About Us
LATEST NEWS: iGEM Paris team wins first price for Foundational Research at iGEM 2007 Jamboree (November 3-4, MIT, Cambridge MA).
The Laboratoire de Biochimie (BIOC) is a mixed research unit belonging to
the École Polytechnique and the Centre National de la Recherche
Scientifique (CNRS) in Palaiseau (France). The École Polytechniqueis an excellence center among the
top in Europe. In fact, in a recent review by The Times (http://www.thes.co.uk/downloads/rankings/world-rankings-16pages.pdf), it was
chosen as the most prestigious academic institution in France, and ranked
6th among all European universities.
The Lab's main research interests are:
molecular enzymology and biocatalysis, protein structure and design,
biological crystallography and structural bioinformatics.
Those topics are treated both experimentally and theoretically.
The Laboratory has conducted extensive research on aminoacyl-ARNt synthetases
and aminoacid recognition.
After a restructuration in 2003, a Bioinformatics group has been created with
two faculty positions (Thomas SIMONSON, Professeur Associe and Alfonso JARAMILLO, Maitre de Conferences), and is still
further developing: the size of the group has doubled in the last
year. The group is composed of 3 permanent members (2 faculty members and a
bioinformatics engineer), 2 postdoc researchers, 4 Ph.D. students and a
sabbatical visitor, many of them working on projects in
close collaboration with experimental groups.
The Bioinformatics group uses computational protein design techniques to explore
aspects of natural evolution that are difficult to address
experimentally. Conversely, the mechanisms of natural evolution are exploited
to design new proteins with a desired function as thermostability, improved
activity to new substrates and tuned specificity.
In particular, the team has worked on approaches to study of the influence of
protein-protein and protein-ligand interactions on protein evolution. Parallel
researches are done using different description levels as proteins on-lattice
and off-lattice, and from amino acid level potentials to the atomic description
of proteins using molecular mechanics force fields. In all cases the
software and algorithms are developed inside the group.
The group has expertise in molecular dynamics simulations and free energy
calculations, which have been applied to binding calculations of aaRS (see
publications by Prof. SIMONSON).
Another research area is computational protein design methodology (see
publications by Prof. JARAMILLO) and the double optimization of binding and
active sites in the design of enzymes. The group is also working on improved
solvation models for ligand-protein interactions in protein design and
develops force field parameters from ab initio quantum mechanics
calculations for small ligands and its applications to tetracycline-protein
interactions.
The group is also developing distributed computing tools through screen
savers, using the SETI@HOME paradigm. This project aims to combine scientific
results with science popularisation, developing distributed
computing protein design Web tools that will coordinate computers of volunteers
that donate their idle CPU cycles.
The Bioinformatics group research is funded by the CEA, Programme de
Toxicologie Nucléaire (2004-2007) and by the French Ministere de la
Recherche, ACI IMPBio, Ëvolution in silico. Evolution de proteines:
simulation et controle" (2003-2005).
The experimental group has a long record of contributions in the field of
aminoacyl-ARNt synthetases. Some selected publications are:
Latest achievements
The group has deposited 16 x-ray structures of aaRS in the last 5 years
(Prof. MECHULAM et al). The high standard of the group is recognized by its
publications (see above), but also by other public distinctions:
Prof. BLANQUET is a member of the French Academy of Sciences, founder member
of the French Academy of Technology, and directs the interdisciplinary CNRS
program "Protéomique et génie des protéines"
(France). Prof. SCHMITT has been awarded the bronze medal of the CNRS 2003 for
her work on the mechanism of enzyme catalysis using aminoacyl-tRNA
synthetases, and on the interaction of enzymes with their ligands using
crystallographic methods.
Prof. SIMONSON is an expert in molecular modelling of proteins and their
interactions with ligands and other proteins. In the last years he has made
important contributions in the field of amino acid recognition by aminoacyl-tRNA
synthetases by computer calculations of binding free energies. In the last 10
years, he has directed 6 Ph.D. students and 5 postdoctoral fellows.
Selected articles:
Prof. JARAMILLO is an expert in computational protein design. He is co-author of
the protein design software DESIGNER. After a Ph.D. on theoretical physics he
moved to biology and he had postdoctoral positions with Prof. Wodak (U. Toronto)
and Prof. Karplus (first at the Univ. Luis Pasteur, Strasbourg, and later at
Harvard U., USA). After 4 years of postdoctoral work he joined the faculty of
the Department of Biology at the Ecole Polytechnique. He continues to
collaborate with Prof. Wodak and Prof. Karplus, and also with the group of
Prof. Hilvert (ETH, Zurich). He has supervised two master thesis in protein
design and is currently supervising the postdoctoral research of Dr. TORTOSA.
Relevant publications of Prof. JARAMILLO:
Finally, it should be noted that of the students and postdocs (many of them of
a nationality other than French) who have been trained in the group, the last
two have obtained a tenure track and a permanent position respectively. The
group is in fact paying attention to offering best chances to young people for
their future career.
(c) Alfonso Jaramillo.
Last modified on 16 November 2007.