Presentation of the LDM

The laboratory 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 laboratory:

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

Research Topics

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

Key Words

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

Techniques

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

Some Recent Publications

Amara P, Fdez Galvan I, Fontecilla-Camps JC and Field MJ. (2007) The enamine intermediate may not be universal to thiamine catalysis. Angewandte Chemie International Edition England 46(47): 9019-9022

Crehuet R and Field MJ. (2007) A transition path sampling study of the reaction catalyzed by the enzyme chorismate mutase. Journal of Physical Chemistry B 111(20): 5708-5718

Field MJ. (2007) A Practical Introduction to the Simulation of Molecular Systems, Second Edition, Cambridge University Press, Cambridge

Lepsik M and Field MJ. (2007) Binding of Calcium and Other Metal Ions to the EF-hand Loops of Calmodulin Studied by Quantum Chemical Calculations and Molecular Dynamics Simulations. Journal of Physical Chemistry B 111(33): 10012-10022

Thomas A and Field MJ. (2006) A comparative QM/MM simulation study of the reaction mechanisms of human and Plasmodium falciparum HG(X)PRTases. Journal of the American Chemical Society 128(31): 10096-10102

(A full list of publications may be consulted here).