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Volumn 105, Issue 30, 2008, Pages 10366-10371

Conformational dynamics of an intact virus: Order parameters for the coat protein of Pf1 bacteriophage

Author keywords

Motion; Side chain; Solid state NMR

Indexed keywords

COAT PROTEIN; GLUTAMINE; GLYCINE; VIRUS PROTEIN;

EID: 48749091080     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0800405105     Document Type: Article
Times cited : (88)

References (46)
  • 1
    • 0013869897 scopus 로고
    • A rod-shaped Pseudomonas phage
    • Takeya K, Amako K (1966) A rod-shaped Pseudomonas phage. Virology 28:163-165.
    • (1966) Virology , vol.28 , pp. 163-165
    • Takeya, K.1    Amako, K.2
  • 2
    • 0015782233 scopus 로고
    • The length of the filamentous Pseudomonas aeruginosa bacteriophage Pf
    • Bradley DE (1973) The length of the filamentous Pseudomonas aeruginosa bacteriophage Pf. Can J Microbiol 19:623-632.
    • (1973) Can J Microbiol , vol.19 , pp. 623-632
    • Bradley, D.E.1
  • 4
    • 0017768320 scopus 로고
    • Different packaging of DNA in filamentous viruses Pf1 and Xf
    • Wiseman RL, Day LA (1977) Different packaging of DNA in filamentous viruses Pf1 and Xf. J Mol Biol 116:607-611.
    • (1977) J Mol Biol , vol.116 , pp. 607-611
    • Wiseman, R.L.1    Day, L.A.2
  • 5
    • 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 LG, Liu DJ, Day LA (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. Biochemistry 33:1694-1703.
    • (1994) Biochemistry , vol.33 , pp. 1694-1703
    • Kostrikis, L.G.1    Liu, D.J.2    Day, L.A.3
  • 6
    • 0019887666 scopus 로고
    • The symmetries of filamentous phage particles
    • Caspar DLD, Makowski L (1981) The symmetries of filamentous phage particles. J Mol Biol 145:611-617.
    • (1981) J Mol Biol , vol.145 , pp. 611-617
    • Caspar, D.L.D.1    Makowski, L.2
  • 7
    • 0023123048 scopus 로고
    • Pf1 Inovirus. Electron density distribution calculated by a maximum entropy algorithm from native fibre diffraction data to 3 A resolution and single isomorphous replacement data to 5 A resolution
    • Marvin DA, Bryan RK, Nave C (1987) Pf1 Inovirus. Electron density distribution calculated by a maximum entropy algorithm from native fibre diffraction data to 3 A resolution and single isomorphous replacement data to 5 A resolution. J Mol Biol 193:315-343.
    • (1987) J Mol Biol , vol.193 , pp. 315-343
    • Marvin, D.A.1    Bryan, R.K.2    Nave, C.3
  • 8
    • 0023148840 scopus 로고
    • Structure and dynamics of the Pf1 filamentous bacteriophage coat protein in micelles
    • Schiksnis RA, Bogusky MJ, Tsang P, Opella SJ (1987) Structure and dynamics of the Pf1 filamentous bacteriophage coat protein in micelles. Biochemistry 26:1373-1381.
    • (1987) Biochemistry , vol.26 , pp. 1373-1381
    • Schiksnis, R.A.1    Bogusky, M.J.2    Tsang, P.3    Opella, S.J.4
  • 10
    • 0024278073 scopus 로고
    • Conformation of the coat protein of filamentous bacteriophage Pf1 determined by neutron diffraction from magnetically oriented gels of specifically deuterated virions
    • Stark W, Glucksman MJ, Makowski L (1988) Conformation of the coat protein of filamentous bacteriophage Pf1 determined by neutron diffraction from magnetically oriented gels of specifically deuterated virions. J Mol Biol 199:171-182.
    • (1988) J Mol Biol , vol.199 , pp. 171-182
    • Stark, W.1    Glucksman, M.J.2    Makowski, L.3
  • 11
    • 0028108799 scopus 로고
    • Pf1 virus structure: Helical coat protein and DNA with paraxial phosphates
