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Intrinsic α helix propensities compact hydrodynamic radii in intrinsically disordered proteins
Author(s) -
English Lance R.,
Tilton Erin C.,
Ricard Benjamin J.,
Whitten Steven T.
Publication year - 2017
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.25222
Subject(s) - intrinsically disordered proteins , polyproline helix , chemistry , dihedral angle , helix (gastropod) , chemical physics , radius of gyration , crystallography , protein structure , sequence (biology) , physics , molecule , peptide , biology , biochemistry , ecology , hydrogen bond , organic chemistry , snail , polymer
ABSTRACT Proteins that lack tertiary stability under normal conditions, known as intrinsically disordered, exhibit a wide range of biological activities. Molecular descriptions for the biology of intrinsically disordered proteins (IDPs) consequently rely on disordered structural models, which in turn require experiments that assess the origins to structural features observed. For example, while hydrodynamic size is mostly insensitive to sequence composition in chemically denatured proteins, IDPs show strong sequence‐specific effects in the hydrodynamic radius ( R h ) when measured under normal conditions. To investigate sequence‐modulation of IDP R h , disordered ensembles generated by a hard sphere collision model modified with a structure‐based parameterization of the solution energetics were used to parse the contributions of net charge, main chain dihedral angle bias, and excluded volume on hydrodynamic size. Ensembles for polypeptides 10–35 residues in length were then used to establish power–law scaling relationships for comparison to experimental R h from 26 IDPs. Results showed the expected outcomes of increased hydrodynamic size from increases in excluded volume and net charge, and compaction from chain–solvent interactions. Chain bias representing intrinsic preferences for α helix and polyproline II (PP II ), however, modulated R h with intricate dependence on the simulated propensities. PP II propensities at levels expected in IDPs correlated with heightened R h sensitivity to even weak α helix propensities, indicating bias for common ( φ , ψ ) are important determinants of hydrodynamic size. Moreover, data show that IDP R h can be predicted from sequence with good accuracy from a small set of physicochemical properties, namely intrinsic conformational propensities and net charge. Proteins 2017; 85:296–311. © 2016 Wiley Periodicals, Inc.