Protein Folding in Contact Map Space
نویسندگان
چکیده
منابع مشابه
Protein Folding in Contact Map Space
We represent a protein's structure by its contact map. Our aim is to identify the unknown fold of a known sequence by minimizing a (free) energy deened in the space of contact maps. To this end we developed an eecient method to search this space and to generate low energy maps that are also physical. We proved that the standard pairwise approximation to the free energy is unable to stabilize th...
متن کاملProtein folding using contact maps.
We discuss the problem of representations of protein structure and give the definition of contact maps. We present a method to obtain a three-dimensional polypeptide conformation from a contact map. We also explain how to deal with the case of nonphysical contact maps. We describe a stochastic method to perform dynamics in contact map space. We explain how the motion is restricted to physical r...
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The effects of cooperativity are studied within Go-Lennard-Jones models of proteins by making the contact interactions dependent on the proximity to the native conformation. The kinetic universality classes are found to remain the same as in the absence of cooperativity. For a fixed native geometry, small changes in the effective contact map may affect the folding times in a chance way, and, to...
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MOTIVATION Starting from linear chains of amino acids, the spontaneous folding of proteins into their elaborate 3D structures is one of the remarkable examples of biological self-organization. We investigated native state structures of 30 single-domain, two-state proteins, from complex networks perspective, to understand the role of topological parameters in proteins' folding kinetics, at two l...
متن کاملProtein folding rates estimated from contact predictions.
Folding rates of small single-domain proteins that fold through simple two-state kinetics can be estimated from details of the three-dimensional protein structure. Previously, predictions of secondary structure had been exploited to predict folding rates from sequence. Here, we estimate two-state folding rates from predictions of internal residue-residue contacts in proteins of unknown structur...
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ژورنال
عنوان ژورنال: Physical Review Letters
سال: 1999
ISSN: 0031-9007,1079-7114
DOI: 10.1103/physrevlett.82.656