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Molecular mechanisms of pH‐driven conformational transitions of proteins: Insights from continuum electrostatics calculations of acid unfolding
Author(s) -
Fitch Carolyn A.,
Whitten Steven T.,
Hilser Vincent J.,
GarcíaMoreno E. Bertrand
Publication year - 2006
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.20797
Subject(s) - electrostatics , molecular dynamics , chemical physics , static electricity , chemistry , biophysics , nanotechnology , physics , statistical physics , computational chemistry , materials science , biology , quantum mechanics
The acid unfolding of staphylococcal nuclease (SNase) is very cooperative (Whitten and García‐Moreno, Biochemistry 2000;39:14292–14304). As many as seven hydrogen ions (H + ) are bound preferentially by the acid‐unfolded state relative to the native (N) state in the pH range 3.2–3.9. To investigate the mechanism of acid unfolding, structure‐based p K a calculations were performed with a variety of continuum electrostatic methods. The calculations reproduced successfully the H + binding properties of the N state between pH 5 and 9, but they systematically overestimated the number of H + bound upon acid unfolding. The calculated p K a values of all carboxylic residues in the N state were more depressed than they should be. The discrepancy between the observed and the calculated H + uptake upon acid unfolding was not improved by using high protein dielectric constants, structures relaxed with molecular dynamics, or other empirical modifications implemented previously by others to maximize agreement between measured and calculated p K a values. This suggests an important role for conformational fluctuations of the backbone as important determinants of p K a values of carboxylic groups. Because no global or subglobal conformational changes have been observed previously for SNase under acidic conditions above the acid‐unfolding region, these fluctuations must be local. The acid unfolding of SNase does not seem to involve the disruption of the N state by accruement of intramolecular repulsive interactions, nor the protonation of key ion paired carboxylic residues. It is more consistent with modest contributions from many H + binding groups, with an important role for local conformational fluctuations in the coupling between H + binding and the global structural transition. Proteins 2006. © 2006 Wiley‐Liss, Inc.