Structural Biology and Chemistry Department Activity Report

With its nine scientific groups (two in organic chemistry, two in biochemistry, three in X-ray crystallography, one in NMR, one in structural bioinformatics) and six technical platforms (sequencing, biophysics, crystallization and X-ray diffraction, electron microscopy, protein expression, proteomics), the department of structural biology and chemistry (Département de Biologie Structurale et Chimie, DBSC) addresses a large variety of biological problems, mostly related to health. The Department’s teams develop their own biological research themes; in addition, the DBSC brings its molecular vision to other projects and laboratories within and outside the Institut Pasteur. Although our research is primarily motivated by fundamental biological questions, many of ongoing research programs have a "biomedical" dimension, and the research spans the space between the elucidation of structure-function relationships and the search for new therapeutic molecules.
Recent work in the Unit of Structural Biochemistry includes the determination of several X-ray crystal structures of potential drug targets, such as the proline racemase of T. cruzi, the total regulator of fatty acid synthesis FapR present in several Gram+ pathogenic bacteria (S. aureus, L monocitogenes), Ser/Thr proteins kinases and phosphatases from M. tuberculosis, or the phosphatydilinositol mannosyl transferase PimA, an essential enzyme for the synthesis of the mycobacterial cellular wall. In a similar spirit, research themes of the Unit of Structural Immunology centre on the structural and functional characterization of antigens from infectious agents that are vaccine candidates or targets for drug design. During 2008, work on antigens from Plasmodium and Shigella flexneri continued, as well as on site-specific recombinases and neurotoxic and anticoagulant phospholipases A2. 

The unit “NMR of Biomolecules” uses NMR to study structure and interactions of biological macromolecules (bacterial proteins implied in the acquisition of heme, antigenic determinants within the framework of the development of a vaccine against shigellosis, viral transcription factors, structure and interactions of domains in the protein NEMO, interactions of PDZ domains in viral infections). 

The studies of the “Enzymatic Regulation of Cellular Activities” unit of the protein NEMO, an essential regulating factor on the NF-KB pathway, have shown major advances at the functional and structural level. The structure of the regulative domain of this protein was solved by X-ray crystallography. This protein is implied in many cancers via the control apoptosis. Studies are under way to find inhibitors of NEMO, which could lead to the development of new anti-cancer drugs.
In collaboration with the department of neuroscience, the “Structural Dynamics of the Macromolecules“ unit determined the structure of a bacterial analogue of the nicotinic acetylcholine receptor, in an obviously open state. The pharmacology associated to these molecules, pentameric ionic channels, the opening of which is triggered by a ligand, is very rich, since GABA, the glycine, serotonin, and acetylcholine receptors belong to the same family. The detailed study of the mechanism of opening of the channel becomes possible, since now structures of both open and closed states of members of this family are known. 

The “Chemistry of Biomolecules” Unit contributes to several multidisciplinary programs involving the synthesis of new chemical entities derived from carbohydrates, peptides, and conjugates thereof. Major focus is on the validation of biological targets of medical interest and on the development of innovative strategies towards glyco-therapeutics and/or glyco-vaccines.
Conformational changes and flexibility play an important role in protein-ligand interactions and are studied by molecular modelling approaches in two units (Structural Dynamics of the Macromolecules, and Structural Bioinformatics). Virtual screening and docking pursued in the Structural Bioinformatics unit led to the identification of several compounds that inhibit essential proteins in the agents of malaria and tuberculosis.

Selected publications:
J Boutet, C Guerreiro, LA Mulard. Synthesis of branched tri- to pentasaccharides representative of fragments of Shigella flexneri serotypes 3a and/or X O-antigens. Tetrahedron (2008) vol. 64 pp 10558-10572.

M Nilges, A Bernard, B Bardiaux,T Malliavin, M Habeck, W Rieping. Accurate NMR structures through minimization of an extended hybrid energy. Structure (2008) vol. 16 pp 1305-1312.

B Vulliez le Normand, FA Saul, A Phalipon, F Belot, F C Guerreiro, LA Mulard, GA Bentley, GA. Structures of synthetic O-antigen fragments from serotype 2a Shigella flexneri in complex with a protective monoclonal antibody. PNAS USA (2008) vol 105 pp 9976-9981.

PA Kaminski, P Dacher, L Dugue, S Pochet. In vivo reshaping the catalytic site of nucleoside 2 ’-deoxyribosyltransferase for dideoxy- and didehydronucleosides via a single amino acid substitution. J. Biol. Chem (2008) vol 283 pp 20053-20059.

J Lefevre, P Delepelaire, M Delepierre, N Izadi-Pruneyre. Modulation by substrates of the interaction between the HasR outer membrane receptor and its specific TonB-like protein, HasB. J. Mol. Biol (2008) vol 378 pp 840-851.

F Cordier, E Vinolo, M Veron, M Delepierre, F Agou. Solution structure of NEMO zinc finger and impact of an anhidrotic ectodermal dysplasia with immunodeficiency-related point mutation. J Mol Biol (2008) vol 377 pp 1419-1432.

F Ahmed, G Andre-Leroux, A Haouz, A Boutonnier, M Delepierre, F Qadri, F Nato, JM Fournier, PM Alzari, PM. Crystal structure of a monoclonal antibody directed against an antigenic determinant common to Ogawa and Inaba serotypes of Vibrio cholerae O1. Proteins (2008) vol 70 pp 284-288.

P England, LF Westblade, F Karimova, V Robbe-Saule, F Norel, A Kolb, A. Binding of the Unorthodox Transcription Activator, Crl, to the Components of the Transcription Machinery. J Biol Chem (2008) vol 283 pp 33455-33464.

N Bocquet, H Nury, M Baaden, C Le Poupon, JP Changeux, M Delarue, PJ Corringer. X-ray structure of a pentameric ligand-gated ion channel in an apparently open conformation. Nature (2009) vol 457 pp 111-114. Epub 2008 Nov 5.