The objective of this proposal is to use a combination of experimental and computational approaches to develop a physically plausible model for the folding of the src SH3 domain capable of accurately predicting the results of further experimental measurements. The rate limiting step in folding will be probed by analyzing the kinetic consequences of both single and multiple amino acid substitutions in combination with both all atom and simplified computational models. The starting point of the folding reaction, the denatured state, will be probed by studying peptide models, the kinetics of exchange from the native state, and by direct NMR characterization. The importance of hydrophobic-hydrophyllic patterning and the relationship between sequence conservation and kinetics will be investigated using phage display selection methods. The experimental data will be compared with the results of computational methods including a recently developed ab initio folding simulation method, a simple model which computes the rate and transition state structure from the sequence and native state using simple physical principles, and all atom MD simulations. The ultimate goal is a therapy for beta sheet proteins capable for predicting the folding rate, the structure in the transition state ensemble, and the residual structure in the denatured state from the sequence and structure of the native protein.
| Karanicolas, John; Corn, Jacob E; Chen, Irwin et al. (2011) A de novo protein binding pair by computational design and directed evolution. Mol Cell 42:250-60 |
| Fleishman, Sarel J; Corn, Jacob E; Strauch, Eva M et al. (2010) Rosetta in CAPRI rounds 13-19. Proteins 78:3212-8 |
| McBeth, Christine; Seamons, Audrey; Pizarro, Juan C et al. (2008) A new twist in TCR diversity revealed by a forbidden alphabeta TCR. J Mol Biol 375:1306-19 |
| Cho, Hyundae D; Sood, Vanita D; Baker, David et al. (2008) On the role of a conserved, potentially helix-breaking residue in the tRNA-binding alpha-helix of archaeal CCA-adding enzymes. RNA 14:1284-9 |
| Korkegian, Aaron; Black, Margaret E; Baker, David et al. (2005) Computational thermostabilization of an enzyme. Science 308:857-60 |
| Chevalier, Brett S; Kortemme, Tanja; Chadsey, Meggen S et al. (2002) Design, activity, and structure of a highly specific artificial endonuclease. Mol Cell 10:895-905 |
