메뉴 건너뛰기




Volumn 7, Issue 1, 2014, Pages

Insights into the mechanism of C5aR inhibition by PMX53 via implicit solvent molecular dynamics simulations and docking

Author keywords

C5a; C5aR; Class A GPCR; Complement system; Docking; Implicit solvent; Membrane protein; Molecular dynamics

Indexed keywords


EID: 84928156402     PISSN: 20461682     EISSN: None     Source Type: Journal    
DOI: 10.1186/2046-1682-7-5     Document Type: Article
Times cited : (22)

References (68)
  • 2
    • 35348821843 scopus 로고    scopus 로고
    • Function, structure and therapeutic potential of complement C5a receptors
    • Monk PN, Scola A-M, Madala P, Fairlie DP. Function, structure and therapeutic potential of complement C5a receptors. British J Pharm 2007, 152:429-448.
    • (2007) British J Pharm , vol.152 , pp. 429-448
    • Monk, P.N.1    Scola, A.-M.2    Madala, P.3    Fairlie, D.P.4
  • 3
    • 84876819390 scopus 로고    scopus 로고
    • International union of basic and clinical pharmacology. LXXXVII. Complement peptide C5a, C4a, and C3a receptors
    • Klos A, Wende E, Wareham KJ, Monk PN. International union of basic and clinical pharmacology. LXXXVII. Complement peptide C5a, C4a, and C3a receptors. Pharm Rev 2013, 65:500-543.
    • (2013) Pharm Rev , vol.65 , pp. 500-543
    • Klos, A.1    Wende, E.2    Wareham, K.J.3    Monk, P.N.4
  • 4
    • 84874623794 scopus 로고    scopus 로고
    • C5L2: a controversial receptor of complement anaphylatoxin, C5a
    • Li R, Coulthard LG, Wu MC, Taylor SM, Woodruff TM. C5L2: a controversial receptor of complement anaphylatoxin, C5a. FASEB J 2013, 27:855-864.
    • (2013) FASEB J , vol.27 , pp. 855-864
    • Li, R.1    Coulthard, L.G.2    Wu, M.C.3    Taylor, S.M.4    Woodruff, T.M.5
  • 6
    • 0036745078 scopus 로고    scopus 로고
    • Antiarthritic activity of an orally active C5a receptor antagonist against antigen-induced monarticular arthritis in the rat
    • Woodruff TM, Strachan AJ, Dryburgh N, Shiels IA, Reid RC, Fairlie DP, Taylor SM. Antiarthritic activity of an orally active C5a receptor antagonist against antigen-induced monarticular arthritis in the rat. Arthritis Rheum 2002, 46:2476-2485.
    • (2002) Arthritis Rheum , vol.46 , pp. 2476-2485
    • Woodruff, T.M.1    Strachan, A.J.2    Dryburgh, N.3    Shiels, I.A.4    Reid, R.C.5    Fairlie, D.P.6    Taylor, S.M.7
  • 8
    • 77956394836 scopus 로고    scopus 로고
    • The role of the complement system and the activation fragment C5a in the central nervous system
    • Woodruff TM, Ager RR, Tenner AJ, Noakes PG, Taylor SM. The role of the complement system and the activation fragment C5a in the central nervous system. Neruomol Med 2010, 12:179-192.
    • (2010) Neruomol Med , vol.12 , pp. 179-192
    • Woodruff, T.M.1    Ager, R.R.2    Tenner, A.J.3    Noakes, P.G.4    Taylor, S.M.5
  • 10
    • 0032572818 scopus 로고    scopus 로고
    • Small molecular probes for G-protein-coupled C5a receptors: conformationally constrained antagonists derived from the C terminus of the human plasma protein C5a
    • Wong KA, Finch AM, Pierens GK, Craik DJ, Taylor SM, Fairlie DP. Small molecular probes for G-protein-coupled C5a receptors: conformationally constrained antagonists derived from the C terminus of the human plasma protein C5a. J Med Chem 1998, 41:3417-3425.
