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Volumn 5, Issue 8, 2013, Pages

MOLE 2.0: Advanced approach for analysis of biomacromolecular channels

Author keywords

BM3; CAM; Channels; Cytochrome P450; Pores; Protein structures; Tunnels

Indexed keywords


EID: 84884364871     PISSN: None     EISSN: 17582946     Source Type: Journal    
DOI: 10.1186/1758-2946-5-39     Document Type: Article
Times cited : (262)

References (61)
  • 1
    • 61449156398 scopus 로고    scopus 로고
    • A review about nothing: Are apolar cavities in proteins really empty?
    • Matthews BW, Liu L: A review about nothing: are apolar cavities in proteins really empty? Protein Sci 2009, 18:494-502.
    • (2009) Protein Sci , vol.18 , pp. 494-502
    • Matthews, B.W.1    Liu, L.2
  • 2
    • 0028275784 scopus 로고
    • The three-dimensional structure of human erythrocyte aquaporin CHIP
    • Walz T, Smith BL, Agre P, Engel A: The three-dimensional structure of human erythrocyte aquaporin CHIP. EMBO J 1994, 13:2985-2993. (Pubitemid 24213450)
    • (1994) EMBO Journal , vol.13 , Issue.13 , pp. 2985-2993
    • Walz, T.1    Smith, B.L.2    Agre, P.3    Engel, A.4
  • 3
    • 0037198626 scopus 로고    scopus 로고
    • Crystal structure and mechanism of a calcium-gated potassium channel
    • DOI 10.1038/417515a
    • Jiang Y, Lee A, Chen J, Cadene M, Chait BT, MacKinnon R: Crystal structure and mechanism of a calcium-gated potassium channel. Nature 2002, 417:515-522. (Pubitemid 34595912)
    • (2002) Nature , vol.417 , Issue.6888 , pp. 515-522
    • Jiang, Y.1    Lee, A.2    Chen, J.3    Cadene, M.4    Chait, B.T.5    MacKinnon, R.6
  • 5
    • 81355156238 scopus 로고    scopus 로고
    • Guide to Receptors and Channels (GRAC), 5th edition
    • Alexander SPH, Mathie A, Peters JA: Guide to Receptors and Channels (GRAC), 5th edition. Br J Pharmacol 2011, 164(Suppl):S1-S324.
    • (2011) Br J Pharmacol , vol.164 , Issue.SUPPL.
    • Alexander, S.P.H.1    Mathie, A.2    Peters, J.A.3
  • 6
    • 4544342928 scopus 로고    scopus 로고
    • Potassium channels and the atomic basis of selective ion conduction (Nobel Lecture)
    • MacKinnon R: Potassium channels and the atomic basis of selective ion conduction (Nobel Lecture). Angewandte Chemie (International ed. in English) 2004, 43:4265-4277.
    • (2004) Angewandte Chemie (International Ed. in English) , vol.43 , pp. 4265-4277
    • Mackinnon, R.1
  • 7
    • 34547116864 scopus 로고    scopus 로고
    • Structural characteristics of channels and pathways in photosystem II including the identification of an oxygen channel
    • DOI 10.1016/j.jsb.2007.01.016, PII S1047847707000238
    • Murray JW, Barber J: Structural characteristics of channels and pathways in photosystem II including the identification of an oxygen channel. J Struct Biol 2007, 159:228-237. (Pubitemid 47096868)
    • (2007) Journal of Structural Biology , vol.159 , Issue.2 , pp. 228-237
    • Murray, J.W.1    Barber, J.2
  • 8
    • 62049085169 scopus 로고    scopus 로고
    • Cyanobacterial photosystem II at 2.9-A resolution and the role of quinones, lipids, channels and chloride
    • Guskov A, Kern J, Gabdulkhakov A, Broser M, Zouni A, Saenger W: Cyanobacterial photosystem II at 2.9-A resolution and the role of quinones, lipids, channels and chloride. Nat Struct Mol Biol 2009, 16:334-342.
