Universität zu Köln

Wolff, Katrin ORCID: 0000-0002-5467-740X, Vendruscolo, Michele ORCID: 0000-0002-3616-1610 and Porto, Markus (2011). Coarse-grained model for protein folding based on structural profiles. Phys. Rev. E, 84 (4). COLLEGE PK: AMER PHYSICAL SOC. ISSN 1550-2376

Full text not available from this repository.

Abstract

We study a coarse-grained protein model whose primary characteristics are (i) a tubelike geometry to describe the self-avoidance effects of the polypeptide chain and (ii) an energy function based on a one-dimensional structural representation. The latter specifies the connectivity of a sequence in a given conformation, so that the energy function, rather than favoring the formation of specific native pairwise contacts, promotes the establishment of a specific target connectivity for each amino acid. We show that the resulting dynamics is in good agreement with both experimental observations and the results of all-atoms simulations. In contrast to the latter, our coarse-grained approach provides the possibility to explore longer time scales and thus enables one to access, albeit in less detail, larger regions of the conformational space. We illustrate our approach by its application to the villin headpiece domain, a three-helix protein, by studying its folding behavior and determining heat capacities and free-energy landscapes in various reaction coordinates.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Wolff, Katrin UNSPECIFIED orcid.org/0000-0002-5467-740X UNSPECIFIED Vendruscolo, Michele UNSPECIFIED orcid.org/0000-0002-3616-1610 UNSPECIFIED Porto, Markus UNSPECIFIED UNSPECIFIED UNSPECIFIED
URN:	urn:nbn:de:hbz:38-486969
DOI:	10.1103/PhysRevE.84.041934
Journal or Publication Title:	Phys. Rev. E
Volume:	84
Number:	4
Date:	2011
Publisher:	AMER PHYSICAL SOC
Place of Publication:	COLLEGE PK
ISSN:	1550-2376
Language:	English
Faculty:	Unspecified
Divisions:	Unspecified
Subjects:	no entry
Uncontrolled Keywords:	Keywords Language FREE-ENERGY LANDSCAPE; DYNAMICS; PATHWAYS; SIMULATION; PREDICTION; ALIGNMENT; ENSEMBLE; FUNNELS; STATE Multiple languages Physics, Fluids & Plasmas; Physics, Mathematical Multiple languages
URI:	http://kups.ub.uni-koeln.de/id/eprint/48696