Group of Marc Delarue

Selected Publications (1989-2009)



Photo: crystals of B. stearothermophilus Tyrosyl-tRNA synthetase
(the protein was a gift from H. Bedouelle, I.P.)

puce   1. Experimental Structural Biology and structure-function relationships

puce 1.1 Structural Molecular Biology (a selection)

1.1.1 DNA and RNA Polymerases

  - O. Poch, I. Sauvaget, M. Delarue and N. Tordo. Identification of four sequence motifs for all RNA-dependent polymerases. EMBO J. (1989) 8: 3867-3874. Link.

  - M. Delarue, O.Poch, N. Tordo, D. Moras and P. Argos. An attempt to unify the structure of polymerase. Prot. Eng. (1990) 3: 461-467. [PDF]

  - R. Muller, O. Poch, M. Delarue, D.H. Bishop, M. Bouloy. Rift Valley fever virus L segment: possible functional role of newly identified regions conserved in RNA-dependent polymerases. J Gen Virol. (1994) 75:1345-52. Link

  - O. Poch and M. Delarue. Structural implication of multialignements and delineation of common motifs. Methods in Enzymology (1996) 266: 662-680. Link

  - N. Sukumar, J.B. Boulé, N. Expert-Bezançon, N. Jourdan, J. Lescar, F. Rougeon, C. Papanicolaou, M. Delarue. Crystallization of the catalytic domain of murine terminal desoxynucleotidyl transferase. Acta Cryst. (2000) D56: 1662-1664. [PDF]

  - M. Delarue, J.B. Boulé, J. Lescar, N. Expert-Bezancon, N. Jourdan, N. Sukumar, F. Rougeon, C. Papanicolaou. X-Ray structure of a template independent DNA polymerase: murine Terminal desoxynucleotidyl Transferase at 2.35 Å resolution. EMBO J. 21: 427-439 (2002). [PDF]

  - F. Romain, I. Barbosa, J. Gouge, F. Rougeon, M. Delarue Conferring a template-dependent polymerase activity to terminal deoxynucleotidyltransferase by mutations in the Loop1 region. Nucleic Acids Res. (2009) 37(14):4642-56. Open Access

1.1.2 Aminocyl-tRNA synthetases

  - G. Eriani, M. Delarue, O. Poch, J. Gangloff and D. Moras. Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs. Nature (1990) 347: 203-206. Link

  - Delarue M, Moras D. The aminoacyl-tRNA synthetase family: modules at work. Bioessays (1993) 15:675-87. Link

  - Delarue M, Poterszman A, Nikonov S, Garber M, Moras D, Thierry JC. Crystal structure of a prokaryotic aspartyl tRNA-synthetase. EMBO J. (1994) 13: 3219-29. [PDF]

  - Poterszman A, Delarue M, Thierry JC, Moras D. Synthesis and recognition of aspartyl-adenylate by Thermus thermophilus aspartyl-tRNA synthetase. J Mol Biol. (1994) 244: 158-67. Link

  - Mosyak L, Reshetnikova L, Goldgur Y, Delarue M, Safro MG. Structure of phenylalanyl-tRNA synthetase from Thermus thermophilus. Nat Struct Biol. (1995) 2: 537-47. Link

  - Delarue M. Aminoacyl-tRNA synthetases. Curr. Op. Str. Biol. 5: 48-55 (1995). Link

  - Snewin VA, Khouri E, Mattei D, Tekaia F, Delarue M, Mendis KN, David PH. Caracterisation of a gene from Plasmodium vivax and P. knowlesi: homology with valine-tRNA synthetase. Gene (1996) 173:137-45. Link

  - Rees B, Webster G, Delarue M, Boeglin M, Moras D. Aspartyl tRNA-synthetase from Escherichia coli: flexibility and adaptability to the substrates. J Mol Biol. (2000) 299: 1157-64. Link

1.1.3 Genetic code

  - M. Delarue. Partition of aminoacyl-tRNA synthetases into two structural classes dating back to early metabolism : implications for the origin of the genetic code and contemporary sequences. J. Mol. Evol. 41:703-711 (1995). PubMed

  - M. Delarue. An asymmetric underlying rule in the assignment of codons: clue to a possible quick early evolution of the genetic code via successive binary choices. RNA 13:161-169 (2007). Open Access

puce 1.2 Structure-Based Drug Design projects.

