Research Article
Protein flexibility from discrete molecular dynamics simulations using quasi-physical potentials† ‡
Agustí Emperador,
Tim Meyer,
Modesto Orozco,
Agustí Emperador
Joint IRB-BSC Program on Computational Biology, Institute of Research in Biomedicine, Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain
Barcelona Supercomputing Centre, Jordi Girona 31, Edifici Torre Girona, Barcelona 08034, Spain
Search for more papers by this authorTim Meyer
Joint IRB-BSC Program on Computational Biology, Institute of Research in Biomedicine, Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain
Barcelona Supercomputing Centre, Jordi Girona 31, Edifici Torre Girona, Barcelona 08034, Spain
Search for more papers by this authorCorresponding Author
Modesto Orozco
Joint IRB-BSC Program on Computational Biology, Institute of Research in Biomedicine, Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain
Barcelona Supercomputing Centre, Jordi Girona 31, Edifici Torre Girona, Barcelona 08034, Spain
National Institute of Bioinformatics, Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain
Departament de Bioquímica, Facultat de Biología, Universitat de Barcelona, Av. Diagonal 647, Barcelona 08028, Spain
Institute of Research in Biomedicine, Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain===Search for more papers by this authorAgustí Emperador,
Tim Meyer,
Modesto Orozco,
Agustí Emperador
Joint IRB-BSC Program on Computational Biology, Institute of Research in Biomedicine, Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain
Barcelona Supercomputing Centre, Jordi Girona 31, Edifici Torre Girona, Barcelona 08034, Spain
Search for more papers by this authorTim Meyer
Joint IRB-BSC Program on Computational Biology, Institute of Research in Biomedicine, Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain
Barcelona Supercomputing Centre, Jordi Girona 31, Edifici Torre Girona, Barcelona 08034, Spain
Search for more papers by this authorCorresponding Author
Modesto Orozco
Joint IRB-BSC Program on Computational Biology, Institute of Research in Biomedicine, Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain
Barcelona Supercomputing Centre, Jordi Girona 31, Edifici Torre Girona, Barcelona 08034, Spain
National Institute of Bioinformatics, Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain
Departament de Bioquímica, Facultat de Biología, Universitat de Barcelona, Av. Diagonal 647, Barcelona 08028, Spain
Institute of Research in Biomedicine, Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain===Search for more papers by this author†
This article is dedicated in memory of Angel Ramirez Ortiz.
‡
The authors state no conflict of interest.
Abstract
We have applied all atoms discrete molecular dynamics (DMD) based on a quasi-physical potential to study the flexibility of an extended set of proteins for which atomistic MD simulations are available. The method uses pure physical potentials supplemented by information on secondary structure and despite its simplicity is able to reproduce with good accuracy the dynamics of proteins in solution. The method presents a clear improvement with respect to coarse-grained methods based on structure potentials and opens the possibility to explore dynamics of proteins out from the equilibrium and to trace conformational changes induced by interaction of proteins with both small and macromolecular ligands. Proteins 2010. © 2009 Wiley-Liss, Inc.
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