PDBsum entry 2hkd

De novo protein

PDB id: 2hkd

Contents

Protein chain

315 a.a.

Ligands

PG4

Waters ×426

References listed in PDB file

Key reference

Title

Atomic structures of peptide self-Assembly mimics.

Authors

K.Makabe, D.Mcelheny, V.Tereshko, A.Hilyard, G.Gawlak, S.Yan, A.Koide, S.Koide.

Ref.

Proc Natl Acad Sci U S A, 2006, 103, 17753-17758. [DOI no: 10.1073/pnas.0606690103]

PubMed id

17093048

Abstract

Although the beta-rich self-assemblies are a major structural class for polypeptides and the focus of intense research, little is known about their atomic structures and dynamics due to their insoluble and noncrystalline nature. We developed a protein engineering strategy that captures a self-assembly segment in a water-soluble molecule. A predefined number of self-assembling peptide units are linked, and the beta-sheet ends are capped to prevent aggregation, which yields a mono-dispersed soluble protein. We tested this strategy by using Borrelia outer surface protein (OspA) whose single-layer beta-sheet located between two globular domains consists of two beta-hairpin units and thus can be considered as a prototype of self-assembly. We constructed self-assembly mimics of different sizes and determined their atomic structures using x-ray crystallography and NMR spectroscopy. Highly regular beta-sheet geometries were maintained in these structures, and peptide units had a nearly identical conformation, supporting the concept that a peptide in the regular beta-geometry is primed for self-assembly. However, we found small but significant differences in the relative orientation between adjacent peptide units in terms of beta-sheet twist and bend, suggesting their inherent flexibility. Modeling shows how this conformational diversity, when propagated over a large number of peptide units, can lead to a substantial degree of nanoscale polymorphism of self-assemblies.

Figure 2.
Fig. 2. Structures of -repeat segments in PSAMs. (A) The backbone structure of the -repeat segment in the crystal structure of OspA+3bh-sm1. The hydrogen bonds between backbone atoms are shown as dashed lines. (B) Side chain conformations of the -repeat segment of OspA+3bh. Only the residues on the front face of the -sheet are shown. The -sheet backbone is shown as arrows. For clarity, the turn regions are omitted. The three cross-strand amino acid ladders are labeled with their respective amino acid compositions ("F/L," "E/K," and "T/I"). These ladders extend short and/or imperfect ones present in wild-type OspA ("FLFV," "EKEK," and "TVTI," respectively) (14). (C) Superposition of a total of 26 copies of the -hairpin unit from the PSAM crystal structures. The backbone of the original -hairpin unit from wild-type OspA is shown in green. Amino acid resides in the -strand regions are labeled with an uppercase letter and residue number. Strand residues labeled in black have their side chain pointing toward the reader, and those labeled in gray have their side chain pointing away from the reader. Residues in the turn regions are labeled with a lowercase letter.

Figure 4.
Fig. 4. Demonstration of the propagation of small conformational differences of -hairpin pairs (i.e., four-stranded building blocks) leading to substantial -ribbon polymorphism. Larger peptide self-assemblies were modeled using six representative -hairpin pairs. Different building blocks are shown in different colors (cyan, 5bh molecule C, -hairpin units 4 and 3; blue, 5bh molecule A, units 3 and2; yellow, 5bh molecule A, units 5 and 4; green, 5bh molecule C, units 3 and 2; red, 2bh units 2 and 1), and only the backbone traces of the -strand regions are shown for clarity. These -hairpin pairs were superimposed using the first two -strands (labeled with "1" and "2," respectively). Different relative orientations of the third and fourth -strands, with respect to the first and second, are evident. -Ribbon superstructures shown at Right were constructed in a step-wise manner. Starting from a four-stranded building block, a copy of the building block was generated. The third and fourth -strands of the original block and the first and second -strands of the copy (which have the identical sequence and nearly identical conformation; Fig. 2C) were then superimposed. In this way, the third and fourth -strands of the copy are now placed as the fifth and sixth -strands of the original building block, and the relative orientation between adjacent two-stranded units (i.e., -strands 1–2 and 3–4, and -strands 3–4 and -strand 5–6) is kept identical. These steps were iterated until a superstructure of sufficient length was generated.