Electrostatic energy is useful to correlate the structure and the function of proteins. For this reason, improved understanding of the molecular determinants of pKa values and electrostatic energies, and the development of computational methods for structure- based electrostatics calculations, continues to be of great interest. Most computational methods are not yet sufficiently accurate to be useful to describe biochemical processes, especially those where the change in the charge of a protein is coupled to a change in conformation. Furthermore, the physical basis of electrostatic effects in proteins is not well understood. The studies that are proposed examine the hypothesis that local conformational fluctuations that involve rearrangement of the backbone contribute significantly to the magnitude of pKa values and electrostatic energies of proteins. Preliminary data suggest that the hypothesis is likely to be correct. Neither local conformational fluctuations of proteins nor the structural responses of proteins to changes in their charged state can be reproduced reliably with existing computational approaches. One of the problems is that the range and character of fluctuations of proteins in the slow time scales characteristic of equilibrium and biological processes have not been characterized. The goal of the equilibrium thermodynamic studies that are proposed is (1) to improve understanding the relationship between local conformational stability and pKa values of surface ionizable residues;(2) to describe the coupling between local structural fluctuations, ligand binding, and global conformational transitions;(3) to examine the contributions from local unfolding to the ionization energetics of internal residues. These experimental studies will contribute the physical insight and the data needed to guide improvements to existing methods for structure-based calculation of electrostatic effects in proteins. They will also be used to test and develop a new method for structure-based calculations of electrostatic effects that combines standard electrostatics continuum methods for pKa calculations with a statistical thermodynamic method to describe the distribution of microstates in the native state ensemble.
The principles and the computational methods emerging from these studies will impact our understanding of pH-driven conformational transitions of medical and biological relevance, such as activation of viruses and toxins. The computational method that will be developed could be useful in problems in drug design, and for the design of proteins and macromolecular switches.
|Richman, Daniel E; Majumdar, Ananya; GarcÃa-Moreno E, Bertrand (2014) pH dependence of conformational fluctuations of the protein backbone. Proteins 82:3132-43|
|Kukic, Predrag; Farrell, Damien; McIntosh, Lawrence P et al. (2013) Protein dielectric constants determined from NMR chemical shift perturbations. J Am Chem Soc 135:16968-76|
|Spencer, Daniel; Bertrand, Garcia-Moreno E; Stites, Wesley E (2013) The pH dependence of staphylococcal nuclease stability is incompatible with a three-state denaturation model. Biophys Chem 180-181:86-94|
|Wu, Xiongwu; Damjanovic, Ana; Brooks, Bernard R (2012) Efficient and Unbiased Sampling of Biomolecular Systems in the Canonical Ensemble: A Review of Self-Guided Langevin Dynamics. Adv Chem Phys 150:255-326|
|Nielsen, Jens E; Gunner, M R; GarcÃa-Moreno, Bertrand E (2011) The pKa Cooperative: a collaborative effort to advance structure-based calculations of pKa values and electrostatic effects in proteins. Proteins 79:3249-59|
|Bell-Upp, Peregrine; Robinson, Aaron C; Whitten, Steven T et al. (2011) Thermodynamic principles for the engineering of pH-driven conformational switches and acid insensitive proteins. Biophys Chem 159:217-26|
|Itoh, Satoru G; DamjanoviÄ‡, Ana; Brooks, Bernard R (2011) pH replica-exchange method based on discrete protonation states. Proteins 79:3420-36|
|DamjanoviÄ‡, Ana; Brooks, Bernard R; GarcÃa-Moreno, Bertrand (2011) Conformational relaxation and water penetration coupled to ionization of internal groups in proteins. J Phys Chem A 115:4042-53|