    • Liu DJ, Day LA (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
  • 12
    • 0028075981 scopus 로고
    • An electrostatic spatial resonance model for coaxial helical structures with applications to the filamentous bacteriophages
    • Marzec CJ, Day LA (1994) An electrostatic spatial resonance model for coaxial helical structures with applications to the filamentous bacteriophages. Biophys J 67:2205-2222.
    • (1994) Biophys J , vol.67 , pp. 2205-2222
    • Marzec, C.J.1    Day, L.A.2
  • 13
    • 0032054113 scopus 로고    scopus 로고
    • Filamentous phage structure, infection and assembly
    • Marvin DA (1998) Filamentous phage structure, infection and assembly. Curr Opin Struct Biol 8:150-158.
    • (1998) Curr Opin Struct Biol , vol.8 , pp. 150-158
    • Marvin, D.A.1
  • 14
    • 0038575449 scopus 로고    scopus 로고
    • Structure and dynamics of a membrane protein in micelles from three solution NMR experiments
    • Lee S, Mesleh MF, Opella SJ (2003) Structure and dynamics of a membrane protein in micelles from three solution NMR experiments. J Biomol NMR 26:327-334.
    • (2003) J Biomol NMR , vol.26 , pp. 327-334
    • Lee, S.1    Mesleh, M.F.2    Opella, S.J.3
  • 15
    • 0037417751 scopus 로고    scopus 로고
    • Protein and DNA residue orientations in the filamentous virus Pf1 determined by polarized Raman and polarized FTIR spectroscopy
    • Tsuboi M, et al. (2003) Protein and DNA residue orientations in the filamentous virus Pf1 determined by polarized Raman and polarized FTIR spectroscopy. Biochemistry 42:940-950.
    • (2003) Biochemistry , vol.42 , pp. 940-950
    • Tsuboi, M.1
  • 16
    • 4344702276 scopus 로고    scopus 로고
    • Structure of the coat protein in Pf1 bacteriophage determined by solid-state NMR spectroscopy
    • Thiriot DS, Nevzorov AA, Zagyanskiy L, Wu CH, Opella SJ (2004) Structure of the coat protein in Pf1 bacteriophage determined by solid-state NMR spectroscopy. J Mol Biol 341:869-879.
    • (2004) J Mol Biol , vol.341 , pp. 869-879
    • Thiriot, D.S.1    Nevzorov, A.A.2    Zagyanskiy, L.3    Wu, C.H.4    Opella, S.J.5
  • 17
    • 15244356304 scopus 로고    scopus 로고
    • Structural basis of the temperature transition of Pf1 bacteriophage
    • Thiriot DS, Nevzorov AA, Opella SJ (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
  • 18
    • 33847628307 scopus 로고    scopus 로고
    • Filamentous phage studied by magic-angle spinning NMR: Resonance assignment and secondary structure of the coat protein in Pf1
    • Goldbourt A, Gross BJ, Day LA, McDermott AE (2007) Filamentous phage studied by magic-angle spinning NMR: Resonance assignment and secondary structure of the coat protein in Pf1. J Am Chem Soc 129:2338-2344.
    • (2007) J Am Chem Soc , vol.129 , pp. 2338-2344
    • Goldbourt, A.1    Gross, B.J.2    Day, L.A.3    McDermott, A.E.4
  • 19
    • 35748970172 scopus 로고    scopus 로고
    • Assignment of congested NMR spectra: Carbonyl backbone enrichment via the Entner-Doudoroff pathway
    • Goldbourt A, Day LA, McDermott AE (2007) Assignment of congested NMR spectra: Carbonyl backbone enrichment via the Entner-Doudoroff pathway. J Magn Reson 189:157-165.
    • (2007) J Magn Reson , vol.189 , pp. 157-165
    • Goldbourt, A.1    Day, L.A.2    McDermott, A.E.3
  • 20
    • 0032538349 scopus 로고    scopus 로고
    • Structure of the capsid of Pf3 filamentous phage determined from X-ray fibre diffraction data at 3.1 angstrom resolution
