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Large Scale Simulation of Membrane Proteins

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Computational and experimental biologists investigate jointly the physical mechanisms underlying the function of the molecular machines in cells. Simulations used to encompass biomolecular systems of 10,000 atoms, but recently the size increased tenfold. For example, simulations of aquaporins, a water channel, published during 2001-2003 (1, 2, 3) involved about 100,000 atoms and had been cited in connection with last year's chemistry Nobel prize; simulations of cadherin, a cell adhesion protein, and of ATPase, a key metabolic protein complex, published 2004 included a similar number of atoms. Simulations of over 200,000 atoms for a protein, lac repressor, that regulates genes, and for a protein, MscS, that is a mechanically gated membrane channel will be published later this year. Simulations involving over 300,000 atoms, on a protein, ankyrin, acting as an elastic spring in hearing, have been completed. The increase in the size of simulated systems is prompted by a revolutionary advance in crystallography that resolves ever larger structures of biomolecules and simulations are made possible through the great increase of computer resources at the NSF centers (PSC, NCSA). This marks the beginning of a new era in which systems like virus capsids and the ribosome, entailing 1-3 million atoms, will be studied, too. NAMD (see Highlight Dec 2002) is ready for the challenge posed by simulations needing 250-500 processors today and 1000-10000 processors in the future, to keep up with the developments in the biology laboratories (more).