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Volumn 582, Issue 25-26, 2008, Pages 3619-3624

Characterization of the papillomavirus α1E2 peptide unfolded to folded transition upon DNA binding

Author keywords

DNA structure; E2 protein; Induced fit; Molecular dynamics; Papillomavirus

Indexed keywords

GLYCOPROTEIN E2;

EID: 53949123299     PISSN: 00145793     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.febslet.2008.09.041     Document Type: Article
Times cited : (5)

References (49)
  • 1
    • 0035193540 scopus 로고    scopus 로고
    • Human papillomaviruses and their role in cervical cancer
    • Dell G., and Gaston K. Human papillomaviruses and their role in cervical cancer. Cell. Mol. Life Sci. 58 (2001) 1923-1942
    • (2001) Cell. Mol. Life Sci. , vol.58 , pp. 1923-1942
    • Dell, G.1    Gaston, K.2
  • 2
    • 0036086459 scopus 로고    scopus 로고
    • The papillomavirus E2 proteins: structure, function and biology
    • Hedge R. The papillomavirus E2 proteins: structure, function and biology. Annu. Rev. Biophys. Biomol. Struct. 31 (2002) 343-360
    • (2002) Annu. Rev. Biophys. Biomol. Struct. , vol.31 , pp. 343-360
    • Hedge, R.1
  • 4
    • 0030667739 scopus 로고    scopus 로고
    • Functional interaction of a novel cellular protein with the papillomavirus E2 transactivation domain
    • Breiding D.E., Sverdrup F., Grossel M.J., Moscufo N., Boonchai W., and Androphy E.J. Functional interaction of a novel cellular protein with the papillomavirus E2 transactivation domain. Mol. Cell Biol. 17 (1997) 7208-7219
    • (1997) Mol. Cell Biol. , vol.17 , pp. 7208-7219
    • Breiding, D.E.1    Sverdrup, F.2    Grossel, M.J.3    Moscufo, N.4    Boonchai, W.5    Androphy, E.J.6
  • 5
    • 0031907715 scopus 로고    scopus 로고
    • Functional interaction of the bovine papillomavirus E2 transactivation domain with TFIIB
    • Yao J.M., Breiding D.E., and Androphy E.J. Functional interaction of the bovine papillomavirus E2 transactivation domain with TFIIB. J. Virol. 72 (1998) 1013-1019
    • (1998) J. Virol. , vol.72 , pp. 1013-1019
    • Yao, J.M.1    Breiding, D.E.2    Androphy, E.J.3
  • 6
    • 0034613274 scopus 로고    scopus 로고
    • The structural basis of DNA target discrimination by papillomavirus E2 proteins
    • Kim S.S., Tam J.K., Wang A.F., and Hegde R.S. The structural basis of DNA target discrimination by papillomavirus E2 proteins. J. Biol. Chem. 275 (2000) 31245-31254
    • (2000) J. Biol. Chem. , vol.275 , pp. 31245-31254
    • Kim, S.S.1    Tam, J.K.2    Wang, A.F.3    Hegde, R.S.4
  • 8
    • 0032545160 scopus 로고    scopus 로고
    • Crystal structure of the E2 DNA-binding domain from human papillomavirus type 16: Implications for its DNA-binding-site selection mechanism
    • Hegde R.S., and Androphy E.J. Crystal structure of the E2 DNA-binding domain from human papillomavirus type 16: Implications for its DNA-binding-site selection mechanism. J. Mol. Biol. 284 (1998) 1479-1489
    • (1998) J. Mol. Biol. , vol.284 , pp. 1479-1489
    • Hegde, R.S.1    Androphy, E.J.2
  • 9
    • 0345304716 scopus 로고    scopus 로고
    • Comparison of the structure and DNA-binding properties of the E2 proteins from an oncogenic and a non-oncogenic human papillomavirus
