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Identification of amyloidogenic peptide sequences using a coarse-grained physicochemical model

✍ Scribed by Oliver J. Clarke; Martin J. Parker

Publisher
John Wiley and Sons
Year
2009
Tongue
English
Weight
605 KB
Volume
30
Category
Article
ISSN
0192-8651

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✦ Synopsis

Abstract

Cross‐β amyloid is implicated in over 20 human diseases. Experiments suggest that specific sequence elements within amyloidogenic proteins play a major role in seeding amyloid formation. Identifying these seeding sequences is important for rationalizing the molecular mechanisms of amyloid formation and for elaborating therapeutic strategies that target amyloid. Theoretical techniques play an important role in facilitating the identification and structural characterization of putative seeding sequences; most amyloid species are not amenable to high resolution experimental structure techniques. In this study we have combined a coarse‐grained physicochemical protein model with a highly efficient Monte Carlo sampling technique to identify amyloidogenic sequences in four proteins for which respective experimental peptide fragmentation data exist. Peptide sequences were defined as amyloidogenic if the ensemble structure predicted for three interacting peptides described a stable and regular three‐stranded β‐sheet. For such peptides, free energies were calculated to provide a measure of amyloid propensity. The overall agreement between the experimental and predicted data is good, and we correctly identify several self‐recognition motifs proposed to define the cross‐β amyloid fibril architectures of two of the proteins. Our results compare very favorably with those obtained using atomistic molecular dynamics methods, though our simulations are 30–40 times faster. © 2008 Wiley Periodicals, Inc. J Comput Chem 2009

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