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Volumn 49, Issue 8, 2010, Pages 1737-1743

A structural model for the single-stranded DNA genome of filamentous bacteriophage Pf1

Author keywords

[No Author keywords available]

Indexed keywords

AVERAGE ANGLE; BASE PLANE; DNA LOOPS; DNA NUCLEOTIDES; FILAMENT AXIS; FLEXIBLE FILAMENTS; MOLECULAR MODELS; NUCLEOTIDE BASIS; POLARIZED RAMAN SPECTRA; PSEUDOMONAS AERUGINOSA; RAMAN BANDS; SINGLE-STRANDED DNA; STRUCTURAL MODELS;

EID: 77749265086     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi901323a     Document Type: Article
Times cited : (20)

References (36)
  • 1
    • 0028108799 scopus 로고
    • Pf1 virus structure: Helical coat protein and DNA with paraxial phosphates
    • Liu, D. J., and Day, L. A. (1994) Pf1 virus structure: helical coat protein and DNA with paraxial phosphates. Science 265, 671-674.
    • (1994) Science , vol.265 , pp. 671-674
    • Liu, D.J.1    Day, L.A.2
  • 2
    • 85069925239 scopus 로고    scopus 로고
    • Mahy, B. W. J., and van Regenmortel, M. H. V., Eds. Elsevier, Oxford, U.K.
    • Overman, S. A., and Thomas, G. J., Jr. (2008) in Encyclopedia of Virology (Mahy, B. W. J., and van Regenmortel, M. H. V., Eds.) pp 190-198, Elsevier, Oxford, U.K.
    • (2008) Encyclopedia of Virology , pp. 190-198
    • Overman, S.A.1    Thomas Jr., G.J.2
  • 4
    • 0034142068 scopus 로고    scopus 로고
    • The molecular structure and structural transition of the alpha-helical capsid in filamentous bacteriophage Pf1
    • (Part 2)
    • Welsh, L. C., Symmons, M. F., and Marvin, D. A. (2000) The molecular structure and structural transition of the alpha-helical capsid in filamentous bacteriophage Pf1. Acta Crystallogr., Sect. D: Biol. Crystallogr. 56 (Part 2), 137-150.
    • (2000) Acta Crystallogr., Sect. D: Biol. Crystallogr. , vol.56 , pp. 137-150
    • Welsh, L.C.1    Symmons, M.F.2    Marvin, D.A.3
  • 5
    • 4344702276 scopus 로고    scopus 로고
    • Structure of the coat protein in Pf1 bacteriophage determined by solid-state NMR spectroscopy
    • Thiriot, D. S., Nevzorov, A. A., Zagyanskly, L., Wu, C. H., and Opella, S. J. (2004) Structure of the coat protein in Pf1 bacteriophage determined by solid-state NMR spectroscopy. J. Mol. Biol. 341, 869879.
    • (2004) J. Mol. Biol. , vol.341 , pp. 869879
    • Thiriot, D.S.1    Nevzorov, A.A.2    Zagyanskly, L.3    Wu, C.H.4    Opella, S.J.5
  • 6
    • 0037417751 scopus 로고    scopus 로고
    • Protein and DNA residue orientations in the filamentous virus PfI determined by polarized Raman and polarized FTIR spectroscopy
    • Tsuboi, M., Kubo, Y., Ikeda, T., Overman, S. A., Osman, O., and Thomas, G. J., Jr. (2003) Protein and DNA residue orientations in the filamentous virus PfI determined by polarized Raman and polarized FTIR spectroscopy. Biochemistry 42, 940-950.
    • (2003) Biochemistry , vol.42 , pp. 940-950
    • Tsuboi, M.1    Kubo, Y.2    Ikeda, T.3    Overman, S.A.4    Osman, O.5    Thomas Jr., G.J.6
  • 7
    • 0034852135 scopus 로고    scopus 로고
    • Characterization of molecular alignment in aqueous suspensions of Pf1 bacteriophage
    • DOI 10.1023/A:1011263920003
    • Zweckstetter, M., and Bax, A. (2001) Characterization of molecular alignment in aqueous suspensions of Pf1 bacteriophage. J. iomol. NMR 20, 365-377. (Pubitemid 32825731)
    • (2001) Journal of Biomolecular NMR , vol.20 , Issue.4 , pp. 365-377
    • Zweckstetter, M.1    Bax, A.2
  • 8
    • 0035955207 scopus 로고    scopus 로고
    • Single-step determination of protein substructures using dipolar couplings: Aid to structural genomics [24]
    • DOI 10.1021/ja016496h
    • Zweckstetter, M., and Bax, A. (2001) Single-step determination of protein substructures using dipolar couplings: aid to structural genomics, J. Am. Chem. Soc. 123, 9490-9491. (Pubitemid 32900338)
