PROJECTS of Dr Philippe HUETZ

First project : theoretical study of protein folding.

Protein folding constitutes one of the most fascinating problems of fundamental biophysics that for a few decades researchers try hard to resolve. Within cells, this change from a state called "denatured", i.e. of a more or less statistical polymer, of the neosynthesized polypeptidic chain, to a state called "native", where the protein adopts the unique and functional (average) conformation which is characteristic of it, is supported by so called chaperone molecules. But for a majority of globular proteins, this phenomenon happens spontaneously in aqueous solution when one goes from denaturing to renaturing conditions, thus revealing an intrinsic property of the polypeptidic chain. A simple calculus shows that a protein, made up of a few tens to several thousands aminoacids, cannot fold by exploring the space of all possible conformations, which would amount to 3100 for a small protein of 100 residues, what would take about 1027 years to realize at the molecular dynamics scale. But the effective time necessary to reach the native conformation varies between the millisecond and the minute.

 

The nature of the driving forces at the origin of this phenomenon is still obscure, and although the progressive positioning of the hydrophobic interactions seems to play a major role, the purely thermodynamic approach comes up against the disconcerting observation that, under physiological conditions, the native state is only marginally more stable with regard to the ensemble of the denatured conformations (about 40 kJ/mol of protein). Even though the native states of different proteins may be quite similar, a given protein will adopt only one and unique folded state, this last being coded by the order of the aminoacids along the polypeptidic chain. The protein folding problem consists in predicting the compact, quasi crystalline three-dimensional structure of a protein, starting from the knowledge of its sequence of monomers.

 

The discovery of this second genetic code would have a fundamental impact for medical biology, for ab initio design of novel proteins (biosensors, enzymes, hormones, medicines...), for decoding the mass of genetic information obtained in the Human Genome project, and for trying to understand the structures and functions of all the protein sequences determined every day in laboratories. Protein crystallization, allowing X-ray analysis, indeed proceeds by trial and error, and it is difficult and most often impossible to crystallize membrane proteins ; whereas multidimensional NMR analysis, allowing the determination of a protein average structure in solution, is subject to the use of models and becomes too complex for high molecular weight molecules.

 

The aim of my project is to try to understand protein folding by tackling the problem under theoretical angles such as : knots theory, numbers theory, deterministic chaos.

Second project : interaction of ultrasounds with biological matter.

This project, of both theoretical and experimental nature, aims to study the interaction of ultrasonic specific waves with healthy/cancerous tissues/cells, viruses or bacteria, to try to determine eigen-resonance frequencies of these systems. This work is conducted in conjunction with the one of Abdeslam Bentaleb who, in an analogous effort, is interested in the use of infrared waves.

 

A few examples of the use of ultrasounds for measuring biophysical parameters :

 

- It has been shown that proteic or nucleoproteic self-assemblies absorb more the ultrasounds than their dissociated subunits. This phenomenon has for instance been observed on small plant icosahedral viruses, the tobacco mosaic virus, or microtubules, hemocyanines, etc. In fact, in an aqueous medium where molar volume changes are important, the ultrasonic relaxation amplitudes are proportional to the volume fluctuations. It is thus possible to apprehend on such systems the sum of the fluctuations directly related to their self-organized state.

- Ultrasounds, which allow to characterize rapid chemical reactions, have been applied to the study of proton transfer reactions, in particular at the catalytic site of serine proteolytic enzymes, such as alpha-lytic protease or alpha-chymotrypsin.

- Study of macromolecular conformational transitions in solution (example : the helix-random coil transition of poly-L-ornithine).

- Determination of the adiabatic compressibility of globular proteins.

- Study of lipidic bilayers (DMPC, DPPC) containing cholesterol (properties of membrane fluctuation, viscoelasticity).