Molecular mechanisms of pH‐driven conformational transitions of proteins: Insights from continuum electrostatics calculations of acid unfolding

摘要: The acid unfolding of staphylococcal nuclease (SNase) is very cooperative (Whitten and Garcia-Moreno, Biochemistry 2000;39:14292-14304). As many as seven hydrogen ions (H+) are bound preferentially by the acid-unfolded state relative to native (N) in pH range 3.2-3.9. To investigate mechanism unfolding, structure-based pKa calculations were performed with a variety continuum electrostatic methods. reproduced successfully H+ binding properties N between 5 9, but they systematically overestimated number upon unfolding. calculated values all carboxylic residues more depressed than should be. discrepancy observed uptake was not improved using high protein dielectric constants, structures relaxed molecular dynamics, or other empirical modifications implemented previously others maximize agreement measured values. This suggests an important role for conformational fluctuations backbone determinants groups. Because no global subglobal changes have been SNase under acidic conditions above acid-unfolding region, these must be local. does seem involve disruption accruement intramolecular repulsive interactions, nor protonation key ion paired residues. It consistent modest contributions from groups, local coupling structural transition.