메뉴 건너뛰기




Volumn 11, Issue 4, 2016, Pages

Molecular dynamics simulations and classical multidimensional scaling unveil new metastable states in the conformational landscape of CDK2

Author keywords

[No Author keywords available]

Indexed keywords

8 ANILINO 1 NAPHTHALENESULFONIC ACID; CYCLIN DEPENDENT KINASE 2; CDK2 PROTEIN, HUMAN;

EID: 84964617582     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0154066     Document Type: Article
Times cited : (26)

References (52)
  • 1
    • 0037032835 scopus 로고    scopus 로고
    • The protein kinase complement of the human genome
    • PMID: 12471243
    • Manning G, Whyte DB, Martinez R, Hunter T, Sudarsanam S. The protein kinase complement of the human genome. Science. 2002; 298:1912-1934. PMID: 12471243
    • (2002) Science , vol.298 , pp. 1912-1934
    • Manning, G.1    Whyte, D.B.2    Martinez, R.3    Hunter, T.4    Sudarsanam, S.5
  • 2
    • 0037013143 scopus 로고    scopus 로고
    • The conformational plasticity of protein kinases
    • PMID: 12015977
    • Huse M, Kuriyan J. The conformational plasticity of protein kinases. Cell. 2002; 109:275-282. PMID: 12015977
    • (2002) Cell , vol.109 , pp. 275-282
    • Huse, M.1    Kuriyan, J.2
  • 4
    • 79551594605 scopus 로고    scopus 로고
    • Protein kinases: Evolution of dynamic regulatory proteins
    • PMID: 20971646
    • Taylor SS, Kornev AP. Protein kinases: evolution of dynamic regulatory proteins. Trends Biochem Sci. 2011; 36:65-77. doi: 10.1016/j.tibs.2010.09.006 PMID: 20971646
    • (2011) Trends Biochem Sci. , vol.36 , pp. 65-77
    • Taylor, S.S.1    Kornev, A.P.2
  • 5
    • 77950482089 scopus 로고    scopus 로고
    • Global consequences of activation loop phosphorylation on protein kinase A
    • PMID: 19965870
    • Steichen JM, Iyer GH, Li S, Saldanha A, Deal MS, Woods VL, et al. Global consequences of activation loop phosphorylation on protein kinase A. J Biol Chem. 2010; 285:3825-3832. doi: 10.1074/jbc.M109.061820 PMID: 19965870
    • (2010) J Biol Chem , vol.285 , pp. 3825-3832
    • Steichen, J.M.1    Iyer, G.H.2    Li, S.3    Saldanha, A.4    Deal, M.S.5    Woods, V.L.6
  • 6
    • 0026342401 scopus 로고
    • Crystal structure of the catalytic subunit of cyclic adenosine monophosphate-dependent protein kinase
    • PMID: 1862342
    • Knighton DR, Zheng JH, Ten Eyck LF, Ashford VA, Xuong NH, Taylor SS, et al. Crystal structure of the catalytic subunit of cyclic adenosine monophosphate-dependent protein kinase. Science. 1991; 253:407-414. PMID: 1862342
    • (1991) Science , vol.253 , pp. 407-414
    • Knighton, D.R.1    Zheng, J.H.2    Ten Eyck, L.F.3    Ashford, V.A.4    Xuong, N.H.5    Taylor, S.S.6
  • 7
    • 0029029617 scopus 로고
    • Mechanism of CDKactivation revealed by the structure of a cyclin A-CDK2 complex
    • PMID: 7630397
    • Jeffrey PD, Russo AA, Polyak K, Gibbs E, Hurwitz J, Massagué J, et al. Mechanism of CDKactivation revealed by the structure of a cyclin A-CDK2 complex. Nature. 1995; 376:313-320 PMID: 7630397
    • (1995) Nature , vol.376 , pp. 313-320
    • Jeffrey, P.D.1    Russo, A.A.2    Polyak, K.3    Gibbs, E.4    Hurwitz, J.5    Massagué, J.6
