Folding of a Small Helical Protein Using Hydrogen Bonds and Hydrophobicity Forces

Simple item page
dc.creatorFavrin, Giorgio
dc.creatorIrbäck, Anders
dc.creatorWallin, Stefan
dc.date2001-11-15
dc.date.accessioned2026-07-07T02:43:31Z
dc.date.available2026-07-07T02:43:31Z
dc.descriptionA reduced protein model with five to six atoms per amino acid and five amino acid types is developed and tested on a three-helix-bundle protein, a 46-amino acid fragment from staphylococcal protein A. The model does not rely on the widely used Go approximation where non-native interactions are ignored. We find that the collapse transition is considerably more abrupt for the protein A sequence than for random sequences with the same composition. The chain collapse is found to be at least as fast as helix formation. Energy minimization restricted to the thermodynamically favored topology gives a structure that has a root-mean-square deviation of 1.8 A from the native structure. The sequence-dependent part of our potential is pairwise additive. Our calculations suggest that fine-tuning this potential by parameter optimization is of limited use.
dc.description18 pages, 8 figures
dc.identifierhttps://arxiv.org/abs/cond-mat/0111291
dc.identifierhttp://arxiv.org/abs/cond-mat/0111291
dc.identifierProteins Struct. Funct. Genet. 47 (2002) 99-105
dc.identifier.urihttp://salesiana.dossiersoluciones.com/handle/123456789/18532
dc.subjectSoft Condensed Matter
dc.subjectBiological Physics
dc.subjectChemical Physics
dc.subjectBiomolecules
dc.titleFolding of a Small Helical Protein Using Hydrogen Bonds and Hydrophobicity Forces
dc.typetext

Files

Collections

arXiv