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Volumn 55, Issue , 2015, Pages 13-24

Principal Component Analysis reveals correlation of cavities evolution and functional motions in proteins

Author keywords

Cavity geometry evolution; Drug design; Functional analysis; Molecular dynamics; Principal component analysis; Protein cavities

Indexed keywords

BIOLOGY; CARBON MONOXIDE; COMPLEX NETWORKS; CONFORMATIONS; FUNCTIONAL ANALYSIS; GEOMETRY; MOLECULAR DYNAMICS; PROTEINS;

EID: 84949114871     PISSN: 10933263     EISSN: 18734243     Source Type: Journal    
DOI: 10.1016/j.jmgm.2014.10.011     Document Type: Article
Times cited : (33)

References (53)
  • 1
    • 0036424666 scopus 로고    scopus 로고
    • Structural basis of macromolecular recognition
    • J. Janin, S.J. Wodak (Eds.), Protein Modules and Protein-Protein Interaction, Academic Press, Amsterdam
    • S.J. Wodak, J. Janin, Structural basis of macromolecular recognition, in: J. Janin, S.J. Wodak (Eds.), Protein Modules and Protein-Protein Interaction, Volume 61 of Advances in Protein Chemistry, Academic Press, Amsterdam, 2002, pp. 9-73.
    • (2002) Advances in Protein Chemistry , vol.61 , pp. 9-73
    • Wodak, S.J.1    Janin, J.2
  • 2
    • 0035659985 scopus 로고    scopus 로고
    • The many faces of Ras: Recognition of small GTP-binding proteins
    • K.D. Corbett, T. Alber, The many faces of Ras: recognition of small GTP-binding proteins, Trends Biochem. Sci. 26 (12) (2001) 710-716.
    • (2001) Trends Biochem. Sci. , vol.26 , Issue.12 , pp. 710-716
    • Corbett, K.D.1    Alber, T.2
  • 3
    • 0023936327 scopus 로고
    • Using shape complementarity as an initial screen in designing ligands for a receptor binding site of known three-dimensional structure
    • R.L. DesJarlais, R.P. Sheridan, G.L. Seibel, S.J. Dixon, I.D. Kuntz, R. Venkataraghavan, Using shape complementarity as an initial screen in designing ligands for a receptor binding site of known three-dimensional structure, J. Med. Chem. 31 (4) (1988) 722-729.
    • (1988) J. Med. Chem. , vol.31 , Issue.4 , pp. 722-729
    • DesJarlais, R.L.1    Sheridan, R.P.2    Seibel, G.L.3    Dixon, S.J.4    Kuntz, I.D.5    Venkataraghavan, R.6
  • 4
    • 0038185277 scopus 로고    scopus 로고
    • A novel shape complementarity scoring function for protein-protein docking
    • R. Chen, Z. Weng, A novel shape complementarity scoring function for protein-protein docking, Proteins 51 (3) (2003) 397-408.
    • (2003) Proteins , vol.51 , Issue.3 , pp. 397-408
    • Chen, R.1    Weng, Z.2
  • 5
    • 0037212102 scopus 로고    scopus 로고
    • Ligandfit: A novel method for the shape-directed rapid docking of ligands to protein active sites
    • C.M. Venkatachalam, X. Jiang, T. Oldfield, M. Waldman, Ligandfit: a novel method for the shape-directed rapid docking of ligands to protein active sites, J. Mol. Gr. Modell. 21 (4) (2003) 289-307.
    • (2003) J. Mol. Gr. Modell. , vol.21 , Issue.4 , pp. 289-307
    • Venkatachalam, C.M.1    Jiang, X.2    Oldfield, T.3    Waldman, M.4
  • 6
    • 0026567907 scopus 로고
    • Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect
    • A. Elisabeth Eriksson, W.A. Baase, X.-J. Zhang, D.W. Heinz, M. Blaber, E.P. Baldwin, B.W. Matthews, Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect, Science 255 (5041) (1992) 178-183.
