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R. CHARBEL MAROUN

dernière mise à jour : 09/04/2015

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Présentation générale

Présentation

STRUCTURAL BIOINFORMATICS OF NORMAL AND PATHOLOGICAL MOLECULES

 

Team leader R. Charbel Maroun, PhD, HDR

Structural bioinformatics methodologies such as molecular modeling and simulation are applied to generate accurate three-dimensional models of biomolecules and their collective motions, leading to the prediction and study of physico-chemical and biological properties that are difficult to access by physical means. Molecular modeling allows the generation of 3D models and molecular dynamics simulations allow the exploration of the conformations and internal movements of the molecules. These methods are also useful to interpret experimental structural data or other source of information related to the atomic structure of biomolecules. The results of structural bioinformatics provide relevant information for fundamental science and the basic mechanisms of (bio)molecular function.

The understanding of the dynamics of microtubules and the role of the protein partners that regulate the cytoskeleton remains incomplete. In this laboratory, our work is aimed at enlightening fundamental processes of critical importance in biology, such as cell cycle and neurodegeneration. For this purpose, the structural bioinformatics group applies and develops methods for the study of the normal and pathological variants of proteins of the microtubule skeleton. The understanding of the difference between both behaviors should lead us to the molecular basis of disease.

 

Molecular basis of pathogenic mutations
     Molecular modeling and dynamics of proteins of the microtubule skeleton: spastin in interaction with its partners

Spastin (Spastic ParapleGia 4, SPG4) is a ubiquitous protein involved in several microtubule-dependent functions such as intracellular membrane traffic, cytokinesis and endoplasmic reticulum morphogenesis. Mutations of SPG4 induce hereditary Human Spastic Paraplegias (HSP) -genetic disorders characterized by progressive lower limb spasticity and weakness. At the cellular level this disease is characterized by a degeneration of cortico-spinal tract axons. To date, only symptomatic treatments partially improving spasticity are available for HSP patients -no preventive or curative treatments exist; thus, the importance of understanding the molecular mechanisms regulated by spastin underlying axon maintenance and function. In our laboratory an interdisciplinary approach (NMR, cell and molecular biology, optical and video microscopy, structural bioinformatics) is used for studying the physiological and pathological role of spastin and its regulation by molecular partners, several of which have been recently identified by us.

The goal of this research project is to analyze, via structural bioinformatics, the 3D structure and dynamics of spastin and its different domains, as well as the biomolecular interactions between these domains and known and unknown promising molecular partners. This knowledge should help us understand the mechanism of action of spastin and its pathogenic mutants, leading eventually to HSP-directed therapy.

     Molecular basis of genetic disorders

In the context of collaboration with medical geneticists from Qatar, we provide, in complement to genetic data showing the association of monogenic mutations to pathological phenotypes, molecular information on the mechanisms behind that may link the observed mutation and the phenotype. Structural bioinformatics in this context accelerates understanding of the pathology, notably when no direct structural data are available.

 

Molecular basis of signal transduction
     GPCRs and the mechanism of signal transduction

In this project we study the structural and dynamical features of a histamine receptor with microsecond-scale all-atom molecular dynamics (MD) simulations as a way to understand better the mechanisms of signal transduction, inactivation and constitutive activity. For this purpose, we embed the receptor in a lipid bilayer membrane surrounded of water and salt ions. Three systems containing (i) the receptor coupled to the endogenous agonist, (ii) the receptor coupled to a specific and powerful inverse agonist, and (iii) the uncoupled receptor were prepared. The results of a detailed multi-level comparative analysis of the trajectories will allow us to propose molecular mechanisms for the different states of the receptor, as well as describe conformational changes taking place.

 

Protein-protein interactions
      integral membrane proteins

Prediction of multimeric complexes of integral cell membrane proteins by computational approaches with the goal of understanding their modulation of cell signaling.

Disciplines

Biology

Physics

Biochemistry

Computer science

Chemistry

Mathematics

Domaines d'expertise

Structural bioinformatics

Model building

Molecular modeling and simulation

Laboratoire

Publications

Publications

Chapters in books:
  • G.Faure, V.T.Gowda, C.Bon & R.C.Maroun. «Etude moléculaire de l'interaction des PLA2 anticoagulantes des venins des serpents avec le Facteur Xa». Dans Explorer, exploiter les toxines et maîtriser les organismes producteurs, F. Goudey-Perrière, Eds.; Editions Elsevier, Paris, 2001; pp. 117-118.

 

Reviews:
  • S.M.T.Serrano, R.C.Maroun (2005). «Snake venom serine peptidases: highly specialized toxins acting on the hemostatic system». Toxicon, 45, 8, 1115-32. Review paper by invitation. PMID: 15922778.

