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Published online before print April 23, 2008, 10.1110/ps.035055.108
Protein Science (2008), 17:1151-1161. Published by Cold Spring Harbor Laboratory Press. Copyright © 2008 The Protein Society
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Structures, basins, and energies: A deconstruction of the Protein Coil Library

Lauren L. Perskie, Timothy O. Street1, and George D. Rose

T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, USA

(RECEIVED February 22, 2008; FINAL REVISION April 9, 2008; ACCEPTED April 15, 2008)

Globular proteins adopt complex folds, composed of organized assemblies of {alpha}-helix and β-sheet together with irregular regions that interconnect these scaffold elements. Here, we seek to parse the irregular regions into their structural constituents and to rationalize their formative energetics. Toward this end, we dissected the Protein Coil Library, a structural database of protein segments that are neither {alpha}-helix nor β-strand, extracted from high-resolution protein structures. The backbone dihedral angles of residues from coil library segments are distributed indiscriminately across the {varphi},{psi} map, but when contoured, seven distinct basins emerge clearly. The structures and energetics associated with the two least-studied basins are the primary focus of this article. Specifically, the structural motifs associated with these basins were characterized in detail and then assessed in simple simulations designed to capture their energetic determinants. It is found that conformational constraints imposed by excluded volume and hydrogen bonding are sufficient to reproduce the observed {phi},{psi} distributions of these motifs; no additional energy terms are required. These three motifs in conjunction with {alpha}-helices, strands of β-sheet, canonical β-turns, and polyproline II conformers comprise ~90% of all protein structure.

Keywords: protein folding; protein structure; protein conformation; random coil; unfolded state


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