    • (2001) Journal of the American Chemical Society , vol.123 , Issue.38 , pp. 9490-9491
    • Zweckstetter, M.1    Bax, A.2
  • 9
    • 0021095333 scopus 로고
    • Structure similarity, difference and variability in the filamentous viruses fd, If1, IKe, PfI, Xf and Pf3
    • Thomas, G. J., Jr., Prescott, B., and Day, L. A. (1983) Structure similarity, difference and variability in the filamentous viruses fd, If1, IKe, PfI, Xf and Pf3. J. Mol. Biol. 165, 321-356.
    • (1983) J. Mol. Biol. , vol.165 , pp. 321-356
    • Thomas Jr., G.J.1    Prescott, B.2    Day, L.A.3
  • 10
    • 0020639043 scopus 로고
    • Comparison of protein and deoxyribonucleic acid backbone structures in fd and Pf1 bacteriophages
    • Cross, T. A., Tsang, P., and Opella, S. J. (1983) Comparison, of protein and deoxyribonucleic acid backbone structures in fd and Pf1 bacteriophages. Biochemistry 22, 721-726. (Pubitemid 13134036)
    • (1983) Biochemistry , vol.22 , Issue.4 , pp. 721-726
    • Cross, T.A.1    Tsang, P.2    Opella, S.J.3
  • 11
    • 0013014485 scopus 로고
    • Structure of the bacterial virus Pf1. An infrared linear dichroism study
    • Fritzsche, H., Tsang, P., Opella, S. J., and Kallenbach, N. R. (1986) Structure of the bacterial virus Pf1. An infrared linear dichroism study. Stud. Biophys. 116, 175-180.
    • (1986) Stud. Biophys. , vol.116 , pp. 175-180
    • Fritzsche, H.1    Tsang, P.2    Opella, S.J.3    Kallenbach, N.R.4
  • 12
    • 0024286078 scopus 로고
    • Sugar pucker and phosphodiester conformations in viral genomes of filamentous bacteriophages: Fd, If1, IKe, Pf1, Xf, and Pf3
    • Thomas, G. J., Jr., Prescott, B., Opella, S. J., and Day, L. A. (1988) Sugar pucker and phosphodiester conformations in viral genomes of filamentous bacteriophages: fd, If1, IKe, Pf1, Xf, and Pf3. Biochemistry 27, 4350-4357.
    • (1988) Biochemistry , vol.27 , pp. 4350-4357
    • Thomas Jr., G.J.1    Prescott, B.2    Opella, S.J.3    Day, L.A.4
  • 13
    • 0025784438 scopus 로고
    • Neutron diffraction studies of the structure of filamentous bacteriophage Pf1. Demonstration that the coat protein consists of a pair of alpha-helices with an intervening, non-helical surface loop. 7
    • Nambudripad, R., Stark, W., and Makowski, L. (1991) Neutron diffraction studies of the structure of filamentous bacteriophage Pf1. Demonstration that the coat protein consists of a pair of alpha-helices with an intervening, non-helical surface loop. 7. Mol. Biol. 220, 359379.
    • (1991) Mol. Biol. , vol.220 , pp. 359-379
    • Nambudripad, R.1    Stark, W.2    Makowski, L.3
  • 14
    • 0026434570 scopus 로고
    • Membrane-mediated assembly of filamentous bacteriophage Pf1 coat protein
    • Nambudripad, R., Stark, W., Opella, S. J., and Makowski, L. (1991) Membrane-mediated assembly of filamentous bacteriophage Pf1 coat protein. Science 252, 1305-1308. (Pubitemid 21917044)
    • (1991) Science , vol.252 , Issue.5010 , pp. 1305-1308
    • Nambudripad, R.1    Stark, W.2    Opella, S.J.3    Makowski, L.4
  • 15
    • 0026899228 scopus 로고
    • Flow linear dichroism spectra of four filamentous bacteriophages: DNA and coat protein contributions
    • Clack, B. A., and Gray, D. M. (1992) Flow linear dichroism spectra of four filamentous bacteriophages: DNA and coat protein contributions. Biopolymers 32, 795-810.
    • (1992) Biopolymers , vol.32 , pp. 795-810
    • Clack, B.A.1    Gray, D.M.2
  • 16
    • 0028213921 scopus 로고
    • Ultraviolet absorbance and circular dichroism of Pf1 virus: Nucleotide/subunit ratio of unity, hyperchromic tyrosines and DNA bases, and high helicity in the subunits
