Soiree on Force measurement and modelling in biological systems

Dr. Sergi Garcia Maynes (Physics KCL )
Conformational dynamics of single proteins under force

Understanding the molecular mechanisms that confer mechanical stability to well-defined biological systems is a major challenge in modern physics, chemistry and biology. Single molecule techniques are now providing a new vista on the molecular mechanisms by which proteins equilibrate under the effect of a constant stretching force. In this vein, force clamp spectroscopy allows us to monitor for the first time, with exquisite sub-Ǻngström sensitivity, the conformational dynamics of a single refolding protein during its individual folding trajectory from highly extended states. Contrary to previous belief, our experiments demonstrate that the acquisition of the protein’s native conformation occurs after dynamic maturation of an ensemble of collapsed states that are mechanically labile and structurally heterogeneous. These results support the validity of statistical mechanics models in describing the folding of a small protein on biological timescales. Remarkably, the existence of such newly discovered ensemble of collapsed states that hold the key to explaining how an extended polypeptide folds while regaining its mechanical stability is likely to have profound implications on the onset of conformational diseases, occurring at the level of a single molecule. Furthermore, mechanical force provides an alternative means to heat or electricity to activate chemical reactions. However, the full reconstruction of the potential energy surface governing a chemical reaction under force remains still largely incomplete. Using a combination of protein engineering techniques with single molecule force-clamp spectroscopy we examined the influence of force on the rate at which a protein disulfide bond is reduced by nucleophiles in a bimolecular substitution reaction (S_N2). Our experiments directly identify a reactivity switch occurring at ~500 pN, resulting from a force-induced conformational change in the ground state of the disulfide bond. The single protein data is providing a new view that will help guide the development of theories on the statistical dynamics of folding and ab-initio studies of a chemical reaction while placed under a stretching force; of common occurrence in nature.

Prof Grubmueller (Max-Planck-Institute for Biophysical Chemistry)
Mechanoenzymatics: Atomistic simulation of biolomolecular nano-machines

Proteins are biological nanomachines. Virtually every function in the cell
is carried out by proteins -- ranging from protein synthesis, ATP synthesis, molecular binding and recognition, selective transport, sensor functions, mechanical stability, and many more.

The combined interdisciplinary efforts of the past years have revealed how many of these functions are effected on the molecular level. Computer simulations of the atomistic dynamics play a pivotal role in this enterprise, as they offer both unparalleled temporal and spatial resolution. Force probe simulations, in particular, serve to access slow events which otherwise would not be accessible through atomistic simulations, and enable direct comparison to single molecule experiments.

In this talk we will address by force probe simulations the mechanisms underlying the molecular force sensor titin kinase, mechanical energy transfer in F-ATP synthase, and the mechanical properties of viral capsids.