Experiment and theory highlight role of native state topology in SH3 folding

Riddle, D.S., Grantcharova, V.P., et al. Nat Struct Biol 6, 1016-1204. (1999)

We use a combination of experiments, computer simulations and simple model calculations to characterize, first, the folding transition state ensemble of the src SH3 domain, and second, the features of the protein that determine its folding mechanism. Kinetic analysis of mutations at 52 of the 57 residues in the src SH3 domain revealed that the transition state ensemble is even more polarized than suspected earlier: no single alanine substitution in the N-terminal 15 residues or the C-terminal 9 residues has more than a two-fold effect on the folding rate, while such substitutions at 15 sites in the central three-stranded beta-sheet cause significant decreases in the folding rate. Molecular dynamics (MD) unfolding simulations and ab initio folding simulations on the src SH3 domain exhibit a hierarchy of folding similar to that observed in the experiments. The similarity in folding mechanism of different SH3 domains and the similar hierarchy of structure formation observed in the experiments and the simulations can be largely accounted for by a simple native state topology-based model of protein folding energy landscapes.

A correlation between folding rate and contact order

Plaxco, K. W., Simons, K. T. et al. J. Mol. Biol. 277, 985-994. (1998)

Our studies have revealed a significant correlation between the average sequence seqaration between contacting residues in the native state (contact order) and the folding rate of simple, single domain proteins.


Calculate the contact order for your protein or a protein in the PDB

Sequences of small proteins are not optimized for rapid folding

Kim, D. E., Gu, H., and Baker, D. Proc. Natl. Acad. Sci, 95, 4982-4986 (1998)

Distributions of free energies of unfolding and refolding rates in randomized protein L variants compared to wild type.

 

 

A folded, functional SH3 domain built largely from a five letter amino acid alphabet

 Riddle, D., Santiago, J., et al. Nature Structural Biology 4, 805-809. (1997)

Diagram showing the positions of simplified residues (I, K, E, A, G) in red for FP2 in the wild type SH3 structure. Side chains of residues involved in ligand binding are displayed and residues where simplification was not attempted are in light blue. The peptide ligand is shown in orange. Residues which did not tolerate simplification are in black.

 

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