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This study investigates how mutations in a specific amino acid residue (phenylalanine F20) within the hydrophobic core of the Fyn SH3 protein domain affect the protein's native state dynamics. The researchers combined NMR order parameters from wild-type and two mutant proteins (F20L and F20V) as restraints in molecular dynamics simulations, enabling an atomistic-level characterization of subtle structural fluctuations induced by the mutations. The resulting structural ensembles allowed estimation of native state entropy changes, which translated into free energy contributions of several kcal/mol, indicating these conformational changes make meaningful contributions to overall protein stability.
Why it matters
Understanding how single amino acid mutations alter protein dynamics and stability at an atomistic level is critical for protein engineering, drug design, and interpreting the functional consequences of disease-associated mutations. This methodology offers a sensitive framework for detecting and quantifying subtle thermodynamic perturbations that conventional structural analyses might overlook.
arXiv:2605.14496v2 Announce Type: replace
Abstract: NMR relaxation experiments have shown that there are small but measurable changes in the native state dynamics of the Fyn SH3 domain associated with the substitution by other amino acids of a phenylalanine residue (F20) in the hydrophobic core. We have here used experimental values of NMR order parameters for the wild type protein and two mutational variants (F20L and F20V) as restraints in molecular dynamics simulations. This approach is highly sensitive and provides an atomistic description of the subtle perturbations in native state fluctuations accompanying the mutations. The structural ensembles that we have determined using this method allow the changes in the native state entropy of the protein caused by each of the mutations to be estimated. These entropy changes correspond to free energy variations of several kcal/mol and therefore represent sizable contributions to the overall changes in stability that are associated with the amino acid mutations.
Source: Detection of residual native state entropy changes upon mutation in Fyn SH3