Karine Bastard

Current position: Research Scientist, Genoscope, Institute of Genomics, Life Science Division, Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Evry, France

 

Education: Ph.D. in Molecular Modeling, 2005, Paris Diderot University, Paris, France

During my undergraduate studies in biochemistry at Nantes University (Nantes, France), I became very interested in structural biology, notably in the recognition mechanism between biological molecules. As I wanted to study this processes “in silico,” I joined Richard Lavery and Chantal Prévost’s group at the Institut de Biologie Physico-Chimique, CNRS (Paris, France), to work on a Ph.D. in the development of docking methods. During this period, I had the opportunity to collaborate actively with Martin Zacharias at Jacobs University Bremen (Bremen, Germany). Having been awarded a Marie Curie post-doctoral fellowship, I continued my work with Michael Levitt’s group at Stanford University (Stanford, CA), focusing on the dynamics of association using molecular dynamics methods. Using my in silico skills to model systems that are difficult to access with experimental tools (such as an antibody-antigen complex and a triple-DNA helix in complex with a protein filament), I set up highly productive collaborations with immunologists, physicists, and chemists. In 2010, I joined Genoscope to complete a multidisciplinary approach aiming at the discovery of new enzymatic activities. As part of the bioinformatics group, I use my expertise in molecular modeling to contribute to a large post-genomic project involving the structural classification and determination of the biological functions of enzymes issued from high-throughput sequencing.

Publications:

Parallel evolution of non-homologous isofunctional enzymes in methionine biosynthesis.

Bastard K*, Perret A*, Mariage A, Bessonnet T, Pinet-Turpault A, Petit JL, Darii E, Bazire P, Vergne-Vaxelaire C, Brewee C, Debard A, Pellouin V, Besnard-Gonnet M, Artiguenave F, Médigue C, Vallenet D, Danchin A, Zaparucha A, Weissenbach J, Salanoubat M, de Berardinis V.

*Co-first authors

Nat Chem Biol. 2017 Aug;13(8):858-866. doi: 10.1038/nchembio.2397.

 

Revealing the hidden functional diversity of an enzyme family.

Bastard K*, Smith AA*, Vergne-Vaxelaire C, Perret A, Zaparucha A, De Melo-Minardi R, Mariage A, Boutard M, Debard A, Lechaplais C, Pelle C, Pellouin V, Perchat N, Petit JL, Kreimeyer A, Medigue C, Weissenbach J, Artiguenave F, De Berardinis V, Vallenet D, Salanoubat M.

*Co-first authors

Nat Chem Biol. 2014 Jan;10(1):42-9. doi: 10.1038/nchembio.1387.

 

A novel acyl-CoA beta-transaminase characterized from a metagenome.

Perret A, Lechaplais C, Tricot S, Perchat N, Vergne C, Pellé C, Bastard K, Kreimeyer A, Vallenet D, Zaparucha A, Weissenbach J, Salanoubat M.

PLoS One. 2011;6(8):e22918. doi: 10.1371/journal.pone.0022918.

 

3-Keto-5-aminohexanoate cleavage enzyme: a common fold for an uncommon Claisen-type condensation.

Bellinzoni M*, Bastard K*, Perret A, Zaparucha A, Perchat N, Vergne C, Wagner T, de Melo-Minardi RC, Artiguenave F, Cohen GN, Weissenbach J, Salanoubat M, Alzari PM.

*Co-first authors

J Biol Chem. 2011 Aug 5;286(31):27399-405. doi: 10.1074/jbc.M111.253260.

 

Accounting for large amplitude protein deformation during in silico macromolecular docking.

Bastard K, Saladin A, Prévost C.

Int J Mol Sci. 2011 Feb 22;12(2):1316-33. doi: 10.3390/ijms12021316.

 

On the characterization and selection of diverse conformational ensembles with applications to flexible docking.

Loriot S, Sachdeva S, Bastard K, Prévost C, Cazals F.

IEEE/ACM Trans Comput Biol Bioinform. 2011 Mar-Apr;8(2):487-98. doi: 10.1109/TCBB.2009.59.

 

Identification of subfamily-specific sites based on active sites modeling and clustering.

de Melo-Minardi RC*, Bastard K*, Artiguenave F.

*Co-first authors

Bioinformatics. 2010 Dec 15;26(24):3075-82. doi: 10.1093/bioinformatics/btq595.

 

Dimorphic motifs in D0 and D1+D2 domains of killer cell Ig-like receptor 3DL1 combine to form receptors with high, moderate, and no avidity for the complex of a peptide derived from HIV and HLA-A*2402.

Sharma D*, Bastard K*, Guethlein LA, Norman PJ, Yawata N, Yawata M, Pando M, Thananchai H, Dong T, Rowland-Jones S, Brodsky FM, Parham P.

*Co-first authors

J Immunol. 2009 Oct 1;183(7):4569-82. doi: 10.4049/jimmunol.0901734. Epub 2009 Sep 14.

 

In silico-in vitro screening of protein-protein interactions: towards the next generation of therapeutics.

Villoutreix BO, Bastard K, Sperandio O, Fahraeus R, Poyet JL, Calvo F, Déprez B, Miteva MA.

Curr Pharm Biotechnol. 2008 Apr;9(2):103-22. Review.

 

Accounting for loop flexibility during protein-protein docking.

Bastard K, Prévost C, Zacharias M.

 

Docking macromolecules with flexible segments.

Bastard K, Thureau A, Lavery R, Prévost C.

J Comput Chem. 2003 Nov 30;24(15):1910-20.