메뉴 건너뛰기




Volumn 22, Issue 6, 2009, Pages 506-515

A Combined atomic force microscopy imaging and docking study to investigate the complex between p53 DNA binding domain and azurin

Author keywords

Atomic force microscopy; Azurin; Docking; Molecular dynamics simulation; P53

Indexed keywords

AZURIN; DNA; GLUTATHIONE TRANSFERASE; GOLD; PROTEIN P53;

EID: 70349931469     PISSN: 09523499     EISSN: 10991352     Source Type: Journal    
DOI: 10.1002/jmr.975     Document Type: Article
Times cited : (15)

References (55)
  • 1
    • 0037076392 scopus 로고    scopus 로고
    • Single-molecule height measurements on microsomal cytochrome P450 in nanometer-scale phospholipid bilayer disks
    • Bayburt TH, Sligar SG. 2002.Single-molecule height measurements on microsomal cytochrome P450 in nanometer-scale phospholipid bilayer disks. Proc. Natl. Acad. Sci. USA 99:6725-6730
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 6725-6730
    • Bayburt, T.H.1    Sligar, S.G.2
  • 3
    • 0035869026 scopus 로고    scopus 로고
    • A method for studying protein orientation with atomic force microscopy using relative protein volumes
    • Bergkvist M, Carlsson J, Oscarsson S. 2001. A method for studying protein orientation with atomic force microscopy using relative protein volumes. J. Phys. Chem. B 105:2062-2069
    • (2001) J. Phys. Chem. B , vol.105 , pp. 2062-2069
    • Bergkvist, M.1    Carlsson, J.2    Oscarsson, S.3
  • 4
    • 0345708206 scopus 로고    scopus 로고
    • A combined study by AFM and MD simulation of a plastocyanin mutant chemisorbed on a gold surface
    • Bizzarri AR, Bonanni B, Costantini G, Cannistraro S. 2003. A combined study by AFM and MD simulation of a plastocyanin mutant chemisorbed on a gold surface. Chem. Phys. Chem. 4:1189-1195
    • (2003) Chem. Phys. Chem. , vol.4 , pp. 1189-1195
    • Bizzarri, A.R.1    Bonanni, B.2    Costantini, G.3    Cannistraro, S.4
  • 5
    • 33746259610 scopus 로고    scopus 로고
    • Topological and dynamical properties of Azurin anchored to a gold substrate as investigated by molecular dynamics simulation
    • Bizzarri AR. 2006. Topological and dynamical properties of Azurin anchored to a gold substrate as investigated by molecular dynamics simulation. Biophys. Chem. 122:206-214
    • (2006) Biophys. Chem. , vol.122 , pp. 206-214
    • Bizzarri, A.R.1
  • 6
    • 34248551488 scopus 로고    scopus 로고
    • Docking and molecular dynamics simulation of the azurin-cytochrome c551 electron transfer complex
    • Bizzarri AR, Brunori E, Bonanni B, Cannistraro S. 2007. Docking and molecular dynamics simulation of the azurin-cytochrome c551 electron transfer complex. J. Mol. Recognit. 20:122-131
    • (2007) J. Mol. Recognit , vol.20 , pp. 122-131
    • Bizzarri, A.R.1    Brunori, E.2    Bonanni, B.3    Cannistraro, S.4
  • 7
    • 0001498695 scopus 로고    scopus 로고
    • Crystal structure of the disulfide bond-deficient azurin mutant C3A/C26A. How important is the S-S bond for folding and stability?
