What is an amyloid protein?

A normal protein that, under pathological circumstances, accumulates in a form of insoluble fibers exhibiting a cross-beta structure. Amyloid proteins or peptides are characteristic of diseases such as Alzheimer, Parkinson, Huntington, Creutzfeldt-Jakob or type 2 diabetes mellitus.

The bioinformatic approach

In the case of amyloid proteins, bioinformatic methods are particularly advisable because insoluble aggregates formed by those proteins are resistant to many biochemical and structural conditions. Moreover, putative amyloid proteins exist in numerous organisms, from yeasts to humans, including fishes or reptiles. An exhaustive knowledge of amyloid proteins is therefore nearly impossible using only biological techniques.

The Amyloid Protein DataBase

AMYPdb is an online database dedicated to amyloid precursor families and to their amino acid sequence signatures.
The last update of the structure and the interface of AMYPdb occurred on April 7th 2008. The protein files are from UniProtKB, release 6.1.

Member access and expert contribution

To create your personal AMYPdb online account, please follow the sign up link in the left-side menu. Members have access to additional tools and they can manage their own working sets of protein sequences and patterns.
We encourage experts to participate to the AMYPdb project. Members can obtain an expert account by sending an email to christian.delamarche@univ-rennes1.fr, or by using links available in the database. A wiki system allows contributors to add accurate biological data to protein and families description. As an example, contributor can annotated proteins with the AMYPdb amyloid classification, associated with a quality rank (yellow stars):

Amyloid in vivo (the precursor protein, or a specific sub-segment, forms fibrils in human, or animals, or is a yeast prion)
Amyloid in vitro (the polypeptide forms fibrils under experimental conditions)
Amyloid in silico (the polypeptide forms fibrils using computational techniques)
Putative amyloid protein (the protein is a member of an amyloid family, but the amyloid properties of that specific member were not assessed)
Unclassified protein (the protein family does not fulfill the definition of amyloid, but sparse data show that at least one member of the family shares some amyloid properties)

Citation

The present work is described in : Pawlicki S., Le Béchec A. and Delamarche C. (in press) AMYPdb: a database dedicated to amyloid precursor proteins. BMC Bioinformatics