    • Kostrikis, L. G., Liu, D. J., and Day, L. A. (1994) Ultraviolet absorbance and circular dichroism of Pf1 virus: nucleotide/subunit ratio of unity, hyperchromic tyrosines and DNA bases, and high helicity in the subunits. Biohemistry 33, 1694-1703.
    • (1994) Biohemistry , vol.33 , pp. 1694-1703
    • Kostrikis, L.G.1    Liu, D.J.2    Day, L.A.3
  • 17
    • 0001592310 scopus 로고    scopus 로고
    • Demonstration by ultraviolet resonance Raman spectroscopy of differences in DNA organization and interactions in filamentous viruses Pf1 and fd
    • Wen, Z. Q., Armstrong, A., and Thomas, G. J., Jr. (1999) Demonstration by ultraviolet resonance Raman spectroscopy of differences in DNA organization and interactions in filamentous viruses Pf1 and fd. Biochemiury 38, 3148-3156.
    • (1999) Biochemiury , vol.38 , pp. 3148-3156
    • Wen, Z.Q.1    Armstrong, A.2    Thomas Jr., G.J.3
  • 18
    • 0033516702 scopus 로고    scopus 로고
    • Raman optical activity of filamentous bacteriophages: Hydration of α-helices
    • DOI 10.1006/jmbi.1999.2871
    • Blanch, E. W., Bell, A. F., Hecht, L., Day, L. A., and Barron, L. D. (1999) Raman optical activity of filamentous bacteriophages: hydration of alpha-helices. J. Mol. Biol. 290, 1-7. (Pubitemid 29308571)
    • (1999) Journal of Molecular Biology , vol.290 , Issue.1 , pp. 1-7
    • Blanch, E.W.1    Bell, A.F.2    Hecht, L.3    Day, L.A.4    Barron, L.D.5
  • 19
    • 0034646323 scopus 로고    scopus 로고
    • -1 as an indicator of protein alpha-helix orientation: Application to Pf1 filamentous virus
    • -1 as an indicator of protein alpha-helix orientation: application to Pf1 filamentous virus. Biochemistry 39, 2677-2684.
    • (2000) Biochemistry , vol.39 , pp. 2677-2684
    • Tsuboi, M.1    Suzuki, M.2    Overman, S.A.3    Thomas Jr., G.J.4
  • 20
    • 5444261667 scopus 로고    scopus 로고
    • Effects of virion and salt concentrations on the Raman signatures of filamentous phages fd, Pf1, Pf3, and PH75
    • Overman, S. A., Kristensen, D. M., Bondre, P., Hewitt, B., and Thomas, G. J., Jr. (2004) Effects of virion and salt concentrations on the Raman signatures of filamentous phages fd, Pf1, Pf3, and PH75. Biochemistry 43, 13129-13136.
    • (2004) Biochemistry , vol.43 , pp. 13129-13136
    • Overman, S.A.1    Kristensen, D.M.2    Bondre, P.3    Hewitt, B.4    Thomas Jr., G.J.5
  • 21
    • 15244356304 scopus 로고    scopus 로고
    • Structural basis of the temperature transition of Pf1 bacteriophage
    • Thiriot, D. S., Nevzorov, A. A., and Opella, S. J. (2005) Structural basis of the temperature transition of Pf1 bacteriophage, Protein Sci. 14, 1064-1070.
    • (2005) Protein Sci. , vol.14 , pp. 1064-1070
    • Thiriot, D.S.1    Nevzorov, A.A.2    Opella, S.J.3
  • 22
    • 0020580625 scopus 로고
    • DNA and protein lattice-lattice interactions in the filamentous bacteriophages
    • Marzec, C. J., and Day, L. A. (1983) DNA and protein lattice-lattice interactions in the filamentous bacteriophages. Biophys. J. 42, 171180.
    • (1983) Biophys. J. , vol.42 , pp. 171180
    • Marzec, C.J.1    Day, L.A.2
  • 23
    • 0024297501 scopus 로고
    • Raman spectroscopy of mercury(II) binding to two filamentous viruses: Ff (fd, M13, f1) and Pf1
    • Day, L. A., Casadevall, A., Prescott, B., and Thomas, G. J., Jr. (1988) Raman spectroscopy of mercury(II) binding to two filamentous viruses: Ff (fd, M13, f1) and Pf1. Biochemistry 27, 706-711.
    • (1988) Biochemistry , vol.27 , pp. 706-711
    • Day, L.A.1    Casadevall, A.2    Prescott, B.3    Thomas Jr., G.J.4
  • 24
    • 2542544330 scopus 로고    scopus 로고
    • Ultraviolet resonance raman spectroscopy of DNA and protein constituents of viruses: Assignments and cross sections for excitations at 257, 244, 238 and 229 nm
