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Volumn 5, Issue 10, 2009, Pages 2886-2897

Binding of an RNA pol II ligand to the ww domain of Pin1 using molecular dynamics docking simulations

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EID: 73949132512     PISSN: 15499618     EISSN: None     Source Type: Journal    
DOI: 10.1021/ct900190n     Document Type: Article
Times cited : (4)

References (50)
  • 1
    • 3543036966 scopus 로고    scopus 로고
    • PINA is essential for growth and positively influences NIMA function in Aspergillus nidulans
    • Joseph, J. D.; Daigle, S. N.; Means, A. R. PINA is essential for growth and positively influences NIMA function in Aspergillus nidulans J. Biol. Chem. 2004, 279, 32373-32384
    • (2004) J. Biol. Chem. , vol.279 , pp. 32373-32384
    • Joseph, J.D.1    Daigle, S.N.2    Means, A.R.3
  • 2
    • 0029916122 scopus 로고    scopus 로고
    • A. human peptidyl-prolyl isomerase essential for regulation of mitosis
    • Lu, K. P.; Hanes, D.; Hunter, T. A. human peptidyl-prolyl isomerase essential for regulation of mitosis Nature 1996, 380, 544-547
    • (1996) Nature , vol.380 , pp. 544-547
    • Lu, K.P.1    Hanes, D.2    Hunter, T.3
  • 3
    • 0035796405 scopus 로고    scopus 로고
    • Pin1 is overexpressed in breast cancer and cooperates with Ras signaling in increasing the transcriptional activity of c-Jun towards cyclin D1
    • Wulf, G. M.; Ryo, A.; Wulf, G. G.; Lee, S. W.; Niu, T.; Petkova, V.; Lu, K. P. Pin1 is overexpressed in breast cancer and cooperates with Ras signaling in increasing the transcriptional activity of c-Jun towards cyclin D1 EMBO J. 2001, 20, 3459-3472
    • (2001) EMBO J , vol.20 , pp. 3459-3472
    • Wulf, G.M.1    Ryo, A.2    Wulf, G.G.3    Lee, S.W.4    Niu, T.5    Petkova, V.6    Lu, K.P.7
  • 4
    • 1842763560 scopus 로고    scopus 로고
    • Pinning down cell signalling, cancer and Alzheimer's disease
    • Lu, K. P. Pinning down cell signalling, cancer and Alzheimer's disease Trends Biochem. Sci. 2004, 29, 200-209
    • (2004) Trends Biochem. Sci. , vol.29 , pp. 200-209
    • Lu, K.P.1
  • 5
    • 0038448924 scopus 로고    scopus 로고
    • Structural analysis of the mitotic regulator hPin1 in solution: Insights into domain architecture and substrate binding
    • Bayer, E.; Goettsch, S.; Mueller, J. W.; Griewel, B.; Guiberman, E.; Mayr, L. M.; Bayer, P. Structural analysis of the mitotic regulator hPin1 in solution: Insights into domain architecture and substrate binding J. Biol. Chem. 2003, 278, 26183-26193
    • (2003) J. Biol. Chem. , vol.278 , pp. 26183-26193
    • Bayer, E.1    Goettsch, S.2    Mueller, J.W.3    Griewel, B.4    Guiberman, E.5    Mayr, L.M.6    Bayer, P.7
  • 6
    • 33847656165 scopus 로고    scopus 로고
    • Substrate recognition reduces side-chain flexibility for conserved hydrophobic residues in human
    • Namanja, A. T.; Peng, T.; Zintsmaster, J. S.; Elson, A. C.; Shakour, M. G.; Peng, J. W.Substrate recognition reduces side-chain flexibility for conserved hydrophobic residues in human Pin1 Structure 2007, 15, 313-327
    • (2007) Pin1 Structure , vol.15 , pp. 313-327
    • Namanja, A.T.1    Peng, T.2    Zintsmaster, J.S.3    Elson, A.C.4    Shakour, M.G.5    Peng, J.W.6
  • 7
    • 53149141784 scopus 로고    scopus 로고
    • Structural characterisation of PinA WW Domain and comparison with other Group IV WW Domains
    • Ng, C. A.; Kato, Y.; Tanokura, M.; Brownlee, R. T. C. Structural characterisation of PinA WW Domain and comparison with other Group IV WW Domains, Pin1 and Ess1 Biochim. Biophys. Acta 2008, 1784, 1208-1214
