Speaker
Dr
Marco Pasi
(BMSSI, Lyon)
Description
We present a new coarse-grain protein model PaLaCe
(Pasi-Lavery-Ceres) that has been developed to allow rapid
studies of protein mechanics and to build up a deeper
understanding of the links between mechanics and function.
PaLaCe uses an intermediate level protein representation
with two or three pseudoatoms per amino acid. Adding
explicit peptide groups and backbone hydrogen bonding allows
changes in secondary structure to be treated. The PaLaCe
force field is composed of physics-based bonded and
non-bonded interactions, combined with an implicit solvent
term. The force field was parameterized using Boltzmann
inversion of the probability distributions derived from a
large database of well-resolved protein structures, and then
optimized by fitting simulated and experimental
distributions using an iterative refinement technique.
PaLaCe has been implemented in the MMTK simulation package
and can be used for energy minimization, normal mode
calculations and molecular or stochastic dynamics. We
illustrate its performance by simulating the forced
unfolding of a titin immunoglobin domain.