    • (1998) J Med Chem , vol.41 , pp. 3417-3425
    • Wong, K.A.1    Finch, A.M.2    Pierens, G.K.3    Craik, D.J.4    Taylor, S.M.5    Fairlie, D.P.6
  • 12
    • 0035007326 scopus 로고    scopus 로고
    • Species dependence for binding of small molecule agonist and antagonists to the C5a receptor on polymorphonuclear leukocytes
    • Woodruff TM, Strachan AJ, Sanderson SD, Monk PN, Wong AK, Fairlie DP, Taylor SM. Species dependence for binding of small molecule agonist and antagonists to the C5a receptor on polymorphonuclear leukocytes. Inflammation 2001, 25:171-177.
    • (2001) Inflammation , vol.25 , pp. 171-177
    • Woodruff, T.M.1    Strachan, A.J.2    Sanderson, S.D.3    Monk, P.N.4    Wong, A.K.5    Fairlie, D.P.6    Taylor, S.M.7
  • 14
    • 84864221004 scopus 로고    scopus 로고
    • A new era of GPCR structural and chemical biology
    • Granier S, Kobilka B. A new era of GPCR structural and chemical biology. Nat Chem Biol 2012, 8:670-673.
    • (2012) Nat Chem Biol , vol.8 , pp. 670-673
    • Granier, S.1    Kobilka, B.2
  • 20
    • 84861367246 scopus 로고    scopus 로고
    • Biomolecular simulation: a computational microscope for molecular biology
    • Dror RO, Dirks RM, Grossman JP, Xu H, Shaw DE. Biomolecular simulation: a computational microscope for molecular biology. Annu Rev Biophys 2012, 41:429-452.
    • (2012) Annu Rev Biophys , vol.41 , pp. 429-452
    • Dror, R.O.1    Dirks, R.M.2    Grossman, J.P.3    Xu, H.4    Shaw, D.E.5
  • 21
    • 77955803232 scopus 로고    scopus 로고
    • FoldGPCR: structure prediction protocol for the transmembrane domain of G protein-coupled receptors from class A
    • Michino M, Chen J, Stevens RC, Brooks CL. FoldGPCR: structure prediction protocol for the transmembrane domain of G protein-coupled receptors from class A. Proteins 2010, 78:2189-2201.
    • (2010) Proteins , vol.78 , pp. 2189-2201
    • Michino, M.1    Chen, J.2    Stevens, R.C.3    Brooks, C.L.4
  • 22
    • 79957973576 scopus 로고    scopus 로고
    • Improving peptides
    • Thayer AM. Improving peptides. Chem Eng News 2011, 89(22):13-20.
    • (2011) Chem Eng News , vol.89 , Issue.22 , pp. 13-20
    • Thayer, A.M.1
  • 23
    • 28444450565 scopus 로고    scopus 로고
    • Modeling flexible loops in the dark-adapted and activated states of rhodopsin, a prototypical G-protein-coupled receptor
    • Nikiforovich GV, Marshall GR. Modeling flexible loops in the dark-adapted and activated states of rhodopsin, a prototypical G-protein-coupled receptor. Biophys J 2005, 89:3780-3789.
    • (2005) Biophys J , vol.89 , pp. 3780-3789
    • Nikiforovich, G.V.1    Marshall, G.R.2
  • 24
    • 34047246323 scopus 로고    scopus 로고
    • A comprehensive structure-function map of the intracellular surface of the human C5a receptor. I. Identification of critical residues
    • Matsumoto ML, Narzinski K, Kiser PD, Nikiforovich GV, Baranski TJ. A comprehensive structure-function map of the intracellular surface of the human C5a receptor. I. Identification of critical residues. J Biol Chem 2007, 282:3105-3121.
    • (2007) J Biol Chem , vol.282 , pp. 3105-3121
    • Matsumoto, M.L.1    Narzinski, K.2    Kiser, P.D.3    Nikiforovich, G.V.4    Baranski, T.J.5
  • 25
    • 40549111917 scopus 로고    scopus 로고
    • Modeling molecular mechanisms of binding of the anaphylatoxin C5a to the C5a receptor
    • Nikiforovich GV, Marshall GR, Baranski TJ. Modeling molecular mechanisms of binding of the anaphylatoxin C5a to the C5a receptor. Biochemistry 2008, 47:3117-3130.