  • 8
    • 16144364951 scopus 로고    scopus 로고
    • Structural basis for activation of human lymphocyte kinase Lck upon tyrosine phosphorylation
    • PMID: 8945479
    • Yamaguchi H, Hendrickson WA. Structural basis for activation of human lymphocyte kinase Lck upon tyrosine phosphorylation. Nature. 1996; 384:484-489. PMID: 8945479
    • (1996) Nature , vol.384 , pp. 484-489
    • Yamaguchi, H.1    Hendrickson, W.A.2
  • 9
    • 0030866897 scopus 로고    scopus 로고
    • Activation mechanism of the MAP kinase ERK2 by dual phosphorylation
    • PMID: 9298898
    • Canagarajah BJ, Khokhlatchev A, Cobb MH, Goldsmith EJ. Activation mechanism of the MAP kinase ERK2 by dual phosphorylation. Cell. 1997; 90:859-869. PMID: 9298898
    • (1997) Cell , vol.90 , pp. 859-869
    • Canagarajah, B.J.1    Khokhlatchev, A.2    Cobb, M.H.3    Goldsmith, E.J.4
  • 10
    • 84861859600 scopus 로고    scopus 로고
    • The structural basis for control of eukaryotic protein kinases
    • PMID: 22482904
    • Endicott JA, Noble MEM, Johnson LN. The structural basis for control of eukaryotic protein kinases. Annu Rev Biochem. 2012; 81:587-613. doi: 10.1146/annurev-biochem-052410-090317 PMID: 22482904
    • (2012) Annu Rev Biochem. , vol.81 , pp. 587-613
    • Endicott, J.A.1    Noble, M.E.M.2    Johnson, L.N.3
  • 11
    • 0033001789 scopus 로고    scopus 로고
    • Crystal structures of c-Src reveal features of its autoinhibitory mechanism
    • PMID: 10360179
    • Xu W, Doshi A, Lei M, Eck MJ, Harrison SC. Crystal structures of c-Src reveal features of its autoinhibitory mechanism. Mol Cell. 1999; 3:629-638. PMID: 10360179
    • (1999) Mol Cell , vol.3 , pp. 629-638
    • Xu, W.1    Doshi, A.2    Lei, M.3    Eck, M.J.4    Harrison, S.C.5
  • 13
    • 84875747743 scopus 로고    scopus 로고
    • αC helix displacement as a general approach for allosteric modulation of protein kinases
    • PMID: 23195331
    • Palmieri L, Rastelli G. αC helix displacement as a general approach for allosteric modulation of protein kinases. Drug Discov Today. 2013; 18:407-414. doi: 10.1016/j.drudis.2012.11.009 PMID: 23195331
    • (2013) Drug Discov Today , vol.18 , pp. 407-414
    • Palmieri, L.1    Rastelli, G.2
  • 14
    • 77950573400 scopus 로고    scopus 로고
    • Through the "gatekeeper door": Exploiting the active kinase conformation
    • PMID: 20000735
    • Zuccotto F, Ardini E, Casale E, Angiolini M. Through the "gatekeeper door": exploiting the active kinase conformation. J Med Chem. 2010; 53:2681-2694. doi: 10.1021/jm901443h PMID: 20000735
    • (2010) J Med Chem. , vol.53 , pp. 2681-2694
    • Zuccotto, F.1    Ardini, E.2    Casale, E.3    Angiolini, M.4
  • 15
    • 84881361773 scopus 로고    scopus 로고
    • Anticancertherapeutic strategies based on CDK inhibitors
    • PMID: 23394082
    • Esposito L, Indovina P, Magnotti F, Conti D, Giordano A. Anticancertherapeutic strategies based on CDK inhibitors. Curr Pharm Des. 2013; 19:5327-5332. PMID: 23394082
    • (2013) Curr Pharm Des , vol.19 , pp. 5327-5332
    • Esposito, L.1    Indovina, P.2    Magnotti, F.3    Conti, D.4    Giordano, A.5
