ArticleJournal of chemical information and modeling2024
Kinetics-Based State Definitions for Discrete Binding Conformations of T4 L99A in MD via Markov State Modeling.
Article in Journal of chemical information and modeling, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
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1 citing paper in PubMed.
- An Automated Workflow for Diagnosing Sampling Issues Caused by Slow Torsional Motions in Molecular Simulations.Journal of chemical information and modeling · 2026Article
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3 authors.
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Abstract
As a model system, the binding pocket of the L99A mutant of T4 lysozyme has been the subject of numerous computational free energy studies. However, previous studies have failed to fully sample and account for the observed changes in the binding pocket of T4 L99A upon binding of a congeneric ligand series, limiting the accuracy of results. In this work, we resolve the closed, intermediate, and open states for T4 L99A previously reported in experiment in MD and establish definitions for these states based on the dynamics of the system. From this analysis, we arrive at two primary conclusions. First, assignment of simulation trajectories into discrete states should not be done simply based on RMSD to crystal structures as this can result in misassignment of states. Second, the different metastable conformations studied here need to be carefully treated, as we estimate the time scales for conformational interconversion to be on the order of 10
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