We propose to develop statistical mechanical theory for protein stability and folding kinetics. Lattice models are unrealistically simplified All- atom simulations don't explore enough conformation space. We propose a graph theoretic (GT) approach that covers conformational space broadly, yet can be used with many different models, including anatomically detailed ones. We are calculating partition functions, so: enthalpies, entropies, heat capacities of folding, m-values for denaturants, pH and salt-induced transitions, transitions to molten globules, thermal factors, and hydrogen exchange protection factors. What is novel here is a proper treatment of the density of states essential for any microscopic theory of stability and kinetics. We are also treating folding kinetics, which we aim to apply to realistic models and specific proteins, including lysozyme, cytochrome C, ribonuclease, and others. Ultimately, understanding the fluctuations and other non-native states of proteins will be essential for predicting protein function and mechanism.
| Perez, Alberto; MacCallum, Justin L; Brini, Emiliano et al. (2015) Grid-based backbone correction to the ff12SB protein force field for implicit-solvent simulations. J Chem Theory Comput 11:4770-9 |
| Pressé, Steve; Peterson, Jack; Lee, Julian et al. (2014) Single molecule conformational memory extraction: p5ab RNA hairpin. J Phys Chem B 118:6597-603 |
| Roy, Arijit; Perez, Alberto; Dill, Ken A et al. (2014) Computing the relative stabilities and the per-residue components in protein conformational changes. Structure 22:168-75 |
| Presse, Steve; Lee, Julian; Dill, Ken A (2013) Extracting conformational memory from single-molecule kinetic data. J Phys Chem B 117:495-502 |
| Peterson, G Jack; Pressé, Steve; Peterson, Kristin S et al. (2012) Simulated evolution of protein-protein interaction networks with realistic topology. PLoS One 7:e39052 |
| Schmit, Jeremy D; Dill, Ken (2012) Growth rates of protein crystals. J Am Chem Soc 134:3934-7 |
| Dill, Ken A; MacCallum, Justin L (2012) The protein-folding problem, 50 years on. Science 338:1042-6 |
| Perez, Alberto; Yang, Zheng; Bahar, Ivet et al. (2012) FlexE: Using elastic network models to compare models of protein structure. J Chem Theory Comput 8:3985-3991 |
| Ge, Hao; Presse, Steve; Ghosh, Kingshuk et al. (2012) Markov processes follow from the principle of maximum caliber. J Chem Phys 136:064108 |
| MacCallum, Justin L; Pérez, Alberto; Schnieders, Michael J et al. (2011) Assessment of protein structure refinement in CASP9. Proteins 79 Suppl 10:74-90 |
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