results available for comparison are typically defined in a diabatic representation—it will typically be much more convenient to work in the adiabatic representation, e.g., when using Born-Oppenheimer potential energy surfaces (PESs) and derivative couplings that come from electronic structure calculations. The canonical equations of motion (EOMs) (i.e., Hamilton’s equations) that come from the adiabatic MM Hamiltonian, however, in addition to the common first-derivative couplings, also involve second-derivative non-adiabatic coupling terms (as does the quantum Schrödinger equation), and the latter are considerably more difficult to calculate. This paper thus revisits the adiabatic version of the MM Hamiltonian and describes a modification of the classical adiabatic EOMs that are entirely equivalent to Hamilton’s equations but that do not involve the second-derivative couplings. The second-derivative coupling terms have not been neglected; they simply do not appear in these modified adiabatic EOMs. This means that SQC/MM calculations can be carried out in the adiabatic representation, without approximation, needing only the PESs and the first-derivative coupling elements. The results of example SQC/MM calculations are presented, which illustrate this point, and also the fact that simply neglecting the second-derivative couplings in Hamilton’s equations (and presumably also in the Schrödinger equation) can cause very significant errors.

Significance: The influenza A M2 channel (AM2) transports protons into the influenza virus upon acid activation. It is an important pharmacological target as well as a prototypical case to study proton conduction through biological channels. The current work provides the most complete computational characterization to date of the physical basis for the acid activation mechanism of the AM2 proton channel. Our results show that lowering the pH value gradually opens the Trp41 gate and decreases the deprotonation barrier of the His37 tetrad, leading to channel activation. Our result also demonstrates that the C-terminal amphipathic helix does not significantly change the proton conduction mechanism in the AM2 transmembrane domain.

Significance: The M2 channel in the influenza A virus is one of three commonly targeted proteins in the viral membrane. Proton permeation across the M2 channel acidifies the virion, releasing the viral RNA and core proteins. This work constitutes, to our knowledge, the first complete characterization of this process by multiscale computer simulation, and the results are in quantitative agreement with prior experimental measurements. The simulations confirm that the mechanism involves a “shuttling” of protons through the His37 tetrad and that the rate-limiting step is histidine deprotonation. The results also reveal several important features, including a large barrier for protons to reach the His37 tetrad and increased conductance for lower pH values due to channel broadening and increased solvent dynamics despite larger charge repulsion.

Significance: The long-studied proton-pumping mechanism in cytochrome c oxidase (C c O) continues to be a source of debate. This work provides a comprehensive computational characterization of the internal proton transport dynamics, while explicitly including Grotthuss shuttling, that lead to both pumping and catalysis. Focusing on the first steps of oxidation of the fully reduced enzyme, our results show that the transfer of the pumped and chemical protons are thermodynamically driven by electron transfer, and explain how proton back-leakage is avoided by large back-leak barriers and kinetic gating. This work also explicitly characterizes the coupling of proton transport with hydration changes in the hydrophobic cavity and D-channel, thus advancing our understanding of proton transport in biomolecules in general.