  • 17
    • 84880564100 scopus 로고    scopus 로고
    • Structural characterization of the cyclin-dependent protein kinase family
    • PMID: 23863171
    • Endicott JA, Noble MEM Structural characterization of the cyclin-dependent protein kinase family. Biochem SocTrans. 2013; 41:1008-1016. doi: 10.1042/BST20130097 PMID: 23863171
    • (2013) Biochem SocTrans , vol.41 , pp. 1008-1016
    • Endicott, J.A.1    Noble, M.E.M.2
  • 18
    • 0031466305 scopus 로고    scopus 로고
    • Cyclin-dependent kinases: Engines, clocks, and microprocessors
    • PMID: 9442875
    • Morgan DO Cyclin-dependent kinases: engines, clocks, and microprocessors. Annu Rev Cell Dev Biol. 1997; 13:261-291. PMID: 9442875
    • (1997) Annu Rev Cell Dev Biol , vol.13 , pp. 261-291
    • Morgan, D.O.1
  • 19
    • 57749188299 scopus 로고    scopus 로고
    • Targeting cancerwith small molecule kinase inhibitors
    • PMID: 19104514
    • Zhang J, Yang PL, Gray NS. Targeting cancerwith small molecule kinase inhibitors. Nat Rev Cancer. 2009; 9:28-39. doi: 10.1038/nrc2559 PMID: 19104514
    • (2009) Nat Rev Cancer , vol.9 , pp. 28-39
    • Zhang, J.1    Yang, P.L.2    Gray, N.S.3
  • 20
    • 36549040859 scopus 로고    scopus 로고
    • The selectivity of protein kinase inhibitors: A further update
    • PMID: 17850214
    • Bain J, Plater L, Elliott M, Shpiro N, Hastie CJ, McLauchlan H, et al. The selectivity of protein kinase inhibitors: a further update. Biochem J. 2007; 408:297-315. PMID: 17850214
    • (2007) Biochem J , vol.408 , pp. 297-315
    • Bain, J.1    Plater, L.2    Elliott, M.3    Shpiro, N.4    Hastie, C.J.5    McLauchlan, H.6
  • 21
    • 84928384482 scopus 로고    scopus 로고
    • Insights on structural characteristics and ligand binding mechanisms of CDK2
    • PMID: 25918937
    • Li Y, Zhang J, Gao W, Zhang L, Pan Y, Zhang S, et al. Insights on structural characteristics and ligand binding mechanisms of CDK2. Int J Mol Sci. 2015; 16:9314-9340. doi: 10.3390/ijms16059314 PMID: 25918937
    • (2015) Int J Mol Sci , vol.16 , pp. 9314-9340
    • Li, Y.1    Zhang, J.2    Gao, W.3    Zhang, L.4    Pan, Y.5    Zhang, S.6
  • 23
    • 0031253655 scopus 로고    scopus 로고
    • Protein kinase inhibition by staurosporine revealed in details of the molecular interaction with CDK2
    • PMID: 9334743
    • Lawrie AM, Noble ME, Tunnah P, Brown NR, Johnson LN, Endicott JA. Protein kinase inhibition by staurosporine revealed in details of the molecular interaction with CDK2. Nat Struct Biol. 1997; 4:796-801. PMID: 9334743
    • (1997) Nat Struct Biol. , vol.4 , pp. 796-801
    • Lawrie, A.M.1    Noble, M.E.2    Tunnah, P.3    Brown, N.R.4    Johnson, L.N.5    Endicott, J.A.6
  • 25
    • 79957497448 scopus 로고    scopus 로고
    • Discovery of a potential allosteric ligand binding site in CDK2
    • PMID: 21291269
    • Betzi S, Alam R, Martin M, Lubbers DJ, Han H, Jakkaraj SR, et al. Discovery of a potential allosteric ligand binding site in CDK2. ACS Chem Biol. 2011; 6:492-501. doi: 10.1021/cb100410m PMID: 21291269
    • (2011) ACS Chem Biol. , vol.6 , pp. 492-501
