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Published online before print June 28, 2007, 10.1110/ps.072867007
Protein Science (2007), 16:1667-1675. Published by Cold Spring Harbor Laboratory Press. Copyright © 2007 The Protein Society
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The role of protein homochirality in shaping the energy landscape of folding

Vikas Nanda, Aina Andrianarijaona, and Chitra Narayanan

Center for Advanced Biotechnology and Medicine, Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, New Jersey 08854, USA

(RECEIVED March 11, 2007; FINAL REVISION May 9, 2007; ACCEPTED May 10, 2007)

The homochirality, or isotacticity, of the natural amino acids facilitates the formation of regular secondary structures such as {alpha}-helices and beta-sheets. However, many examples exist in nature where novel polypeptide topologies use both L- and D-amino acids. In this study, we explore how stereochemistry of the polypeptide backbone influences basic properties such as compactness and the size of fold space by simulating both lattice and all-atom polypeptide chains. We formulate a rectangular lattice chain model in both two and three dimensions, where monomers are chiral, having the effect of restricting local conformation. Syndiotactic chains with alternating chirality of adjacent monomers have a very large ensemble of accessible conformations characterized predominantly by extended structures. Isotactic chains on the other hand, have far fewer possible conformations and a significant fraction of these are compact. Syndiotactic chains are often unable to access maximally compact states available to their isotactic counterparts of the same length. Similar features are observed in all-atom models of isotactic versus syndiotactic polyalanine. Our results suggest that protein isotacticity has evolved to increase the enthalpy of chain collapse by facilitating compact helical states and to reduce the entropic cost of folding by restricting the size of the unfolded ensemble of competing states.

Keywords: lattice chain model; tacticity; folding funnel; protein design


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