Molecular dynamic simulation of mGluR5 amino terminal domain: Essential dynamics analysis captures the agonist or antagonist behaviour of ligands

Journal of Molecular Graphics and Modelling

Volumn 41, Issue , 2013, Pages 72-78

  Casoni, Alessandro ^a   Clerici, Francesca ^a   Contini, Alessandro ^a  

^a UNIVERSITY OF MILAN   (Italy)

Author keywords

Essential dynamics; Glutamate metabotropic receptor; Molecular dynamic simulations; Principal component analysis

Indexed keywords

AMINO-TERMINAL DOMAIN; DESCRIPTORS; EIGENVALUES; ESSENTIAL DYNAMICS; GLUTAMATE METABOTROPIC RECEPTOR; INTER-DOMAIN; LIGAND BINDING DOMAIN;

COMPUTER SIMULATION; EIGENVALUES AND EIGENFUNCTIONS; ENZYME ACTIVITY; LIGANDS; PRINCIPAL COMPONENT ANALYSIS;

MOLECULAR DYNAMICS;

2 AMINO 2 (2 CARBOXYCYCLOPROPYL) 3 (XANTHEN 9 YL)PROPIONIC ACID; 2 CHLORO 5 HYDROXYPHENYLGLYCINE; 4 CARBOXYPHENYLGLYCINE; ALPHA METHYL 4 CARBOXYPHENYLGLYCINE; GLUTAMIC ACID; LIGAND; METABOTROPIC RECEPTOR 5; QUISQUALIC ACID;

AGONIST; AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ANALYTIC METHOD; ARTICLE; CONTROLLED STUDY; DRUG BINDING; ESSENTIAL DYNAMICS; LIGAND BINDING; LIGAND BINDING DOMAIN; MOLECULAR DOCKING; MOLECULAR DYNAMICS; MOLECULAR MODEL; PRINCIPAL COMPONENT ANALYSIS; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN FUNCTION;

AMINO ACIDS; BINDING SITES; GLUTAMIC ACID; GLYCINE; HUMANS; LIGANDS; MOLECULAR DYNAMICS SIMULATION; PHENYLACETATES; PRINCIPAL COMPONENT ANALYSIS; PROTEIN BINDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; QUISQUALIC ACID; RECEPTORS, METABOTROPIC GLUTAMATE; XANTHENES;

EID: 84874939905     PISSN: 10933263     EISSN: 18734243     Source Type: Journal    
DOI: 10.1016/j.jmgm.2013.02.002     Document Type: Article

References (43)

