Molecular dynamics simulation of chemokine receptors in lipid bilayer: A case study on C-C chemokine receptor type 2

Chemical Biology and Drug Design

Volumn 82, Issue 5, 2013, Pages 534-545

  Shahlaei, Mohsen ^a   Fassihi, Afshin ^b   Papaleo, Elena ^c   Pourfarzam, Morteza ^b  

^a KERMANSHAH UNIVERSITY OF MEDICAL SCIENCES   (Iran)

^b ISFAHAN UNIVERSITY OF MEDICAL SCIENCES   (Iran)

^c UNIVERSITY OF MILANO BICOCCA   (Italy)

Author keywords

C C chemokine receptor type 2; Homology modeling; INCB3344; Molecular docking; Molecular dynamics simulation

Indexed keywords

CC CHEMOKINE RECEPTOR TYPE 2; CHEMOKINE RECEPTOR; GLUTAMIC ACID; HISTIDINE; LIGAND; N [2 [[1 [4 (1,3 BENZODIOXOL 5 YL) 4 HYDROXYCYCLOHEXYL] 4 ETHOXY 3 PYRROLIDINYL]AMINO] 2 OXOETHYL] 3 (TRIFLUOROMETHYL)BENZAMIDE; TRYPTOPHAN; TYROSINE; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; CONFORMATIONAL TRANSITION; LIGAND BINDING; LIPID BILAYER; MOLECULAR DOCKING; MOLECULAR DYNAMICS; PRIORITY JOURNAL;

C-C CHEMOKINE RECEPTOR TYPE 2; HOMOLOGY MODELING; INCB3344; MOLECULAR DOCKING; MOLECULAR DYNAMICS SIMULATION;

AMINO ACID SEQUENCE; BINDING SITES; CATALYTIC DOMAIN; HUMANS; HYDROGEN BONDING; LIPID BILAYERS; MOLECULAR DYNAMICS SIMULATION; MOLECULAR SEQUENCE DATA; PROTEIN BINDING; PYRROLIDINES; RECEPTORS, CCR2; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 84885836131     PISSN: 17470277     EISSN: 17470285     Source Type: Journal    
DOI: 10.1111/cbdd.12179     Document Type: Article

References (54)