    • (1992) Science , vol.255 , Issue.5041 , pp. 178-183
    • Elisabeth Eriksson, A.1    Baase, W.A.2    Zhang, X.-J.3    Heinz, D.W.4    Blaber, M.5    Baldwin, E.P.6    Matthews, B.W.7
  • 7
    • 0025600834 scopus 로고
    • Enhanced sampling in molecular dynamics: Use of the time-dependent hartree approximation for a simulation of carbon monoxide diffusion through myoglobin
    • R. Elber, M. Karplus, Enhanced sampling in molecular dynamics: use of the time-dependent hartree approximation for a simulation of carbon monoxide diffusion through myoglobin, J. Am. Chem. Soc. 112 (25) (1990) 9161-9175.
    • (1990) J. Am. Chem. Soc. , vol.112 , Issue.25 , pp. 9161-9175
    • Elber, R.1    Karplus, M.2
  • 8
    • 77951298113 scopus 로고    scopus 로고
    • Ligand diffusion in globins: Simulations versus experiment
    • R. Elber, Ligand diffusion in globins: simulations versus experiment, Curr. Opin. Struct. Biol. 20 (2) (2010) 162-167.
    • (2010) Curr. Opin. Struct. Biol. , vol.20 , Issue.2 , pp. 162-167
    • Elber, R.1
  • 9
    • 3042587451 scopus 로고    scopus 로고
    • A survey of active site access channels in cytochromes {P450}
    • R.C. Wade, P.J. Winn, I. Schlichting, Sudarko, A survey of active site access channels in cytochromes {P450}, J. Inorg. Biochem. 98 (7) (2004) 1175-1182.
    • (2004) J. Inorg. Biochem. , vol.98 , Issue.7 , pp. 1175-1182
    • Wade, R.C.1    Winn, P.J.2    Schlichting, I.3    Sudarko4
  • 10
    • 80053107447 scopus 로고    scopus 로고
    • Active-site hydration and water diffusion in cytochrome p450cam: A highly dynamic process
    • Y. Miao, J. Baudry, Active-site hydration and water diffusion in cytochrome p450cam: a highly dynamic process, Biophys. J. 101 (6) (2011) 1493-1503.
    • (2011) Biophys. J. , vol.101 , Issue.6 , pp. 1493-1503
    • Miao, Y.1    Baudry, J.2
  • 11
    • 0038546856 scopus 로고    scopus 로고
    • Trypanosoma cruzi trans-sialidase operates through a covalent sialylenzyme intermediate: Tyrosine is the catalytic nucleophile
    • A.G. Watts, I. Damager, M.L. Amaya, A. Buschiazzo, P. Alzari, A.C. Frasch, S.G. Withers, Trypanosoma cruzi trans-sialidase operates through a covalent sialylenzyme intermediate: tyrosine is the catalytic nucleophile, J. Am. Chem. Soc. 125 (25) (2003) 7532-7533.
    • (2003) J. Am. Chem. Soc. , vol.125 , Issue.25 , pp. 7532-7533
    • Watts, A.G.1    Damager, I.2    Amaya, M.L.3    Buschiazzo, A.4    Alzari, P.5    Frasch, A.C.6    Withers, S.G.7
  • 12
    • 33750045457 scopus 로고    scopus 로고
    • Allosteric inhibition of Staphylococcus aureus D-alanine:D-alanine ligase revealed by crystallographic studies
    • S. Liu, J.S. Chang, J.T. Herberg, M.-M. Horng, P.K. Tomich, A.H. Lin, K.R. Marotti, Allosteric inhibition of Staphylococcus aureus D-alanine:D-alanine ligase revealed by crystallographic studies, Proc. Natl. Acad. Sci. U. S. A. 103 (41) (2006) 15178-15183.
    • (2006) Proc. Natl. Acad. Sci. U. S. A. , vol.103 , Issue.41 , pp. 15178-15183
    • Liu, S.1    Chang, J.S.2    Herberg, J.T.3    Horng, M.-M.4    Tomich, P.K.5    Lin, A.H.6    Marotti, K.R.7
  • 13
    • 0343415156 scopus 로고    scopus 로고
    • The way things move: Looking under the hood of molecular motor proteins
    • R.D. Vale, R.A. Milligan, The way things move: looking under the hood of molecular motor proteins, Science 288 (5463) (2000) 88-95.
