The DOI matches its Crossref record; 37 of the 37 references it cites were found in a registry or an index.
Rotamer libraries of spin labelled cysteines for protein studies
Open accessAbstract
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.
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Self-citationParallel Tempering: Theory, Applications, and New PerspectivesPreprint
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Metadata
- Authors
- Polyhach, Y., Bordignon, E., & Jeschke, G.
- Venue
- Phys. Chem. Chem. Phys.
- Publisher
- Royal Society of Chemistry (RSC)
- Published
- 2011
- Volume
- 13
- Issue
- 6
- Pages
- 2356-2366
- ISSN
- 1463-9076 (ISSN-L)
- 1463-9084
- OpenAlex
- W2040595716
- Cited by
- 425
- References
- 37
- FWCI
- 14.02
- Type
- journal article
- Language
- en
- Open access
- green
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