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Issue 6, 2011
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Rotamer libraries of spin labelled cysteines for protein studies

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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

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The article was received on 19 Sep 2010, accepted on 08 Nov 2010 and first published on 30 Nov 2010

Article type: Paper
DOI: 10.1039/C0CP01865A
Phys. Chem. Chem. Phys., 2011,13, 2356-2366

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    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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