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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