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The Project:

The Project:

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The Project:

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  1. The Project: Find all nonlocal contact clusters for the several globular proteins (barnase, fibronectin type III domain, the immunophilin FKBP12, azurin, chymotrypsin inhibitor 2, and ribosomal protein L9) whose folding nucleus is identified experimentally by mutational Φ-value analysis. Identify the strong clusters form the nonlocal contact clusters you obtained. Examine whether the strong clusters identified are coincident with the folding nucleation sites identified experimentally by the mutational Φ-value analysis.

  2. i j i k j l Non-local Contact Clusters(J. Mol. Biol.357, 1647-1654 (2004)) • The number of non-local contact exhibits a strikingly high correlation with the logarithmic rate constant of folding in non-two-state proteins. (a) Relationships of the logarithmic rate constants, log(kI) and log(kN), for the formation of the intermediate (○) and native state (■), respectively, with the number of non-local contact clusters, Nc. • Non-local contacting residue pairs: • A contact cluster should contain at least three contacting residue pairs, and the following two pairs are involved in the same contact cluster.

  3. Contact Strength and Strong Clusters • We introduced a parameter "contact strength" to investigate a role of strongly contacting residues pairs in determining the folding initiation sites of the two proteins. The contact strength is defined as the number of atom-atom contacts between two contacting residues. • We define a strongly contacting residue pair as a contacting residue pair that has a contact strength number larger than or equal to 4. • The non-local contact clusters that have at least four strongly contacting residues pairs; we call these non-local contact clusters the strong clusters.

  4. Barnase: 1A2p.pdb (110, 879), J. Mol. Biol. (1992) 224, 819-835. Fibronectin type III domain: 1FNA.pdb (96, 825), J. Mol. Biol. (2001) 305, 1185-1194. FKBP12: 1FKK.pdb (107, 830), J. Mol. Biol. (1999) 291, 445-461. Azurin: 1AZU.pdb (128, 930), Biochemistry (2005) 44, 10054-10062. Chymotrypsin inhibitor 2: 3CI2.pdb (83, 1061), Biochemistry (1993) 32, 11270-11278. Ribosomal protein L9: 1DIV.pdb (149, 1435), Biochemistry (2007) 46, 1013-1021.

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