A minimal physically realistic protein-like lattice model: designing an energy landscape that ensures all-or-none folding to a unique native state

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CSSB_BJ_2003_001.pdf (215.02 KB)
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Pokarowski, Piotr
Kolinski, Andrzej
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School of Biological Sciences
School established in 2016 with the merger of the Schools of Applied Physiology and Biology
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http://hdl.handle.net/1853/41959
Abstract
A simple protein model restricted to the face-centered cubic lattice has been studied. The model interaction scheme includes attractive interactions between hydrophobic (H) residues, repulsive interactions between hydrophobic and polar (P) residues, and orientation-dependent P-P interactions. Additionally, there is a potential that favors extended b-type conformations. A sequence has been designed that adopts a native structure, consisting of an antiparallel, six-member Greekkey b-barrel with protein-like structural degeneracy. It has been shown that the proposed model is a minimal one, i.e., all the above listed types of interactions are necessary for cooperative (all-or-none) type folding to the native state. Simulations were performed via the Replica Exchange Monte Carlo method and the numerical data analyzed via a multihistogram method.
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2003-03
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