    • (2009) Nat Struct Mol Biol , vol.16 , pp. 334-342
    • Guskov, A.1    Kern, J.2    Gabdulkhakov, A.3    Broser, M.4    Zouni, A.5    Saenger, W.6
  • 9
    • 33745628037 scopus 로고    scopus 로고
    • The Geometry of the Ribosomal Polypeptide Exit Tunnel
    • DOI 10.1016/j.jmb.2006.05.023, PII S002228360600605X
    • Voss NR, Gerstein M, Steitz TA, Moore PB: The geometry of the ribosomal polypeptide exit tunnel. J Mol Biol 2006, 360:893-906. (Pubitemid 43993916)
    • (2006) Journal of Molecular Biology , vol.360 , Issue.4 , pp. 893-906
    • Voss, N.R.1    Gerstein, M.2    Steitz, T.A.3    Moore, P.B.4
  • 10
    • 3042587451 scopus 로고    scopus 로고
    • A survey of active site access channels in cytochromes P450
    • DOI 10.1016/j.jinorgbio.2004.02.007, PII S0162013404000431
    • Wade RC, Winn PJ, Schlichting I, Sudarko: A survey of active site access channels in cytochromes P450. J Inorg Biochem 2004, 98:1175-1182. (Pubitemid 38833595)
    • (2004) Journal of Inorganic Biochemistry , vol.98 , Issue.7 , pp. 1175-1182
    • Wade, R.C.1    Winn, P.J.2    Schlichting, I.3    Sudarko4
  • 12
    • 84857569031 scopus 로고    scopus 로고
    • Is there a relationship between the substrate preferences and structural flexibility of cytochromes P450?
    • Otyepka M, Berka K, Anzenbacher P: Is there a relationship between the substrate preferences and structural flexibility of cytochromes P450? Curr Drug Metab 2012, 13:130-142.
    • (2012) Curr Drug Metab , vol.13 , pp. 130-142
    • Otyepka, M.1    Berka, K.2    Anzenbacher, P.3
  • 13
    • 80054709526 scopus 로고    scopus 로고
    • Membrane position of ibuprofen agrees with suggested access path entrance to cytochrome P450 2C9 active site
    • Berka K, Hendrychová T, Anzenbacher P, Otyepka M: Membrane position of ibuprofen agrees with suggested access path entrance to cytochrome P450 2C9 active site. J Phys Chem A 2011, 115:11248-11255.
    • (2011) J Phys Chem A , vol.115 , pp. 11248-11255
    • Berka, K.1    Hendrychová, T.2    Anzenbacher, P.3    Otyepka, M.4
  • 14
    • 84857532829 scopus 로고    scopus 로고
    • Dynamics and hydration of the active sites of mammalian cytochromes P450 probed by molecular dynamics simulations
    • Hendrychova T, Berka K, Navratilova V, Anzenbacher P, Otyepka M: Dynamics and hydration of the active sites of mammalian cytochromes P450 probed by molecular dynamics simulations. Curr Drug Metab 2012, 13:177-189.
    • (2012) Curr Drug Metab , vol.13 , pp. 177-189
    • Hendrychova, T.1    Berka, K.2    Navratilova, V.3    Anzenbacher, P.4    Otyepka, M.5
  • 17
    • 34547795897 scopus 로고    scopus 로고
    • Acetylcholinesterases-The structural similarities and differences
    • Wiesner J, Kriz Z, Kuca K, Jun D, Koca J: Acetylcholinesterases-the structural similarities and differences. J Enzyme Inhib Med Chem 2007, 22:417-424.
    • (2007) J Enzyme Inhib Med Chem , vol.22 , pp. 417-424
    • Wiesner, J.1    Kriz, Z.2    Kuca, K.3    Jun, D.4    Koca, J.5
  • 18
    • 79959357752 scopus 로고    scopus 로고
    • Backdoor opening mechanism in acetylcholinesterase based on X-ray crystallography and molecular dynamics simulations
    • Sanson B, Colletier J-P, Xu Y, Lang PT, Jiang H, Silman I, Sussman JL, Weik M: Backdoor opening mechanism in acetylcholinesterase based on X-ray crystallography and molecular dynamics simulations. Protein Sci 2011, 20:1114-1118.
