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Compactness determines protein folding type


Compactness determines protein folding type



Journal of Bioinformatics and Computational Biology 6(4): 667-680



ISSN/ISBN: 0219-7200

PMID: 18763735

DOI: 10.1142/s0219720008003618

We have demonstrated here that protein compactness, which we define as the ratio of the accessible surface area of a protein to that of the ideal sphere of the same volume, is one of the factors determining the mechanism of protein folding. Proteins with multi-state kinetics, on average, are more compact (compactness is 1.49+/-0.02 for proteins within the size range of 101-151 amino acid residues) than proteins with two-state kinetics (compactness is 1.59+/-0.03 for proteins within the same size range of 101-151 amino acid residues). We have shown that compactness for homologous proteins can explain both the difference in folding rates and the difference in folding mechanisms.

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