 

Journal articles:
  • R.C.Maroun & R.T.Keys (1976). «Estudio Teorico Conformacional de un Complejo de Adicion Inorganico», Rev. Soc. Quim. Méx.  5, 16-25.
  • R.Maroun & W.L.Mattice (1981). «Solution Conformations of the Pituitary Opioid Peptide Dynorphin-(1-13)», Biochem. and Biophys. Research. Comm.  103, 442-446. PMID: 7332550
  • G.Santiago, R.C.Maroun, E.R.Hawkins & W.L.Mattice (1981). «Electrostatic Interactions in Ionic Homopolypeptides in Solutions of Moderate Ionic Strength», Biopolymers  10, 2181-2194. DOI: 10.1002/bip.1981.360201011
  • R.C.Maroun,& W.L.Mattice (1984). «Influence of L-cystinyl Side Chain Configurations on the Melting of Crosslinked alpha-Tropomyosin Dimers», Biochim. Biophys. Acta   784, 133-139. PMID: 6691991
  • R.C.Maroun, R.W.McCord & W.L.Mattice (1986). «Triangular Matrix Representation of Dimensionless Helical Hydrophobic Moment Ratios», Int. .J. Biol. Macromol.  8, 73-78. DOI: 10.1016/0141-8130(86)90002-4
  • R.C.Maroun & W.K.Olson (1986); «Theoretical Studies on B-DNA Dimensions and Flexibility – their Base Sequence and Chain-length dependence», Biophysical J 2, A124-A124, part 2.
  • R.C.Maroun & W.K.Olson (1988). «Base Sequence Effects in Double-Helical DNA. II. Configurational Statistics of Rodlike Chains», Biopolymers  27, 561-584. PMID: 3370294
  • R.C.Maroun & W.K.Olson (1988). «Base Sequence Effects in Double-Helical DNA. III. Average Properties of Curved DNA», Biopolymers  27, 585-603. PMID: 3370295
  • R.Maroun & N.Gresh (1989). «A Theoretical Investigation of the Intercalative Binding of 7-H Pyrido[4,3C]Carbazole Chromophore into a d(CpG)2 Minihelix», Biopolymers  28, 835-849. PMID: 2720126
  • M.Delepierre, R.Maroun, C.Garbay-Jaureguiberry, J.Igolen & B.P.Roques (1989). «1H and 31P Nuclear Magnetic Resonance Studies of the Differences in DNA Deformation Induced by Anti-tumoral 7H-pyrido[4,3-c]carbazole Dimers» J. Mol. Biol.  210, 211-228. PMID: 2585517
  • R.Maroun, M.Delepierre & B.P.Roques (1989). «Intercalative Binding of Ditercalinium to d(CpGpCpG)2: A Theoretical Study», J. Biom. Str. Dyn.  7, 607-622. PMID: 2627301
  • R.C.Maroun & B.P.Roques (1991). «Induction of DNA Bending by Bifunctional Intercalating Agents of the 7H-Pyridocarbazole Family», Biophysical Chemistry  39, 45-56. PMID: 2012833
  • A.Dorville, I.McCort-Tranchepain, D.Vichard, W.Sather, R.Maroun, P. Ascher & B. P. Roques (1992). «Preferred Antagonistic Binding State of the NMDA Receptor: Synthesis, Pharmacology and Computer Modeling of Phosphonomethyl Phenylalanine Derivatives», J. Med. Chem.  35, 2551-2562. PMID: 1386112
  • H.Chen, J.Boiziau, F.Parker, R.Maroun, B.Tocqué, B.P.Roques & C. Garbay-Jaurreguiberry (1993). «Synthesis and Structure-Activity Studies of a Series of [(Hydroxybenzyl)amino]salicylates as Inhibitors of EGF Receptor-Associated Tyrosine Kinase Activity», J. Med. Chem.  36, 4094-4098. PMID: 8258833
  • Y.Zhang, A.Wisner, R.C.Maroun, V.Choumet, Y.Xiong & C.Bon (1997). «Trimeresurus stejnegeri Snake Venom Plasminogen Activator: Site-directed Mutagenesis and Molecular Modeling», J. Biol. Chem.  272, 20531-20537. PMID: 9252366
  • S.Karray, L.Juompan, R.C.Maroun, D.Isenberg, G.J.Silverman & M.Zouali (1998). «Structural Basis of the gp120 Superantigen Binding Site on Human Immunoglobulins», J. Imm. 161, 6681-6688. PMID: 9862697
  • R.C.Maroun (1999). «Molecular Modeling of a Loop Structure in Lysozyme: Sequence Effects vs. Crystal Packing», J. Biom. Str. Dyn. 16, 873-889. PMID: 10217456