    • (2011) Protein Sci , vol.20 , pp. 1114-1118
    • Sanson, B.1    Colletier, J.-P.2    Xu, Y.3    Lang, P.T.4    Jiang, H.5    Silman, I.6    Sussman, J.L.7    Weik, M.8
  • 19
    • 35748972048 scopus 로고    scopus 로고
    • MOLE: A Voronoi Diagram-Based Explorer of Molecular Channels, Pores, and Tunnels
    • DOI 10.1016/j.str.2007.10.007, PII S0969212607003759
    • Petrek M, Kosinová P, Koca J, Otyepka M: MOLE: a Voronoi diagram-based explorer of molecular channels, pores, and tunnels. Structure 2007, 15:1357-1363. (Pubitemid 350051932)
    • (2007) Structure , vol.15 , Issue.11 , pp. 1357-1363
    • Petrek, M.1    Kosinova, P.2    Koca, J.3    Otyepka, M.4
  • 21
    • 84865201962 scopus 로고    scopus 로고
    • A single mutation in a tunnel to the active site changes the mechanism and kinetics of product release in haloalkane dehalogenase LinB
    • Biedermannová L, Prokop Z, Gora A, Chovancová E, Kovács M, Damborsky J, Wade RC: A single mutation in a tunnel to the active site changes the mechanism and kinetics of product release in haloalkane dehalogenase LinB. J Biol Chem 2012, 287:29062-29074.
    • (2012) J Biol Chem , vol.287 , pp. 29062-29074
    • Biedermannová, L.1    Prokop, Z.2    Gora, A.3    Chovancová, E.4    Kovács, M.5    Damborsky, J.6    Wade, R.C.7
  • 23
    • 84855653879 scopus 로고    scopus 로고
    • Identifying continuous pores in protein structures with PROPORES by computational repositioning of gating residues
    • Lee P-H, Helms V: Identifying continuous pores in protein structures with PROPORES by computational repositioning of gating residues. Proteins 2011, 80:421-432.
    • (2011) Proteins , vol.80 , pp. 421-432
    • Lee, P.-H.1    Helms, V.2
  • 24
    • 0027053611 scopus 로고
    • POCKET: A computer graphics method for identifying and displaying protein cavities and their surrounding amino acids
    • DOI 10.1016/0263-7855(92)80074-N
    • Levitt DG, Banaszak LJ: POCKET: a computer graphies method for identifying and displaying protein cavities and their surrounding amino acids. J Mol Graph 1992, 10:229-234. (Pubitemid 23018967)
    • (1992) Journal of Molecular Graphics , vol.10 , Issue.4 , pp. 229-234
    • Levitt, D.G.1    Banaszak, L.J.2
  • 25
    • 0031370977 scopus 로고    scopus 로고
    • LIGSITE: Automatic and efficient detection of potential small molecule-binding sites in proteins
    • DOI 10.1016/S1093-3263(98)00002-3, PII S1093326398000023
    • Hendlich M, Rippmann F, Barnickel G: LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins. J Mol Graphics Model 1997, 15:359-363. (Pubitemid 28409807)
    • (1997) Journal of Molecular Graphics and Modelling , vol.15 , Issue.6 , pp. 359-363
    • Hendlich, M.1    Rippmann, F.2    Barnickel, G.3
  • 26
    • 33750029942 scopus 로고    scopus 로고
    • LIGSITEcsc: Predicting ligand binding sites using the Connolly surface and degree of conservation
    • Huang B, Schroeder M: LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation. BMC Struct Biol 2006, 6:19.
    • (2006) BMC Struct Biol , vol.6 , pp. 19
    • Huang, B.1    Schroeder, M.2
  • 27
    • 79955795138 scopus 로고    scopus 로고
    • DxTuber: Detecting protein cavities, tunnels and clefts based on protein and solvent dynamics
    • Raunest M, Kandt C: dxTuber: detecting protein cavities, tunnels and clefts based on protein and solvent dynamics. J Mol Graph Model 2011, 29:895-905.