    • Wen, Z. Q., and Thomas, G. J., Jr. (1998) Ultraviolet resonance raman spectroscopy of DNA and protein constituents of viruses: assignments and cross sections for excitations at 257, 244, 238 and 229 nm. Biopolymers 45, 247-256.
    • (1998) Biopolymers , vol.45 , pp. 247-256
    • Wen, Z.Q.1    Thomas Jr., G.J.2
  • 27
    • 33750829427 scopus 로고    scopus 로고
    • On structural transitions, thermodynamic equilibrium, and the phase diagram of DNA and RNA duplexes under torque and tension
    • DOI 10.1073/pnas.0603850103
    • Wereszczynski, J., and Andricioaei, I. (2006) On structural transitions, thermodynamic equilibrium, and the phase diagram of DNA and RNA duplexes under torque and tension, Proc. Natl. Acad. Sci. U.S.A. 103. 103, 16200-16205. (Pubitemid 44715174)
    • (2006) Proceedings of the National Academy of Sciences of the United States of America , vol.103 , Issue.44 , pp. 16200-16205
    • Wereszczynski, J.1    Andricioaei, I.2
  • 29
    • 0001766135 scopus 로고    scopus 로고
    • Raman scattering tensors in biological molecules and their assemblies
    • Tsuboi, M., and Thomas, G. J., Jr. (1997) Raman scattering tensors in biological molecules and their assemblies, Appl. Spectrosc. Rev. 32, 263-299.
    • (1997) Appl. Spectrosc. Rev. , vol.32 , pp. 263-299
    • Tsuboi, M.1    Thomas Jr., G.J.2
  • 30
    • 0017260974 scopus 로고
    • Mass, length, composition and structure of the filamentous bacterial virus fd
    • Berkowitz, S. A., and Day, L. A. (1976) Mass, length, composition and structure of the filamentous bacterial virus fd. J. Mol. Biol. 102, 531-547.
    • (1976) J. Mol. Biol. , vol.102 , pp. 531-547
    • Berkowitz, S.A.1    Day, L.A.2
  • 31
    • 0029971090 scopus 로고    scopus 로고
    • Subunit orientation in the filamentous virus Ff(fd, f1, M 13)
    • Overman, S. A., Tsuboi, M., and Thomas, G. J., Jr. (1996) Subunit orientation in the filamentous virus Ff(fd, f1, M 13). J. Mol. Biol. 259, 331-336.
    • (1996) J. Mol. Biol. , vol.259 , pp. 331-336
    • Overman, S.A.1    Tsuboi, M.2    Thomas Jr., G.J.3
  • 32
    • 0028986185 scopus 로고
    • Polarized Raman, spectra of oriented fibers of A DNA and B DNA: Anisotropic and isotropic local Raman tensors of base and backbone vibrations
    • Thomas, G. J., Jr., Benevides, J. M., Overman, S. A., Ueda, T., Ushizawa, K., Saitoh, M. and Tsuboi, M. (1995) Polarized Raman, spectra of oriented fibers of A DNA and B DNA: anisotropic and isotropic local Raman tensors of base and backbone vibrations. Biophys. J. 68, 1073-1088.
    • (1995) Biophys. J. , vol.68 , pp. 1073-1088
    • Thomas Jr., G.J.1    Benevides, J.M.2    Overman, S.A.3    Ueda, T.4    Ushizawa, K.5    Saitoh, M.6    Tsuboi, M.7
  • 34
    • 0000568172 scopus 로고
    • Pf1 filamentous bacteriophage; refinement of a molecular model by simulated annealing using 3.3 A resolution X-ray fibre diffraction data
    • Gonzalez, A., Nave, C., and Marvin, D. A. (1995) Pf1 filamentous bacteriophage; refinement of a molecular model by simulated annealing using 3.3 A resolution X-ray fibre diffraction data, Acta Crystallogr., Sect. D: Biol. Crystallogr. 51, 792-804.
    • (1995) Acta Crystallogr., Sect. D: Biol. Crystallogr. , vol.51 , pp. 792-804
    • Gonzalez, A.1    Nave, C.2    Marvin, D.A.3
  • 36
    • 0033616633 scopus 로고    scopus 로고
    • Raman markers of nonaromatic side chains in an alpha-helix assembly: Ala, Asp, Glu, Gly, lie, Leu, Lys, Ser, and Val residues of phage fd subunits
    • Overman, S. A., and Thomas, G. J., Jr. (1999) Raman markers of nonaromatic side chains in an alpha-helix assembly: Ala, Asp, Glu, Gly, lie, Leu, Lys, Ser, and Val residues of phage fd subunits. Biochemistry 38, 4018-4027
    • (1999) Biochemistry , vol.38 , pp. 4018-4027
    • Overman, S.A.1    Thomas Jr., G.J.2


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