title: A structural model for unfolded proteins from residual dipolar couplings and small-angle x-ray scattering.
abstract: Natively unfolded proteins play key roles in normal and pathological biochemical processes. Despite their importance for function, this category of proteins remains beyond the reach of classical structural biology because of their inherent conformational heterogeneity. We present a description of the intrinsic conformational sampling of unfolded proteins based on residue-specific /Psi propensities from loop regions of a folded protein database and simple volume exclusion. This approach is used to propose a structural model of the 57-aa, natively disordered region of the nucleocapsid-binding domain of Sendai virus phosphoprotein. Structural ensembles obeying these simple rules of conformational sampling are used to simulate averaged residual dipolar couplings (RDCs) and small-angle x-ray scattering data. This protein is particularly informative because RDC data from the equally sized folded and unfolded domains both report on the unstructured region, allowing a quantitative analysis of the degree of order present in this part of the protein. Close agreement between experimental and simulated RDC and small-angle x-ray scattering data validates this simple model of conformational sampling, providing a precise description of local structure and dynamics and average dimensions of the ensemble of sampled structures. RDC data from two urea-unfolded systems are also closely reproduced. The demonstration that conformational behavior of unfolded proteins can be accurately predicted from the primary sequence by using a simple set of rules has important consequences for our understanding of the structure and dynamics of the unstructured state.
authors.affiliation: Institut de Biologie Structurale Jean-Pierre Ebel, Commissariat à l'Energie Atomique-Centre National de la Recherche Scientifique-Universite Joseph Fourier, 41 Rue Jules Horowitz, 38027 Grenoble, France.
authors.forename: Pau
authors.initials: P
authors.lastname: Bernadó
authors.forename: Laurence
authors.initials: L
authors.lastname: Blanchard
authors.forename: Peter
authors.initials: P
authors.lastname: Timmins
authors.forename: Dominique
authors.initials: D
authors.lastname: Marion
authors.forename: Rob W H
authors.initials: RW
authors.lastname: Ruigrok
authors.forename: Martin
authors.initials: M
authors.lastname: Blackledge
mesh_terms: D008958:Models, Molecular; D010750:Phosphoproteins / Q000737:chemistry*; D011489:Protein Denaturation; D017434:Protein Structure, Tertiary; D012542:Scattering, Radiation; D029082:Sendai virus / Q000737:chemistry*; D020539:Sequence Analysis, Protein; D014508:Urea; D014764:Viral Proteins / Q000737:chemistry*; D014961:X-Ray Diffraction; D014965:X-Rays
chemical_list: D010750:Phosphoproteins; D014764:Viral Proteins; D014508:Urea