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Published online on January 10, 2007, 10.1073/pnas.0605534104
PNAS | January 16, 2007 | vol. 104 | no. 3 | 796-801


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PHYSICAL SCIENCES / BIOLOGICAL SCIENCES / COMPUTER SCIENCES / BIOPHYSICS
A consensus view of protein dynamics

Manuel Rueda*,{dagger}, Carles Ferrer-Costa*,{dagger}, Tim Meyer*,{dagger},{ddagger}, Alberto Pérez*,{dagger}, Jordi Camps{dagger},§, Adam Hospital*,{dagger},§, Josep Lluis Gelpí*,{dagger},{ddagger}, and Modesto Orozco*,{dagger},{ddagger},§,¶

*Molecular Modelling and Bioinformatics Unit and §Structural Biology Node, Institut de Recerca Biomèdica, Parc Científic de Barcelona, Josep Samitier 1-5, 08028 Barcelona, Spain; {dagger}Computational Biology Program, Barcelona Supercomputing Center, Jordi Girona 31, Edifici Nexus II, 08028 Barcelona, Spain; and {ddagger}Departament de Bioquímica i Biologia Molecular, Facultat de Biologia, Universitat de Barcelona, Avgda Diagonal 645, 08028 Barcelona, Spain

Edited by Harold A. Scheraga, Cornell University, Ithaca, NY, and approved November 10, 2006 (received for review July 6, 2006)

The dynamics of proteins in aqueous solution has been investigated through a massive approach based on "state of the art" molecular dynamics simulations performed for all protein metafolds using the four most popular force fields (OPLS, CHARMM, AMBER, and GROMOS). A detailed analysis of the massive database of trajectories (>1.5 terabytes of data obtained using {approx}50 years of CPU) allowed us to obtain a robust-consensus picture of protein dynamics in aqueous solution.

force field | molecular dynamics | molecular modeling | protein structure

Author contributions: M.R., C.F.-C., and T.M. contributed equally to this work; M.R., C.F.-C., A.H., J.L.G., and M.O. designed research; M.R., C.F.-C., T.M., A.P., and J.C. performed research; M.R., C.F.-C., T.M., and A.P. analyzed data; and M.O. wrote the paper.

The authors declare no conflict of interest.

This article is a PNAS direct submission.

This article contains supporting information online at www.pnas.org/cgi/content/full/0605534104/DC1.

To whom correspondence should be addressed. E-mail: modesto{at}mmb.pcb.ub.es

© 2007 by The National Academy of Sciences of the USA


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