Institut de Biologie StructuraleGrenoble / France

Contact person(s) related to this article / FIELD Martin

Presentation

Responsable: Martin Field

Presentation

The Dynamo team has the goal of developing and applying theoretical tools for studying the structure and function of biological macromolecules and their complexes. Most of our work is done on proteins.

Three themes cover the majority of research done in the team:

  • The study of processes in proteins that require the use of both quantum chemical and classical mechanical simulation tools. Work in this area focuses upon the development and the application of hybrid quantum chemical/molecular mechanical (QC/MM) methods for the simulation of enzymatic reaction mechanisms.
  • Molecular modeling of various aspects of the structure, function and dynamics of proteins.
  • Multiscale modeling of cellular processes, notably those involving reaction-diffusion.

Most developmental work is done within the team’s modeling and simulation program, pDynamo (http://www.pdynamo.org).

Staff

Permanent Staff:

Martin Field (CEA)

Post-doctoral Scientists:

Nicholus Bhattacharjee
Mikolaj Feliks

Research Topics:

  • Modeling the structure and the function of proteins.
  • Development of simulation algorithms.
  • Simulating enzymatic reaction mechanisms.
  • Protein dynamics.
  • Reaction-diffusion processes.

Keywords:

Molecular modeling, molecular simulation, enzymatic reaction mechanisms, protein dynamics.

Specialized Techniques:

Molecular modeling, molecular dynamics, quantum chemistry, statistical mechanics, high-performance computing.

Major Publications:

  • Marcos E, Field MJ, Crehuet R. Pentacoordinated phosphorus revisited by high-level QM/MM calculations. Proteins : Structure, Function, and Bioinformatics (2010) 78 : 2405-2411.
  • Canaguier S, Field M, Oudart Y, Pecaut J, Fontecave M and Artero V. A structural and functional mimic of the active site of NiFe hydrogenases. Chemical Communications (2010) 46 : 5876-5878.
  • Hagiwara Y, Field MJ, Nureki O and Tateno M. Editing mechanism of aminoacyl-tRNA synthetases operates by a hybrid ribozyme/protein catalyst. Journal of the American Chemical Society (2010) 132 : 2751-2758.
  • Vaccaro L, Artero V, Canaguier S, Fontecave M and Field MJ. Mechanism of hydrogen evolution catalyzed by NiFe hydrogenases : insights from a Ni-Ru model compound. Dalton Transactions (2010) 39 : 3043-3049.
  • Lelimousin M, Adam V, Nienhaus GU, Bourgeois D and Field MJ. Photoconversion of the fluorescent protein EosFP : A hybrid potential simulation study reveals intersystem crossings. Journal of the American Chemical Society (2009) 131 : 16814-16823.