  • S.Braud, M.A.A.Parry, R.C.Maroun, C.Bon & A.Wisner (2000). «The Contribution of Residues 192 and 193 to the Specificity of Snake Venom Serine Proteinases», J. Biol. Chem. 275, 1823-1828. PMID: 10636881
  • R.C.Maroun, C.Demangel, S.Rouyre, C.Bon, J.C.Mazié & V.Choumet (2000). «Combining Phage Display and Molecular Modeling to Map the Epitope of a Neutralizing Anti-Toxin Antibody», European J. Biochem. 267, 2345-2353. PMID: 10759860
  • Z.Yuan, C.Rang, R.C.Maroun, V.Juarez, R.Frutos, N.Pasteur, C Vendrely, J.-F.Charles & C.Nielsen-LeRoux (2001). «Identification and molecular structural analysis of a toxicity determinant for the Bacillus sphaericus crystal toxin», European J. Biochem. 268, 2751-2760. PMID: 11322897
  • R.C.Maroun (2001). «Molecular Basis for the Partition of the Essential Functions of Thrombin among Snake Venom Serine Proteinases. The case of thrombin-like enzymes», Haemostasis 31, 247-256. PMID: 11910192
  • V. Jan, R.C.Maroun, A.Robbe-Vincent, L.De Haro & V.Choumet (2002). «Toxicity Evolution of Vipera Aspis Aspis Venom: Identification and Molecular Modeling of a Novel Phospholipase A2 Heterodimeric Neurotoxin», FEBS Letters 527, 263-268. PMID: 12220671
  • S.M.T.Serrano & R.C.Maroun (2004). «Identification of the substrate-binding exosites of two snake venom serine proteinases : molecular basis for the partition of two essential functions of thrombin», J. Mol. Recognition 17, 51-61. PMID: 14872537
  • A.Aguilar-Rojas, M.-J.Almaraz-Barrera, M.Krzeminski, M.Robles-Flores, R.Hernández-Rivas, N.Guillén, R.C.Maroun & M.Vargas (2005). « Entamoeba histolytica: inhibition of cellular functions by overexpression of EhGEF1, a novel Rho/Rac guanine nucleotide exchange factor », Experimental Parasitology, 109, 3, 150-162. PMID: 15713446
  • G.Faure, V.T.Gowda & R.C.Maroun (2007). «Characterization of a human coagulation factor Xa-binding site on Viperidae snake venom phospholipases A2 by affinity binding studies and molecular bioinformatics». BMC Struct Biol 7, 82. PMID: 18062812.
  • C.Weber, S.Blazquez, S.Marion, C.Ausseur, M.Krzeminski, D.Vats, A.Bhattacharya, M.-C.Rigothier, R.C.Maroun and N.Guillén. (2008). «Bioinformatics and Functional Analysis of an Entamoeba histolytica Mannosyltransferase Necessary for Parasite Complement Resistance and Hepatical Infection», PLoS Neglected Tropical Diseases 2(2), e165.
  • L.Moreno-Vargas, J.Correa-Basurto, R.C.Maroun & F.J.Fernández (2012). «Homology modeling of the structure of acyl coA:isopenicillin N-acyltransferase (IAT) from Penicillium chrysogenum. IAT interaction studies with isopenicillin-N, combining molecular dynamics simulations and docking», J Mol Model 3, 1189-205. PMID: 21695507.
  • M. Kambouris, R.C. Maroun, T.Ben-Omran, Y. Al-Sarraj, K. Errafi,i R. Ali, H. Boulos, P.A. Curmi & H. El-Shanti (2014). “Mutations in Zinc Finger 407 [ZNF407] Cause a Novel Autosomal Recessive Cognitive Impairment Syndrome”, Orphanet Journal of Rare Diseases 9, 80.PMID: 24907849. Highly accessed.
  • Méndez-Luna D, Martínez-Archundia M, Maroun RC, Ceballos-Reyes G, Fragoso-Vázquez MJ, González-Juárez DE, Correa-Basurto J. (2015). “Deciphering the GPER/GPR30-agonist and antagonists interactions using molecular modeling studies, molecular dynamics, and docking simulations.” J Biomol Struct Dyn. Jan 14:1-12. [Epub ahead of print] PMID: 25587872.

