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Molecular dynamics study of amyloid formation of two Abl‐SH3 domain peptides
Author(s) -
Liepina Inta,
Ventura Salvador,
Czaplewski Cezary,
Liwo Adam
Publication year - 2006
Publication title -
journal of peptide science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.475
H-Index - 66
eISSN - 1099-1387
pISSN - 1075-2617
DOI - 10.1002/psc.813
Subject(s) - sh3 domain , molecular dynamics , beta sheet , peptide , biophysics , chemistry , biology , biochemistry , receptor , proto oncogene tyrosine protein kinase src , computational chemistry
Abstract Molecular dynamics (MD) simulations were carried out for two‐strand and ten‐strand β‐sheets constructed from two peptides corresponding to the diverging turn of two homologous Abl‐SH3 domains, DLSFMKGE (MK; from Drosophila) and DLSFKKGE (KK; from man), in explicit water at the temperatures of 30, 170/190 and 300 K. It was found that the 2 × MK β‐sheet is more stable than the 2 × KK β‐sheet, and that the 10 × MK β‐sheet is more stable than the 10 × KK β‐sheet; this suggests that the MK systems are fibril‐creating and the KK systems are not. These results might explain why most SH3 domains possess two conserved basic residues at the diverging turn, which may act as gatekeepers in order to avoid aggregation. Copyright © 2006 European Peptide Society and John Wiley & Sons, Ltd.