title: Hydrodynamic Radii of Intrinsically Disordered Proteins Determined from Experimental Polyproline II Propensities.
abstract: The properties of disordered proteins are thought to depend on intrinsic conformational propensities for polyproline II (PPII) structure. While intrinsic PPII propensities have been measured for the common biological amino acids in short peptides, the ability of these experimentally determined propensities to quantitatively reproduce structural behavior in intrinsically disordered proteins (IDPs) has not been established. Presented here are results from molecular simulations of disordered proteins showing that the hydrodynamic radius (Rh) can be predicted from experimental PPII propensities with good agreement, even when charge-based considerations are omitted. The simulations demonstrate that Rh and chain propensity for PPII structure are linked via a simple power-law scaling relationship, which was tested using the experimental Rh of 22 IDPs covering a wide range of peptide lengths, net charge, and sequence composition. Charge effects on Rh were found to be generally weak when compared to PPII effects on Rh. Results from this study indicate that the hydrodynamic dimensions of IDPs are evidence of considerable sequence-dependent backbone propensities for PPII structure that qualitatively, if not quantitatively, match conformational propensities measured in peptides.
authors.affiliation: Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas, United States of America.
authors.forename: Maria E
authors.initials: ME
authors.lastname: Tomasso
authors.affiliation: Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas, United States of America.
authors.forename: Micheal J
authors.initials: MJ
authors.lastname: Tarver
authors.affiliation: Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas, United States of America.
authors.forename: Deepa
authors.initials: D
authors.lastname: Devarajan
authors.affiliation: Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas, United States of America.
authors.forename: Steven T
authors.initials: ST
authors.lastname: Whitten
mesh_terms: D019295:Computational Biology; D003198:Computer Simulation; D057446:Hydrodynamics; D064267:Intrinsically Disordered Proteins / Q000737:chemistry*; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry*; D017433:Protein Structure, Secondary
chemical_list: D064267:Intrinsically Disordered Proteins; D010455:Peptides; C011083:polyproline