TrendBio

#37 · Structural bio & protein design

MD-informed models map allosteric couplings in receptors and AAA+ ATPases

3 preprints
Items per day, last 8 weekstoday: 3

The common thread across these three preprints is the use of molecular dynamics to resolve allosteric coupling at residue resolution, followed by a statistical or kinetic layer that ranks or validates the resulting pathways. The AT1R study applies interpretable Bayesian network modeling to MD ensembles, mapping residue-level allosteric couplings that are validated by mutational scanning and that yield a negative allosteric modulator. The AAA+ ATPase study pairs comparative MD with SHAP feature ranking to trace allosteric paths in katanin and ClpB. The acetylcholine receptor study combines kinetic modelling, phi-value and activation energy estimates from single-channel recordings with MD to map parallel gating pathways. What is new across these items is the explicit coupling of simulation-derived pathways to interpretability methods or experimental kinetics that constrain them, rather than MD alone.

Preprints

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