    • Dell G., Wilkinson K.W., Tranter R., Parish J., Brady L., and Gaston K. Comparison of the structure and DNA-binding properties of the E2 proteins from an oncogenic and a non-oncogenic human papillomavirus. J. Mol. Biol. 334 (2003) 979-991
    • (2003) J. Mol. Biol. , vol.334 , pp. 979-991
    • Dell, G.1    Wilkinson, K.W.2    Tranter, R.3    Parish, J.4    Brady, L.5    Gaston, K.6
  • 10
    • 0032489427 scopus 로고    scopus 로고
    • Subunit rearrangement accompanies sequence-specific DNA-binding by the bovine papillomavirus-1 E2 protein
    • Hedge R.S., Wang A.F., Kim S.S., and Shapira M. Subunit rearrangement accompanies sequence-specific DNA-binding by the bovine papillomavirus-1 E2 protein. J. Mol. Biol. 276 (1998) 797-808
    • (1998) J. Mol. Biol. , vol.276 , pp. 797-808
    • Hedge, R.S.1    Wang, A.F.2    Kim, S.S.3    Shapira, M.4
  • 11
    • 33748579930 scopus 로고    scopus 로고
    • The recognition of local DNA conformational by the human papillomavirus type 6 E2 protein
    • Hooley E., Fairweather V., Clarke A.R., Gaston K., and e Brady R.L. The recognition of local DNA conformational by the human papillomavirus type 6 E2 protein. Nucl. Acids Res. 14 (2006) 3897-3908
    • (2006) Nucl. Acids Res. , vol.14 , pp. 3897-3908
    • Hooley, E.1    Fairweather, V.2    Clarke, A.R.3    Gaston, K.4    e Brady, R.L.5
  • 12
    • 0026656038 scopus 로고
    • Crystal structure at 1.7 A of the bovine papillomavirus-1 E2 DNA-binding domain bound to its DNA target
    • Hegde R.S., Grossman S.R., Laimins L.A., and e Sigler P.B. Crystal structure at 1.7 A of the bovine papillomavirus-1 E2 DNA-binding domain bound to its DNA target. Nature 359 (1992) 505-512
    • (1992) Nature , vol.359 , pp. 505-512
    • Hegde, R.S.1    Grossman, S.R.2    Laimins, L.A.3    e Sigler, P.B.4
  • 13
    • 0033522799 scopus 로고    scopus 로고
    • Crystal structure of the human papillomavirus type 18 E2 activation domain
    • Harris S.F., and Botchan M.R. Crystal structure of the human papillomavirus type 18 E2 activation domain. Science 284 (1999) 1673-1677
    • (1999) Science , vol.284 , pp. 1673-1677
    • Harris, S.F.1    Botchan, M.R.2
  • 14
    • 0033534152 scopus 로고    scopus 로고
    • Structural correlates for enhanced stability in the E2 DNA-binding domain from bovine papillomavirus
    • Veeraraghavan S., Mello C.C., Androphy E.J., and Baleja J.D. Structural correlates for enhanced stability in the E2 DNA-binding domain from bovine papillomavirus. Biochemistry 38 (1999) 16115-16124
    • (1999) Biochemistry , vol.38 , pp. 16115-16124
    • Veeraraghavan, S.1    Mello, C.C.2    Androphy, E.J.3    Baleja, J.D.4
  • 15
    • 0030068229 scopus 로고    scopus 로고
    • Solution structure of the DNA-binding domain of a human papillomavirus E2 protein: evidence for flexible DNA-binding regions
    • Liang H., Petros A.M., Meadows R.P., Yoon H.S., Egan D.A., Walter K., Holzman T.F., Robins T., and Fesik S.W. Solution structure of the DNA-binding domain of a human papillomavirus E2 protein: evidence for flexible DNA-binding regions. Biochemistry 35 (1996) 2095-2103
    • (1996) Biochemistry , vol.35 , pp. 2095-2103
    • Liang, H.1    Petros, A.M.2    Meadows, R.P.3    Yoon, H.S.4    Egan, D.A.5    Walter, K.6    Holzman, T.F.7    Robins, T.8    Fesik, S.W.9
  • 16
    • 22544471479 scopus 로고    scopus 로고
    • Solution structure of the HPV-16 E2 DNA-binding domain, a transcriptional regulator with a dimeric beta-barrel fold