1. Berger O., Edholm O., Jähnig F. (1997) Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature. Biophys J.;72:2002-2013.
2. Arkan E., Shahlaei M., Pourhossein A., Fakhri K., Fassihi A. (2010) Validated QSAR analysis of some diaryl substituted pyrazoles as CCR2 inhibitors by various linear and nonlinear multivariate chemometrics methods. Eur J Med Chem;45:3394-3406.
3. Saghaie L., Shahlaei M., Fassihi A., Madadkar-Sobhani A., Gholivand M., Pourhossein A. (2011) QSAR analysis for some diaryl-substituted pyrazoles as CCR2 inhibitors by GA-stepwise MLR. Chem Biol Drug Des;77:75-85.
4. Shahlaei M., Fassihi A., Saghaie L. (2010) Application of PC-ANN and PC-LS-SVM in QSAR of CCR1 antagonist compounds: a comparative study. Eur J Med Chem;45:1572-1582.
5. Shahlaei M., Madadkar-Sobhani A., Mahnam K., Fassihi A., Saghaie L., Mansourian M. (2011) Homology modeling of human CCR5 and analysis of its binding properties through molecular docking and molecular dynamics simulation. BBA - Biomembranes;1808:802-817.
6. Tak P. (2006) Chemokine inhibition in inflammatory arthritis. Best Pract Res Clin Rheumatol;20:929-939.
7. Coll B., Alonso-Villaverde C., Joven J. (2007) Monocyte chemoattractant protein-1 and atherosclerosis: is there room for an additional biomarker? Clin Chim Acta;383:21-29.
8. Mahad D., Ransohoff R. (2003) The role of MCP-1 (CCL2) and CCR2 in multiple sclerosis and experimental autoimmune encephalomyelitis (EAE). Semin Immunol;15:23-32.
9. Ivetac A., Sansom M. (2008) Molecular dynamics simulations and membrane protein structure quality. Eur Biophys J;37:403-409.
10. Shin N., Baribaud F., Wang K., Yang G., Wynn R., Covington M.B., Feldmanet P., Gallaghera K.B., Leffeta L.M., Loa Y.Y., Wangc A., Xuec C.-B., Newtona R.C., Scherle P.A. (2009) Pharmacological characterization of INCB3344, a small molecule antagonist of human CCR2. Biochem Biophys Res Commun;387:251-255.
11. Izikson L., Klein R., Charo I., Weiner H., Luster A. (2000) Resistance to experimental autoimmune encephalomyelitis in mice lacking the CC. J Exp Med;192:1075-1080.
12. Brodmerkel C.M., Huber R., Covington M., Diamond S., Hall L., Collins R., Leffet L. et al. (2005) Discovery and pharmacological characterization of a novel rodent-active CCR2 antagonist, INCB3344. J Immunol;175:5370-5378.
13. Kabsch W., Sander C. (1983) Dictionary of protein secondary structure - pattern-recognition of hydrogen-bonded and geometrical features. Biopolymers;22:2577-2637.
14. Singh R., Sobhia M.E. (2011) Homology modeling of human CCR2 receptor. Med Chem Res;20:1704-1712.
15. Singh R., Sobhia M.E. (2012) Structure prediction and molecular dynamics simulations of a G-protein coupled receptor: human CCR2 receptor. J Biomol Struct Dyn;31:694-715.
16. Chavan S., Pawar S., Singh R., Sobhia M.E. (2012) Binding site characterization of G protein-coupled receptor by alanine-scanning mutagenesis using molecular dynamics and binding free energy approach: application to CC chemokine receptor-2 (CCR2). Mol Divers;16:401-413.
17. Wu B., Chien E.Y.T., Mol C.D., Fenalti G., Liu W., Katritch V., Abagyan R. et al. (2010) Structures of the CXCR4 chemokine GPCR with small-molecule and cyclic peptide antagonists. Science;330:1066-1071.
18. Altschul S.F., Madden T.L., Schäffer1 A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res;25:3389-3402.
19. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., Bourne P.E., (2000) The protein data bank. Nucleic Acids Res;28:235-242.
20. Cserzö M., Wallin E., Simon I., von Heijne G., Elofsson A. (1997) Prediction of transmembrane alpha-helices in prokaryotic membrane proteins: the dense alignment surface method. Protein Eng;10:673-676.
21. Tusnády G., Simon I. (1998) Principles governing amino acid composition of integral membrane proteins: application to topology prediction. J Mol Biol;283:489-506.
22. Viklund H., Elofsson A. (2008) OCTOPUS: improving topology prediction by two-track ANN-based preference scores and an extended topological grammar. Bioinformatics;24:1662-1668.
23. Sonnhammer E.L., von Heijne G., Krogh A. (1998) A hidden Markov model for predicting transmembrane helices in protein sequences. Proc ISMB;6:175-182.
24. Kahsay R., Gao G., Liao L. (2005) An improved hidden Markov model for transmembrane protein detection and topology prediction and its applications to complete genomes. Bioinformatics;21:1853-1858.
25. Hofmann K., Stoffel W. (1993) TMbase - A database of membrane spanning proteins segments. Biol Chem Hoppe-Seyler;347:166.
26. Juretić D., Lee B., Trinajstić N., Williams R. (1993) Conformational preference functions for predicting helices in membrane proteins. Biopolymers;33:255-273.
27. Pollastri G., McLysaght A. (2005) Porter: a new, accurate server for protein secondary structure prediction. Bioinformatics;21:1719-1720.
