title: Block-restraining of residual dipolar couplings to allow fluctuating relative alignments of molecular subdomains.
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.
authors.affiliation: Centre for Theoretical Chemistry and Physics, Massey University Auckland, Private Bag 102904, 0632 Auckland, New Zealand; Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Oslo, P.O.Box 1033, Blindern, 0315 Oslo, Norway.
authors.forename: Lukas N
authors.initials: LN
authors.lastname: Wirz
authors.affiliation: Centre for Theoretical Chemistry and Physics, Massey University Auckland, Private Bag 102904, 0632 Auckland, New Zealand; Institute for Natural and Mathematical Sciences, Massey University Auckland, Private Bag 102904, 0632 Auckland, New Zealand; Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Private Bag 92019, Auckland, New Zealand. Electronic address: j.allison@massey.ac.nz.
authors.forename: Jane R
authors.initials: JR
authors.lastname: Allison
mesh_terms: D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry*; D000072417:Protein Domains; D016415:Sequence Alignment
chemical_list: D010455:Peptides
keywords: Alignment; Molecular dynamics; Nuclear magnetic resonance; Peptides; Proteins; Residual dipolar couplings