    • Betzi, S.1    Alam, R.2    Martin, M.3    Lubbers, D.J.4    Han, H.5    Jakkaraj, S.R.6
  • 26
    • 84905658166 scopus 로고    scopus 로고
    • Modeling conformational transitions in kinases by molecular dynamics simulations: Achievements, difficulties, and open challenges
    • PMID: 24860596
    • D'Abramo M, Besker N, Chillemi G, Grottesi A. Modeling conformational transitions in kinases by molecular dynamics simulations: achievements, difficulties, and open challenges. Front Genet. 2014; 5:128. doi: 10.3389/fgene.2014.00128 PMID: 24860596
    • (2014) Front Genet , vol.5 , pp. 128
    • D'Abramo, M.1    Besker, N.2    Chillemi, G.3    Grottesi, A.4
  • 27
    • 80052499578 scopus 로고    scopus 로고
    • Cyclin-dependent kinases: Bridging their structure and function through computations
    • PMID: 21882947
    • De Vivo M, Bottegoni G, Berteotti A, Recanatini M, Gervasio FL, Cavalli A. Cyclin-dependent kinases: bridging their structure and function through computations. Future Med Chem. 2011; 3:1551-1559. doi: 10.4155/fmc.11.113 PMID: 21882947
    • (2011) Future Med Chem , vol.3 , pp. 1551-1559
    • De Vivo, M.1    Bottegoni, G.2    Berteotti, A.3    Recanatini, M.4    Gervasio, F.L.5    Cavalli, A.6
  • 28
    • 84921901999 scopus 로고    scopus 로고
    • Computational study of the "DFG-flip" conformational transition in c-Abl and c-Src tyrosine kinases
    • PMID: 25548962
    • Meng Y, Lin Y, Roux B. Computational study of the "DFG-flip" conformational transition in c-Abl and c-Src tyrosine kinases. J Phys Chem B. 2015; 119:1443-1456. doi: 10.1021/jp511792a PMID: 25548962
    • (2015) J Phys Chem B , vol.119 , pp. 1443-1456
    • Meng, Y.1    Lin, Y.2    Roux, B.3
  • 29
    • 62549151081 scopus 로고    scopus 로고
    • Protein conformational transitions: The closure mechanism of a kinase explored by atomistic simulations
    • PMID: 19067513
    • Berteotti A, Cavalli A, Branduardi D, Gervasio FL, Recanatini M, Parrinello M. Protein conformational transitions: the closure mechanism of a kinase explored by atomistic simulations. J Am Chem Soc. 2009; 131:244-250. doi: 10.1021/ja806846q PMID: 19067513
    • (2009) J Am Chem Soc. , vol.131 , pp. 244-250
    • Berteotti, A.1    Cavalli, A.2    Branduardi, D.3    Gervasio, F.L.4    Recanatini, M.5    Parrinello, M.6
  • 30
    • 84950351930 scopus 로고
    • Multidimensional Scaling: I. Theory and Method
    • Torgerson WS Multidimensional Scaling: I. Theory and Method. Psychometrika. 1952; 17: 401-419.
    • (1952) Psychometrika , vol.17 , pp. 401-419
    • Torgerson, W.S.1
  • 31
    • 82455166726 scopus 로고
    • Some properties of clasical multi-dimesional scaling
    • Mardia KV Some properties of clasical multi-dimesional scaling. Commun Stat Methods. 1978; 7: 1233-1241.
    • (1978) Commun Stat Methods , vol.7 , pp. 1233-1241
    • Mardia, K.V.1
  • 32
    • 44349104257 scopus 로고    scopus 로고
    • The out-of-sample problem for classical multidimensional scaling
    • Trosset MW, Priebe CE. The out-of-sample problem for classical multidimensional scaling. Comput Stat Data Anal. 2008; 52: 4635-4642.
