Mechanistic Evidence Matrix
Cross-references each mechanistic claim with structural, dynamic, energetic, quantitative, and uncertainty evidence.
B293 changes between alternative polar microenvironments
High-pKa state places B293 near B289; low-pKa state places B293 near the B128 backbone oxygen
Contact–pKa and distance time-series analyses support state-dependent local rearrangement
Ensemble PROPKA identifies an unusually high and heterogeneous B293 pKa
B324 exhibits strong pKa-coupled microenvironment remodeling
High-pKa B324 state forms close contacts with B285 GLU; lower-pKa states adopt different local arrangements
Distance and contact analyses link B324 environment to conformational state
Ensemble PROPKA shows broad pKa heterogeneity and strong pH-sensitive protonation propensity
Module B is more compact and internally contacted at pH 6.8
Average and representative structures indicate altered Module B organization
Module B contacts, radius of gyration, and shape descriptors consistently differ between conditions
No direct free-energy proof; interpretation is based primarily on conformational metrics
The histidine-rich regions reorganize dynamically between pH conditions
Clean histidine-network views place selected pH-sensitive histidines within the global architecture
ANM, DCCM, and network analyses identify condition-dependent changes in fluctuation and communication patterns
Ensemble PROPKA identifies several histidines with predicted pKa values within or near the physiological switching range
Global A–B PB-MMPBSA energy is directionally more favorable at pH 6.8
Global overlays show substantial conformational divergence between trajectory-derived averages
DCCM and intermodule network analyses indicate altered coupling between conditions
PB-MMPBSA endpoint calculations were completed using 1001 frames per pH condition; configurational entropy was not included