title: Residual dipolar couplings measured in unfolded proteins are sensitive to amino-acid-specific geometries as well as local conformational sampling.
abstract: Many functional proteins do not have well defined folded structures. In recent years, both experimental and computational approaches have been developed to study the conformational behaviour of this type of protein. It has been shown previously that experimental RDCs (residual dipolar couplings) can be used to study the backbone sampling of disordered proteins in some detail. In these studies, the backbone structure was modelled using a common geometry for all amino acids. In the present paper, we demonstrate that experimental RDCs are also sensitive to the specific geometry of each amino acid as defined by energy-minimized internal co-ordinates. We have modified the FM (flexible-Meccano) algorithm that constructs conformational ensembles on the basis of a statistical coil model, to account for these differences. The modified algorithm inherits the advantages of the FM algorithm to efficiently sample the potential energy landscape for coil conformations. The specific geometries incorporated in the new algorithm result in a better reproduction of experimental RDCs and are generally applicable for further studies to characterize the conformational properties of intrinsically disordered proteins. In addition, the internal-co-ordinate-based algorithm is an order of magnitude more efficient, and facilitates side-chain construction, surface osmolyte simulation, spin-label distribution sampling and proline cis/trans isomer simulation.
authors.affiliation: Institut de Biologie Structurale Jean-Pierre Ebel, CEA-CNRS-UJF UMR 5075, 41 Rue Jules Horowitz, Grenoble 38027, France.
authors.forename: Jie-rong
authors.initials: JR
authors.lastname: Huang
authors.forename: Martin
authors.initials: M
authors.lastname: Gentner
authors.forename: Navratna
authors.initials: N
authors.lastname: Vajpai
authors.forename: Stephan
authors.initials: S
authors.lastname: Grzesiek
authors.forename: Martin
authors.initials: M
authors.lastname: Blackledge
mesh_terms: D000465:Algorithms; D000596:Amino Acids / Q000737:chemistry* / Q000378:metabolism*; D019295:Computational Biology; D019906:Nuclear Magnetic Resonance, Biomolecular; D011487:Protein Conformation; D058767:Protein Unfolding; D011506:Proteins / Q000737:chemistry* / Q000302:isolation & purification / Q000378:metabolism
chemical_list: D000596:Amino Acids; D011506:Proteins