    • Nadra A.D., Eliseo T., Mok Y.K., Almeida F.C.L., Bycroft M., Paci M., Prat-Gay G., and Cicero D.O. Solution structure of the HPV-16 E2 DNA-binding domain, a transcriptional regulator with a dimeric beta-barrel fold. J. Biomol. NMR 30 (2004) 211-214
    • (2004) J. Biomol. NMR , vol.30 , pp. 211-214
    • Nadra, A.D.1    Eliseo, T.2    Mok, Y.K.3    Almeida, F.C.L.4    Bycroft, M.5    Paci, M.6    Prat-Gay, G.7    Cicero, D.O.8
  • 17
    • 51049122626 scopus 로고    scopus 로고
    • MD simulations of papillomavirus DNA-E2 protein complexes hints at a protein structural code for DNA deformation
    • Falconi M., Oteri F., Eliseo T., Cicero D.O., and Desideri A. MD simulations of papillomavirus DNA-E2 protein complexes hints at a protein structural code for DNA deformation. Biophys. J. 95 (2008) 1108-1117
    • (2008) Biophys. J. , vol.95 , pp. 1108-1117
    • Falconi, M.1    Oteri, F.2    Eliseo, T.3    Cicero, D.O.4    Desideri, A.5
  • 18
    • 33645220778 scopus 로고    scopus 로고
    • Specificity in DNA recognition by a peptide from papillomavirus E2 protein
    • Faber-Barata J., Mohana-Borges R., and Lima L.M.T.R. Specificity in DNA recognition by a peptide from papillomavirus E2 protein. FEBS Lett. 580 (2006) 1919-1924
    • (2006) FEBS Lett. , vol.580 , pp. 1919-1924
    • Faber-Barata, J.1    Mohana-Borges, R.2    Lima, L.M.T.R.3
  • 19
    • 0025155512 scopus 로고
    • Folding transition in the DNA-binding domain of Gcn4 on specific binding to DNA
    • Weiss M.A., Ellenberger T., Wobbe C.R., Lee J.P., Harrison S.C., and Struhl K. Folding transition in the DNA-binding domain of Gcn4 on specific binding to DNA. Nature 347 (1990) 575-578
    • (1990) Nature , vol.347 , pp. 575-578
    • Weiss, M.A.1    Ellenberger, T.2    Wobbe, C.R.3    Lee, J.P.4    Harrison, S.C.5    Struhl, K.6
  • 20
    • 0028915928 scopus 로고
    • Solution dynamics of the Trp repressor - a study of amide proton-exchange by T-1 relaxation
    • Gryk M.R., Finucane M.D., Zheng Z.W., and Jardetzky O. Solution dynamics of the Trp repressor - a study of amide proton-exchange by T-1 relaxation. J. Mol. Biol. 246 (1995) 618-627
    • (1995) J. Mol. Biol. , vol.246 , pp. 618-627
    • Gryk, M.R.1    Finucane, M.D.2    Zheng, Z.W.3    Jardetzky, O.4
  • 21
    • 0028036594 scopus 로고
    • The secondary structure of the Ets domain of human Fli-1 resembles that of the helix-turn-helix DNA-binding motif of the Escherichia coli catabolite gene activator protein
    • Liang H., Olejniczak E.T., Mao X.H., Nettesheim D.G., Yu L.P., Thompson C.B., and Fesik S.W. The secondary structure of the Ets domain of human Fli-1 resembles that of the helix-turn-helix DNA-binding motif of the Escherichia coli catabolite gene activator protein. Proc. Natl. Acad. Sci. USA 91 (1994) 11655-11659
    • (1994) Proc. Natl. Acad. Sci. USA , vol.91 , pp. 11655-11659
    • Liang, H.1    Olejniczak, E.T.2    Mao, X.H.3    Nettesheim, D.G.4    Yu, L.P.5    Thompson, C.B.6    Fesik, S.W.7
  • 22
    • 33744795425 scopus 로고    scopus 로고
    • Structural and thermodynamic basis for the enhanced transcriptional control by the human papillomavirus strain-16 E2 protein
    • Cicero D.O., Nadra A.D., Eliseo T., Dellarole M., Paci M., and de Prat-Gay G. Structural and thermodynamic basis for the enhanced transcriptional control by the human papillomavirus strain-16 E2 protein. Biochemistry 45 (2006) 6551-6560