    • (2011) J Mol Graph Model , vol.29 , pp. 895-905
    • Raunest, M.1    Kandt, C.2
  • 28
    • 57649229060 scopus 로고    scopus 로고
    • HOLLOW: Generating accurate representations of channel and interior surfaces in molecular structures
    • Ho BK, Gruswitz F: HOLLOW: generating accurate representations of channel and interior surfaces in molecular structures. BMC Struct Biol 2008, 8:49.
    • (2008) BMC Struct Biol , vol.8 , pp. 49
    • Ho, B.K.1    Gruswitz, F.2
  • 29
    • 77954262905 scopus 로고    scopus 로고
    • 3V: Cavity, channel and cleft volume calculator and extractor
    • Voss NR, Gerstein M: 3V: cavity, channel and cleft volume calculator and extractor. Nucleic Acids Res 2010, 38:W555-W562.
    • (2010) Nucleic Acids Res , vol.38
    • Voss, N.R.1    Gerstein, M.2
  • 31
    • 58849142521 scopus 로고    scopus 로고
    • Finding and characterizing tunnels in macromolecules with application to ion channels and pores
    • Coleman RG, Sharp KA: Finding and characterizing tunnels in macromolecules with application to ion channels and pores. Biophys J 2009, 96:632-645.
    • (2009) Biophys J , vol.96 , pp. 632-645
    • Coleman, R.G.1    Sharp, K.A.2
  • 32
    • 0342424187 scopus 로고    scopus 로고
    • Fast prediction and visualization of protein binding pockets with PASS
    • DOI 10.1023/A:1008124202956
    • Brady GP, Stouten PFW, Brady GP Jr: Fast prediction and visualization of protein binding pockets with PASS. J Comput Aided Mol Des 2000, 14:383-401. (Pubitemid 30219399)
    • (2000) Journal of Computer-Aided Molecular Design , vol.14 , Issue.4 , pp. 383-401
    • Brady Jr., G.P.1    Stouten, P.F.W.2
  • 33
    • 0028881975 scopus 로고
    • SURFNET: A program for visualizing molecular surfaces, cavities, and intermolecular interactions
    • Laskowski RA: SURFNET: A program for visualizing molecular surfaces, cavities, and intermolecular interactions. J Mol Graph 1995, 13:323-330.
    • (1995) J Mol Graph , vol.13 , pp. 323-330
    • Laskowski, R.A.1
  • 34
    • 0030404988 scopus 로고    scopus 로고
    • HOLE: A program for the analysis of the pore dimensions of ion channel structural models
    • DOI 10.1016/S0263-7855(97)00009-X, PII S026378559700009X
    • Smart OS, Neduvelil JG, Wang X, Wallace BAA, Sansom MSP: HOLE: a program for the analysis of the pore dimensions of ion channel structural models. J Mol Graph 1996, 14:354-360. (Pubitemid 27302826)
    • (1996) Journal of Molecular Graphics , vol.14 , Issue.6 , pp. 354-360
    • Smart, O.S.1    Neduvelil, J.G.2    Wang, X.3    Wallace, B.A.4    Sansom, M.S.P.5
  • 35
    • 68249097450 scopus 로고    scopus 로고
    • PoreWalker: A novel tool for the identification and characterization of channels in transmembrane proteins from their three-dimensional structure
    • Pellegrini-Calace M, Maiwald T, Thornton JM: PoreWalker: a novel tool for the identification and characterization of channels in transmembrane proteins from their three-dimensional structure. PLoS Comput Biol 2009, 5:e1000440.
    • (2009) PLoS Comput Biol , vol.5
    • Pellegrini-Calace, M.1    Maiwald, T.2    Thornton, J.M.3
  • 36
    • 50849107731 scopus 로고    scopus 로고
    • MolAxis: Efficient and accurate identification of channels in macromolecules
    • Yaffe E, Fishelovitch D, Wolfson HJ, Halperin D, Nussinov R: MolAxis: efficient and accurate identification of channels in macromolecules. Proteins 2008, 73:72-86.
