Work carried out under this proposal will focus on the characterization of non-native states and unfolding pathways for a series of proteins with varying topology and secondary structure. The methods of molecular dynamics and newly developed approaches of radius of gyration umbrella sampling will be used to investigate non-native states of apomyoglobin, fragment B of staphylococcal protein A, lysozyme and apo-alpha-lactalbumin. Models for the protonation states of titratable side chains which are representative of key pH states for the protein apomyoglobin will be developed and studied - models for the system at neutral pH, pH 4 and lower pH values will be considered. These systems will then be investigated using techniques of equilibrium and non-equilibrium (T-jump) molecular dynamics in explicit aqueous solvent. Similar studies will be carried out for lysozyme, apo-alpha-lactalbumin and protein A. Using recently developed techniques of radius of gyration umbrella sampling, the unfolding pathway followed by each of these protein systems (in explicit solvent) when incremental increases in the radius of gyration are induced by changes in the radius of gyration biasing potential will be examined. This pathway, and the intermediates which develop at intermediate values of radius of gyration, will be compared to experimentally determined pathways and intermediates as well as those we find from equilibrium and T-jump simulations. The initial focus of these studies will be to characterize the unfolding pathway for the small three helical bundle protein, protein A, because of its simplified topology. The folding pathway of this system is currently being studied experimentally using fast kinetic methods and NMR hydrogen exchange.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
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Molecular and Cellular Biophysics Study Section (BBCA)
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Scripps Research Institute
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Hills Jr, Ronald D; Kathuria, Sagar V; Wallace, Louise A et al. (2010) Topological frustration in beta alpha-repeat proteins: sequence diversity modulates the conserved folding mechanisms of alpha/beta/alpha sandwich proteins. J Mol Biol 398:332-50
Arora, Karunesh; Brooks Iii 3rd, Charles L (2009) Functionally important conformations of the Met20 loop in dihydrofolate reductase are populated by rapid thermal fluctuations. J Am Chem Soc 131:5642-7
Hills Jr, Ronald D; Brooks 3rd, Charles L (2008) Subdomain competition, cooperativity, and topological frustration in the folding of CheY. J Mol Biol 382:485-95
Chen, Jianhan; Brooks 3rd, Charles L; Khandogin, Jana (2008) Recent advances in implicit solvent-based methods for biomolecular simulations. Curr Opin Struct Biol 18:140-8
Hills Jr, Ronald D; Brooks 3rd, Charles L (2008) Coevolution of function and the folding landscape: correlation with density of native contacts. Biophys J 95:L57-9
Shahrezaei, Vahid; Swain, Peter S (2008) The stochastic nature of biochemical networks. Curr Opin Biotechnol 19:369-74
Khandogin, Jana; Raleigh, Daniel P; Brooks 3rd, Charles L (2007) Folding intermediate in the villin headpiece domain arises from disruption of a N-terminal hydrogen-bonded network. J Am Chem Soc 129:3056-7
Hills Jr, Ronald D; Brooks 3rd, Charles L (2007) Hydrophobic cooperativity as a mechanism for amyloid nucleation. J Mol Biol 368:894-901
Khandogin, Jana; Brooks 3rd, Charles L (2007) Linking folding with aggregation in Alzheimer's beta-amyloid peptides. Proc Natl Acad Sci U S A 104:16880-5
Arora, Karunesh; Brooks 3rd, Charles L (2007) Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism. Proc Natl Acad Sci U S A 104:18496-501

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