    • (2008) Comput Stat Data Anal. , vol.52 , pp. 4635-4642
    • Trosset, M.W.1    Priebe, C.E.2
  • 33
    • 0000802374 scopus 로고
    • The approximation of one matrix by another of lower rank
    • Eckart C, Young G. The approximation of one matrix by another of lower rank. Psychometrika. 1936; 1: 211-218.
    • (1936) Psychometrika , vol.1 , pp. 211-218
    • Eckart, C.1    Young, G.2
  • 35
    • 0036890178 scopus 로고    scopus 로고
    • Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation
    • PMID: 12395429
    • Jakalian A, Jack DB, Bayly CI. Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation. J Comput Chem. 2002; 23:1623-1641. PMID: 12395429
    • (2002) J Comput Chem. , vol.23 , pp. 1623-1641
    • Jakalian, A.1    Jack, D.B.2    Bayly, C.I.3
  • 36
    • 33748538349 scopus 로고    scopus 로고
    • Automatic atom type and bond type perception in molecular mechanical calculations
    • PMID: 16458552
    • Wang J, Wang W, Kollman PA, Case DA. Automatic atom type and bond type perception in molecular mechanical calculations. J Mol Graph Model. 2006; 25:247-60. PMID: 16458552
    • (2006) J Mol Graph Model , vol.25 , pp. 247-260
    • Wang, J.1    Wang, W.2    Kollman, P.A.3    Case, D.A.4
  • 37
    • 84938930908 scopus 로고    scopus 로고
    • ff14SB: Improving the accuracy of protein side chain and backbone parameters from ff99SB
    • PMID: 26574453
    • Maier JA, Martinez C, Kasavajhala K, Wickstrom L, Hauser KE, Simmerling C. ff14SB: improving the accuracy of protein side chain and backbone parameters from ff99SB. J Chem Theory Comput. 2015; 11:3696-3713. doi: 10.1021/acs.jctc.5b00255 PMID: 26574453
    • (2015) J Chem Theory Comput , vol.11 , pp. 3696-3713
    • Maier, J.A.1    Martinez, C.2    Kasavajhala, K.3    Wickstrom, L.4    Hauser, K.E.5    Simmerling, C.6
  • 38
  • 40
    • 33846823909 scopus 로고
    • Particle mesh Ewald: An N log(N) method for Ewald sums in large systems
    • Darden T, York D, Pedersen L. Particle mesh Ewald: An N log(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
  • 41
    • 33646940952 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 HJ. 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.3
  • 42
    • 84986440341 scopus 로고
    • SETTLE: An analytical version of the SHAKE and RATTLE algorithm for rigid water models
    • Miyamoto S, Kollman PA. SETTLE: an analytical version of the SHAKE and RATTLE algorithm for rigid water models. J Comput Chem. 1992; 13: 952-962.
