pH-Dependence of Protein Stability: Absolute Electrostatic Free Energy Differences between Conformations

@article{citeulike:2371020, abstract = {Abstract: A method for calculating the absolute electrostatic free energy of a titrating system as a function of pH is proposed, and a concise formula for the free energy is presented. Based on the theory of linked functions, the electrostatic free energy is calculated by integration of the titration curve. The approach uses pH = , at which the system is in the unprotonated state, as the reference pH for the integration. The finite-difference Poisson-Boltzmann method is used for the electrostatic free energy, and the titration curve is obtained by the Monte Carlo approach of Beroza et al.1 The method is applied to the native and denatured state of hen egg-white lysozyme in aqueous solution. A dielectric constant of 20 is assigned to the protein interior, in accord with the work of Antosiewicz et al.2 X-ray structures are used for the native state, and an extended -structure is used for the unfolded reference state; good agreement with experiment is obtained. Comparison of the results for the extended -structure and for a "null" model of noninteracting sites for the unfolded state shows significant differences. This indicates that there are important interactions between titrating sites in the unfolded state, in agreement with recent experimental estimates by Oliveberg et al.3 A number of structures obtained by in vacuo minimization of the native and unfolded protein are compared, and it is shown that the absolute pH-stability curve has a strong conformational dependence, although the relative stability curve does not. Calculations of absolute free energy differences, rather than relative changes as a function of pH, are of general interest; for example, they can be used to study the binding energy of ligands involving small titratable compounds.}, address = {Department of Chemistry, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, and Laboratoire de Chimie Biophysique, Institut le Bel, Universit\'{e} Louis Pasteur, 4 rue Blaise Pascal, 67000 Strasbourg, France}, author = {Schaefer, M. and Sommer, M. and Karplus, M. }, citeulike-article-id = {2371020}, doi = {10.1021/jp962972s}, journal = {J. Phys. Chem. B}, keywords = {computation, md, ph-calculations}, month = {February}, number = {9}, pages = {1663--1683}, posted-at = {2008-02-13 17:27:43}, priority = {2}, title = {pH-Dependence of Protein Stability: Absolute Electrostatic Free Energy Differences between Conformations}, url = {http://dx.doi.org/10.1021/jp962972s}, volume = {101}, year = {1997} }

TY - JOUR ID - citeulike:2371020 L3 - citeulike-article-id:2371020 TI - pH-Dependence of Protein Stability: Absolute Electrostatic Free Energy Differences between Conformations JF - J. Phys. Chem. B VL - 101 IS - 9 SP - 1663 EP - 1683 AD - Department of Chemistry, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, and Laboratoire de Chimie Biophysique, Institut le Bel, Université Louis Pasteur, 4 rue Blaise Pascal, 67000 Strasbourg, France N2 - Abstract: A method for calculating the absolute electrostatic free energy of a titrating system as a function of pH is proposed, and a concise formula for the free energy is presented. Based on the theory of linked functions, the electrostatic free energy is calculated by integration of the titration curve. The approach uses pH = , at which the system is in the unprotonated state, as the reference pH for the integration. The finite-difference Poisson-Boltzmann method is used for the electrostatic free energy, and the titration curve is obtained by the Monte Carlo approach of Beroza et al.1 The method is applied to the native and denatured state of hen egg-white lysozyme in aqueous solution. A dielectric constant of 20 is assigned to the protein interior, in accord with the work of Antosiewicz et al.2 X-ray structures are used for the native state, and an extended -structure is used for the unfolded reference state; good agreement with experiment is obtained. Comparison of the results for the extended -structure and for a "null" model of noninteracting sites for the unfolded state shows significant differences. This indicates that there are important interactions between titrating sites in the unfolded state, in agreement with recent experimental estimates by Oliveberg et al.3 A number of structures obtained by in vacuo minimization of the native and unfolded protein are compared, and it is shown that the absolute pH-stability curve has a strong conformational dependence, although the relative stability curve does not. Calculations of absolute free energy differences, rather than relative changes as a function of pH, are of general interest; for example, they can be used to study the binding energy of ligands involving small titratable compounds. KW - computation KW - md KW - ph-calculations AU - Schaefer, M AU - Sommer, M AU - Karplus, M PY - 1997/02/27/ UR - http://dx.doi.org/10.1021/jp962972s ER -