    • (2008) Biochemistry , vol.47 , pp. 3117-3130
    • Nikiforovich, G.V.1    Marshall, G.R.2    Baranski, T.J.3
  • 26
    • 43149124854 scopus 로고    scopus 로고
    • Structure of the complement factor 5a receptor-ligand complex studied by disulfide trapping and molecular modeling
    • Hagemann IS, Miller DL, Kico JM, Nikiforovich GV, Baranski TJ. Structure of the complement factor 5a receptor-ligand complex studied by disulfide trapping and molecular modeling. J Biol Chem 2008, 283:7763-7775.
    • (2008) J Biol Chem , vol.283 , pp. 7763-7775
    • Hagemann, I.S.1    Miller, D.L.2    Kico, J.M.3    Nikiforovich, G.V.4    Baranski, T.J.5
  • 27
    • 83455179211 scopus 로고    scopus 로고
    • Structural mechanisms of constitutive activation in the C5a receptors with mutations in the extracellular loops: molecular modeling study
    • Nikiforovich GV, Baranski TJ. Structural mechanisms of constitutive activation in the C5a receptors with mutations in the extracellular loops: molecular modeling study. Proteins 2012, 80:71-80.
    • (2012) Proteins , vol.80 , pp. 71-80
    • Nikiforovich, G.V.1    Baranski, T.J.2
  • 28
    • 60849099080 scopus 로고    scopus 로고
    • Structural study of Ac-Phe-[Orn-Pro-dCha-Trp-Arg], a potent C5a recptor antagonist by NMR
    • Zhang L, Mallik B, Morikis D. Structural study of Ac-Phe-[Orn-Pro-dCha-Trp-Arg], a potent C5a recptor antagonist by NMR. Peptide Sci 2008, 90:803-815.
    • (2008) Peptide Sci , vol.90 , pp. 803-815
    • Zhang, L.1    Mallik, B.2    Morikis, D.3
  • 29
    • 0242322528 scopus 로고    scopus 로고
    • An implicit membrane generalized born theory for the study of structure, stability, and interactions of membrane proteins
    • Im W, Feig M, Brooks CL. An implicit membrane generalized born theory for the study of structure, stability, and interactions of membrane proteins. Biophys J 2003, 85:2900-2918.
    • (2003) Biophys J , vol.85 , pp. 2900-2918
    • Im, W.1    Feig, M.2    Brooks, C.L.3
  • 30
    • 0038792211 scopus 로고    scopus 로고
    • New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations
    • Lee MS, Feig M, Salzbury FR, Brooks CL. New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations. J Comp Chem 2003, 24:1348-1356.
    • (2003) J Comp Chem , vol.24 , pp. 1348-1356
    • Lee, M.S.1    Feig, M.2    Salzbury, F.R.3    Brooks, C.L.4
  • 31
    • 17444426051 scopus 로고    scopus 로고
    • A generalized Born formalism for heterogeneous dielec- tric environments: application to the implicit modeling of biological membranes
    • Tanizaki S, Feig M. A generalized Born formalism for heterogeneous dielec- tric environments: application to the implicit modeling of biological membranes. J Chem Phys 2005, 122:124706.
    • (2005) J Chem Phys , vol.122 , pp. 124706
    • Tanizaki, S.1    Feig, M.2
  • 32
    • 1942456697 scopus 로고    scopus 로고
    • Recent advances in the development and application of implicit solvent models in biomolecule simulations
    • Feig M, Brooks CL. Recent advances in the development and application of implicit solvent models in biomolecule simulations. Curr Op Struct Biol 2004, 14:217-224.
    • (2004) Curr Op Struct Biol , vol.14 , pp. 217-224
    • Feig, M.1    Brooks, C.L.2
  • 33
    • 84874665665 scopus 로고    scopus 로고
    • Membrane protein native state discrimination by implicit membrane models
    • Yuzlenko O, Lazaridis T. Membrane protein native state discrimination by implicit membrane models. J Comp Chem 2013, 34:731-738.
