RSS

PDB:2e8d

Protein Name

Amyloid fibrils of K3 peptide

Species

Human (Homo sapiens)

Biological Context

Amyloid fibrils are highly ordered filamentous aggregates formed by the self-assembly of monomeric polypeptides. It has been currently reported that depositions and formation processes of amyloid fibrils are associated with about 40 diseases including Alzheimer's disease, dialysis-related amyloidosis, type II diabetes, Parkinson's disease, and prion disease.

In this context, it is significantly important to understand the structure of amyloid fibrils and their molecular mechanism of fibrilliogenesis for preventing diseases caused by amyloidogenesis, and to obtain in-depth insight into the mechanism of protein folding and misfolding.

In this study, the authors determined the fibrous structures of K3 peptides, one of the amyloidogenic fragments of beta2-microglobulin, a protein responsible for dialysis-related amyloidosis.

Structure Description

2e8d2e8d_x2e8d_y

Interestingly, the K3 fibril formation is accompanied by the structural reorganization. Nonpolar residues, Val27, Cys25, and Leu23, buried in the interior of the native Ig fold are exposed to the surface of the K3 fibrils. Conversely, aromatic Phe22 and Tyr26 and polar Gln24 and Ser28 are buried between the beta-strands in the fibrils.

K3 fibril conformations are stabilized by intermolecular interactions as follows. The Phe rings are aligned and separated by a distance of 4.5–4.7 angstrom, i.e., the interstrand spacing, a distance favorable for pi-pi interactions. In addition, Tyr26 buried between the beta-sheets also is stabilized by pi-pi interactions by making the phenol ring of Tyr26 run parallel to the plane of the beta-sheets. On the other hand, the amide groups of aligned Asn24 residues are likely to form an intermolecular hydrogen bond network with adjacent molecules, referred to as "Asn ladder". These intermolecular interactions between the side chain of Asn24 result from minimizing thermodynamically unfavorable interactions between the isolated polar amide groups in the hydrophobic interior of the fibrils.

Protein Data Bank (PDB)

References

Source

  • Iwata, K. Fujiwara, T. Matsuki, Y. Akutsu, H. Takahashi, S. Naiki, H. Goto, Y.; "3D structure of amyloid protofilaments of beta2-microglobulin fragment probed by solid-state NMR"; Proc.Natl.Acad.Sci.Usa; (2006) 103:18119-18124 PubMed:17108084.

Others

author: Young-Ho Lee


Japanese version:PDB:2e8d