    • Bonander N, Leckner J, Guo H,Karlsson BG, Sjölin L. 2000. Crystal structure of the disulfide bond-deficient azurin mutant C3A/C26A. How important is the S-S bond for folding and stability? Eur. J. Biochem. 267:4511-4519
    • (2000) Eur. J. Biochem , vol.267 , pp. 4511-4519
    • Bonander, N.1    Leckner, J.2    Guo, H.3    Karlsson, B.G.4    Sjölin, L.5
  • 9
    • 44649117345 scopus 로고    scopus 로고
    • Nanoparticles on modified glass surface as height calibration standard for atomic force microscopy operating in contact and tapping mode
    • Bonanni B, Cannistraro S. 2005. Nanoparticles on modified glass surface as height calibration standard for atomic force microscopy operating in contact and tapping mode. J. Nanotechnol. a0106:1-14
    • (2005) J. Nanotechnol. a , vol.106 , pp. 1-14
    • Bonanni, B.1    Cannistraro, S.2
  • 10
    • 33748323194 scopus 로고    scopus 로고
    • Optimized biorecognition of cytochrome c 551 and azurin immobilized on thiol-terminated monolayers assembled on Au(111) substrates
    • Bonanni B, Bizzarri AR, Cannistraro S. 2006. Optimized biorecognition of cytochrome c 551 and azurin immobilized on thiol-terminated monolayers assembled on Au(111) substrates. J. Phys. Chem. B 110:14574-14580
    • (2006) J. Phys. Chem. B , vol.110 , pp. 14574-14580
    • Bonanni, B.1    Bizzarri, A.R.2    Cannistraro, S.3
  • 11
    • 34249789018 scopus 로고    scopus 로고
    • Functional metalloproteins integrated with conductive substrates: Detecting single molecules and sensing individual recognition events
    • Bonanni B, Andolfi L,Bizzarri AR, Cannistraro S. 2007. Functional metalloproteins integrated with conductive substrates: Detecting single molecules and sensing individual recognition events. J. Phys. Chem. B 111:5062-5075
    • (2007) J. Phys. Chem. B , vol.111 , pp. 5062-5075
    • Bonanni, B.1    Andolfi, L.2    Bizzarri, A.R.3    Cannistraro, S.4
  • 12
    • 27744587245 scopus 로고    scopus 로고
    • Force measurements with the atomic force microscope: Technique, interpretation, and applications
    • Butt HJ, Cappella B, Kappl M. 2005. Force measurements with the atomic force microscope: technique, interpretation, and applications. Surf. Sci. Rep. 59: 1-152.
    • (2005) Surf. Sci. Rep. , vol.59 , pp. 1-152
    • Butt, H.J.1    Cappella, B.2    Kappl, M.3
  • 13
    • 33644625284 scopus 로고    scopus 로고
    • CysxHisy-Zn2+ interactions: Possibilities and limitations of a simple pairwise force field
    • Calumet N, Simonson T. 2006. CysxHisy-Zn2+ interactions: possibilities and limitations of a simple pairwise force field. J. Mol. Graph. Model. 24:404-411
    • (2006) J. Mol. Graph. Model. , vol.24 , pp. 404-411
    • Calumet, N.1    Simonson, T.2
  • 14
    • 0037093643 scopus 로고    scopus 로고
    • Docking unbound proteins using shape complementarity, desolvation, and electrostatics. Proteins: Struct
    • Chen R, Weng Z. 2002. Docking unbound proteins using shape complementarity, desolvation, and electrostatics. Proteins: Struct. Funct. Genet. 47:281-294
    • (2002) Funct. Genet , vol.47 , pp. 281-294
    • Chen, R.1    Weng, Z.2
  • 15
    • 0038185277 scopus 로고    scopus 로고
    • A novel shape complementarity scoring function for protein-protein docking. Proteins: Struct
    • Chen R, Weng Z. 2003. A novel shape complementarity scoring function for protein-protein docking. Proteins: Struct. Funct. Genet. 51: 397-408.
