Designed Local Electric Fields-Promising Tools for Enzyme Engineering

Designing efficient catalysts is one of the ultimate goals of chemists. In this Perspective, we discuss how local electric fields (LEFs) can be exploited to improve the catalytic performance of supramolecular catalysts, such as enzymes. More specifically, this Perspective starts by laying out the fundamentals of how local electric fields affect chemical reactivity and review the computational tools available to study electric fields in various settings. Subsequently, the advances made so far in optimizing enzymatic electric fields through targeted mutations are discussed critically and concisely. The Perspective ends with an outlook on some anticipated evolutions of the field in the near future. Among others, we offer some pointers on how the recent data science/machine learning revolution, engulfing all science disciplines, could potentially provide robust and principled tools to facilitate rapid inference of electric field effects, as well as the translation between optimal electrostatic environments and corresponding chemical modifications.

When the Dust Has Settled: Calculation of Binding Affinities from First Principles for SARS-CoV-2 Variants with Quantitative Accuracy

Accurate determination of binding free energy is pivotal for the study of many biological processes and has been applied in a number of theoretical investigations to compare the affinity of severe acute respiratory syndrome coronavirus 2 variants toward the host cell. Diversity of these variants challenges the development of effective general therapies, their transmissibility relying either on an increased affinity toward their dedicated human receptor, the angiotensin-converting enzyme 2 (ACE2), or on escaping the immune response. Now that robust structural data are available, we have determined with utmost accuracy the standard binding free energy of the receptor-binding domain to the most widespread variants, namely, Alpha, Beta, Delta, and Omicron BA.2, as well as the wild type (WT) in complex either with ACE2 or with antibodies, namely, S2E12 and H11-D4, using a rigorous theoretical framework that combines molecular dynamics and potential-of-mean-force calculations. Our results show that an appropriate starting structure is crucial to ensure appropriate reproduction of the binding affinity, allowing the variants to be compared. They also emphasize the necessity to apply the relevant methodology, bereft of any shortcut, to account for all the contributions to the standard binding free energy. Our estimates of the binding affinities support the view that while the Alpha and Beta variants lean on an increased affinity toward the host cell, the Delta and Omicron BA.2 variants choose immune escape. Moreover, the S2E12 antibody, already known to be active against the WT (Starr et al., 2021; Mlcochova et al., 2021), proved to be equally effective against the Delta variant. In stark contrast, H11-D4 retains a low affinity toward the WT compared to that of ACE2 for the latter. Assuming robust structural information, the methodology employed herein successfully addresses the challenging protein-protein binding problem in the context of coronavirus disease 2019 while offering promising perspectives for predictive studies of ever-emerging variants.

Mechanisms of Spectrotemporal Modulation Detection for Normal- and Hearing-Impaired Listeners

Spectrotemporal modulations (STM) are essential features of speech signals that make them intelligible. While their encoding has been widely investigated in neurophysiology, we still lack a full understanding of how STMs are processed at the behavioral level and how cochlear hearing loss impacts this processing. Here, we introduce a novel methodological framework based on psychophysical reverse correlation deployed in the modulation space to characterize the mechanisms underlying STM detection in noise. We derive perceptual filters for young normal-hearing and older hearing-impaired individuals performing a detection task of an elementary target STM (a given product of temporal and spectral modulations) embedded in other masking STMs. Analyzed with computational tools, our data show that both groups rely on a comparable linear (band-pass)-nonlinear processing cascade, which can be well accounted for by a temporal modulation filter bank model combined with cross-correlation against the target representation. Our results also suggest that the modulation mistuning observed for the hearing-impaired group results primarily from broader cochlear filters. Yet, we find idiosyncratic behaviors that cannot be captured by cochlear tuning alone, highlighting the need to consider variability originating from additional mechanisms. Overall, this integrated experimental-computational approach offers a principled way to assess suprathreshold processing distortions in each individual and could thus be used to further investigate interindividual differences in speech intelligibility.