PDBsum entry 2oy7

Membrane protein

PDB id

2oy7

Contents

			Protein chain

					315 a.a.

			Waters ×396

References listed in PDB file

Key reference

Title

Aromatic cross-Strand ladders control the structure and stability of beta-Rich peptide self-Assembly mimics.

Authors

M.Biancalana, K.Makabe, A.Koide, S.Koide.

Ref.

J Mol Biol, 2008, 383, 205-213. [DOI no: 10.1016/j.jmb.2008.08.031]

PubMed id

18762191

Abstract

Though beta-rich self-assemblies comprise a major structural class of polypeptides, a detailed understanding of the determinants of their structure and stability is lacking. In particular, the roles of repetitive stretches of side chains running the long axis of these beta-sheets, termed "cross-strand ladders," remain poorly characterized due to the inherently insoluble and heterogeneous nature of self-assemblies. To overcome these experimental challenges, we have established a complementary experimental system termed "peptide self-assembly mimics" (PSAMs). The PSAMs capture a defined number of self-assembly-like peptide repeats within a soluble beta-rich protein, making structural and energetic studies possible. In this work, we investigated the role of cross-strand ladders containing aromatic residues, which are prominent in self-assembling peptides. A combination of solution data and high-resolution crystal structures revealed that a single cross-strand ladder consisting solely of Tyr significantly stabilized, rigidified, and flattened the PSAM beta-sheet. These characteristics would stabilize each beta-sheet layer of a self-assembly and direct sheet conformations compatible with lamination. Our results therefore provide a rationale for the abundance of aromatic amino acids in fibril-forming peptides and establish important roles of cross-strand Tyr ladders in the structure and stability of beta-rich peptide self-assemblies.



	Figure 1. Fig. 1. Cross-stand ladders in self-assembled β-sheets and the PSAM system. (a) Schematic drawings showing how the sequence and register of a self-assembling peptide determine ladder composition. A simplified β-sheet is shown as a connection of α-carbons, with side-chain spheres colored to indicate chemical identity. Only an antiparallel assembly is shown. (b) Scheme illustrating the PSAM concept and ladder mutations: a segment of peptide self-assembly is excised, linked, and capped. Mutations, shown as green spheres, can then be introduced into ladder positions within the PSAM scaffold. (c) Cartoon representations of the PSAM scaffolds used (left: large scaffold, i.e., OspA + 3bh; right: small scaffold, i.e., natural OspA). The SLB in each scaffold is colored blue with the α-carbons of mutated ladder positions shown as spheres. The side chains of these ladders are all located on the same face of the β-sheet.		Figure 4. Fig. 4. Perturbations of backbone conformation introduced by the Tyr ladders. (a) Each PSAM mutant was aligned using the most C-terminal β-hairpin of the SLB, denoted as 0 (residues 187–209). Wild-type (EK)[4] is shown in gray and (YY)[4] in blue. (YK)[4] overlays almost perfectly with wild type, and its structure is not depicted. The N- and C-terminal domains along with the turn regions are omitted for clarity. The backbones of the β-strands are shown as sticks. (b) Values of the three parameters, Twist, Bend, and Bend′, describing the three-dimensional rotations of each β-hairpin in the SLB. Zero values define a perfectly flat, rectangular β-sheet. Wild-type (EK)[4] is shown in gray, (YY)[4] in blue, and (YK)[4] in red. (c) Overpacking of Tyr ladders revealed by hybrid analysis. Each strand from (YY)[4] was aligned separately with its homologous strand in wild-type (EK)[4] using all backbone atoms. The adjusted coordinates of the aromatic side chains were then grafted onto the wild-type (EK)[4] backbone to form the (YY)[4] hybrid. Severe steric conflicts (shown as red dots in the insets) were judged using Probe.^21 Y182 has two side-chain conformers, and the conflicts were observed for its gauche conformer but not for its trans conformer.

PROCHECK

	Headers