PDBsum entry 3eex

Membrane protein

PDB id: 3eex

Contents

Protein chains

316 a.a.

Ligands

P6G ×3

References listed in PDB file

Key reference

Title

Minimalist design of water-Soluble cross-{Beta} architecture.

Authors

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

Ref.

Proc Natl Acad Sci U S A, 2010, 107, 3469-3474. [DOI no: 10.1073/pnas.0912654107]

PubMed id

20133689

Abstract

Demonstrated successes of protein design and engineering suggest significant potential to produce diverse protein architectures and assemblies beyond those found in nature. Here, we describe a new class of synthetic protein architecture through the successful design and atomic structures of water-soluble cross-beta proteins. The cross-beta motif is formed from the lamination of successive beta-sheet layers, and it is abundantly observed in the core of insoluble amyloid fibrils associated with protein-misfolding diseases. Despite its prominence, cross-beta has been designed only in the context of insoluble aggregates of peptides or proteins. Cross-beta's recalcitrance to protein engineering and conspicuous absence among the known atomic structures of natural proteins thus makes it a challenging target for design in a water-soluble form. Through comparative analysis of the cross-beta structures of fibril-forming peptides, we identified rows of hydrophobic residues ("ladders") running across beta-strands of each beta-sheet layer as a minimal component of the cross-beta motif. Grafting a single ladder of hydrophobic residues designed from the Alzheimer's amyloid-beta peptide onto a large beta-sheet protein formed a dimeric protein with a cross-beta architecture that remained water-soluble, as revealed by solution analysis and x-ray crystal structures. These results demonstrate that the cross-beta motif is a stable architecture in water-soluble polypeptides and can be readily designed. Our results provide a new route for accessing the cross-beta structure and expanding the scope of protein design.

Figure 3.
The x-ray crystal structures of cross-β PSAMs. (A) The overall structure of the YY/LF PSAM dimer is shown in surface and cartoon representations, in two orthogonal views. Molecule A is in green and molecule B in blue. The N- and C-terminal domains are indicated. The two molecules are related by pseudo-two-fold symmetry (dashed line). (B) The arrangement of the laminated β-sheet segment of YY/LF PSAM. Residues 118–209 are shown in orthogonal orientations, with the same coloring scheme as in A. The Cα-Cα distances across the β-sheets and the positions of the YY and LF ladders are indicated. (C) Comparisons of the backbone conformations of the central β-sheet regions of the YY/KE (Orange), YY/LF (Blue), FL/LF (Magenta) PSAMs. (D) Comparisons of the cross-β PSAM dimers, showing alignments of molecule A (Left) and an orthogonal view of the entire dimer complex (Right). Proteins are shown as Cα traces, with YY/LF in blue and FL/LF in pink.

Figure 4.
The interface structures of synthetic cross-β. (A) The dimer interface of the YY/LF PSAM dimer. The dimer has been opened like a book along the axis indicated, with molecule A on the right and molecule B on the left. The red coloration indicates surfaces in the LF ladder that are buried in the interface (defined as atoms within 5 Å of the adjacent molecule). The yellow surfaces are for those atoms in the LF ladder that are not buried in the interface. All other contacts are colored orange. The insert shows how the hydrophobic ladder from subunit B (shown as stick models) overlays on the subunit A surface. (B) The dimer interface of the FL/LF PSAM dimer. The coloring scheme is the same as in A, but the red and yellow surfaces are for atoms in both hydrophobic ladders. (C) The packing of the cross-β segment of YY/LF. At left, the side chains of the YY and LF ladders are shown as spheres. For clarity, only two adjacent β-strands from molecules A and B are shown. At Center and Right are shown orthogonal representations of all side chains of the YY and LF ladders. The β-strands are shown as cartoons. The loop regions have been omitted for clarity. Side-chain carbons are colored green and blue for molecule A and molecule B, respectively. (D) The packing of the cross-β segment of FL/LF depicted in the same manner as in C.