Enseignements

Enseignements

 TEACHING EXPERIENCE

 

  • TEACHING ASSISTANT 1977 - 1981. Louisiana State University, Chemistry Department.

 

  • LECTURER 1984 - 1986. Rutgers University, Chemistry Department.

 

  • LECTURER 1990 - 1993. Université de Paris V, Faculté de Pharmacie. Master (DEA) of molecular pharmacochemistry, experimental  pharmacology and metabolism.

 

  • LECTURER 1999-2004. Institut Pasteur. DEA de Structure, Fonction et Ingénierie des Protéines, U. De Paris VII.

 

  • INSTRUCTOR 2003-2009. Departamento de Biotecnologia, Universidad Autonoma Metropolitana (UAM), Mexico, and Centro de Biotecnologia, Universidad Autonoma del Estado de Morelos (UAEM), Cuernavaca, Mexico. « Molecular structural bioinformatics: Theoretical and computational methods for the study of biological macromolecules ».

 

  • LECTURER 2004. International School on Computational Sciences for Complex Systems in Biology (CSSB 2004). Rovereto, Italy. « Theoretical methods for the study of the 3D structure, the function and the recognition mechanisms of biological macromolecules ».
  • INSTRUCTOR 2004 EMBO course « Biomolecular Simulation », Institut Pasteur, Paris, France.

 

  • INSTRUCTOR 2004 UAM's 30th anniversary. Mexico City, Mexico. Course in Molecular Structural Bioinformatics “Theoretical and computational methods for the study of biological macromolecules”.

 

  • INSTRUCTOR 2005-présent. UAM, Dept. of Biotechnology; Universidad Autonoma del Estado de Morelos, Centro de Biotecnologia; Escuela Superior de Medicina y Homéopatia, Instituto Politécnico Nacional, “Molecular Structural Bioinformatics: Theoretical and computational methods for the study of biological macromolecules”.

Curriculum vitae

Formations

  • B.Sc. in Chemistry (Licenciatura de Quimica). National Autonomous University of Mexico (UNAM), Mexico, Mexico, May 1977.  Thesis: «A theoretical study in quantum chemistry on the conformations of an inorganic addition complex» (in Spanish).

 

  • Ph.D. in Physical-chemistry/Physics. Louisiana State University, Baton Rouge, Louisiana, USA, May 1983.  Thesis «Statistical mechanics of conformational transitions in biopolymers » in Diss. Abst. Intnl. (in English).

 

  • H.D.R. in Structural Bioinformatics. Université de Paris VII Denis Diderot, January 2004. Thesis «Theoretical methods for the study of the structure, the function and the mechanisms of molecular recognition in biology» (in French).

 

Parcours professionnel

 PROFESSIONAL EXPERIENCE - LABORATORIES

 

  • GRADUATE STUDENT 1977 - 1983. Louisiana State University, Baton Rouge, Louisiana, USA. Chemistry Department.

 

  • POSTDOCTORAL FELLOW 1983 - 1986. Rutgers University, New Brunswick, New Jersey, USA. Chemistry Department.

 

  • ASSOCIATED RESEARCH FELLOW (CNRS) 1986 - 1987.  Institut de Biologie Physico-chimique, Laboratoire de Biochimie Théorique, Paris, France.

 

  • RESEARCH FELLOW (INSERM, FRM, ARC) 1987 - 1991. Unité de Pharmaco-chimie Moléculaire, UER des Sciences Pharmaceutiques et Biologiques, Université de Paris V, Paris, France.

 

  • CHARGE DE RECHERCHE 1ère classe (INSERM) 1991 - 1993: Unité de Pharmaco-chimie Moléculaire, UER des Sciences Pharmaceutiques et Biologiques, Université de Paris V, Paris, France.
  • 1993-1995: Unité d'Immunologie Structurale, Institut Pasteur,
  • 1995-1998: Unité de Physico-chimie de Macromolécules Biologiques, Institut Pasteur. (Unit ceased to exist).
  • 1995-2001: Unité des Venins, Institut Pasteur. (Unit ceased to exist).
  • 2002-2005 : Unité de Bioinformatique Structurale, Institut Pasteur.
  • 2006: Laboratoire d’Informatique (LIP6), Université de Paris VI. (Team ceased to exist).
  • 2007-2010: Centre de Psychiatrie et de Neurosciences Broca-Ste. Anne, équipe Neurobiologie et Pharmacologie Moléculaire, INSERM U573, U894. (Unit ceased to exist).
  • 2011-2012 : Centre Interdisciplinaire de Recherche en Biologie (CIRB; CNRS UMR 7241/INSERM U1050), Collège de France.
  • 2012-present : Structure-activité des biomolécules normales et pathologiques (SABNP), U829 INSERM/Université d’Evry-Val d’Essonne

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