This proposal requests support for an ongoing collaboration among three faculty members, aimed at the development of molecular simulation protocols to study the conformations and energetics of both native and non-native states of peptides and proteins, and to explore the details of pH- and salt-induced conformational transitions. The primary computational tools will be explicit and continuum solvent models for conformational energetics and molecular dynamics in "extended" ensembles for conformational sampling. Critical tests of the continuum solvent models will concentrate on pH- and salt effects for titration of amino acid side-chains (including difficult cases with buried charges and water penetration effects) and on folding/unfolding and monomer/dimer transitions in selected proteins and peptides. Based on these studies, new generalized Born solvation models will be developed, which can represent mixed membrane/water environments, and which will be better-tested for salt-dependence predictions. These will be incorporated into the CHARMM and Amber molecular dynamics packages, and a major effort will be made to improve the efficiency and robustness of constant pH simulations, in which the protonation state of amino acid side chains is brought to equilibrium with an external bath of protons at a given pH at the same time that the conformational states of the system are sampled via molecular dynamics. This combination of continuum solvent ideas and more sophisticated sampling techniques should allow us to develop practical simulation tools in which the user specifies pH and salt concentration as external thermodynamic variables, in much the same way that temperature and pressure are specified currently. This will facilitate MD simulations under these more relevant biochemical conditions to be easily accessible to a wider community.
This project will develop and test new computational methods for carrying out computer simulations of the properties of proteins under varying conditions of acid and external salt. Applications will be made to order-disorder transitions in peptides, folded proteins, and protein-protein assemblies. Aspects related to human health include detailed studies of p53 and p27 domains, of importance in cancer, and acid-based changes in conformation in peptides related to Alzheimer's disease and other aggregation-related disorders.
|Goh, Garrett B; Hulbert, Benjamin S; Zhou, Huiqing et al. (2014) Constant pH molecular dynamics of proteins in explicit solvent with proton tautomerism. Proteins 82:1319-31|
|Goh, Garrett B; Laricheva, Elena N; Brooks 3rd, Charles L (2014) Uncovering pH-dependent transient states of proteins with buried ionizable residues. J Am Chem Soc 136:8496-9|
|Giamba?u, George M; Luchko, Tyler; Herschlag, Daniel et al. (2014) Ion counting from explicit-solvent simulations and 3D-RISM. Biophys J 106:883-94|
|Bharatham, Nagakumar; Bharatham, Kavitha; Shelat, Anang A et al. (2014) Ligand binding mode prediction by docking: mdm2/mdmx inhibitors as a case study. J Chem Inf Model 54:648-59|
|Goh, Garrett B; Knight, Jennifer L; Brooks 3rd, Charles L (2013) pH-dependent dynamics of complex RNA macromolecules. J Chem Theory Comput 9:935-943|
|Joung, In Suk; Luchko, Tyler; Case, David A (2013) Simple electrolyte solutions: comparison of DRISM and molecular dynamics results for alkali halide solutions. J Chem Phys 138:044103|
|Cheatham 3rd, Thomas E; Case, David A (2013) Twenty-five years of nucleic acid simulations. Biopolymers 99:969-77|
|Laricheva, Elena N; Arora, Karunesh; Knight, Jennifer L et al. (2013) Deconstructing activation events in rhodopsin. J Am Chem Soc 135:10906-9|
|Nikolova, Evgenia N; Goh, Garrett B; Brooks 3rd, Charles L et al. (2013) Characterizing the protonation state of cytosine in transient GýýC Hoogsteen base pairs in duplex DNA. J Am Chem Soc 135:6766-9|
|Foit, Linda; George, Jenny S; Zhang, Bin W et al. (2013) Chaperone activation by unfolding. Proc Natl Acad Sci U S A 110:E1254-62|
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