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Structures, Basins and Energies: A Deconstruction of the Protein Coil Library

¹ Johns Hopkins University;
² Univ. Cal., S.F.;
³ Johns Hopkin University

(RECEIVED February 22, 2008; ACCEPTED April 15, 2008)

Globular proteins adopt complex folds, comprised of organized assemblies of 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 -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 , 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 paper. 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 ,-distributions of these motifs; no additional energy terms are required. These three motifs in conjunction with -helices, strands of β sheet, canonical β-turns, and polyproline II conformers comprise ~90% of all protein structure.

Keywords: Protein Structure/Folding; Correlation of structure with spectra and other properties; Computational Analysis of Protein Structure; Forces and stability; Hydrogen bonds; inverse gamma-turns; random coil; unfolded state

⁴ E-mail: grose{at}jhu.edu

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