Date : 20/04/2009

Laboratory
Laboratoire de RMN
ENS/UPMC/CNRS
Departement de Chimie
Ecole Normale Superieure
24, rue Lhomnd
75231 Paris Cedex 05
Director UMR 7203 - Solange Lavielle

PhD Supervisor
Daniel Abergel
email : This e-mail address is being protected from spam bots, you need JavaScript enabled to view it
phone : +33 1 44 32 33 44

Subjects / Tools-Methodologies:
1 : Prediction of Protein Dynamics / Computational (non-MD) Approaches
2 :Analysis of NMR Relaxation Data / Computational (non-MD) Approaches
3 : Protein Conformational Entropy / Computational (non-MD) Approaches

Summary of lab's interests

The primary interest of the lab is the investigation of the dynamics of proteins. Our experimental approaches rely on solution- and solid-state Nuclear Magnetic Resonance (NMR)spectroscopy. We are very active in the field of NMR methodology and have developed a host of methods to characterize many dynamic effects over a wide range of time scales: from sub-nanosecond motions of protein backbones and side-chains to acide-base reactions and conformational exchange on micro-, millisecond and second timescales. We have also developed theoretical models employed to predict and analyze fast (sub-ns to several ns) motions in proteins. Our experimental and computational approaches are often tested on well-known proteins for validation and then used to unravel the molecular mechanisms underlying the function of proteins involved in important biological processes (Human Centrin and DNA repair; Engrailed 2 and development; T. brucei 6-PGL, a potential target against sleeping sickness).

Summary of project

The role of the 3D structure of a protein in its function at the molecular level has been amply demonstrated. A number of sudies, however, have shown the fundamental contribution of internal dynamics to the protein mechanism of action. Thus, beyond the well-known links between structure and function, an additional structure/dynamics/function relationship has been demonstrated. In this respect, liquid-state high-field NMR has proven to be a unique tool for the study of protein dynamics, particularly through spin-relaxation measurements that provide invaluable information on internal mobility. Thus, following an initial perturbation, spins return to thermodynamic equilibrium by loosing magnetic energy through internal and overall molecular motions. Experimental measurement of various relaxation rates (by cross-relaxation or interference effects, nuclear Overhauser effect, ...) thus allows to better picture internal motions that occur on the pico-second to second time scales. The aim of this proposal will be to investigate several aspects of protein fast dynamics modeling (pico- to nanosecond time scales), from the NMR viewpoint. This encompasses various phenomena such as vibration, rotation, libration of chemical bonds, as well as molecular overall motion in solution. We have developed a simple model that allows one to predict the dynamics of chemical bond vectors, considered as rotators coupled throuh potentials, which depend solely on the molecular structure (NCR model, for Network of coupled rotators). This approach allowed us to model 15N relaxation rates on several proteins. Our model also permits to estimate local disorder through calculation of backbone conformational entropy associated with amide NH vectors. The NCR model will be developed in several ways. First, it will be extended to the case of interference relaxation effects involving two different interactions (dipoles, chemical shift tensors or a combination of both). These methods, some of which were previously developed in the lab, have been mostly used to obtain structural constraints, but their dynamic content has been largely neglected so far. One of the goals will be to extract this information to provide improved analysis of the dynamics. The project will also focus on the extension of the model to the study of side-chain dynamics. Predictions will be compared to various experiments performed on proteins under studied in the lab (human centrin 2, 6PGL, Calbindin). In addition, the NCR model will be developed so that the approach can be used to interpret NMR dynamics studies of proteins in the solid state, where the molecule does not undergo overall motions, so that relaxation rates represent a direct probe to internal dynamics. Thus, preliminary backbone amide nitrogen 15 relaxation studies were recently published, that showed that longitudinal relaxation rates range through an order of magnitude, which is much larger than what is observed in solution. Moreover, the absence of overall mobility makes the assumption of uncorrelated overall and internal motions unnecessary. During the course of this project, the theoretical model will be devised and adapted to various experiments to be developed in the lab.