    • (2013) J Comp Chem , vol.34 , pp. 731-738
    • Yuzlenko, O.1    Lazaridis, T.2
  • 35
    • 3142714765 scopus 로고    scopus 로고
    • Extending the treatment of backbone energetics in protein force fields: limitations of gas- phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations
    • Mackerell AD, Feig M, Brooks CL. Extending the treatment of backbone energetics in protein force fields: limitations of gas- phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J Comput Chem 2004, 25:1400-1415.
    • (2004) J Comput Chem , vol.25 , pp. 1400-1415
    • Mackerell, A.D.1    Feig, M.2    Brooks, C.L.3
  • 37
    • 0027393187 scopus 로고
    • Statistical clustering techniques for analysis of long molecular dynamics trajectories. I: analysis of 2.2 ns trajectories of YPGDV
    • Karpen ME, Tobias DJ, Brooks CL. Statistical clustering techniques for analysis of long molecular dynamics trajectories. I: analysis of 2.2 ns trajectories of YPGDV. Biochemistry 1993, 32:412-420.
    • (1993) Biochemistry , vol.32 , pp. 412-420
    • Karpen, M.E.1    Tobias, D.J.2    Brooks, C.L.3
  • 38
    • 84973857317 scopus 로고
    • ART-2: self-organization of stable category recognition codes for analog input patterns
    • Carpenter GA, Grossberg S. ART-2: self-organization of stable category recognition codes for analog input patterns. Appl Opt 1987, 26:4919-4930.
    • (1987) Appl Opt , vol.26 , pp. 4919-4930
    • Carpenter, G.A.1    Grossberg, S.2
  • 39
    • 34247550299 scopus 로고    scopus 로고
    • Modeling of the complex between transducin and photoactivated rhodopsin, a prototypical G-protein-coupled receptor
    • Nikiforovich GV, Taylor CM, Marshall GR. Modeling of the complex between transducin and photoactivated rhodopsin, a prototypical G-protein-coupled receptor. Biochemistry 2007, 46:4734-4744.
    • (2007) Biochemistry , vol.46 , pp. 4734-4744
    • Nikiforovich, G.V.1    Taylor, C.M.2    Marshall, G.R.3
  • 40
    • 84874724662 scopus 로고    scopus 로고
    • Update on activities at the Universal Protein Resource (UniProt) in 2013
    • The UniProt Consortium
    • The UniProt Consortium Update on activities at the Universal Protein Resource (UniProt) in 2013. Nucleic Acids Res 2013, 41:D43-D47. The UniProt Consortium.
    • (2013) Nucleic Acids Res , vol.41 , pp. D43-D47
  • 42
    • 33646940952 scopus 로고    scopus 로고
    • Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes
    • Ryckaert JP, Ciccotti G, Berendsen HJC. Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys 1997, 23:327-341.
    • (1997) J Comput Phys , vol.23 , pp. 327-341
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 43
    • 0001368373 scopus 로고
    • Étude comparative de la distribution florale dans une portion des Alpes et des Jura
    • Jaccard P. Étude comparative de la distribution florale dans une portion des Alpes et des Jura. Bulletin de la Société Vaudoise des Sciences Naturelles 1901, 37:547-579.
    • (1901) Bulletin de la Société Vaudoise des Sciences Naturelles , vol.37 , pp. 547-579
    • Jaccard, P.1
  • 45
    • 84907095419 scopus 로고    scopus 로고
    • R: A language and environment for statistical computing
    • Vienna, Austria: R Development Core Team
    • R Development Core Team R: A language and environment for statistical computing. R Foundation for Statistical Computing 2011, Vienna, Austria: R Development Core Team, R Development Core Team.
    • (2011) R Foundation for Statistical Computing
  • 48
    • 0017429069 scopus 로고
    • Areas, volumes, packing, and protein structure
    • Richards FM. Areas, volumes, packing, and protein structure. Ann Rev Biophys Bioeng 1977, 6:151-176.
    • (1977) Ann Rev Biophys Bioeng , vol.6 , pp. 151-176
    • Richards, F.M.1
  • 49
    • 0034084991 scopus 로고    scopus 로고
    • Combined molecular mechanical and con- tinuum solvent approach (MM-PBSA/GBSA) to predict ligand binding
    • Massova I, Kollman PA. Combined molecular mechanical and con- tinuum solvent approach (MM-PBSA/GBSA) to predict ligand binding. Perspect Drug Discov Des 2000, 18:113-135.