    • (2008) Proteins , vol.73 , pp. 72-86
    • Yaffe, E.1    Fishelovitch, D.2    Wolfson, H.J.3    Halperin, D.4    Nussinov, R.5
  • 42
    • 47849083143 scopus 로고    scopus 로고
    • A comparison of five implementations of 3D Delaunay tessellation in combinatorial and computational geometry
    • Liu Y, Snoeyink J: A comparison of five implementations of 3D Delaunay tessellation in combinatorial and computational geometry. Combinatorial Computational Geometry 2005, 52:439-458.
    • (2005) Combinatorial Computational Geometry , vol.52 , pp. 439-458
    • Liu, Y.1    Snoeyink, J.2
  • 43
    • 0020475449 scopus 로고
    • A simple method for displaying the hydropathic character of a protein
    • Kyte J, Doolittle RF: A simple method for displaying the hydropathic character of a protein. J Mol Biol 1982, 157:105-132.
    • (1982) J Mol Biol , vol.157 , pp. 105-132
    • Kyte, J.1    Doolittle, R.F.2
  • 45
    • 0026691182 scopus 로고
    • The rapid generation of mutation data matrices from protein sequences
    • Jones DT, Taylor WR, Thornton JM: The rapid generation of mutation data matrices from protein sequences. Bioinformatics 1992, 8:275-282.
    • (1992) Bioinformatics , vol.8 , pp. 275-282
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 46
    • 0014349825 scopus 로고
    • The characterization of amino acid sequences in proteins by statistical methods
    • Zimmerman JM, Eliezer N, Simha R: The characterization of amino acid sequences in proteins by statistical methods. J Theor Biol 1968, 21:170-201.
    • (1968) J Theor Biol , vol.21 , pp. 170-201
    • Zimmerman, J.M.1    Eliezer, N.2    Simha, R.3
  • 47
    • 51249175171 scopus 로고
    • Higher-dimensional voronoi diagrams in linear expected time
    • Dwyer RA: Higher-dimensional voronoi diagrams in linear expected time. Discrete Comput Geom 1991, 6:343-367.
    • (1991) Discrete Comput Geom , vol.6 , pp. 343-367
    • Dwyer, R.A.1
  • 48
    • 33746124556 scopus 로고    scopus 로고
    • Biomolecules in the computer: Jmol to the rescue
    • Herráez A: Biomolecules in the computer: Jmol to the rescue. Bioch Mol Biol Educ 2006, 34:255-261.
    • (2006) Bioch Mol Biol Educ , vol.34 , pp. 255-261
    • Herráez, A.1
  • 49
    • 0345864027 scopus 로고    scopus 로고
    • The Catalytic Site Atlas: A resource of catalytic sites and residues identified in enzymes using structural data
    • Porter CT, Bartlett GJ, Thornton JM: The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data. Nucleic Acids Res 2004, 32:D129-D133. (Pubitemid 38081621)
    • (2004) Nucleic Acids Research , vol.32
    • Porter, C.T.1    Bartlett, G.J.2    Thornton, J.M.3
  • 51
    • 57049180108 scopus 로고    scopus 로고
    • Cytochrome c oxidase: Exciting progress and remaining mysteries
    • Brzezinski P, Gennis RB: Cytochrome c oxidase: exciting progress and remaining mysteries. J Bioenerg Biomembr 2008, 40:521-531.
    • (2008) J Bioenerg Biomembr , vol.40 , pp. 521-531
    • Brzezinski, P.1    Gennis, R.B.2
  • 52
    • 13444271681 scopus 로고    scopus 로고
    • Refined structure of the nicotinic acetylcholine receptor at 4 A resolution
    • DOI 10.1016/j.jmb.2004.12.031
    • Unwin N: Refined structure of the nicotinic acetylcholine receptor at 4A resolution. J Mol Biol 2005, 346:967-989. (Pubitemid 40215523)
    • (2005) Journal of Molecular Biology , vol.346 , Issue.4 , pp. 967-989
    • Unwin, N.1
  • 54
    • 77956314063 scopus 로고    scopus 로고
    • Conformational plasticity and structure/ function relationships in cytochromes P450
    • Pochapsky TC, Kazanis S, Dang M: Conformational plasticity and structure/ function relationships in cytochromes P450. Antioxid Redox Signal 2010, 13:1273-1296.