    • (2008) Pin1 and Ess1 Biochim. Biophys. Acta , vol.1784 , pp. 1208-1214
    • Ng, C.A.1    Kato, Y.2    Tanokura, M.3    Brownlee, R.T.C.4
  • 8
    • 17644385551 scopus 로고    scopus 로고
    • The structure of the Candida albicans Ess1 prolyl isomerase reveals a well-ordered linker that restricts domain mobility
    • Li, Z.; Li, H.; Devasahayam, G.; Gemmill, T.; Chaturvedi, V.; Hanes, S. D.; Van Roey, P. The structure of the Candida albicans Ess1 prolyl isomerase reveals a well-ordered linker that restricts domain mobility Biochemistry 2005, 44, 6180-6189
    • (2005) Biochemistry , vol.44 , pp. 6180-6189
    • Li, Z.1    Li, H.2    Devasahayam, G.3    Gemmill, T.4    Chaturvedi, V.5    Hanes, S.D.6    Van Roey, P.7
  • 10
    • 0033885803 scopus 로고    scopus 로고
    • Structural basis for phosphoserine-proline recognition by group IV WW domains
    • Verdecia, M. A.; Bowman, M. E.; Lu, K. P.; Hunter, T.; Noel, J. P. Structural basis for phosphoserine-proline recognition by group IV WW domains Nat. Struct. Biol. 2000, 7, 639-643
    • (2000) Nat. Struct. Biol. , vol.7 , pp. 639-643
    • Verdecia, M.A.1    Bowman, M.E.2    Lu, K.P.3    Hunter, T.4    Noel, J.P.5
  • 11
    • 0036535975 scopus 로고    scopus 로고
    • Pinning down proline-directed phosphorylation signaling
    • Lu, K. P.; Liou, Y. C.; Zhou, X. Z. Pinning down proline-directed phosphorylation signaling Trends Cell Biol. 2002, 12, 164-172
    • (2002) Trends Cell Biol , vol.12 , pp. 164-172
    • Lu, K.P.1    Liou, Y.C.2    Zhou, X.Z.3
  • 12
    • 0029775570 scopus 로고    scopus 로고
    • Structure of the WW domain of a kinase-associated protein complexed with a proline-rich peptide
    • Macias, M. J.; HyvÖnen, M.; Baraldi, E.; Schultz, J.; Sudol, M.; Saraste, M.; Oschkinat, H. Structure of the WW domain of a kinase-associated protein complexed with a proline-rich peptide Nature 1996, 382, 646-649
    • (1996) Nature , vol.382 , pp. 646-649
    • Macias, M.J.1    HyvÖnen, M.2    Baraldi, E.3    Schultz, J.4    Sudol, M.5    Saraste, M.6    Oschkinat, H.7
  • 13
    • 0033546329 scopus 로고    scopus 로고
    • A single point mutation in a group I WW domain shifts its specificity to that of group II WW domains J
    • Espanel, X.; Sudol, M. A single point mutation in a group I WW domain shifts its specificity to that of group II WW domains J. Biol. Chem. 1999, 274, 17284-17289
    • (1999) Biol. Chem. , vol.274 , pp. 17284-17289
    • Espanel, X.1    Sudol, M.2
  • 15
    • 0034714176 scopus 로고    scopus 로고
    • NMR solution structure of hPar14 reveals similarity to the peptidyl prolyl cis/trans isomerase domain of the mitotic regulator hPin1 but indicates a different functionality of the protein
    • Sekerina, E.; Rahfeld, J. U.; Müller, J.; Fangḧ Anel, J.; Rascher, C.; Fischer, G.; Bayer, P. NMR solution structure of hPar14 reveals similarity to the peptidyl prolyl cis/trans isomerase domain of the mitotic regulator hPin1 but indicates a different functionality of the protein J. Mol. Biol. 2000, 301, 1003-1017
    • (2000) J. Mol. Biol. , vol.301 , pp. 1003-1017
    • Sekerina, E.1    Rahfeld, J.U.2    Müller, J.3    Fangḧ4    Anel, J.5    Rascher, C.6    Fischer, G.7    Bayer, P.8
  • 19
    • 0037155792 scopus 로고    scopus 로고
    • Determinants of ligand specificity in groups I and IV WW domains as studied by surface plasmon resonance and model building
    • Kato, Y.; Ito, M.; Kawai, K.; Nagata, K.; Tanokura, M. Determinants of ligand specificity in groups I and IV WW domains as studied by surface plasmon resonance and model building J. Biol. Chem. 2002, 277, 10173-10177
