Relationships between unfolded configurations of proteins and dynamics of folding to the native state

Authors

  • Attila Gursoy,

    1. College of Engineering and Center for Computational Biology and Bioinformatics, Koç University, İstanbul 34450, Turkey
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  • Ozlem Keskin,

    1. College of Engineering and Center for Computational Biology and Bioinformatics, Koç University, İstanbul 34450, Turkey
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  • Metin Turkay,

    1. College of Engineering and Center for Computational Biology and Bioinformatics, Koç University, İstanbul 34450, Turkey
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  • Burak Erman

    Corresponding author
    1. College of Engineering and Center for Computational Biology and Bioinformatics, Koç University, İstanbul 34450, Turkey
    • College of Engineering and Center for Computational Biology and Bioinformatics, Koç University, İstanbul 34450, Turkey
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Abstract

We compare folding trajectories of chymotrypsin inhibitor (CI2) using a dynamic Monte Carlo scheme with Go-type potentials. The model considers the four backbone atoms of each residue and a sphere centered around Cβ the diameter of which is chosen according to the type of the side group. Bond lengths and bond angles are kept fixed. Folding trajectories are obtained by giving random increments to the φ and ψ torsion angles with some bias toward the native state. Excluded volume effects are considered. Two sets of 20 trajectories are obtained, with different initial configurations. The first set is generated from random initial configurations. The initial configurations of the second set are generated according to knowledge-based neighbor dependent torsion probabilities derived from triplets in the Protein Data Bank. Compared to chains with randomly generated initial configurations, those generated with neighbor-dependent probabilities (i) fold faster, (ii) have better defined secondary structure elements, and (iii) have less number of non-native contacts during folding. © 2006 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 3667–3678, 2006

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