- Samama J.P., Delarue M., Mourey L., Choay J., Moras D. Crystallization and preliminary crystallographic data for bovine antithrombin III. J Mol Biol. (1989) 210: 877-9. Link

- Delarue M., Samama J.-P., Mourey L. and Moras D. Crystal structure of bovine antithrombin III: the molecular replacement solution. Acta Cryst. (1990). B46: 550-556. PDF

- Mourey L., Samama J.P., Delarue M., Petitou M., Choay J., Moras D. Refined crystal structure of cleaved bovine antithrombin III at 3.2 A resolution. J Mol Biol. (1993) 232:223-41. Link

- I. Li de la Sierra, H. Munier-Lehmann, A.M. Gilles, O. Barzu and M. Delarue. Crystallization of M. tuberculosis  TMP Kinase and preliminary X-Ray data analysis. Acta Cryst. (2000) D56: 1662-1664. PDF

- I. Li de la Siera, H. Munier-Lehmann, A.M. Gilles, O. Barzu and M. Delarue. Crystal structure of M. tuberculosis TMP kinase at 1.95 Å resolution. J. Mol. Biol. 311: 87-100 (2001). [PDF]

- D.T. Manallack, W.R. Pitt, P. Herdewijn, J. Balzarini, E. De Clercq, M.R. Sanderson, M. Sohi, F. Wien, H. Munier-Lehmann, A. Haouz, M. Delarue. Database searching for thymidine and thymidylate kinase inhibitors using three-dimensional structure-based methods. J Enzyme Inhib Med Chem. (2002) 17(3):167-74. Link

- A. Haouz, V. Vanheusden, H. Munier-Lehmann, M. Freuyen, P. Herdewijn, S. van Calenbergh and M. Delarue. Enzymatic and structural analysis of inhibitors designed against Mycobacterium tuberculosis thymidylate kinase. J. Biol. Chem. 278: 49-63 (2003). [PDF]

- E. Fioravanti, A. Haouz, T. Ursby, H. Munier-Lehmann, M. Delarue, D. Bourgeois. Mycobacterium tuberculosis thymidylate kinase: structural studies of intermediates along the reaction pathway. J Mol Biol. (2003) 327(5):1077-92. Link

- M. Delarue, N. Duclert-Savatier, E. Miclet, A. Haouz, D. Giganti, J. Ouazzani, P. Lopez, M. Nilges and V. Stoven. X-Ray structure and catalytic mechanism of T. brucei 6-phosphogluconolactonase at 2.10 Å resolution. J. Mol. Biol. 366:868-81 (2007). Link

- N. Duclert-Savatier, L. Poggi, E. Miclet, P. Lopez, J, Ouazzani, N. Chevalier, M. Nilges, M. Delarue and V. Stoven. Insights into the enzymatic mechanism of 6-phosphogluconolactonase from Trypanosoma brucei using structural data and molecular dynamics simulation. J. Mol. Biol. (2009) 388:1009-21. Link

puce 1.3 Structural Studies in Solution: SAXS

- M. Bada, D. Walther, B. Arcangioli, S. Doniach and M. Delarue. Solution structural studies and low resolution model of the SAP1 protein from S. pombe. J. Mol. Biol. (2000) 300: 563-574.[PDF]

puce   2. Methods: Optimisation by Mean Field Techniques

puce 2.1 Optimisation Methods for Crystallography

- M. Delarue. On the resolution of phase ambiguity in P-1 space group by Monte Carlo minimization methods. Acta Cryst. (2000) A56: 553-561.  [PDF]

- M. Delarue and H. Orland. General formalism for phase combination and refinement in protein crystallography: self-consistent Mean-Field optimization methods in reciprocal space. Acta Cryst. (2000) A56:562-574.  [PDF]

- M. Delarue and Ph. Dumas. On the use of low-frequency normal modes to enforce large amplitude and collective movements in the refinement of macromolecular models. P.N.A.S. (2004) 101: 6957-6961.  [PDF]

- M. Delarue. Molecular Replacement techniques in the context of structural genomics. M.R. Sanderson and J. Skelly, Eds. Oxford University Press. Practical Approaches Series (2007). [PDF]

- M. Delarue. Dealing with structural variability in molecular replacement and crystallographic refinement through normal-mode analysis. Acta Crystallogr D (2008) 64:40-8. [PDF]

puce 2.2 Side chain conformation prediction, homology modelling and sequence design by MFT