    • (2002) J. Biol. Chem. , vol.277 , pp. 10173-10177
    • Kato, Y.1    Ito, M.2    Kawai, K.3    Nagata, K.4    Tanokura, M.5
  • 20
    • 48249138715 scopus 로고    scopus 로고
    • How to efficiently include receptor flexibility during computational docking Curr
    • May, A.; Sieker, F.; Zacharias, M. How to efficiently include receptor flexibility during computational docking Curr. Comput.-Aided Drug Des. 2008, 4, 143-153
    • (2008) Comput.-Aided Drug Des. , vol.4 , pp. 143-153
    • May, A.1    Sieker, F.2    Zacharias, M.3
  • 21
    • 43349086737 scopus 로고    scopus 로고
    • Computational approaches to protein-protein docking Curr
    • Lee, K.; Lee, J. W. Computational approaches to protein-protein docking Curr. Proteomics 2008, 5, 10-19
    • (2008) Proteomics , vol.5 , pp. 10-19
    • Lee, K.1    Lee, J.W.2
  • 22
    • 33644948688 scopus 로고    scopus 로고
    • HIV-1 protease flaps spontaneously close to the correct structure in simulations following manual placement of an inhibitor into the open state
    • Hornak, V.; Okur, A.; Rizzo, R. C.; Simmerling, C. HIV-1 protease flaps spontaneously close to the correct structure in simulations following manual placement of an inhibitor into the open state J. Am. Chem. Soc. 2006, 128, 2812-2813
    • (2006) J. Am. Chem. Soc. , vol.128 , pp. 2812-2813
    • Hornak, V.1    Okur, A.2    Rizzo, R.C.3    Simmerling, C.4
  • 23
    • 73949106052 scopus 로고    scopus 로고
    • Maestro, version Schrodinger, LLC: New York, NY
    • Maestro, version 8; Schrodinger, LLC: New York, NY, 2007
    • (2007) , pp. 8
  • 25
    • 33644753023 scopus 로고    scopus 로고
    • AMBER force field parameters for phosphorylated amino acids in different protonation states: phosphoserine, phosphothreonine, phosphotyrosine and phosphohistidine
    • Homeyer, N.; Horn, A. H. C.; Lanig, H.; Sticht, H. AMBER force field parameters for phosphorylated amino acids in different protonation states: phosphoserine, phosphothreonine, phosphotyrosine and phosphohistidine J. Mol. Model. 2006, 12, 281-289
    • (2006) J. Mol. Model. , vol.12 , pp. 281-289
    • Homeyer, N.1    Horn, A.H.C.2    Lanig, H.3    Sticht, H.4
  • 27
    • 73949088104 scopus 로고    scopus 로고
    • AMBER University of California: San Francisco, CA
    • Case, D. A. et al. AMBER 9; University of California: San Francisco, CA, 2006.
    • (2006) , pp. 9
    • Case, D.A.1
  • 28
    • 0002121327 scopus 로고
    • Stochastic problems in Physics and Astronomy
    • Chandrasekhar, S. Stochastic problems in Physics and Astronomy Rev. Mod. Phys 1943, 15, 1-89
    • (1943) Rev. Mod. Phys. , vol.15 , pp. 1-89
    • Chandrasekhar, S.1
  • 29
    • 33646940952 scopus 로고
    • Numerical integration of the cartesian equations of motion of a system with constraints: Molecular Dynamics of n-alkanes
    • Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. Numerical integration of the cartesian equations of motion of a system with constraints: Molecular Dynamics of n-alkanes J. Comput. Phys. 1977, 23, 327-341
    • (1977) J. Comput. Phys. , vol.23 , pp. 327-341
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 30
    • 58149163268 scopus 로고    scopus 로고
    • Vulnerability in popular molecular dynamics packages concerning Langevin and Andersen dynamics
    • Cerutti, D. S.; Duke, R.; Freddolino, P. L.; Fan, H.; Lybrand, T. P. A. Vulnerability in popular molecular dynamics packages concerning Langevin and Andersen dynamics J. Chem. Theory Comput. 2008, 4, 1669-1680
