We studied the structure and thermodynamics of several polypeptides using Hamiltonian and temperature replica exchange molecular dynamics (HT-REMD) and standard temperature replica exchange molecular dynamics(T-REMD). We used a coarse grained protein force field, OPEP (Optimized Potential for Efficient structure Prediction, an implicit solvent with simplified side chains representation by a single bead). For details about the OPEP force field and its parameters see: J. Maupetit, P. Tuffery, and P. Derreumaux, Proteins: Struct., Funct.,Bioinf. 2007, 69, 394–408.
We first showed that T-REMD coupled with OPEP is able to recover the proper thermodynamics and structure of six polypeptides ranging in length from 10 to 28 residues: two alanine-based peptides, the second b-hairpin from protein G, the Trp-cage and zinc-finger motif, and a dimer of a coiled coil peptide. This method was tested on the aggregation of Aβ1−40, Aβ1−42, Aβ1−40(D23N), amylin and α-synuclein proteins Refs. [15,16, 19 and 20] which leading to good agreement with
experiments.
Replica Exchange Molecular Dynamics Simulations of Coarse-grained Proteins in Implicit Solvent.
Yassmine Chebaro, Xiao Dong, Rozita Laghaei, Philippe Derreumaux and Normand Mousseau J. Phys. Chem. B, 2008; 113, 267.
The Effect of Disulfide Bond on the Monomeric Structure of Human Amylin Studied by Combined Hamiltonian and Temperature Replica Exchange Molecular Dynamics Simulations. Rozita Laghaei, Normand Mousseau and Guanghong Wei, J. Phys. Chem. B, 2010; 114 , 7071.
Structure
and thermodynamics of amylin dimer studied by
Hamiltonian-temperature replica exchange molecular dynamics
simulations, Rozita Laghaei, Normand Mousseau and Guanghong Wei, J. Phys. Chem. B 115, 3146–3154 (2011).
Distinct dimerization for various alloforms
of the Amyloid-beta protein: Aβ1-40, Aβ1-42 and
Aβ1-40(D23N), Sébastien Côté, Rozita Laghaei, Philippe Derreumaux and
Normand Mousseau, J. Phys. Chem. B 116, 4043-4055 (2012).
Early Oligomerization Stages for the Non-Amyloid Component of Alpha-Synuclein Amyloid.
Cindie Eugène, Rozita Laghaei and Normand Mousseau J. Chem. Phys. 2014; 141,135103