    • (2000) Science , vol.288 , Issue.5463 , pp. 88-95
    • Vale, R.D.1    Milligan, R.A.2
  • 14
    • 0028607523 scopus 로고
    • Cavities and packing at protein interfaces
    • J. Simon, Hubbard, Patrick Argos, Cavities and packing at protein interfaces, Protein Sci. 3 (12) (1994) 2194-2206.
    • (1994) Protein Sci. , vol.3 , Issue.12 , pp. 2194-2206
    • Hubbard, J.S.1    Argos, P.2
  • 15
    • 52949132638 scopus 로고    scopus 로고
    • Cavities and atomic packing in protein structures and interfaces
    • Shrihari Sonavane, Pinak Chakrabarti, Cavities and atomic packing in protein structures and interfaces, PLoS Comput. Biol. 4 (9) (2008) e1000188, 09.
    • (2008) PLoS Comput. Biol. , vol.4 , Issue.9
    • Sonavane, S.1    Chakrabarti, P.2
  • 16
    • 58149333699 scopus 로고    scopus 로고
    • What induces pocket openings on protein surface patches involved in protein-protein interactions?
    • Susanne Eyrisch, Volkhard Helms, What induces pocket openings on protein surface patches involved in protein-protein interactions? J. Comput. Aided Mol. Des. 23 (2) (2009) 73-86.
    • (2009) J. Comput. Aided Mol. Des. , vol.23 , Issue.2 , pp. 73-86
    • Eyrisch, S.1    Helms, V.2
  • 17
    • 23244457434 scopus 로고    scopus 로고
    • Molecular dynamics simulation of sperm whale myoglobin: Effects of mutations and trapped CO on the structure and dynamics of cavities
    • Cecilia Bossa, Andrea Amadei, Isabella Daidone, Massimiliano Anselmi, Beatrice Vallone, Maurizio Brunori, Alfredo Di Nola, Molecular dynamics simulation of sperm whale myoglobin: effects of mutations and trapped CO on the structure and dynamics of cavities, Biophys. J. 89 (1) (2005) 465-474.
    • (2005) Biophys. J. , vol.89 , Issue.1 , pp. 465-474
    • Bossa, C.1    Amadei, A.2    Daidone, I.3    Anselmi, M.4    Vallone, B.5    Brunori, M.6    Nola, A.D.7
  • 18
    • 48249120004 scopus 로고    scopus 로고
    • Atomic level computational identification of ligand migration pathways between solvent and binding site in myoglobin
    • J.Z. Ruscio, D. Kumar, M. Shukla, M.G. Prisant, T.M. Murali, A.V. Onufriev, Atomic level computational identification of ligand migration pathways between solvent and binding site in myoglobin, Proc. Natl. Acad. Sci. U. S. A. 105 (27) (2008) 9204-9209.
    • (2008) Proc. Natl. Acad. Sci. U. S. A. , vol.105 , Issue.27 , pp. 9204-9209
    • Ruscio, J.Z.1    Kumar, D.2    Shukla, M.3    Prisant, M.G.4    Murali, T.M.5    Onufriev, A.V.6
  • 19
    • 69049084556 scopus 로고    scopus 로고
    • Breathing motions of a respiratory protein revealed by molecular dynamics simulations
    • M.A. Scorciapino, A. Robertazzi, M. Casu, P. Ruggerone, M. Ceccarelli, Breathing motions of a respiratory protein revealed by molecular dynamics simulations, J. Am. Chem. Soc. 131 (33) (2009) 11825-11832.
    • (2009) J. Am. Chem. Soc. , vol.131 , Issue.33 , pp. 11825-11832
    • Scorciapino, M.A.1    Robertazzi, A.2    Casu, M.3    Ruggerone, P.4    Ceccarelli, M.5
  • 21
    • 34547583152 scopus 로고    scopus 로고
    • Transient pockets on protein surfaces involved in protein-protein interaction
    • Susanne Eyrisch, Volkhard Helms, Transient pockets on protein surfaces involved in protein-protein interaction, J. Med. Chem. 50 (15) (2007) 3457-3464.