    • (2000) Perspect Drug Discov Des , vol.18 , pp. 113-135
    • Massova, I.1    Kollman, P.A.2
  • 50
    • 28144441347 scopus 로고    scopus 로고
    • Evaluating the molecular mechanics Poisson-Boltzmann surface area free energy method using a congeneric series of ligands to p38 MAP kinase
    • Pearlman DA. Evaluating the molecular mechanics Poisson-Boltzmann surface area free energy method using a congeneric series of ligands to p38 MAP kinase. J Med Chem 2005, 48:7796-7807.
    • (2005) J Med Chem , vol.48 , pp. 7796-7807
    • Pearlman, D.A.1
  • 51
    • 84880020995 scopus 로고    scopus 로고
    • MM-GB (PB) SA Calculations of Protein-Ligand Binding Free Energies, Molecular Dynamics - Studies of Synthetic and Biological Macromolecules
    • Tech, Chapter 9 Edited by Wang L
    • Hayes JM, Archontis G. MM-GB (PB) SA Calculations of Protein-Ligand Binding Free Energies, Molecular Dynamics - Studies of Synthetic and Biological Macromolecules. Tech, Chapter 9 2012, 171-190. Wang L.
    • (2012) , pp. 171-190
    • Hayes, J.M.1    Archontis, G.2
  • 52
    • 79952498871 scopus 로고    scopus 로고
    • Wordom: a user-friendly program for the analysis of molecular structures, trajectories, and free energy surfaces
    • Seeber M, Felline A, Raimondi F, Muff S, Friedman R, Rao F, Caflisch A, Fanelli F. Wordom: a user-friendly program for the analysis of molecular structures, trajectories, and free energy surfaces. J Comp Chem 2011, 32:1183-1194.
    • (2011) J Comp Chem , vol.32 , pp. 1183-1194
    • Seeber, M.1    Felline, A.2    Raimondi, F.3    Muff, S.4    Friedman, R.5    Rao, F.6    Caflisch, A.7    Fanelli, F.8
  • 53
    • 77955839358 scopus 로고    scopus 로고
    • Species specificity of the complement inhibitor compstatin investigated by all-atom molecular dynamics simulations
    • Tamamis P, Morikis D, Floudas CA, Archontis G. Species specificity of the complement inhibitor compstatin investigated by all-atom molecular dynamics simulations. Proteins 2010, 78:2655-2667.
    • (2010) Proteins , vol.78 , pp. 2655-2667
    • Tamamis, P.1    Morikis, D.2    Floudas, C.A.3    Archontis, G.4
  • 54
    • 80053938364 scopus 로고    scopus 로고
    • Design of a modified mouse protein with ligand binding properties of its human analog by molecular dynamics simulations: the case of C3 inhibition by compstatin
    • Tamamis P, Pierou P, Mytidou C, Floudas CA, Morikis D, Archontis G. Design of a modified mouse protein with ligand binding properties of its human analog by molecular dynamics simulations: the case of C3 inhibition by compstatin. Proteins 2011, 79:3166-3179.
    • (2011) Proteins , vol.79 , pp. 3166-3179
    • Tamamis, P.1    Pierou, P.2    Mytidou, C.3    Floudas, C.A.4    Morikis, D.5    Archontis, G.6
  • 55
    • 0023050369 scopus 로고
    • The Opsin family of proteins
    • Findlay JB, Pappin DJ. The Opsin family of proteins. Biochem J 1986, 238:625-642.
    • (1986) Biochem J , vol.238 , pp. 625-642
    • Findlay, J.B.1    Pappin, D.J.2
  • 56
    • 79551494718 scopus 로고    scopus 로고
    • Simplified modeling approach suggests structural mechanisms for constitutive activation of the C5a receptor
    • Nikiforovich GV, Marshall GR, Baranski TJ. Simplified modeling approach suggests structural mechanisms for constitutive activation of the C5a receptor. Proteins 2011, 79:787-802.
