Scientific article
English

Rotamer libraries of spin labelled cysteines for protein studies

Published inPCCP. Physical chemistry chemical physics, vol. 13, no. 6, p. 2356-2366
Publication date2011
First online date2011
Abstract

Studies of structure and dynamics of proteins using site-directed spin labelling rely on explicit modelling of spin label conformations. The large computational effort associated with such modelling with molecular dynamics (MD) simulations can be avoided by a rotamer library approach based on a coarse-grained representation of the conformational space of the spin label. We show here that libraries of about 200 rotamers, obtained by iterative projection of a long MD trajectory of the free spin label onto a set of canonical dihedral angles, provide a representation of the underlying trajectory adequate for EPR distance measurements. Rotamer analysis was performed on selected X-ray structures of spin labelled T4 lysozyme mutants to characterize the spin label rotamer ensemble on a single protein site. Furthermore, predictions based on the rotamer library approach are shown to be in nearly quantitative agreement with electron paramagnetic resonance (EPR) distance data on the Na+/H+ antiporter NhaA and on the light-harvesting complex LHCII whose structures are known from independent cryo electron microscopy and X-ray studies, respectively. Suggestions for the selection of labelling sites in proteins are given, limitations of the approach discussed, and requirements for further development are outlined.

Affiliation entities Not a UNIGE publication
Citation (ISO format)
POLYHACH, Yevhen, BORDIGNON, Enrica, JESCHKE, Gunnar. Rotamer libraries of spin labelled cysteines for protein studies. In: PCCP. Physical chemistry chemical physics, 2011, vol. 13, n° 6, p. 2356–2366. doi: 10.1039/C0CP01865A
Main files (1)
Article (Published version)
accessLevelRestricted
Identifiers
Additional URL for this publicationhttp://xlink.rsc.org/?DOI=C0CP01865A
Journal ISSN1463-9076
62views
0downloads

Technical informations

Creation28/11/2023 13:40:15
First validation29/11/2023 13:42:29
Update time29/11/2023 13:42:29
Status update29/11/2023 13:42:29
Last indexation01/11/2024 06:54:01
All rights reserved by Archive ouverte UNIGE and the University of GenevaunigeBlack