"In the near future, a biochemist will be able to understand the behaviour of a protein, or design a drug that can interact with that protein, drawing on not only the knowledge of a single structure, but of an entire repertory spontaneously occurring in physiological conditions", stated project director Modesto Orozco.
The goal of this study is to define a map of the dynamic properties of a very representative group of proteins. This involves taking stock of the basic rules that govern the flexibility of proteins and allows scientists to predict the structures that these proteins can form based on the presence of ligands or modifications. This allows scientists to go beyond the traditional simple static vision of proteins, which has not been able to capture the subtle conformational changes necessary for proteins to function. These changes modify, for example, how proteins bind to metabolites or drugs.
This is the first study of a larger scientific project, called MoDel - Molecular Dynamics Extended Library, the scope of which is even more ambitious. "MoDel aims to establish a fourth dimension for protein structures thereby providing a complete landscape of possible conformations for the entire proteome - the complete network of protein interactions in a cell, over time. In the near future, a biochemist will be able to understand the behaviour of a protein, or design a drug that can interact with that protein, drawing on not only the knowledge of a single structure, but of an entire repertory spontaneously occurring in physiological conditions", stated project director Modesto Orozco, principal investigator of the Molecular Modelling and Bioinformatics group at IRB Barcelona, director of the Department of Life Sciences of the BSC, and Professor in the Department of Biochemistry at the University of Barcelona.
The project, financed by Genome España through the National Institute for Bioinformatics, the Ministry of Education and Science, and the Government of Catalonia, is the joint effort of a multi-disciplinary team of 15 scientists using the computing resources of the MareNostrum supercomputer, the most powerful computer in Europe, and ranked 5th in the world. During the past year, the study has involved half a million hours of computing time and 200 processors working in parallel - the equivalent of 57 years of computing time on a personal computer. "To attempt this project without the MareNostrum supercomputer would have simply been impossible", affirmed Professor Orozco. Indeed, powerful tools such as MareNostrum are allowing bioinformaticists to make unprecedented advances in the understanding of biological processes.
The source article is written by M. Rueda, C. Ferrer, T. Meyer, A. Pérez, J. Camps, A. Hospital, J.L. Gelpí and M.Orozco. It is titled "A consensus view of protein dynamics" and appears in the Proceedings of the National Academy of Sciences USA (2007) 104, 796-801.