    • (2011) Proteins , vol.79 , pp. 787-802
    • Nikiforovich, G.V.1    Marshall, G.R.2    Baranski, T.J.3
  • 57
    • 77449146970 scopus 로고    scopus 로고
    • Modeling the possible conformations of the extracellular receptors in G-protein-coupled receptors
    • Nikiforovich GV, Taylor CM, Marshall G, Baranski TJ. Modeling the possible conformations of the extracellular receptors in G-protein-coupled receptors. Proteins 2010, 78:271-285.
    • (2010) Proteins , vol.78 , pp. 271-285
    • Nikiforovich, G.V.1    Taylor, C.M.2    Marshall, G.3    Baranski, T.J.4
  • 59
    • 0035923408 scopus 로고    scopus 로고
    • Mapping the ligand-binding site on the C5a receptor: arginine 74 of C5a contacts aspartate 282 of the C5a receptor
    • Cain SA, Coughlan T, Monk PN. Mapping the ligand-binding site on the C5a receptor: arginine 74 of C5a contacts aspartate 282 of the C5a receptor. Biochemistry 2001, 40:14047-14052.
    • (2001) Biochemistry , vol.40 , pp. 14047-14052
    • Cain, S.A.1    Coughlan, T.2    Monk, P.N.3
  • 60
    • 0141922889 scopus 로고    scopus 로고
    • Characterisation of C5a receptor agonists from phage display libraries
    • Cain SA, Higginbottom A, Monk PN. Characterisation of C5a receptor agonists from phage display libraries. Biochem Pharmacol 2003, 66:1833-1840.
    • (2003) Biochem Pharmacol , vol.66 , pp. 1833-1840
    • Cain, S.A.1    Higginbottom, A.2    Monk, P.N.3
  • 62
    • 3242881211 scopus 로고    scopus 로고
    • SuperPose: a simple server for sophisticated structural superposition
    • Maiti R, Van Domselaar GH, Zhang H, Wishart DS. SuperPose: a simple server for sophisticated structural superposition. Nucleic Acids Res 2004, 32(Web Server issue):W590W594.
    • (2004) Nucleic Acids Res , vol.32 , Issue.Web Server Issue , pp. W590W594
    • Maiti, R.1    Van Domselaar, G.H.2    Zhang, H.3    Wishart, D.S.4
  • 65
    • 84884316483 scopus 로고    scopus 로고
    • Molecular recognition of CXCR4 by a dual tropic HIV-1 gp120 V3 loop
    • Tamamis P, Floudas CA. Molecular recognition of CXCR4 by a dual tropic HIV-1 gp120 V3 loop. Biophys J 2013, 105:1502-1514.
    • (2013) Biophys J , vol.105 , pp. 1502-1514
    • Tamamis, P.1    Floudas, C.A.2
  • 66
    • 84899740016 scopus 로고    scopus 로고
    • Molecular recognition of CCR5 by an HIV-1 gp120 V3 Loop
    • Tamamis P, Floudas CA. Molecular recognition of CCR5 by an HIV-1 gp120 V3 Loop. PLoS ONE 2014, 9:e95767.
    • (2014) PLoS ONE , vol.9 , pp. e95767
    • Tamamis, P.1    Floudas, C.A.2
  • 67
    • 84899708038 scopus 로고    scopus 로고
    • Elucidating a key component of cancer metastasis: CXCL12 (SDF-1α) binding to CXCR4
    • Tamamis P, Floudas CA. Elucidating a key component of cancer metastasis: CXCL12 (SDF-1α) binding to CXCR4. J Chem Inf Model 2014, 54:1174-1188.
    • (2014) J Chem Inf Model , vol.54 , pp. 1174-1188
    • Tamamis, P.1    Floudas, C.A.2
  • 68
    • 84903289235 scopus 로고    scopus 로고
    • Elucidating a key anti-HIV-1 and cancer-associated axis: the structure of CCL5 (Rantes) in complex with CCR5
    • Tamamis P, Floudas CA. Elucidating a key anti-HIV-1 and cancer-associated axis: the structure of CCL5 (Rantes) in complex with CCR5. Sci Rep 2014, 4:5447.
    • (2014) Sci Rep , vol.4 , pp. 5447
    • Tamamis, P.1    Floudas, C.A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.