    • (2007) J. Med. Chem. , vol.50 , Issue.15 , pp. 3457-3464
    • Eyrisch, S.1    Helms, V.2
  • 22
    • 82255164267 scopus 로고    scopus 로고
    • MDpocket: Open-source cavity detection and characterization on molecular dynamics trajectories
    • P. Schmidtke, A. Bidon-Chanal, F. Javier Luque, X. Barril, MDpocket: open-source cavity detection and characterization on molecular dynamics trajectories, Bioinformatics 27 (23) (2011) 3276-3285.
    • (2011) Bioinformatics , vol.27 , Issue.23 , pp. 3276-3285
    • Schmidtke, P.1    Bidon-Chanal, A.2    Javier Luque, F.3    Barril, X.4
  • 24
    • 84857291408 scopus 로고    scopus 로고
    • Hot spots and transient pockets: Predicting the determinants of small-molecule binding to a protein-protein interface
    • Alexander Metz, Christopher Pfleger, Hannes Kopitz, Stefania Pfeiffer-Marek, Karl-Heinz Baringhaus, Holger Gohlke, Hot spots and transient pockets: predicting the determinants of small-molecule binding to a protein-protein interface, J. Chem. Inf. Model. 52 (1) (2012) 120-133.
    • (2012) J. Chem. Inf. Model. , vol.52 , Issue.1 , pp. 120-133
    • Metz, A.1    Pfleger, C.2    Kopitz, H.3    Pfeiffer-Marek, S.4    Baringhaus, K.-H.5    Gohlke, H.6
  • 25
    • 84863393146 scopus 로고    scopus 로고
    • Visualisation of variable binding pockets on protein surfaces by probabilistic analysis of related structure sets
    • P. Ashford, D. Moss, A. Alex, S. Yeap, A. Povia, I. Nobeli, M. Williams, Visualisation of variable binding pockets on protein surfaces by probabilistic analysis of related structure sets, BMC Bioinformatics 13 (1) (2012) 39.
    • (2012) BMC Bioinformatics , vol.13 , Issue.1 , pp. 39
    • Ashford, P.1    Moss, D.2    Alex, A.3    Yeap, S.4    Povia, A.5    Nobeli, I.6    Williams, M.7
  • 27
    • 0015222647 scopus 로고
    • The interpretation of protein structures: Estimation of static accessibility
    • B. Lee, F.M. Richards, The interpretation of protein structures: estimation of static accessibility, J. Mol. Biol. 55 (3) (1971) 379-400.
    • (1971) J. Mol. Biol. , vol.55 , Issue.3 , pp. 379-400
    • Lee, B.1    Richards, F.M.2
  • 28
    • 0021107965 scopus 로고
    • Solvent-accessible surfaces of proteins and nucleic acids
    • M.L. Connolly, Solvent-accessible surfaces of proteins and nucleic acids, Science 221 (4612) (1983) 709-713.
    • (1983) Science , vol.221 , Issue.4612 , pp. 709-713
    • Connolly, M.L.1
  • 29
    • 0031687653 scopus 로고    scopus 로고
    • Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design
    • J. Liang, C. Woodward, C. Woodward, H. Edelsbrunner, H. Edelsbrunner, Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design, Protein Sci. 7 (9) (1998) 1884-1897.
    • (1998) Protein Sci. , vol.7 , Issue.9 , pp. 1884-1897
    • Liang, J.1    Woodward, C.2    Woodward, C.3    Edelsbrunner, H.4    Edelsbrunner, H.5
  • 30
    • 84874191086 scopus 로고    scopus 로고
    • Control of substrate access to the active site in methane monooxygenase
    • S.J. Lee, M.S. McCormick, S.J. Lippard, U.-S. Cho, Control of substrate access to the active site in methane monooxygenase, Nature 494 (7437) (2013) 380-384, 02.
    • (2013) Nature , vol.494 , Issue.7437
    • Lee, S.J.1    McCormick, M.S.2    Lippard, S.J.3    Cho, U.-S.4
  • 31
    • 0030045089 scopus 로고    scopus 로고
    • Structural and genetic analysis of the folding and function of t4 lysozyme
    • B.W. Matthews, Structural and genetic analysis of the folding and function of t4 lysozyme, FASEB J. 10 (1) (1996) 35-41.