    • (2008) J. Chem. Theory Comput. , vol.4 , pp. 1669-1680
    • Cerutti, D.S.1    Duke, R.2    Freddolino, P.L.3    Fan, H.4    Lybrand, T.P.A.5
  • 31
    • 33846823909 scopus 로고
    • Particle mesh Ewald: an Nlog(N) method for Ewald sums in large systems
    • Darden, T.; York, D.; Pedersen, L. Particle mesh Ewald: an Nlog(N) method for Ewald sums in large systems J. Chem. Phys. 1993, 98, 10089-10092
    • (1993) J. Chem. Phys. , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 32
    • 0029878720 scopus 로고    scopus 로고
    • VMD -visual molecular dynamics
    • Humphrey, W.; Dalke, A.; Schulten, K. VMD -visual molecular dynamics J. Mol. Graph. 1996, 14, 33-38 27-28
    • (1996) J. Mol. Graph. , vol.14 , Issue.33-38 , pp. 27-28
    • Humphrey, W.1    Dalke, A.2    Schulten, K.3
  • 33
    • 0043245780 scopus 로고    scopus 로고
    • Insights into Protein-Protein Binding by binding Free Energy Calculation and Free Energy Decomposition for the Ras-Raf and Ras-RalGDS Complexes
    • Gohlke, H.; Kiel, C.; Case, D. A.Insights into Protein-Protein Binding by binding Free Energy Calculation and Free Energy Decomposition for the Ras-Raf and Ras-RalGDS Complexes J. Mol. Biol. 2003, 330, 891-913
    • (2003) J. Mol. Biol. , vol.330 , pp. 891-913
    • Gohlke, H.1    Kiel, C.2    Case, D.A.3
  • 35
    • 0032560959 scopus 로고    scopus 로고
    • Continuum Solvent Studies of the Stability of DNA, RNA, and Phosphoramidate-DNA helices
    • Srinivasan, J.; Cheatham, T. E., III; Cieplak, P.; Kollman, P. A.; Case, D. A. Continuum Solvent Studies of the Stability of DNA, RNA, and Phosphoramidate-DNA helices J. Am. Chem. Soc. 1998, 120 (37) 9401-9409
    • (1998) J. Am. Chem. Soc. , vol.120 , Issue.37 , pp. 9401-9409
    • Srinivasan, J.1    Cheatham T.E. III2    Cieplak, P.3    Kollman, P.A.4    Case, D.A.5
  • 36
    • 20644449471 scopus 로고    scopus 로고
    • Modification of the Generalized Born Model Suitable for Macromolecules
    • Onufirev, A.; Bashford, D.; Case, D. A. Modification of the Generalized Born Model Suitable for Macromolecules J. Phys. Chem. 2000, 104, 3712-3720
    • (2000) J. Phys. Chem. , vol.104 , pp. 3712-3720
    • Onufirev, A.1    Bashford, D.2    Case, D.A.3
  • 37
    • 34249298006 scopus 로고    scopus 로고
    • Two-stage Folding of HP-35 from Ab Initio Simulations
    • Lei, H.; Duan, Y. Two-stage Folding of HP-35 from Ab Initio Simulations J. Mol. Biol. 2007, 370, 196-206
    • (2007) J. Mol. Biol. , vol.370 , pp. 196-206
    • Lei, H.1    Duan, Y.2
  • 38
    • 0347602124 scopus 로고    scopus 로고
    • Converging Free Energy Estimates: MM-PB(GB)SA Studies on the Protein-Protein Complex Ras-Raf
    • Gohlke, H.; Case, D. A. Converging Free Energy Estimates: MM-PB(GB)SA Studies on the Protein-Protein Complex Ras-Raf J. Comput. Chem. 2004, 25, 238-250
    • (2004) J. Comput. Chem. , vol.25 , pp. 238-250
    • Gohlke, H.1    Case, D.A.2
  • 39
    • 84961980685 scopus 로고    scopus 로고
    • Binding of a Diverse Set of Ligands to Avidin and Streptavidin: An Accurate Quantitative Prediction of Their Relative Affinities by a Combination of Molecular Mechanics and Continuum Solvent Models
    • Kuhn, B.; Kollman, P. A. Binding of a Diverse Set of Ligands to Avidin and Streptavidin: An Accurate Quantitative Prediction of Their Relative Affinities by a Combination of Molecular Mechanics and Continuum Solvent Models J. Med. Chem. 2000, 43, 3786-3791
    • (2000) J. Med. Chem. , vol.43 , pp. 3786-3791
    • Kuhn, B.1    Kollman, P.A.2
  • 40
    • 0034811498 scopus 로고    scopus 로고