    • (1992) J Comput Chem. , vol.13 , pp. 952-962
    • Miyamoto, S.1    Kollman, P.A.2
  • 43
    • 3142716857 scopus 로고    scopus 로고
    • Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules
    • PMID: 15268227
    • Hamelberg D, Mongan J, McCammon JA. Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules. J Chem Phys. 2004; 120:11919-11929. PMID: 15268227
    • (2004) J Chem Phys. , vol.120 , pp. 11919-11929
    • Hamelberg, D.1    Mongan, J.2    McCammon, J.A.3
  • 44
    • 79957788878 scopus 로고    scopus 로고
    • ProDy: Protein dynamics inferred from theory and experiments
    • PMID: 21471012
    • Bakan A, Meireles LM, Bahar I. ProDy: protein dynamics inferred from theory and experiments. Bioinformatics. 2011; 27:1575-1577. doi: 10.1093/bioinformatics/btr168 PMID: 21471012
    • (2011) Bioinformatics , vol.27 , pp. 1575-1577
    • Bakan, A.1    Meireles, L.M.2    Bahar, I.3
  • 45
    • 84880022273 scopus 로고    scopus 로고
    • PTRAJ and CPPTRAJ: Software for processing and analysis of molecular dynamics trajectory data
    • PMID: 26583988
    • Roe DR, Cheatham TE. PTRAJ and CPPTRAJ: software for processing and analysis of molecular dynamics trajectory data. J Chem Theory Comput. 2013; 9:3084-3095. doi: 10.1021/ct400341p PMID: 26583988
    • (2013) J Chem Theory Comput. , vol.9 , pp. 3084-3095
    • Roe, D.R.1    Cheatham, T.E.2
  • 46
    • 0029878720 scopus 로고    scopus 로고
    • VMD: Visual molecular dynamics
    • PMID: 8744570
    • Humphrey W, Dalke A, Schulten K. VMD: Visual molecular dynamics. J Mol Graph. 1996; 14:33-38. PMID: 8744570
    • (1996) J Mol Graph , vol.14 , pp. 33-38
    • Humphrey, W.1    Dalke, A.2    Schulten, K.3
  • 47
    • 84870403285 scopus 로고    scopus 로고
    • Python Software Foundation
    • Python Software Foundation. Python Language Reference, version 2.7. Python Software Foundation. 2013. Available: http://www.python.org
    • (2013) Python Language Reference, Version 2.7
  • 48
    • 79952595565 scopus 로고    scopus 로고
    • The NumPy array: A structure for efficient numerical computation
    • Van Der Walt S, Colbert SC, Varoquaux G. The NumPy array: a structure for efficient numerical computation. Comput Sci Eng. 2011; 13: 22-30.
    • (2011) Comput Sci Eng. , vol.13 , pp. 22-30
    • Van Der Walt, S.1    Colbert, S.C.2    Varoquaux, G.3
  • 49
    • 84919832780 scopus 로고    scopus 로고
    • Activation pathway of Src kinase reveals intermediate states as targets for drug design
    • PMID: 24584478
    • Shukla D, Meng Y, Roux B, Pande VS. Activation pathway of Src kinase reveals intermediate states as targets for drug design. Nat Commun. 2014; 5: 3397. doi: 10.1038/ncomms4397 PMID: 24584478
    • (2014) Nat Commun. , vol.5 , pp. 3397
    • Shukla, D.1    Meng, Y.2    Roux, B.3    Pande, V.S.4
  • 50
    • 62649161772 scopus 로고    scopus 로고
    • Mapping the conformational transition in Src activation by cumulating the information from multiple molecular dynamics trajectories
    • PMID: 19225111
    • Yang S, Banavali NK, Roux B. Mapping the conformational transition in Src activation by cumulating the information from multiple molecular dynamics trajectories. Proc Natl Acad Sci USA. 2009; 106:3776-3781. doi: 10.1073/pnas.0808261106 PMID: 19225111
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 3776-3781
    • Yang, S.1    Banavali, N.K.2    Roux, B.3
  • 51
    • 0035128033 scopus 로고    scopus 로고
    • Energy landscapes of conformationally constrained peptides
    • Levy Y, Becker OM. Energy landscapes of conformationally constrained peptides. J Chem Phys. 2001; 114: 993-1009.
    • (2001) J Chem Phys. , vol.114 , pp. 993-1009
    • Levy, Y.1    Becker, O.M.2
  • 52
    • 84891836984 scopus 로고    scopus 로고
    • Locking the active conformation of c-Src kinase through the phosphorylation of the activation loop
    • PMID: 24103328
    • Meng Y, Roux B. Locking the active conformation of c-Src kinase through the phosphorylation of the activation loop. J Mol Biol. 2014; 426:423-435. doi: 10.1016/j.jmb.2013.10.001 PMID: 24103328
    • (2014) J Mol Biol , vol.426 , pp. 423-435
    • Meng, Y.1    Roux, B.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.