Physics‐based enzyme design: Predicting binding affinity and catalytic activity

Abstract

Computational enzyme design is an emerging field that has yielded promising success stories, but where numerous challenges remain. Accurate methods to rapidly evaluate possible enzyme design variants could provide significant value when combined with experimental efforts by reducing the number of variants needed to be synthesized and speeding the time to reach the desired endpoint of the design. To that end, extending our computational methods to model the fundamental physical-chemical principles that regulate activity in a protocol that is automated and accessible to a broad population of enzyme design researchers is essential. Here, we apply a physics-based implicit solvent MM-GBSA scoring approach to enzyme design and benchmark the computational predictions against experimentally determined activities. Specifically, we evaluate the ability of MM-GBSA to predict changes in affinity for a steroid binder protein, catalytic turnover for a Kemp eliminase, and catalytic activity for α-Gliadin peptidase variants. Using the enzyme design framework developed here, we accurately rank the most experimentally active enzyme variants, suggesting that this approach could provide enrichment of active variants in real-world enzyme design applications.

Chemical basis for the recognition of trimethyllysine by epigenetic reader proteins

“…Despite the universally recognized phenomenon that biomolecular processes take place in aqueous media and that the hydrophobic effect is a primary determinant of biomolecular association, the role of explicit water molecules has often been ignored in analyses of biomolecular recognition events 48 49 , although recent advances have enabled more detailed analysis of the role of water molecules in binding 46 50 51 . Energetically favourable desolvation of protein-binding sites, however, often determines the magnitude of protein–ligand association 52 53 . Our observations that binding affinities of H3G4 with JARID1A and TAF3 are drastically reduced when compared with H3K4me3 led to the hypothesis that the aromatic cages are occupied by high-energy water molecules.…”

Rapid Evolution of Reduced Susceptibility against a Balanced Dual-Targeting Antibiotic through Stepping-Stone Mutations

“…where G MM is the calculated molecular mechanics energy for the force field applied and G Solv is the solvation energy in the generalized Born approximation. Different variations of this method are widely used in large-scale drug design studies (56)(57)(58), as it accurately predicts mutational effects in drugprotein interaction analyses with a manageable computational demand (see, e.g., references 59 and 60). In our study, MM-GBSA calculations were carried out with the thermal_mmgbsa.py script in the Schrödinger package (55) from 100 evenly spaced structures from the second 50 ns of our previously performed molecular dynamics simulation between the wild-type enzyme (DNA gyrase and topoisomerase IV) and gepotidacin.…”

Mechanistic insights into Zika virus NS3 helicase inhibition by Epigallocatechin-3-gallate

“…The structures of the protein and complex were imported in the Desmond setup wizard and were solvated in a cubic periodic box of TIP3P water molecules. The structures were neutralized by adding a suitable number of counter ions and 0.15 M of salt concentration (41). Steepest descent, a hybrid method is implemented for the local energy minimization of the system.…”