    • (2006) Biochemistry , vol.45 , pp. 6551-6560
    • Cicero, D.O.1    Nadra, A.D.2    Eliseo, T.3    Dellarole, M.4    Paci, M.5    de Prat-Gay, G.6
  • 23
    • 34247393616 scopus 로고    scopus 로고
    • Molecular dynamics of the DNA-binding domain of the papillomavirus E2 transcriptional regulator uncover differential properties for DNA target accommodation
    • Falconi M., Santolamazza A., Eliseo T., de Prat-Gay G., Cicero D.O., and Desideri A. Molecular dynamics of the DNA-binding domain of the papillomavirus E2 transcriptional regulator uncover differential properties for DNA target accommodation. FEBS J. 204 (2007) 2385-2395
    • (2007) FEBS J. , vol.204 , pp. 2385-2395
    • Falconi, M.1    Santolamazza, A.2    Eliseo, T.3    de Prat-Gay, G.4    Cicero, D.O.5    Desideri, A.6
  • 24
    • 0033597729 scopus 로고    scopus 로고
    • The cap-binding protein eIF4E promotes folding of a functional domain of yeast translation initiation factor eIF4G1
    • Hershey P.E.C., McWhirter S.M., Gross J.D., Wagner G., Alber T., and Sachs A.B. The cap-binding protein eIF4E promotes folding of a functional domain of yeast translation initiation factor eIF4G1. J. Biol. Chem. 274 (1999) 21297-21304
    • (1999) J. Biol. Chem. , vol.274 , pp. 21297-21304
    • Hershey, P.E.C.1    McWhirter, S.M.2    Gross, J.D.3    Wagner, G.4    Alber, T.5    Sachs, A.B.6
  • 25
    • 25844495843 scopus 로고    scopus 로고
    • Molecular dynamics studies on free and bound targets of the bovine papillomavirus type I E2 protein: the protein binding effect on DNA and the recognition mechanism
    • Djuranovic D., and Hartmann B. Molecular dynamics studies on free and bound targets of the bovine papillomavirus type I E2 protein: the protein binding effect on DNA and the recognition mechanism. Biophys. J. 89 (2005) 2542-2551
    • (2005) Biophys. J. , vol.89 , pp. 2542-2551
    • Djuranovic, D.1    Hartmann, B.2
  • 26
    • 0014966180 scopus 로고
    • Commission on biochemical nomenclature, abbreviations and symbols for description of conformation of polypeptide chains
    • UB I.-I. Commission on biochemical nomenclature, abbreviations and symbols for description of conformation of polypeptide chains. J. Mol. Biol. 52 (1970) 1-17
    • (1970) J. Mol. Biol. , vol.52 , pp. 1-17
    • UB, I.-I.1
  • 27
    • 0029878720 scopus 로고    scopus 로고
    • VMD - visual molecular dynamics
    • Humphrey W., Dalke A., and Schulten K. VMD - visual molecular dynamics. J. Mol. Graph. 14 (1996) 33-38. http://www.ks.uiuc.edu/Research/vmd/
    • (1996) J. Mol. Graph. , vol.14 , pp. 33-38
    • Humphrey, W.1    Dalke, A.2    Schulten, K.3
  • 29
    • 0031473847 scopus 로고    scopus 로고
    • Swiss-model modeling the Swiss-Pdb viewer: an environment for comparative protein
    • Guex N., and Peitsch M.C. Swiss-model modeling the Swiss-Pdb viewer: an environment for comparative protein. Electrophoresis 18 (1997) 2714-2723. http://www.expasy.org/spdbv
    • (1997) Electrophoresis , vol.18 , pp. 2714-2723
    • Guex, N.1    Peitsch, M.C.2
  • 30
    • 53949120694 scopus 로고    scopus 로고
    • van der Spoel, D., Lindahl, E., Hess, B., van Buuren, A.R., Apol, E., Meulenhoff, P.J., Tieleman, D.P., Sijbers, A.L.T.M., Freenstra, K.A., van Drunen, R. and Berendsen, H.J.C. (2005) GROMACS user manual 3.3. .
