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Alexandre de Brevern, 2 june 2016, ENSCBP

The seminar will take place, the 2 of June 2016 at 14h, at the  ENSCBP amphitheater, Building B,  allée Geoffroy Saint-Hilaire, Pessac.

 

Some examples of protein 3D structural models (and problems).

 

Alexandre G. de Brevern, research director

 

INSERM UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cité, Laboratoire d’excellence GR-Ex, Institut National de Transfusion Sanguine (INTS), 6, rue Alexandre Cabanel, 75015 Paris - France

 

Abstract

 

Protein 3D structures are directly implicated in the majority of the essential biological functions. To have access to the protein structures can help to understand the precise mechanisms of protein functions. Nonetheless, the number of protein structures available in the Protein DataBank (PDB) remains quite limited in regards to the never-ending increasing number of protein sequences predicted from intense genome sequencing project. It is so particularly interesting to use in silico approaches to propose, to analyze and to use pertinent 3D structural models. They are useful to try to apprehend / to predict the atomistic mechanism of protein functions for protein – protein (or ligand, DNA …) interactions and to perform drug design.

 

The proposition of 3D structural models depends on the availability of related proteins with protein structures. If these proteins are close, comparative / homology modeling can be used other way threading and de novo approaches can be tested. Models obtained from comparative / homology modeling are the most used, even they could be more tricky than expected. Models from threading and de novo need a strong expertise to ensure their quality.

 

Different features need to be assessed to ensure the quality of the obtained models. I will so present the different ways to obtain good 3D protein structural models for globular or transmembrane proteins, and especially looking at limitations and difficulties to do it using personal examples on: (i) camel VHHs [1], integrin complexes [2-4], transcription factors [5], transmembrane protein [6, 7], enzymes [8, 9] and proteins with PolyProline II helix [10, 11].

 

[1] Smolarek D., Hattab C., Hassanzadeh-Ghassabeh G., Cochet S., Gutiérrez C., de Brevern A.G., Udomsangpetch R., Picot J., Grodecka M., Wasniowska K., Muyldermans S., Colin Y., Le Van Kim C., Czerwinski M., Bertrand O. (2010), Cell Mol Life Sciences, 67(19):3371-87.

[2] Jallu V., Dusseaux M., Panzer S., Torchet M.F., Hezard N, Goudemand J., de Brevern A.G., Kaplan C. (2010), Human Mutation, 31(3):237-46

[3] Jallu V., Poulain P., Fuchs P., Kaplan C., de Brevern A.G. (2012), Plos One, 7(11):e47304.

[4] Jallu V., Poulain P., Fuchs P., Kaplan C., de Brevern A.G. (2014), Biochimie, 7(11):105:84-90.

[5] Arnaud L. et al.(2010), The American Journal of Human Genetics, 87(5):721-7.

[6] de Brevern A.G., Wong H., Tournamille C., Cartron J.-P., Colin Y., Le Van Kim C., Etchebest C. (2005), Biochem Biophys Acta 1724:288-306.

[7] Barrault A., de Brevern A.G., J Martret, A Le Floch, G Bodivit, P Bierling, F Pirenne, C Tournamille, allo immunization of risk assessment associated with the substitution of the amino acid 223 of the protein RH: If the new variant RHD * 668, in preparation.

[8] Rebhemed J, Alphand V, de Berardinis V, de Brevern A.G. (2013) Biochimie 95(7):1394-402.

[9] de Brevern A.G., Leonard S., Fadeev T., Craveur P., Rebhemed J, BVMOdb : Baeyer-Villiger monooxygenases enzyme family database of strucural models and dynamics, , in preparation.

[10] Mansiaux Y., Joseph A.P., Gelly J.-C., de Brevern A.G. (2011), Plos One 6(3): e18401.

[11] Chevrier L., de Brevern A.G., Hernandez E., Leprince J., Vaudry H., Guedj A.M., de Roux N. (2013), Mol Endocr, 27(6):1004-14.

 

CV

 

Alexandre G. de Brevern - http://www.dsimb.inserm.fr/~debrevern/

INSERM UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cité, Laboratoire d’excellence GR-Ex, Institut National de Transfusion Sanguine (INTS), 6, rue Alexandre Cabanel, 75015 Paris - France

 

 

Cell biologist and physiologist per training, he extended his skills through training in molecular biology (INSERM U419 / U450), cellular biology (UPR CNRS 9042), analytical chemistry (LCA Navy) and bioinformatics (master and PhD). He had acquired a solid training in sequence analysis and modelling of protein structures. In 2002, he joined the INSERM within the Bioinformatics Team Genomics & Molecular (U436, then U726 and E346 INSERM). In 2009, his team joined the UMR-S 665 (now 1134) at the National Institute of Blood Transfusion (INTS), following a long collaboration.

 

The heart of his work has focused on analysing and predicting the three-dimensional structure of proteins, the headquarters of major biological functions. Understand and analyse 3D structures are of major interest in the context of medical research. Obtaining protein structure by biophysical approaches is a long, complex and expensive. Structural bioinformatics offers an alternative approach for obtaining structural models. Understanding the biological functions of proteins and their dysfunctions associated with a disease and through the design of reliable structural models, especially in the absence of close counterpart structure.

 

His research and his projects are balanced on two areas: (i) innovative methodological developments, and (ii) biomedical applications of interest on the themes of INSERM and INTS. He continues methodological research on the sequence relationship - structure of globular proteins, which he extends to transmembrane proteins. The objective is the development and use of innovative bioinformatics approaches in close collaboration with experimentalists. Within the INTS, he expanded his work to pathologies of importance in blood transfusion and haematology.

 

He is Senior Researcher at INSERM since 2014. He had published more than 80 papers in peer review journals and provided to the scientific community more than ten webservers and databases. He is also a referee for several international scientific journals and in editorial boards of 8 of them. He is deeply implicated in CNRS national committee (previously in section 16 – Chemistry and CID 43 – Bioinformatics, now in in section 20 – Biology and CID 51 – Bioinformatics, and also member of the council of this last).

 

He had received the Price of French Graphical and Modelling Society (GGMM, 2001) and Maurice Nicloux Price of French Biochemistry & Molecular Biology Society (SFBBM, 2010).

 

Contact: Véronique TREZEGUET v.trezeguet@cbmn.u-bordeaux.fr

 

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