Analysis of fragments induced by simulated lattice protein folding

dc.contributor.author	Chomilier, J	en
dc.contributor.author	Lamarine, M	en
dc.contributor.author	Mornon, J-P	en
dc.contributor.author	Hernandez Torres, J	en
dc.contributor.author	Eliopoulos, E	en
dc.contributor.author	Papandreou, N	en
dc.date.accessioned	2014-06-06T06:45:54Z
dc.date.available	2014-06-06T06:45:54Z
dc.date.issued	2004	en
dc.identifier.issn	16310691	en
dc.identifier.uri	http://dx.doi.org/10.1016/j.crvi.2004.02.002	en
dc.identifier.uri	http://62.217.125.90/xmlui/handle/123456789/2699
dc.subject.other	Monte Carlo analysis	en
dc.subject.other	protein	en
dc.subject.other	algorithm	en
dc.subject.other	alpha helix	en
dc.subject.other	amino acid sequence	en
dc.subject.other	amino terminal sequence	en
dc.subject.other	article	en
dc.subject.other	carboxy terminal sequence	en
dc.subject.other	computer program	en
dc.subject.other	controlled study	en
dc.subject.other	correlation analysis	en
dc.subject.other	crystal structure	en
dc.subject.other	geometry	en
dc.subject.other	hydrophobicity	en
dc.subject.other	mathematical computing	en
dc.subject.other	molecular interaction	en
dc.subject.other	Monte Carlo method	en
dc.subject.other	probability	en
dc.subject.other	protein folding	en
dc.subject.other	protein secondary structure	en
dc.subject.other	quantitative analysis	en
dc.subject.other	statistical analysis	en
dc.subject.other	structure analysis	en
dc.subject.other	validation process	en
dc.subject.other	Computer Simulation	en
dc.subject.other	Models, Molecular	en
dc.subject.other	Peptide Fragments	en
dc.subject.other	Protein Conformation	en
dc.subject.other	Protein Folding	en
dc.subject.other	Proteins	en
dc.subject.other	Thermodynamics	en
dc.title	Analysis of fragments induced by simulated lattice protein folding	en
heal.type	journalArticle	en
heal.identifier.primary	10.1016/j.crvi.2004.02.002	en
heal.publicationDate	2004	en
heal.abstract	The folding process of a set of 42 proteins, representative of the various folds, has been simulated by means of a Monte Carlo method on a discrete lattice, using two different potentials of mean force. Multiple compact fragments of contiguous residues are formed in the simulation, stable in composition, but not in geometry. During time, the number of fragments decreases until one final compact globular state is reached. We focused on the early steps of the folding in order to evidence the maximum number of fragments, provided they are sufficiently stable in sequence. A correlation has been established between these proto fragments and regular secondary-structure elements, whatever their nature, alpha helices or beta strands. Quantitatively, this is revealed by an overall mean one-residue quality factor of nearly 60%, which is better for proteins mainly composed of alpha helices. The correspondence between the number of fragments and the number of secondary-structure elements is of 77% and the regions separating successive fragments are mainly located in loops. Besides, hydrophobic clusters deduced from HCA correspond to fragments with an equivalent accuracy. These results suggest that folding pathways do not contain structurally static intermediate. However, since the beginning of folding, most residues that will later form one given secondary structure are kept close in space by being involved in the same fragment. This aggregation may be a way to accelerate the formation of the native state and enforces the key role played by hydrophobic residues in the formation of the fragments, thus in the folding process itself. © 2004 Académie des sciences. Published by Elsevier SAS. All rights reserved.	en
heal.journalName	Comptes Rendus - Biologies	en
dc.identifier.issue	5	en
dc.identifier.volume	327	en
dc.identifier.doi	10.1016/j.crvi.2004.02.002	en
dc.identifier.spage	431	en
dc.identifier.epage	443	en