    • (2003) Funct. Genet , vol.51 , pp. 397-408
    • Chen, R.1    Weng, Z.2
  • 16
    • 0027983669 scopus 로고
    • Crystal structure of a p53 tumor suppressor-DNA complex: Understanding tumorigenic mutations
    • Cho Y, Gorina S, Jeffrey PD, Pavletich NP. 1994. Crystal structure of a p53 tumor suppressor-DNA complex: understanding tumorigenic mutations. Science 265:346-355
    • (1994) Science , vol.265 , pp. 346-355
    • Cho, Y.1    Gorina, S.2    Jeffrey, P.D.3    Pavletich, N.P.4
  • 18
    • 0037034815 scopus 로고    scopus 로고
    • The scanning probe microscopy of metalloproteins and metalloenzymes
    • Davis JJ, Hill HAO. 2002. The scanning probe microscopy of metalloproteins and metalloenzymes. Chem. Commun. 1:393-401
    • (2002) Chem. Commun , vol.1 , pp. 393-401
    • Davis, J.J.1    Hill, H.A.O.2
  • 19
    • 34948865835 scopus 로고    scopus 로고
    • Docking study and free energy simulation of the complex between p53 DNA-binding domain and Azurin
    • De Grandis V, Bizzarri AR, Cannistraro S. 2007. Docking study and free energy simulation of the complex between p53 DNA-binding domain and Azurin. J. Mol. Recognit. 20:215-226
    • (2007) J. Mol. Recognit , vol.20 , pp. 215-226
    • De Grandis, V.1    Bizzarri, A.R.2    Cannistraro, S.3
  • 20
    • 33748211158 scopus 로고    scopus 로고
    • Gain of function of mutant p53: The mutant p53/NF-Y protein complex reveals an aberrant transcriptional mechanism of cell cycle regulation
    • Di Agostino S, Strano S, Emiliozzi V, Zerbini V, Mottolese M, Sacchi A, Blandino G, Piaggio G. 2006. Gain of function of mutant p53: the mutant p53/NF-Y protein complex reveals an aberrant transcriptional mechanism of cell cycle regulation. Cancer Cell 10:191-202
    • (2006) Cancer Cell , vol.10 , pp. 191-202
    • Di Agostino, S.1    Strano, S.2    Emiliozzi, V.3    Zerbini, V.4    Mottolese, M.5    Sacchi, A.6    Blandino, G.7    Piaggio, G.8
  • 21
    • 33745170683 scopus 로고    scopus 로고
    • Effect of Zn2+ on DNA recognition and stability of the p53 DNA-binding domain
    • Duan J, Nilsson L. 2006. Effect of Zn2+ on DNA recognition and stability of the p53 DNA-binding domain. Biochemistry 45:7483-7492
    • (2006) Biochemistry , vol.45 , pp. 7483-7492
    • Duan, J.1    Nilsson, L.2
  • 23
    • 0037239225 scopus 로고    scopus 로고
    • Induction of apoptosis in macrophages by Pseudomonas aeruginosa Azurin: Tumour-suppressor protein p53 and reactive oxygen species, but not redox activity, as critical elements in cytotoxicity
    • Goto M, Yamada T, Kimbara K, Horner J, Newcomb M, Das Gupta TK, Chakrabarty AM. 2003. Induction of apoptosis in macrophages by Pseudomonas aeruginosa Azurin: tumour-suppressor protein p53 and reactive oxygen species, but not redox activity, as critical elements in cytotoxicity. Mol. Microbiol. 47:549-559
    • (2003) Mol. Microbiol , vol.47 , pp. 549-559
    • Goto, M.1    Yamada, T.2    Kimbara, K.3    Horner, J.4    Newcomb, M.5    Das Gupta, T.K.6    Chakrabarty, A.M.7
  • 24
    • 0031473847 scopus 로고    scopus 로고
    • SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modelling
    • Guex N, Peitsch MC. 1997. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modelling. Electrophoresis 18:2714-2723
    • (1997) Electrophoresis , vol.18 , pp. 2714-2723
    • Guex, N.1    Peitsch, M.C.2
  • 26
    • 2942602100 scopus 로고    scopus 로고
    • Molecular recognition imaging and force spectroscopy of single biomolecules
    • Hoerber JK, Miles MJ. 2003. Molecular recognition imaging and force spectroscopy of single biomolecules. Science 302:1002-1005
    • (2003) Science , vol.302 , pp. 1002-1005
    • Hoerber, J.K.1    Miles, M.J.2
  • 30
    • 33750036093 scopus 로고    scopus 로고
    • Structural basis for understanding oncogenic p53 mutations and designing rescue drugs