    • van der Spoel, D., Lindahl, E., Hess, B., van Buuren, A.R., Apol, E., Meulenhoff, P.J., Tieleman, D.P., Sijbers, A.L.T.M., Freenstra, K.A., van Drunen, R. and Berendsen, H.J.C. (2005) GROMACS user manual 3.3. .
  • 31
    • 20544435097 scopus 로고    scopus 로고
    • Exploring the helix-coil transition via all-atom equilibrium ensemble simulations
    • Sorin E.J., and Pande V.S. Exploring the helix-coil transition via all-atom equilibrium ensemble simulations. Biophys. J. 88 (2005) 2472-2493. http://folding.stanford.edu/ffamber/
    • (2005) Biophys. J. , vol.88 , pp. 2472-2493
    • Sorin, E.J.1    Pande, V.S.2
  • 32
    • 0024058085 scopus 로고
    • The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids
    • Lavery R., and Sklenar H. The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids. J. Biomol. Struct. Dyn. 6 (1988) 63-91
    • (1988) J. Biomol. Struct. Dyn. , vol.6 , pp. 63-91
    • Lavery, R.1    Sklenar, H.2
  • 33
    • 0028261555 scopus 로고
    • Modelling DNA conformational mechanics
    • Lavery R., and Hartmann B. Modelling DNA conformational mechanics. Biophys. Chem. 50 (1994) 33-45
    • (1994) Biophys. Chem. , vol.50 , pp. 33-45
    • Lavery, R.1    Hartmann, B.2
  • 34
    • 0000243829 scopus 로고
    • PROCHECK: a program to check the stereochemical quality of protein structures
    • Laskowski R.A., MacArthur M.W., Moss D.S., and Thornton J.M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Cryst. 26 (1993) 283-291
    • (1993) J. Appl. Cryst. , vol.26 , pp. 283-291
    • Laskowski, R.A.1    MacArthur, M.W.2    Moss, D.S.3    Thornton, J.M.4
  • 35
    • 0000020246 scopus 로고    scopus 로고
    • A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions
    • Mahoney M.W., and Jorgensen W.L. A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions. J. Chem. Phys. 112 (2000) 8910-8922
    • (2000) J. Chem. Phys. , vol.112 , pp. 8910-8922
    • Mahoney, M.W.1    Jorgensen, W.L.2
  • 36
    • 0035861454 scopus 로고    scopus 로고
    • Water permeation across biological membranes: mechanism and dynamics of aquaporin-1 and GlpF
    • de Groot B.L., and Grubmüller H. Water permeation across biological membranes: mechanism and dynamics of aquaporin-1 and GlpF. Science 294 (2001) 2353-2357
    • (2001) Science , vol.294 , pp. 2353-2357
    • de Groot, B.L.1    Grubmüller, H.2
  • 38
    • 84986440341 scopus 로고
    • SETTLE: an analytical version of the SHAKE and RATTLE algorithm for rigid water models
    • Miyamoto S., and Kollman P.A. SETTLE: an analytical version of the SHAKE and RATTLE algorithm for rigid water models. J. Comput. Chem. 13 (1992) 952-962
    • (1992) J. Comput. Chem. , vol.13 , pp. 952-962
    • Miyamoto, S.1    Kollman, P.A.2
  • 40
    • 33846823909 scopus 로고
    • Particle Mesh Ewald -an N.log(N) method for Ewald sums in large systems
    • Darden T., York D., and Pedersen L. Particle Mesh Ewald -an N.log(N) method for Ewald sums in large systems. J. Chem. Phys 98 (1992) 10089-10092