- P. Koehl and M. DelarueJ. Mol. Biol. 239:249-275 (1994). On the use of a self-consistent Mean Field theory to predict protein side chain conformations and estimate their entropies. [PDF]

- P. Koehl and M. DelarueNature Structural Biology. 2:163-169 (1995). A new Mean-Field self-consistent formalism providing simultaneously both gap closure and side chain positioning in protein homology modelling. PDF

- P. Koehl and M. DelarueCurr. Op. Str. Biol. 6:222-226 (1996). Mean-field optimization techniques for biological macromolecules. [PDF]

- M. Delarue and P. Koehl (1997) The inverse protein folding problem: self-consistent Mean Field optimization of a structure specific mutation matrix. In: Altman R.B., Dunker A.K., Hunter L. and Klein T., eds. Proceedings of the Pacific Symposium on Biocomputing, World Scientific, Singapore. p 109-121. Link

- P. Koehl and M. Delarue (1997) The native sequence determines sidechain packing in a protein, but does optimal sidechain packing determine the native sequence? Pac Symp Biocomput. pp198-209. Link

- P. Koehl and M. Delarue (1998) Minimisation of protein lattice model distortions based on self-consistent Mean Field theory. J. Chem. Phys. 108: 9540-9549. PDF

puce 2.3 Macromolecular Electrostatics and Solvation

- P. Koehl and M. Delarue. Polar and nonpolar atomic environments in the protein core: implications for folding and binding. Proteins (1994) 20:264-78. Link

- M. Delarue and P. Koehl. Atomic environment energies in proteins defined from statistics of accessible and contact surface areas. J Mol Biol. (1995) 249:675-90. PDF.

- C. Azuara, E. Lindahl, P. Koehl, H. Orland and M. Delarue. PDB_Hydro: Incorporating dipolar solvents with variable density in the Poisson-Boltzmann treatment of macromolecular electrostatics. Nucleic Acids Res. (2006) 34: W38-42. [PDF].

- C. Azuara, H. Orland, M. Bon, P. Koehl and M. Delarue. Incorporating dipolar solvents with variable density in Poisson-Boltzmann electrostatics. Biophys J. (2008) 95:5587-5607. Open Access.

- P. Koehl, H. Orland, M. Delarue. Computing ion solvation free energies using the dipolar Poisson model. J. Phys. Chem. B (2009) 113:5694-7. Open Access.

- P. Koehl, H. Orland, M. Delarue. Beyond the Poisson-Boltzmann model: modeling biomolecule-water and water-water interactions. Phys Rev Lett. (2009) 102:087801. Pubmed and PDF.

puce   3. Modelling and Stucture-Encoded Dynamics: Normal Modes and the Elastic Network Model

- M. Delarue and Y.-H. Sanejouand. Simplified normal mode analysis of the open-closed transition in DNA-dependent polymerases. J. Mol. Biol. (2002) 320: 1011-1024. [PDF]

- M. Delarue and Ph. Dumas. On the use of low-frequency normal modes to enforce large amplitude and collective movements in the refinement of macromolecular models. P.N.A.S. (2004) 101: 6957-6961. [PDF]

- A. Taly, M. Delarue, T. Grutter, M. Nilges, N. Le Novere, P.J. Corringer and J.P. Changeux. Low-frequency normal modes predict a quaternary twist motion for nicotinic receptors gating mechanism. Biophys. J. (2005) 88: 3954-65. Link

- E. Lindahl and M. Delarue. Docking Refinement using Low Frequency Normal Mode Amplitude Optimization. Nucleic Acids Res. (2005) 33: 4496-506. [PDF]

- E. Lindahl, C. Azuara, P. Koehl and M. Delarue. NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom Normal Mode Analysis. Nucleic Acids Res. (2006) 34: W52-56. [PDF].

- J. Franklin, P. Koehl, S. Doniach, and M. Delarue. MinActionPath: maximum likelihood trajectory for large-scale structural transitions in a coarse-grained locally harmonic energy landscape. Nucleic Acids Res. (2007) 35:W477-82. Open Access.

- M. Delarue. Dealing with structural variability in molecular replacement and crystallographic refinement through normal-mode analysis. Acta Crystallogr D (2008) 64:40-8. [PDF]


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