    • Joerger AC,Ang HC, Fersht AR. 2006. Structural basis for understanding oncogenic p53 mutations and designing rescue drugs. Proc. Natl. Acad. Sci. USA 103:15056-15061
    • (2006) Proc. Natl. Acad. Sci. USA , vol.103 , pp. 15056-15061
    • Joerger, A.C.1    Ang, H.C.2    Fersht, A.R.3
  • 31
    • 0030028728 scopus 로고    scopus 로고
    • Principles of protein-protein interactions derived from structural studies
    • Jones S, Thornton JM. 1996. Principles of protein-protein interactions derived from structural studies. Proc. Natl. Acad. Sci. USA 93:13-20
    • (1996) Proc. Natl. Acad. Sci. USA , vol.93 , pp. 13-20
    • Jones, S.1    Thornton, J.M.2
  • 32
    • 0000473453 scopus 로고    scopus 로고
    • A smooth-particle mesh Ewald method for DL-POLY molecular dynamics simulation package on the Fujitsu VPP700
    • Kholmurodov K, Smith W, Yasuoka K, Darden T, Ebisuzaki T. 2000. A smooth-particle mesh Ewald method for DL-POLY molecular dynamics simulation package on the Fujitsu VPP700. J. Comput. Chem. 21:1187-1191
    • (2000) J. Comput. Chem , vol.21 , pp. 1187-1191
    • Kholmurodov, K.1    Smith, W.2    Yasuoka, K.3    Darden, T.4    Ebisuzaki, T.5
  • 33
    • 34250165021 scopus 로고    scopus 로고
    • Nanotechnology platforms and physiological challenges for cancer therapeutics
    • Kim KY. 2007. Nanotechnology platforms and physiological challenges for cancer therapeutics. Nanomed. Nanotechnol. Biol. Med. 3:103-110
    • (2007) Nanomed. Nanotechnol. Biol. Med. , vol.3 , pp. 103-110
    • Kim, K.Y.1
  • 34
    • 0030941458 scopus 로고    scopus 로고
    • The cellular gatekeeper for growth and division
    • 323-331
    • Levine AJ. 1997. p53, the cellular gatekeeper for growth and division. Cell 88:323-331
    • (1997) Cell , vol.88 , pp. 53
    • Levine, A.J.1
  • 35
    • 0035857417 scopus 로고    scopus 로고
    • Reactivity of zinc finger cores: Analysis of protein packing and electrostatic screening
    • Maynard AT, Covell DG. 2001. Reactivity of zinc finger cores: analysis of protein packing and electrostatic screening. J. Am. Chem. Soc. 123:1047-1058
    • (2001) J. Am. Chem. Soc. , vol.123 , pp. 1047-1058
    • Maynard, A.T.1    Covell, D.G.2
  • 36
    • 0025953438 scopus 로고
    • Crystal structure analysis of oxidized Pseudomonas aeruginosa Azurin at pH 5.5 and pH 9.0
    • Nar H, Messerschmidt A, Huber R, Van de Kamp M, Canters GW. 1991. Crystal structure analysis of oxidized Pseudomonas aeruginosa Azurin at pH 5.5 and pH 9.0. J. Mol. Biol. 221:765-772
    • (1991) J. Mol. Biol , vol.221 , pp. 765-772
    • Nar, H.1    Messerschmidt, A.2    Huber, R.3    Van De Kamp, M.4    Canters, G.W.5
  • 38
    • 0032493846 scopus 로고    scopus 로고
    • Three-dimensional structure of Escherichia coli glutathione S-transferase complexed with glutathione sulfonate: Catalytic roles of Cys10 and His106
    • Nishida M, Harada S, Noguchi S, Satow Y, Inoue H, Takahashi K. 1998. Three-dimensional structure of Escherichia coli glutathione S-transferase complexed with glutathione sulfonate: catalytic roles of Cys10 and His106. J. Mol. Biol. 281:135-147
    • (1998) J. Mol. Biol , vol.281 , pp. 135-147
    • Nishida, M.1    Harada, S.2    Noguchi, S.3    Satow, Y.4    Inoue, H.5    Takahashi, K.6
  • 39
    • 0037474541 scopus 로고    scopus 로고
    • Structural characterization and functional significance of transient protein-protein interactions
    • Nooren IMA, Thornton JM. 2003. Structural characterization and functional significance of transient protein-protein interactions. J. Mol. Biol. 325:991-1018
    • (2003) J. Mol. Biol , vol.325 , pp. 991-1018
    • Nooren, I.M.A.1    Thornton, J.M.2
  • 40
    • 84943502952 scopus 로고
    • A molecular dynamics method for simulations in the canonical ensemble
    • Nose' S. 1984. A molecular dynamics method for simulations in the canonical ensemble. Mol. Phys. 52:255-268
    • (1984) Mol. Phys. , vol.52 , pp. 255-268