    • Use of MM-PBSA in Reproducing the Binding Free Energies to HIV-1 RT of TIBO Derivatives and Predicting the Binding Mode to HIV-1 RT of Efavirenz by Docking and MM-PBSA
    • Wang, J.; Morin, P.; Wang, W.; Kollman, P. A. Use of MM-PBSA in Reproducing the Binding Free Energies to HIV-1 RT of TIBO Derivatives and Predicting the Binding Mode to HIV-1 RT of Efavirenz by Docking and MM-PBSA J. Am. Chem. Soc. 2001, 123, 5221-5230
    • (2001) J. Am. Chem. Soc. , vol.123 , pp. 5221-5230
    • Wang, J.1    Morin, P.2    Wang, W.3    Kollman, P.A.4
  • 41
    • 0028204490 scopus 로고
    • Do salt bridges stabilize proteins? A continuum electrostatic analysis
    • Hendsch, Z. S.; Tidor, B. Do salt bridges stabilize proteins? A continuum electrostatic analysis Protein Sci. 1994, 3 (2) 211-226
    • (1994) Protein Sci , vol.3 , Issue.2 , pp. 211-226
    • Hendsch, Z.S.1    Tidor, B.2
  • 42
    • 0032789936 scopus 로고    scopus 로고
    • Electrostatic interactions in the GCN4 leucine zipper: substantial contributions arise from intramolecular interactions enhanced on binding
    • Hendsch, Z. S.; Tidor, B. Electrostatic interactions in the GCN4 leucine zipper: substantial contributions arise from intramolecular interactions enhanced on binding Protein Sci. 1999, 8 (7) 1381-1392
    • (1999) Protein Sci , vol.8 , Issue.7 , pp. 1381-1392
    • Hendsch, Z.S.1    Tidor, B.2
  • 43
    • 0036306236 scopus 로고    scopus 로고
    • On the Role of Electrostatic Interactions in the Design of Protein-Protein Interfaces
    • Sheinerman, F. B.; Honig, B. On the Role of Electrostatic Interactions in the Design of Protein-Protein Interfaces J. Mol. Biol. 2002, 318, 161-177
    • (2002) J. Mol. Biol. , vol.318 , pp. 161-177
    • Sheinerman, F.B.1    Honig, B.2
  • 44
    • 0033137131 scopus 로고    scopus 로고
    • Prediction of the binding energy for small molecules, peptides and proteins
    • Schapira, M.; Totrov, M.; Abagyan, R. Prediction of the binding energy for small molecules, peptides and proteins J. Mol. Recognit. 1999, 12 (3) 177-190
    • (1999) J. Mol. Recognit. , vol.12 , Issue.3 , pp. 177-190
    • Schapira, M.1    Totrov, M.2    Abagyan, R.3
  • 47
    • 18144380285 scopus 로고    scopus 로고
    • Effect of Inorganic Phosphate on FMN Binding and Loop Flexibility in Desulfovibrio desulfuricans Apo-flavodoxin
    • Muralidhara, B. K.; Chen, M.; Ma, J.; Wittung-Stafshede, P. Effect of Inorganic Phosphate on FMN Binding and Loop Flexibility in Desulfovibrio desulfuricans Apo-flavodoxin J. Mol. Biol. 2005, 349, 89-97
    • (2005) J. Mol. Biol. , vol.349 , pp. 89-97
    • Muralidhara, B.K.1    Chen, M.2    Ma, J.3    Wittung-Stafshede, P.4
  • 48
    • 0037169479 scopus 로고    scopus 로고
    • Critical role of WW domain phosphorylation in regulating phosphoserine binding activity and Pin1 function
    • Lu, P. J.; Zhou, X. Z.; Liou, Y. C.; Noel, J. P.; Lu, K. P. Critical role of WW domain phosphorylation in regulating phosphoserine binding activity and Pin1 function J. Biol. Chem. 2002, 277, 2381-2384
    • (2002) J. Biol. Chem. , vol.277 , pp. 2381-2384
    • Lu, P.J.1    Zhou, X.Z.2    Liou, Y.C.3    Noel, J.P.4    Lu, K.P.5
  • 49
    • 0033900164 scopus 로고    scopus 로고
    • Converging on proline: the mechanism of WW domain peptide recognition
    • Zarrinpar, A.; Lim, W. A. Converging on proline: the mechanism of WW domain peptide recognition Nat. Struct. Biol. 2000, 7, 611-613
    • (2000) Nat. Struct. Biol. , vol.7 , pp. 611-613
    • Zarrinpar, A.1    Lim, W.A.2


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