Issue 6, 2011

Rotamer libraries of spin labelled cysteines for protein studies

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.

Graphical abstract: Rotamer libraries of spin labelled cysteines for protein studies

Supplementary files

Article information

Article type
Paper
Submitted
19 Sep 2010
Accepted
08 Nov 2010
First published
30 Nov 2010

Phys. Chem. Chem. Phys., 2011,13, 2356-2366

Rotamer libraries of spin labelled cysteines for protein studies

Y. Polyhach, E. Bordignon and G. Jeschke, Phys. Chem. Chem. Phys., 2011, 13, 2356 DOI: 10.1039/C0CP01865A

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