Accuracy of Molecular Simulation-Based Predictions of k(off) Values: A Metadynamics Study

The k(off) values of ligands unbinding to proteins are key parameters for drug discovery. Their predictions based on molecular simulation may under- or overestimate experiment in a system- and/or technique-dependent way. Here we use an established method-infrequent metadynamics, based on the AMBER force field-to compute the k(off )of the ligand iperoxo (in clinical use) targeting the muscarinic receptor M-2. The ligand charges are calculated by either (i) the Amber standard procedure or (ii) B3LYP-DFT. The calculations using (i) turn out not to provide a reasonable estimation of the transition-state free energy. Those using (ii) differ from experiment by 2 orders of magnitude. On the basis of B3LYP DFT QM/MM simulations, we suggest that the observed discrepancy in (ii) arises, at least in part, from the lack of electronic polarization and/or charge transfer in biomolecular force fields. These issues might be present in other systems, such as DNA-protein complexes.

Polymer-theory insights into biomolecular systems

Salvatore Assenza

Boosted by the technological advances in experimental techniques, cellular biology is nowadays facing the need for quantitative approaches in order to rationalize the huge amount of collected data. A particularly succesfull theoretical framework is provided by Polymer Theory which, combined with molecular simulations, can capture the essential features of biomacromolecules and describe the cellular processes they participate to. This thesis provides a compendium of works showing the strength of this combination. In a first project, we model the twisting properties of amyloid fibrils by means of a simple coarse-grained approach, based on the competition between elasticity and electrostatic repulsion of nearby portions of the fibrils. The model quantitatively recapitulates the evolution of fibril periodicity as a function of the ionic strength of the solution and of the fibril width. A universal mesoscopic structural signature of the fibrils emerges from this picture, predicting a general, parameter-free law for the periodicity of the fibrils which is validated on several experimental results. A second work is focused on the role played by mitochondrial Hsp70 chaperone in the import of cytoplasmic proteins. Particularly, we computed by means of molecular simulations the effective free-energy profile for substrate translocation upon chaperone binding. We then used the resulting free energy to quantitatively characterize the kinetics of the import process and outline the essential role played by Hsp70 in this context. Finally, in a third project we studied the shape properties of a polymer under tension, a physical condition typically realized both in single-molecule experiments and in vivo. By means of analytical calculations and Monte Carlo simulations, we develop a theoretical framework which quantitatively describes these properties, highlighting the interplay between external force and chain size in determining the spatial distribution of a stretched chain.

EPFL2015

Polymer-theory insights into biomolecular systems

Salvatore Assenza

EPFL2015