Computer design of idealized β-motifs

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Title: Computer design of idealized β-motifs
Author: Kolinski, Andrzej ; Galazka, Wojciech ; Skolnick, Jeffrey
Abstract: A lattice model of protein conformation and dynamics is used to explore the requirements for the de novo folding from an arbitrary random coil state of idealized models of four and six-member β-barrels. A number of possible conjectures for the factors giving rise to the structural uniqueness of globular proteins are examined. These include the relative role of generic hydrophilic/ hydrophobic amino acid patterns, the relative importance of the specific identity of the hydrophobic amino acids that form the core of the protein and the possible role played by polar groups in destabilizing alternative, misfolded conformations. These studies may also provide some insights into the relative importance of short range interactions, cooperative hydrogen bonding and tertiary interactions in determining the uniqueness of the native state, as well as the cooperativity of the folding process. Thus, these simulations may provide guidelines for the early stages of the protein design process. Possible applications to the general protein folding problem are also briefly discussed.
Description: ©1995 American Institute of Physics The electronic version of this article is the complete one and can be found online at: DOI:10.1063/1.469930
Type: Article
ISSN: 0021-9606
Citation: Journal of Chemical Physics, 1995:103: 10286-10297
Date: 1995-12-15
Contributor: Uniwersytet Warszawski. Wydział Chemii
Scripps Research Institute. Dept. of Molecular Biology
Publisher: Georgia Institute of Technology
American Institute of Physics
Subject: Amino acids
Protein structure
Short-range interactions

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