    • Nose, S.1
  • 41
    • 0019707626 scopus 로고
    • Polymorphic transitions in single crystals: A new molecular dynamics method
    • Parrinello M, Rahman A. 1981. Polymorphic transitions in single crystals: a new molecular dynamics method. J. Appl. Phys. 52:7182-7190
    • (1981) J. Appl. Phys , vol.52 , pp. 7182-7190
    • Parrinello, M.1    Rahman, A.2
  • 42
    • 0037066262 scopus 로고    scopus 로고
    • Force spectroscopy of single biomolecules
    • Rief M, Grubmueller H. 2002. Force spectroscopy of single biomolecules. ChemPhysChem. 3:255-261
    • (2002) ChemPhysChem , vol.3 , pp. 255-261
    • Rief, M.1    Grubmueller, H.2
  • 43
    • 3042609738 scopus 로고    scopus 로고
    • Fast contact-mode atomic force microscopy on biological specimen by model-based control
    • Schitter G, Stark RW, Stemmer A. 2004. Fast contact-mode atomic force microscopy on biological specimen by model-based control. Ultramicroscopy 100:253-257
    • (2004) Ultramicroscopy , vol.100 , pp. 253-257
    • Schitter, G.1    Stark, R.W.2    Stemmer, A.3
  • 44
    • 34247628555 scopus 로고    scopus 로고
    • Exploiting nanotechnology to target cancer
    • Sengupta S, Sasisekharan R. 2007. Exploiting nanotechnology to target cancer. Br. J. Cancer 96:1315-1319
    • (2007) Br. J. Cancer , vol.96 , pp. 1315-1319
    • Sengupta, S.1    Sasisekharan, R.2
  • 46
    • 0004221058 scopus 로고
    • McGraw-Hill Book Company: New York.
    • Spieger MR. 1961. Statistics. McGraw-Hill Book Company: New York.
    • (1961) Statistics
    • Spieger, M.R.1
  • 47
    • 33947281541 scopus 로고    scopus 로고
    • Developing scanning probe-based nanodevices - Stepping out of the laboratory into the clinic
    • Stolz M, Aebi U, Stoffler D. 2007. Developing scanning probe-based nanodevices - stepping out of the laboratory into the clinic. Nanomed. Nanotechnol. Biol. Med. 3:53-62
    • (2007) Nanomed. Nanotechnol. Biol. Med , vol.3 , pp. 53-62
    • Stolz, M.1    Aebi, U.2    Stoffler, D.3
  • 48
    • 39749143144 scopus 로고    scopus 로고
    • Probing the interaction between p53 and the bacterial protein azurin by single molecule force spectroscopy
    • Taranta M, Bizzarri AR, Cannistraro S. 2008. Probing the interaction between p53 and the bacterial protein azurin by single molecule force spectroscopy. J. Mol. Recognit. 21:63-70
    • (2008) J. Mol. Recognit , vol.21 , pp. 63-70
    • Taranta, M.1    Bizzarri, A.R.2    Cannistraro, S.3
  • 49
    • 1242270553 scopus 로고    scopus 로고
    • Protein - Protein docking: Is the glass half-full or half-empty?
    • Vajda S, Camacho CJ. 2004. Protein - protein docking: is the glass half-full or half-empty? Trends Biotechnol. 22:110-116
    • (2004) Trends Biotechnol , vol.22 , pp. 110-116
    • Vajda, S.1    Camacho, C.J.2
  • 50
    • 0025252558 scopus 로고
    • Involvement of the hydrophobic patch of azurin in the electron-transfer reactions with cytochrome 551 and nitrite reductase
    • Van de Kamp M, Silvestrini MC, Brunori M, Beeumen JV, Hali FC, Canters GW. 1990. Involvement of the hydrophobic patch of azurin in the electron-transfer reactions with cytochrome 551 and nitrite reductase. Eur. J. Biochem. 194:109-118
    • (1990) Eur. J. Biochem , vol.194 , pp. 109-118
    • Van De Kamp, M.1    Silvestrini, M.C.2    Brunori, M.3    Beeumen, J.V.4    Hali, F.C.5    Canters, G.W.6
  • 55
    • 2342460218 scopus 로고    scopus 로고
    • Exploring the electronic and mechanical properties of protein using conducting atomic force microscopy
    • Zhao J, Davis JJ, Sansom MSP, Hung A. 2004. Exploring the electronic and mechanical properties of protein using conducting atomic force microscopy. J. Am. Chem. Soc. 126:5601-5609.
    • (2004) J. Am. Chem. Soc , vol.126 , pp. 5601-5609
    • Zhao, J.1    Davis, J.J.2    Sansom, M.S.P.3    Hung, A.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.