    • (1996) FASEB J. , vol.10 , Issue.1 , pp. 35-41
    • Matthews, B.W.1
  • 32
    • 0030590215 scopus 로고    scopus 로고
    • A functional role for protein cavities in domain:Domain motions
    • S.J. Hubbard, P. Argos, A functional role for protein cavities in domain:domain motions, J. Mol. Biol. 261 (2) (1996) 289-300.
    • (1996) J. Mol. Biol. , vol.261 , Issue.2 , pp. 289-300
    • Hubbard, S.J.1    Argos, P.2
  • 33
    • 1642499388 scopus 로고    scopus 로고
    • Structure of the dengue virus envelope protein after membrane fusion
    • Y. Modis, S. Ogata, D. Clements, S.C. Harrison, Structure of the dengue virus envelope protein after membrane fusion, Nature 427 (6972) (2004) 313-319.
    • (2004) Nature , vol.427 , Issue.6972 , pp. 313-319
    • Modis, Y.1    Ogata, S.2    Clements, D.3    Harrison, S.C.4
  • 36
    • 77955517509 scopus 로고    scopus 로고
    • Druggable pockets and binding site centric chemical space: A paradigm shift in drug discovery
    • S. Pérot, S. Olivier, M.A. Miteva, A.-C. Camproux, B.O. Villoutreix, Druggable pockets and binding site centric chemical space: a paradigm shift in drug discovery, Drug Discov. Today 15 (15-16) (2010) 656-667.
    • (2010) Drug Discov. Today , vol.15 , Issue.15-16 , pp. 656-667
    • Pérot, S.1    Olivier, S.2    Miteva, M.A.3    Camproux, A.-C.4    Villoutreix, B.O.5
  • 37
    • 63149162777 scopus 로고    scopus 로고
    • Managing protein flexibility in docking and its applications
    • C. B-Rao, J. Subramanian, S.D. Sharma, Managing protein flexibility in docking and its applications, Drug Discov. Today 14 (7-8) (2009) 394-400.
    • (2009) Drug Discov. Today , vol.14 , Issue.7-8 , pp. 394-400
    • B-Rao, C.1    Subramanian, J.2    Sharma, S.D.3
  • 38
    • 78149495244 scopus 로고    scopus 로고
    • Computer-aided drug-discovery techniques that account for receptor flexibility
    • J.D. Durrant, J.A. McCammon, Computer-aided drug-discovery techniques that account for receptor flexibility, Curr. Opin. Pharmacol. 10 (6) (2010) 770-774.
    • (2010) Curr. Opin. Pharmacol. , vol.10 , Issue.6 , pp. 770-774
    • Durrant, J.D.1    McCammon, J.A.2
  • 40
    • 49449112578 scopus 로고    scopus 로고
    • Active site pressurization: A new tool for structure-guided drug design and other studies of protein flexibility
    • I.M. Withers, M.P. Mazanetz, H. Wang, P.M. Fischer, C.A. Laughton, Active site pressurization: a new tool for structure-guided drug design and other studies of protein flexibility, J. Chem. Inf. Model. 48 (7) (2008) 1448-1454.
    • (2008) J. Chem. Inf. Model. , vol.48 , Issue.7 , pp. 1448-1454
    • Withers, I.M.1    Mazanetz, M.P.2    Wang, H.3    Fischer, P.M.4    Laughton, C.A.5
  • 41
    • 75549087466 scopus 로고    scopus 로고
    • The flexible pocketome engine for structural chemogenomics
    • E. Jacoby (Ed.), Chemogenomics, Humana Press, Clifton, NJ
    • R. Abagyan, I. Kufareva, The flexible pocketome engine for structural chemogenomics, in: E. Jacoby (Ed.), Chemogenomics, Volume 575 of Methods in Molecular Biology, Humana Press, Clifton, NJ, 2009, pp. 249-279.
