A coarse-grained α-carbon protein model with anisotropic hydrogen-bonding

Authors

  • Eng-Hui Yap,

    1. UCSF/UCB Joint Graduate Group in Bioengineering, Berkeley, California 94720
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  • Nicolas Lux Fawzi,

    1. UCSF/UCB Joint Graduate Group in Bioengineering, Berkeley, California 94720
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  • Teresa Head-Gordon

    Corresponding author
    1. UCSF/UCB Joint Graduate Group in Bioengineering, Berkeley, California 94720
    2. Department of Bioengineering, University of California, Berkeley, California 94720
    • UCSF/UCB Joint Graduate Group in Bioengineering, Berkeley, CA 94720 and Department of Bioengineering, University of California, Berkeley, CA 94720
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Abstract

We develop a sequence based α-carbon model to incorporate a mean field estimate of the orientation dependence of the polypeptide chain that gives rise to specific hydrogen bond pairing to stabilize α-helices and β-sheets. We illustrate the success of the new protein model in capturing thermodynamic measures and folding mechanism of proteins L and G. Compared to our previous coarse-grained model, the new model shows greater folding cooperativity and improvements in designability of protein sequences, as well as predicting correct trends for kinetic rates and mechanism for proteins L and G. We believe the model is broadly applicable to other protein folding and protein–protein co-assembly processes, and does not require experimental input beyond the topology description of the native state. Even without tertiary topology information, it can also serve as a mid-resolution protein model for more exhaustive conformational search strategies that can bridge back down to atomic descriptions of the polypeptide chain. Proteins 2008. © 2007 Wiley-Liss, Inc.

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