Abstract
BackgroundMany β-strands are not flat but bend and/or twist. However, although almost all β-strands have a twist, not all have a bend, suggesting that the underlying force(s) driving β-strand bending is distinct from that for the twist. We, therefore, investigated the physical origin(s) of β-strand bends.MethodsWe calculated rotation, twist and bend angles for a four-residue short frame. Fixed-length fragments consisting of six residues found in three consecutive short frames were used to evaluate the twist and bend angles of full-length β-strands.ResultsWe calculated and statistically analyzed the twist and bend angles of β-strands found in globular proteins with known three-dimensional structures. The results show that full-length β-strand bend angles are related to the nearby aromatic residue content, whereas local bend angles are related to the nearby aliphatic residue content. Furthermore, it appears that β-strands bend to maximize their hydrophobic contacts with an abutting hydrophobic surface or to form a hydrophobic side-chain cluster when an abutting hydrophobic surface is absent.ConclusionsWe conclude that the dominant driving force for full-length β-strand bends is the hydrophobic interaction involving aromatic residues, whereas that for local β-strand bends is the hydrophobic interaction involving aliphatic residues.Electronic supplementary materialThe online version of this article (doi:10.1186/s12900-015-0048-y) contains supplementary material, which is available to authorized users.
Highlights
Many β-strands are not flat but bend and/or twist
The small GTPase Ras homolog enriched in brain (Rheb)—which belongs to the P-loop– containing nucleoside triphosphate hydrolase fold as defined in the Structural Classification of Proteins database (SCOP [4])—has a large twisted β-sheet surrounded by four α-helices (Fig. 1)
The main cluster (41,977 frames) is closer to the center of the circle with bend angles of
Summary
Many β-strands are not flat but bend and/or twist. Many β-strands have a right-hand twist and a bend, which have been suggested to induce a twist in the corresponding β-sheet [1,2,3]. In the early 1980s, simple energy minimization calculations were used to attribute the preference for a righthanded twist to intra-strand and inter-strand nonbonded side-chain interactions [5,6,7]. These studies suggested that, for Ala and Val β-sheets, the major driving force that favors a right-handed twist could be attributed to intrastrand interactions. Wang et al used molecular dynamics simulations to confirm the tendency of isolated β-strands to assume a twisted conformation, they reported a very small difference in free energy between twisted and nontwisted conformations of a single strand; this suggested
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