28. Käll L., Krogh A., Sonnhammer E. (2005) An HMM posterior decoder for sequence feature prediction that includes homology information. Bioinformatics;1:i251-i257.
29. Jones D.T. (1999) Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol;292:195-202.
30. Claros M.G., Von Heijne G. (1994) TopPred II: an improved software for membrane protein structure predictions. Comput Appl Biosci;10:685-686.
31. Thompson J., Higgins D., Gibson T. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment. Nucleic Acids Res;22:4673-4680.
32. Baldwin J., Schertler G., Unger V. (1997) An alpha-carbon template for the transmembrane helices in the rhodopsin family of. J Mol Biol;272:144-164.
33. Sali A., Blundell T. (1993) Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol;234:779-815.
34. Laskowski R.A., MacArthur M.W., Moss D.S., Thornton J.M. (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Crystallogr;26:283-291.
35. Morris G.M., Goodsell D.S., Halliday R.S., Huey R., Hart W.E., Belew R.K., Olson A.J. (1998) Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J Comput Chem;19:1639-1662.
36. Berkhout T.A., Blaney F.E., Bridges A.M., Cooper D.G., Forbes I.T., Gribble A.D., Groot P.H.E., Hardy A., Ife R. J., Kaur R., Moores K.E., Shillito H., Willetts J., Witherington J. (2003) CCR2: characterization of the antagonist binding site from a combined receptor modeling/mutagenesis approach. J Med Chem;46:4070-4086.
37. Kim J.H., Lim J.W., Lee S.W., Kim K., No K.T. (2010) Ligand supported homology modeling and docking evaluation of CCR2: docked pose selection by consensus scoring. J Mol Model;17:2707-2716.
38. Van Der Spoel D., Lindahl E., Hess B., Groenhof G., Mark A.E., Berendsen H.J.C. (2005) GROMACS: fast, flexible, and free. J Comput Chem;26:1701-1718.
39. Tieleman D.P., Berendsen H.J.C. (1996) Molecular dynamics simulations of a fully hydrated dipalmitoylphosphatidylcholine bilayer with different macroscopic boundary conditions and parameters. J Chem Phys;105:4871-4880.
40. van Gunsteren W.F., Billeter S.R., Eising A.A., Hünenberger P.H., Krüger P., Mark A.E., Scott W.R.P., Tironi I.G. (1996) Biomolecular Simulation: the GROMOS96 Manual and User Guide. Zurich, Switzerland: Biomos, Groningen and Hochschulverlag AG, Germany and er ETH Zü rich.
41. Tieleman P., MacCallum J., Ash W., Kandt C., Xu Z., Monticelli L. (2006) Membrane protein simulations with a united-atom lipid and all-atom protein model: lipid-protein interactions, side chain transfer free energies and model proteins. J Phys Condens Matter;18:S1221-S1234.
42. Van Aalten D.M., Bywater R., Findlay J.B., Hendlich M., Hooft R.W., Vriend G. (1996) PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules. J Comput Aided Mol Des;10:255-262.
43. Darden T., York D., Pedersen L. (1993) Particle mesh Ewald: an N [center-dot] log(N) method for Ewald sums in large systems. J Chem Phys;98:10089-10092.
44. Hess B., Bekker H., Berendsen H.J.C., Fraaije J.G.E.M. (1997) LINCS: a linear constraint solver for molecular simulations. J Comput Chem;18:1463-1472.
45. Humphrey W., Dalke A., Schulten K. (1996) VMD: visual molecular dynamics. J Mol Graph;14:33-38.
46. Blanpain C., Lee B., Vakili J., Doranz B.J., Govaerts C., Migeotte I., Sharron M., Dupriez V., Vassart G., Doms R.W., Parmentier M. (1999) Extracellular cysteines of CCR5 are required for chemokine binding, but. J Biol Chem;274:18902-18908.
47. Genoud S., Kajumo F., Guo Y., Thompson D., Dragic T. (1999) CCR5-Mediated human immunodeficiency virus entry depends on an amino-terminal. J Virol;73:1645-1648.
48. Pease J.E., Wang J., Ponath P.D., Murphy P.M. (1998) The N-terminal extracellular segments of the chemokine receptors CCR1 and CCR3. J Biol Chem;273:19972-19976.
49. Ji T.H., Grossmann M., Ji I. (1998) G protein-coupled receptors. I. Diversity of receptor-ligand interactions. J Biol Chem;273:17299-17302.
50. Liu S., Shi X., Liu C., Sun Z. (2004) Characterize dynamic conformational space of human CCR5 extracellular domain by molecular modeling and molecular dynamics simulation. J Mol Struct (Thoechem);673:133-143.
51. Hall S.E., Mao A., Nicolaidou V., Finelli M., Wise E.L., Nedjai B., Kanjanapangka J., Harirchian P., Chen D., Selchau V., Ribeiro S., Schyler S., Pease J.E., Horuk R., Vaidehi N. (2009) Elucidation of binding sites of dual antagonists in the human chemokine receptors CCR2 and CCR5. Mol Pharmacol;75:1325-1336.
52. Liapakis G., Chan W.C., Papadokostaki M., Javitch J.A. (2004) Synergistic contributions of the functional groups of epinephrine to its affinity and efficacy at the ß2 adrenergic receptor. Mol Pharmacol;65:1181-1190.
53. Kenakin T. (1997) Agonist-specific receptor conformations. Trends Pharmacol Sci;18:416-417.
54. Peleg G., Ghanouni P., Kobilka B., Zare R. (2001) Single-molecule spectroscopy of the beta(2) adrenergic receptor: observation of conformational substrates in a membrane protein. Proc Natl Acad Sci USA;98:8469-8474.