Addressing functionally relevant large-scale motions in proteins by molecular-dynamics simulation: The ArtJ case

ITQB- Seminar

Title: " Addressing functionally relevant large-scale motions in proteins by molecular-dynamics simulation: The ArtJ case"

Speaker: Xavier Daura

Affiliation: ICREA Research Professor at Universitat Autònoma de Barcelona

Host: António M. Baptista (Molecular Simulation Lab)

Abstract:

Extended access to High Performance Computing (be it large commodity clusters or supercomputers) has been, together with algorithm (and code) optimisation and parallelisation, a major component to the recent advancement of biomolecular simulation, even more so than the new developments at the methodological and force field levels have. Despite the spectacular increase in time scales and system sizes, the capacity to answer questions of biological relevance remains, however, very limited. Model assumptions aside, reaching the system complexity and time scale relevant to the process of interest were thought to be the main, if not only, bottleneck. Now that this has been reached for some remarkable biomolecular systems (although still very simple when put on biological perspective), it has become evident that, due to the statistical nature of these processes, a very large number of independent events need to be sampled before arriving to consistent results. Here, we present an example study of protein dynamics that illustrates the importance of statistics: an analysis of the conformational dynamics of a bacterial protein of the Periplasmic-Binding family (PBPs) and its relation to ligand binding.

Acknowledgement:
This project is supported by funding under the Sixth Research Framework Programme of the European Union (ref. LSHB-CT-2006-037325) and by the Spanish Ministry for Education and Science/FEDER (ref. BIO2007-62954). We thank the Barcelona Supercomputing Center (BSC) for computing resources made available through grant BCV-2009-1-0024, and the Port d’Informació Científica (PIC) for providing cluster-computing and data-storage resources.

Short CV:

Xavier Daura is Ph.D. in Biological Sciences by the Autonomous University of Barcelona (UAB). In 1996 he moved to the Laboratory of Physical Chemistry, Swiss Federal Insitute of Technology Zurich (ETHZ), where he performed research on computational modelling and simulation of biomolecular systems under the direction of Prof. Wilfred van Gusnteren.  In 2002 he was appointed Research Professor by the Catalan Institution for Research and Advanced Studies (ICREA) and took this position to the Institute of Biotechnology and Biomedicine (IBB) of UAB, where he leads the group of Biomolecular Simulation and Pathogen Proteomics (gSiP). Since 2005 he is also Associate Professor at UAB and Vice-Director of IBB.