Analysis of fragments induced by simulated lattice protein folding. Analyse des fragments obtenus par simulation du repliement protéique sur réseau.
type: Dataset
description: 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. Le repliement protéique a été simulé par une méthode de Monte Carlo appliquée à un réseau discret, et deux potentiels statistiques ont été employés. Un jeu de 42 protéines représentant les différents types de repliement a été utilisé. Au cours de la simulation, de multiples fragments compacts, composés de résidus contigus en séquence, se forment. Ils …
issued: 2026-05-09T10:52:19.611099
language: en
modified: 2026-05-09T10:52:19.611104
contact point: Organization
  fn: CCSD
keyword: hydrophobic-cluster-analysis
keyword: infoeu-reposemanticsarticle
keyword: journal-articles
keyword: lattice-simulation
keyword: monte-carlo
keyword: protein-folding
keyword: secondary-structure
landing page: 1631-0691

Analysis of fragments induced by simulated lattice protein folding. Analyse des fragments obtenus par simulation du repliement protéique sur réseau.
type: Distribution
format: HTML
issued: 2026-05-09T10:52:19.613593
modified: 2026-05-09T10:52:19.598870
access URL: https://hal.science/hal-00087092

test_moissonnage_selune
type: Agent