    • (1992) J. Chem. Phys , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 41
    • 0032996542 scopus 로고    scopus 로고
    • Molecular dynamics simulations of a protein-protein dimmer: particle-mesh Ewald electrostatic model yields far superior results to standard cutoff model
    • Norberto de Souza O., and Ornstein R.L. Molecular dynamics simulations of a protein-protein dimmer: particle-mesh Ewald electrostatic model yields far superior results to standard cutoff model. J. Biomol. Struct. Dyn. 16 (1999) 1205-1218
    • (1999) J. Biomol. Struct. Dyn. , vol.16 , pp. 1205-1218
    • Norberto de Souza, O.1    Ornstein, R.L.2
  • 42
    • 0028072364 scopus 로고
    • Pseudodihedrals: simplified protein backbone representation with knowledge-based energy
    • de Witte R.S., and Shakhnovich E.J. Pseudodihedrals: simplified protein backbone representation with knowledge-based energy. Protein Sci. 3 (1994) 1570-1581
    • (1994) Protein Sci. , vol.3 , pp. 1570-1581
    • de Witte, R.S.1    Shakhnovich, E.J.2
  • 43
    • 0028019116 scopus 로고
    • Helicity, circular dichroism and molecular dynamics of proteins
    • Hirst J.D., and Brooks III C.L. Helicity, circular dichroism and molecular dynamics of proteins. J. Mol. Biol. 243 (1994) 173-178
    • (1994) J. Mol. Biol. , vol.243 , pp. 173-178
    • Hirst, J.D.1    Brooks III, C.L.2
  • 45
    • 41449113042 scopus 로고    scopus 로고
    • The role of DNA twist in the packaging of viral genomes
    • Rollins G.C., Petrov A.S., and Harvey S.C. The role of DNA twist in the packaging of viral genomes. Biophys. J. 94 (2008) L38-40
    • (2008) Biophys. J. , vol.94
    • Rollins, G.C.1    Petrov, A.S.2    Harvey, S.C.3
  • 46
    • 0036286321 scopus 로고    scopus 로고
    • Simulations of nucleic acids and their complexes
    • Giudice E., and Lavery R. Simulations of nucleic acids and their complexes. Acc. Chem. Res. 35 (2002) 350-357
    • (2002) Acc. Chem. Res. , vol.35 , pp. 350-357
    • Giudice, E.1    Lavery, R.2
  • 47
    • 3042581815 scopus 로고    scopus 로고
    • The structural basis of DNA flexibility
    • Travers A.A. The structural basis of DNA flexibility. Phil. Trans. Roy. Soc. Lond. 362 (2004) 1423-1438
    • (2004) Phil. Trans. Roy. Soc. Lond. , vol.362 , pp. 1423-1438
    • Travers, A.A.1
  • 48
    • 0024454946 scopus 로고
    • Definitions and nomenclature of nucleic acids structure parameters
    • Dickerson R.E. Definitions and nomenclature of nucleic acids structure parameters. EMBO J. 8 (1989) 1-4
    • (1989) EMBO J. , vol.8 , pp. 1-4
    • Dickerson, R.E.1
  • 49
    • 27144559598 scopus 로고    scopus 로고
    • Insights into the induced fit mechanism in antithrombin-heparin interaction using molecular dynamics simulations
    • Verli H., and Guimarães J.A. Insights into the induced fit mechanism in antithrombin-heparin interaction using molecular dynamics simulations. J. Mol. Graph. Mod. 24 (2005) 203-212
    • (2005) J. Mol. Graph. Mod. , vol.24 , pp. 203-212
    • Verli, H.1    Guimarães, J.A.2


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