    • (2009) Methods in Molecular Biology , vol.575 , pp. 249-279
    • Abagyan, R.1    Kufareva, I.2
  • 42
    • 47249102090 scopus 로고    scopus 로고
    • A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE)
    • G. Bottegoni, I. Kufareva, M. Totrov, R. Abagyan, A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE), J. Comput. Aided Mol. Des. 22 (5) (2008) 311-325.
    • (2008) J. Comput. Aided Mol. Des. , vol.22 , Issue.5 , pp. 311-325
    • Bottegoni, G.1    Kufareva, I.2    Totrov, M.3    Abagyan, R.4
  • 43
    • 77951217659 scopus 로고    scopus 로고
    • Detection of multiscale pockets on protein surfaces using mathematical morphology
    • T. Kawabata, Detection of multiscale pockets on protein surfaces using mathematical morphology, Proteins 78 (5) (2010) 1195-1211.
    • (2010) Proteins , vol.78 , Issue.5 , pp. 1195-1211
    • Kawabata, T.1
  • 44
    • 0021766921 scopus 로고
    • Cavities in proteins: Structure of a metmyoglobin xenon complex solved to 1.9. ang
    • R.F. Tilton, I.D. Kuntz, G.A. Petsko, Cavities in proteins: structure of a metmyoglobin xenon complex solved to 1.9. ang, Biochemistry 23 (13) (1984) 2849-2857.
    • (1984) Biochemistry , vol.23 , Issue.13 , pp. 2849-2857
    • Tilton, R.F.1    Kuntz, I.D.2    Petsko, G.A.3
  • 46
    • 0032802062 scopus 로고    scopus 로고
    • On the convergence of the conformational coordinates basis set obtained by the essential dynamics analysis of proteins' molecular dynamics simulations
    • A. Amadei, M.A. Ceruso, A. Di Nola, On the convergence of the conformational coordinates basis set obtained by the essential dynamics analysis of proteins' molecular dynamics simulations, Proteins 36 (4) (1999) 419-424.
    • (1999) Proteins , vol.36 , Issue.4 , pp. 419-424
    • Amadei, A.1    Ceruso, M.A.2    Di Nola, A.3
  • 51
    • 0041353145 scopus 로고    scopus 로고
    • Structure and mechanism of the lactose permease of Escherichia coli
    • J. Abramson, I. Smirnova, V. Kasho, G. Verner, H. Ronald Kaback, S. Iwata, Structure and mechanism of the lactose permease of Escherichia coli, Science 301 (5633) (2003) 610-615.
    • (2003) Science , vol.301 , Issue.5633 , pp. 610-615
    • Abramson, J.1    Smirnova, I.2    Kasho, V.3    Verner, G.4    Ronald Kaback, H.5    Iwata, S.6
  • 52
    • 80053056248 scopus 로고    scopus 로고
    • Opening the periplasmic cavity in lactose permease is the limiting step for sugar binding
    • I. Smirnova, V. Kasho, J. Sugihara, H. Ronald Kaback, Opening the periplasmic cavity in lactose permease is the limiting step for sugar binding, Proc. Natl. Acad. Sci. U. S. A. 108 (37) (2011) 15147-15151.
    • (2011) Proc. Natl. Acad. Sci. U. S. A. , vol.108 , Issue.37 , pp. 15147-15151
    • Smirnova, I.1    Kasho, V.2    Sugihara, J.3    Ronald Kaback, H.4
  • 53
    • 79959349280 scopus 로고    scopus 로고
    • Crystal structure of lactose permease in complex with an affinity inactivator yields unique insight into sugar recognition
    • V. Chaptal, S. Kwon, M.R. Sawaya, L. Guan, H. Ronald Kaback, J. Abramson, Crystal structure of lactose permease in complex with an affinity inactivator yields unique insight into sugar recognition, Proc. Natl. Acad. Sci. U. S. A. 108 (23) (2011) 9361-9366.
    • (2011) Proc. Natl. Acad. Sci. U. S. A. , vol.108 , Issue.23 , pp. 9361-9366
    • Chaptal, V.1    Kwon, S.2    Sawaya, M.R.3    Guan, L.4    Ronald Kaback, H.5    Abramson, J.6


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