    • (2010) Antioxid Redox Signal , vol.13 , pp. 1273-1296
    • Pochapsky, T.C.1    Kazanis, S.2    Dang, M.3
  • 55
    • 0023645035 scopus 로고
    • High-resolution crystal structure of cytochrome P450cam
    • Poulos TL, Finzel BC, Howard AJ: High-resolution crystal structure of cytochrome P450cam. J Mol Biol 1987, 195:687-700.
    • (1987) J Mol Biol , vol.195 , pp. 687-700
    • Poulos, T.L.1    Finzel, B.C.2    Howard, A.J.3
  • 56
    • 0027326717 scopus 로고
    • Crystal structure of hemoprotein domain of P450BM-3, a prototype for microsomal P450's
    • Ravichandran K, Boddupalli S, Hasermann C, Peterson J, Deisenhofer J: Crystal structure of hemoprotein domain of P450BM-3, a prototype for microsomal P450's. Science 1993, 261:731-736. (Pubitemid 23278388)
    • (1993) Science , vol.261 , Issue.5122 , pp. 731-736
    • Ravichandran, K.G.1    Boddupalli, S.S.2    Hasemann, C.A.3    Peterson, J.A.4    Deisenhofer, J.5
  • 57
    • 84864531088 scopus 로고    scopus 로고
    • Nicotine and 4-(methylnitrosamino)-1-(3-pyridyl)- 1-butanone binding and access channel in human cytochrome P450 2A6 and 2A13 enzymes
    • DeVore NM, Scott EE: Nicotine and 4-(methylnitrosamino)-1-(3-pyridyl)- 1-butanone binding and access channel in human cytochrome P450 2A6 and 2A13 enzymes. J Biol Chem 2012, 287:26576-26585.
    • (2012) J Biol Chem , vol.287 , pp. 26576-26585
    • Devore, N.M.1    Scott, E.E.2
  • 58
    • 0034634393 scopus 로고    scopus 로고
    • How do substrates enter and products exit the buried active site of cytochrome P450cam? 1. Random expulsion molecular dynamics investigation of ligand access channels and mechanisms
    • Ludemann SK, Lounnas V, Wade RC: How do substrates enter and products exit the buried active site of cytochrome P450cam? 1. Random expulsion molecular dynamics investigation of ligand access channels and mechanisms. J Mol Biol 2000, 303:797-811.
    • (2000) J Mol Biol , vol.303 , pp. 797-811
    • Ludemann, S.K.1    Lounnas, V.2    Wade, R.C.3
  • 59
    • 0034634391 scopus 로고    scopus 로고
    • How do substrates enter and products exit the buried active site of cytochrome P450cam? 2. Steered molecular dynamics and adiabatic mapping of substrate pathways
    • Lüdemann SK, Lounnas V, Wade RC: How do substrates enter and products exit the buried active site of cytochrome P450cam? 2. Steered molecular dynamics and adiabatic mapping of substrate pathways. J Mol Biol 2000, 303:813-830.
    • (2000) J Mol Biol , vol.303 , pp. 813-830
    • Lüdemann, S.K.1    Lounnas, V.2    Wade, R.C.3
  • 61
    • 49149089445 scopus 로고    scopus 로고
    • Flexibility of human cytochromes P450: Molecular dynamics reveals differences between CYPs 3A4, 2C9, and 2A6, which correlate with their substrate preferences
    • Skopalík J, Anzenbacher P, Otyepka M: Flexibility of human cytochromes P450: molecular dynamics reveals differences between CYPs 3A4, 2C9, and 2A6, which correlate with their substrate preferences. J Phys Chem B 2008, 112:8165-8173.
    • (2008) J Phys Chem B , vol.112 , pp. 8165-8173
    • Skopalík, J.1    Anzenbacher, P.2    Otyepka, M.3


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