1. P.J. Conn, and J.P. Pin Pharmacology and functions of metabotropic glutamate receptors Annual Review of Pharmacology and Toxicology 37 1997 205 237
2. J.C. Watkins, P. Krogsgaard-Larsen, and T. Honore Structure-activity relationships in the development of excitatory amino acid receptor agonists and competitive antagonists Trends in Pharmacological Sciences 11 1990 25 33
3. P. Malherbe, F. Knoflach, C. Broger, S. Ohresser, C. Kratzeisen, and G. Adam Identification of essential residues involved in the glutamate binding pocket of the group II metabotropic glutamate receptor Molecular Pharmacology 60 2001 944 954
4. N. Kunishima, Y. Shimada, Y. Tsuji, T. Sato, M. Yamamoto, and T. Kumasaka Structural basis of glutamate recognition by a dimeric metabotropic glutamate receptor Nature 407 2000 971 977
5. P.J. O'Hara, P.O. Sheppard, H. Thogersen, D. Venezia, B.A. Haldeman, and V. McGrane The ligand-binding domain in metabotropic glutamate receptors is related to bacterial periplasmic binding proteins Neuron 11 1993 41 52
6. C.B. Felder, R.C. Graul, A.Y. Lee, H.P. Merkle, and W. Sadee The Venus flytrap of periplasmic binding proteins: an ancient protein module present in multiple drug receptors AAPS PharmSci 1 1999 E2
7. D. Tsuchiya, N. Kunishima, N. Kamiya, H. Jingami, and K. Morikawa Structural views of the ligand-binding cores of a metabotropic glutamate receptor complexed with an antagonist and both glutamate and Gd3+ Proceedings of the National Academy of Sciences 99 2002 2660 2665
8. T. Muto, D. Tsuchiya, K. Morikawa, and H. Jingami Structures of the extracellular regions of the group II/III metabotropic glutamate receptors Proceedings of the National Academy of Sciences 104 2007 3759 3764
9. R. Enz Metabotropic glutamate receptors and interacting proteins: evolving drug targets Current Drug Targets 13 2012 145 156
10. I.V. Belozertseva, T. Kos, P. Popik, W. Danysz, and A.Y. Bespalov Antidepressant-like effects of mGluR1 and mGluR5 antagonists in the rat forced swim and the mouse tail suspension tests European Neuropsychopharmacology 17 2007 172 179
11. J. Kotlinska, and M. Bochenski Comparison of the effects of mGluR1 and mGluR5 antagonists on the expression of behavioral sensitization to the locomotor effect of morphine and the morphine withdrawal jumping in mice European Journal of Pharmacology 558 2007 113 118
12. W. Spooren, T. Ballard, F. Gasparini, M. Amalric, V. Mutel, and R. Schreiber Insight into the function of group I and group II metabotropic glutamate (mGlu) receptors: behavioural characterization and implications for the treatment of CNS disorders Behavioural Pharmacology 14 2003 257 277
13. A. Contini, G. Cappelletti, D. Cartelli, G. Fontana, and M.L. Gelmi Molecular dynamics and tubulin polymerization kinetics study on 1,14-heterofused taxanes: evidences of stabilization of the tubulin head-to-tail dimer-dimer interaction Molecular BioSystems 8 2012 3254 3261
14. N. Ferri, T. Radice, M. Antonino, E.M. Beccalli, S. Tinelli, and F. Zunino Synthesis, structural, and biological evaluation of bis- heteroarylmaleimides and bis-heterofused imides Bioorganic and Medicinal Chemistry 19 2011 5291 5299
15. J.L. Klepeis, K. Lindorff-Larsen, R.O. Dror, and D.E. Shaw Long-timescale molecular dynamics simulations of protein structure and function Current Opinion in Structural Biology 19 2009 120 127
16. C. Baldoli, C. Oldani, S. Maiorana, P. Ferruti, E. Ranucci, and M. Bencini Functionalization and molecular dynamics study of carboxy-terminated poly(1-vinylpyrrolidin-2-one): a potential soluble carrier of biomolecules Journal of Polymer Science Part A: Polymer Chemistry 46 2008 1683 1698
17. Y. Arinaminpathy, M.S.P. Sansom, and P.C. Biggin Molecular dynamics simulations of the ligand-binding domain of the ionotropic glutamate receptor GluR2 Biophysical Journal 82 2002 676 683
18. J. Mendieta, G. Ramírez, and F. Gago Molecular dynamics simulations of the conformational changes of the glutamate receptor ligand-binding core in the presence of glutamate and kainate Proteins 44 2001 460 469
19. G. Costantino, A. Macchiarulo, M. Belenikin, and R. Pellicciari Molecular dynamics simulation of the ligand binding domain of mGluR1 in response to agonist and antagonist binding Journal of Computer-Aided Molecular Design 16 2002 779 784
20. J.J. Falke Enzymology: a moving story Science 295 2002 1480 1481
