Computational Modelling Group

Seminar  7th March 2011 2 p.m.  27:2003

Free energy surfaces of proteins: folding, dynamics and mechanics

Dr Emanuele Paci
Institute of Molecular Biophysics, University of Leeds

AMBER, Bioinformatics, Biomathematics, Biomedical, Biomolecular Organisation, C, Complex fluids, Complex Systems, Computer Science, GPU-libs, HECToR, HPC, HPCx, Linux, Molecular Dynamics, Molecular Mechanics, Monte Carlo, MPI, Multi-physics, Multi-scale, Multigrid solvers, Quantum Chemistry, Scientific Computing, Software Engineering, Vim
Chris-Kriton Skylaris

Dr Emanuele Paci

Proteins have fascinated and puzzled generations of chemists, biochemists and physicists. While the folding problem seems unsolvable to some, and ill formulated or already solved to others, our knowledge of proteins increases steadily, as well as our ability to make practical use of proteins, for example in nanotechnology and synthetic biology applications. The most effective way to understand statistical and kinetic properties of polypeptides, and their folding or their intrinsically disordered nature, is in terms of diffusion on a free energy surface. The latter is not directly accessible from experiment, but it is, in principle, from simulation. The mechanical properties of proteins, while increasingly recognised as biologically important, are an interesting example of the relation between free-energy surface and the response of a protein to an external perturbation. In this talk I will present recent and less recent work that show how theory and numerical modeling have answered questions raised by mechanical experiments on single proteins and anticipated a numbers of interesting findings.