Premium
Multiple β‐sheet molecular dynamics of amyloid formation from two ABl‐SH3 domain peptides
Author(s) -
Lapidus Dmitrijs,
Duka Vita,
Stonkus Vladislavs,
Czaplewski Cezary,
Liwo Adam,
Ventura Salvador,
Liepina Inta
Publication year - 2012
Publication title -
peptide science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.22161
Subject(s) - antiparallel (mathematics) , beta sheet , chemistry , molecular dynamics , stack (abstract data type) , sh3 domain , sequence (biology) , crystallography , peptide , stereochemistry , biophysics , receptor , biochemistry , computational chemistry , proto oncogene tyrosine protein kinase src , physics , quantum mechanics , magnetic field , computer science , biology , programming language
Molecular dynamics simulations in explicit water were carried out for two stacks, each composed of six 10‐strand antiparallel β‐sheets for two peptides corresponding to the diverging turn of two homologous Abl‐SH3 domains. The first system, referred to as 10×6×MK contained the DLSFMKGE sequence from the Drosophila, while the second one, referred to as 10×6×KK , contained the human DLSFKKGE sequence. It was found that the 10×6×MK β‐sheet stack is stable, but the 10×6×KK β‐sheet stack is not. The stability of the 10×6×MK β‐sheet stack results from the hydrophobic interactions of the methionine and phenylalanine residues and the leucine residues of the neighboring sheets. The Met , Phe , and Leu hydrophobic units make a hydrophobic core for the stack of β‐sheets. During the MD run, the Met , Phe , and Leu residues of the neighboring β‐sheets acted as a conformational switch moving the β‐sheets so that the Phe residue interacted with the Met residue from the neighboring β‐sheet. Replacement of Met by Lys destroys the hydrophobic core, which is the stability factor of the β‐sheet stack. For the 10×6×KK system, individual β‐sheets were preserved during simulations, but the interactions between the β‐sheets were lost. The calculations of a six β‐sheet stack confirm the conclusion drawn from our earlier studies of single β‐sheet systems that the β‐sheets must form stacks to be stabilized. These results suggest that the two conserved basic residues at the diverging turn of SH3 domains could act as gatekeepers to avoid aggregation. © 2012 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 98: 557–566, 2012.