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Aggregation of small peptides studied by molecular dynamics simulations
Author(s) -
Flöck Dagmar,
Rossetti Giulia,
Daidone Isabella,
Amadei Andrea,
Nola Alfredo Di
Publication year - 2006
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.21168
Subject(s) - molecular dynamics , amyloid (mycology) , amyloid fibril , protein aggregation , fibril , chemistry , biophysics , intermolecular force , cluster (spacecraft) , computational biology , aggregate (composite) , biology , biochemistry , nanotechnology , amyloid β , disease , materials science , molecule , computer science , medicine , computational chemistry , inorganic chemistry , organic chemistry , pathology , programming language
Peptides and proteins tend to aggregate under appropriate conditions. The amyloid fibrils that are ubiquitously found among these structures are associated with major human diseases like Alzheimer's disease, type II diabetes, and various prion diseases. Lately, it has been observed that even very short peptides like tetra and pentapeptides can form ordered amyloid structures. Here, we present aggregation studies of three such small polypeptide systems, namely, the two amyloidogenic peptides DFNKF and FF, and a control (nonamyloidogenic) one, the AGAIL. The respective aggregation process is studied by all‐atom Molecular Dynamics simulations, which allow to shed light on the fine details of the association and aggregation process. Our analysis suggests that naturally aggregating systems exhibit significantly diverse overall cluster shape properties and specific intermolecular interactions. Additional analysis was also performed on the previously studied NFGAIL system. Proteins 2006. © 2006 Wiley‐Liss, Inc.