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Exploring the sequence determinants of amyloid structure using position-specific scoring matrices

journal contribution
posted on 2023-06-08, 04:57 authored by Sebastian Maurer-Stroh, Maja Debulpaep, Nico Kuemmerer, Manuela Lopez de la Paz, Ivo Cristiano Martins, Joke Reumers, Kyle L Morris, Alastair Copland, Louise SerpellLouise Serpell, Luis Serrano, Joost W H Schymkowitz, Frederic Rousseau
Protein aggregation results in beta-sheet-like assemblies that adopt either a variety of amorphous morphologies or ordered amyloid-like structures. These differences in structure also reflect biological differences; amyloid and amorphous beta-sheet aggregates have different chaperone affinities, accumulate in different cellular locations and are degraded by different mechanisms. Further, amyloid function depends entirely on a high intrinsic degree of order. Here we experimentally explored the sequence space of amyloid hexapeptides and used the derived data to build Waltz, a web-based tool that uses a position-specific scoring matrix to determine amyloid-forming sequences. Waltz allows users to identify and better distinguish between amyloid sequences and amorphous beta-sheet aggregates and allowed us to identify amyloid-forming regions in functional amyloids.

History

Publication status

  • Published

Journal

Nature Methods

ISSN

1548-7091

Publisher

Nature Publishing Group

Issue

3

Volume

7

Page range

237-U109

Department affiliated with

  • Biochemistry Publications

Full text available

  • No

Peer reviewed?

  • Yes

Legacy Posted Date

2012-02-06

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