21. T. Horiuchi, and N. Gō Projection of monte carlo and molecular dynamics trajectories onto the normal mode axes: human lysozyme Proteins: Structure, Function, and Genetics 10 1991 106 116
22. A. Kitao The effects of solvent on the conformation and the collective motions of protein: normal mode analysis and molecular dynamics simulations of melittin in water and in vacuum Chemical Physics 158 1991 447 472
23. A. Amadei, A.B. Linssen, and H.J. Berendsen Essential dynamics of proteins Proteins 17 1993 412 425
24. García Large-amplitude nonlinear motions in proteins Physical Review Letters 68 1992 2696 2699
25. A. Kitao, and N. Go Investigating protein dynamics in collective coordinate space Current Opinion in Structural Biology 9 1999 164 169
26. H.J. Berendsen, and S. Hayward Collective protein dynamics in relation to function Current Opinion in Structural Biology 10 2000 165 169
27. A. Amadei, A.B. Linssen, B.L. de Groot, D.M. van Aalten, and H.J. Berendsen An efficient method for sampling the essential subspace of proteins Journal of Biomolecular Structure & Dynamics 13 1996 615 625
28. B. John, and A. Sali Comparative protein structure modeling by iterative alignment, model building and model assessment Nucleic Acids Research 31 2003 3982 3992
29. M.Y. Shen, and A. Sali Statistical potential for assessment and prediction of protein structures Protein Science 15 2006 2507 2524
30. W.R.P. Scott, P.H. Hünenberger, I.G. Tironi, A.E. Mark, S.R. Billeter, and J. Fennen The GROMOS biomolecular simulation program package The Journal of Physical Chemistry A 103 1999 3596 3607
31. D. Van Der Spoel, E. Lindahl, B. Hess, G. Groenhof, A.E. Mark, and H.J.C. Berendsen Gromacs: fast, flexible, and free Journal of Computational Chemistry 26 2005 1701 1718
32. Z. Chu, and J.J. Hablitz Quisqualate induces an inward current via mGluR activation in neocortical pyramidal neurons Brain Research 879 2000 88 92
33. A.J. Doherty, M.J. Palmer, J.M. Henley, G.L. Collingridge, and D.E. Jane (RS)-2-chloro-5-hydroxyphenylglycine (CHPG) activates mGlu5, but no mGlu1, receptors expressed in CHO cells and potentiates NMDA responses in the hippocampus Neuropharmacology 36 1997 265 267
34. A. Buisson, and D.W. Choi The inhibitory mGluR agonist, S-4-carboxy-3-hydroxy-phenylglycine selectively attenuates NMDA neurotoxicity and oxygen-glucose deprivation-induced neuronal death Neuropharmacology 34 1995 1081 1087
35. A.J. Doherty, M.J. Palmer, Z.A. Bortolotto, A. Hargreaves, A.E. Kingston, and P.L. Ornstein A novel, competitive mGlu(5) receptor antagonist (LY344545) blocks DHPG-induced potentiation of NMDA responses but not the induction of LTP in rat hippocampal slices British Journal of Pharmacology 131 2000 239 244
36. A.J. Doherty, G.L. Collingridge, and D.E. Jane Antagonist activity of alpha-substituted 4-carboxyphenylglycine analogues at group I metabotropic glutamate receptors expressed in CHO cells British Journal of Pharmacology 126 1999 205 210
37. G.M. Morris, D.S. Goodsell, R.S. Halliday, R. Huey, W.E. Hart, and R.K. Belew Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function Journal of Computational Chemistry 19 1998 1639 1662
38. A.W. Schuttelkopf, and D.M. van Aalten PRODRG: a tool for high-throughput crystallography of protein-ligand complexes Acta Crystallographica. Section D, Biological Crystallography 60 2004 1355 1363
39. C. Oostenbrink, A. Villa, A.E. Mark, and W.F. van Gunsteren A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6 Journal of Computational Chemistry 25 2004 1656 1676
40. H.J.C. Berendsen, J.P.M. Postma, W.F. van Gunsteren, and J. Hermans Interaction models for water in relation to protein hydration Intermolecular Forces 1981 331 342
41. D. Janežič, R.M. Venable, and B.R. Brooks Harmonic analysis of large systems. III. Comparison with molecular dynamics Journal of Computational Chemistry 16 1995 1554 1566
42. E.K.G. Dobrovetsky, A. Seitova, D. Cossar, A.M. Edwards, C.H. Arrowsmith, C. Bountra, J. Weigelt, A. Bochkarev, Ligand binding domain of metabotropoc glutamate receptor mGluR5 complexed with glutamate, Unpublished, http://dx.doi.org/10.2210/pdb3lmk/pdb
43. E.K.G. Dobrovetsky, A. Seitova, D. Cossar, A.M. Edwards, C.H. Arrowsmith, C. Bountra, J. Weigelt, A. Bochkarev, Metabotropic glutamate receptor mglur1 complexed with LY341495 antagonist, Unpublished, http://dx.doi.org/10.2210/ pdb3ks9/pdb