Block-restraining of residual dipolar couplings to allow fluctuating relative alignments of molecular subdomains.

Show simple item record Wirz, Lukas N Allison, Jane R
dc.coverage.spatial England 2022-05-18T04:05:40Z 2022-05-18T04:05:40Z 2017-09
dc.identifier.citation (2017). Progress in Biophysics and Molecular Biology, 128, 133-141.
dc.identifier.issn 0079-6107
dc.description.abstract Residual dipolar couplings (RDCs), unlike most other types of NMR observables, provide orientational information, reporting on the alignment of inter-spin vectors (ISVs) relative to the magnetic field. A great challenge in using experimental RDCs to restrain molecular dynamics (MD) simulations is how to represent this alignment. An alignment tensor is often used to parameterise the contribution of molecular alignment to the angular dependence of RDCs. All ISVs that share the same tensor have fixed relative alignment, i.e. if just one tensor is used, the molecule is internally rigid. Here we propose and illustrate a method for subdividing molecules into individually aligned blocks during MD simulations restrained to fit RDCs. This allows the relative orientation of each block to vary during the simulation, which in turn ensures that the internal structure of each block is more realistically reproduced.
dc.format.medium Print-Electronic
dc.language eng
dc.publisher Elsevier BV
dc.relation.ispartofseries Progress in biophysics and molecular biology
dc.rights Items in ResearchSpace are protected by copyright, with all rights reserved, unless otherwise indicated. Previously published items are made available in accordance with the copyright policy of the publisher.
dc.subject Peptides
dc.subject Sequence Alignment
dc.subject Molecular Dynamics Simulation
dc.subject Protein Domains
dc.subject Alignment
dc.subject Molecular dynamics
dc.subject Nuclear magnetic resonance
dc.subject Proteins
dc.subject Residual dipolar couplings
dc.subject Science & Technology
dc.subject Life Sciences & Biomedicine
dc.subject Biochemistry & Molecular Biology
dc.subject Biophysics
dc.subject HIV-1 PROTEASE
dc.subject FORCE-FIELD
dc.subject DYNAMICS
dc.subject NMR
dc.subject TIME
dc.subject 0306 Physical Chemistry (incl. Structural)
dc.subject 0601 Biochemistry and Cell Biology
dc.title Block-restraining of residual dipolar couplings to allow fluctuating relative alignments of molecular subdomains.
dc.type Journal Article
dc.identifier.doi 10.1016/j.pbiomolbio.2017.02.006
pubs.begin-page 133
pubs.volume 128 2022-04-27T23:15:30Z
dc.rights.holder Copyright: The author en
dc.identifier.pmid 28223155 (pubmed)
pubs.end-page 141
pubs.publication-status Published
dc.rights.accessrights en
pubs.subtype Research Support, Non-U.S. Gov't
pubs.subtype Journal Article
pubs.elements-id 739551 Science Biological Sciences
dc.identifier.eissn 1873-1732
dc.identifier.pii S0079-6107(16)30045-1
pubs.record-created-at-source-date 2022-04-28 2017-02-20

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