Molecular Dynamics Simulations and NMR : A Perfect Match ?
Vendredi 10 novembre 2017 11:00
- Duree : 1 heure
Lieu : Salle des séminaires de l’IBS - 71, avenue des Martyrs - Grenoble
Orateur : Kresten LINDORFF-LARSEN (Department of Biology, University of Copenhagen, Denmark)
Proteins are dynamic molecules and their ability to adopt alternative conformations is often central to their biological function. Examples include motions that underlie allosteric regulation or ligand binding, or protein dynamics in enzymes that can modulate the overall catalytic efficiency. In my talk I will discuss how simulations and experiments can be used synergistically to study protein dynamics.
Recent years have seen substantial progress in the ability of simulations to capture protein dynamics on a wide range of timescales. This progress is due both to improvements in sampling methods as well as in the accuracy of the force fields used. In particular, I will discuss how the ability to benchmark and optimize force fields against experimental NMR data on peptide and protein systems has resulted
in substantial improvements of the physical models used in simulations.
Functional protein motions are often described as an exchange between a dominant, ground state structure and one or more minor states. The structural and biophysical properties of these transiently
and sparsely populated states are, however, difficult to study, and an atomic-level description of those states is challenging. In an attempt to determine how well molecular dynamics simulations can capture
slow, conformational changes in protein molecules we have studied several different protein systems, which are known to undergo conformational exchange on the millisecond timescale. By comparison
with structural and dynamical information from X-ray crystallography and NMR spectroscopy, I will discuss how current force fields and sampling methods allow us to sample experimentally-determined alternative conformations with surprisingly high accuracy.
Despite the progress in simulation methods, one may still find that simulations do not always match quantitatively experimental measurements. In such cases, experiments and simulations may be combined
in a very direct fashion to provide a description of protein motions that combines the details of atomic simulations with the accuracy afforded by experimental measurements. The resulting conformational
ensembles may provide novel insight into biomolecular systems that are not obtainable by simulations of experiments alone. Here I will discuss recent examples from my laboratory on such integration
of experiments and simulations.
Contact : ibs.seminaires@ibs.fr
Discipline évènement : (Biologie / Chimie)
Entité organisatrice : (IBS)
Nature évènement : (Séminaire)
Evènement répétitif : (Séminaire IBS)
Site de l'évènement : Polygone scientifique
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