    • Welsh LC, Symmons MF, Sturtevant JM, Marvin DA, Perham RN (1998) Structure of the capsid of Pf3 filamentous phage determined from X-ray fibre diffraction data at 3.1 angstrom resolution. J Mol Biol 283:155-177.
    • (1998) J Mol Biol , vol.283 , pp. 155-177
    • Welsh, L.C.1    Symmons, M.F.2    Sturtevant, J.M.3    Marvin, D.A.4    Perham, R.N.5
  • 21
    • 0035954376 scopus 로고    scopus 로고
    • Solid-state NMR investigation of the dynamics of the soluble and membrane-bound colicin Ia channel-forming domain
    • Huster D, Xiao LS, Hong M (2001) Solid-state NMR investigation of the dynamics of the soluble and membrane-bound colicin Ia channel-forming domain. Biochemistry 40:7662-7674.
    • (2001) Biochemistry , vol.40 , pp. 7662-7674
    • Huster, D.1    Xiao, L.S.2    Hong, M.3
  • 22
    • 33644846256 scopus 로고    scopus 로고
    • 3 heteronuclear dipolar powder patterns: A comparison of MAS-based solid-state NMR sequences
    • 3 heteronuclear dipolar powder patterns: A comparison of MAS-based solid-state NMR sequences. Magn Reson Chem 44:334-347.
    • (2006) Magn Reson Chem , vol.44 , pp. 334-347
    • Lorieau, J.L.1    McDermott, A.E.2
  • 23
    • 33748344482 scopus 로고    scopus 로고
    • Conformational flexibility of a microcrystalline globular protein: Order parameters by solid-state NMR spectroscopy
    • Lorieau JL, McDermott A (2006) Conformational flexibility of a microcrystalline globular protein: Order parameters by solid-state NMR spectroscopy. J Am Chem Soc 128:11505-11512.
    • (2006) J Am Chem Soc , vol.128 , pp. 11505-11512
    • Lorieau, J.L.1    McDermott, A.2
  • 24
    • 0032545177 scopus 로고    scopus 로고
    • Analysis of X-ray diffraction from fibres of Pf1 Inovirus (filamentous bacteriophage) shows that the DNA in the virion is not highly ordered
    • Welsh LC, Marvin DA, Perham RN (1998) Analysis of X-ray diffraction from fibres of Pf1 Inovirus (filamentous bacteriophage) shows that the DNA in the virion is not highly ordered. J Mol Biol 284:1265-1271.
    • (1998) J Mol Biol , vol.284 , pp. 1265-1271
    • Welsh, L.C.1    Marvin, D.A.2    Perham, R.N.3
  • 25
    • 0034142068 scopus 로고    scopus 로고
    • The molecular structure and structural transition of the alpha-helical capsid in filamentous bacteriophage Pf1
    • Welsh LC, Symmons MF, Marvin DA (2000) The molecular structure and structural transition of the alpha-helical capsid in filamentous bacteriophage Pf1. Acta Crystallogr D 56:137-150.
    • (2000) Acta Crystallogr D , vol.56 , pp. 137-150
    • Welsh, L.C.1    Symmons, M.F.2    Marvin, D.A.3
  • 26
    • 0032564447 scopus 로고    scopus 로고
    • Stretched and overwound DNA forms a Pauling-like structure with exposed bases
    • Allemand JF, Bensimon D, Lavery R, Croquette V (1998) Stretched and overwound DNA forms a Pauling-like structure with exposed bases. Proc Natl Acad Sci USA 95:14152-14157.
    • (1998) Proc Natl Acad Sci USA , vol.95 , pp. 14152-14157
    • Allemand, J.F.1    Bensimon, D.2    Lavery, R.3    Croquette, V.4
  • 27
    • 0020639043 scopus 로고
    • Comparison of protein and deoxyribonucleic acid backbone structures in fd and Pf1 bacteriophages
    • Cross TA, Tsang P, Opella SJ (1983) Comparison of protein and deoxyribonucleic acid backbone structures in fd and Pf1 bacteriophages. Biochemistry 22:721-726.
    • (1983) Biochemistry , vol.22 , pp. 721-726
    • Cross, T.A.1    Tsang, P.2    Opella, S.J.3
  • 28
    • 0024974913 scopus 로고
    • Visualization of protein-nucleic acid interactions in a virus. Refined structure of intact tobacco mosaic virus at 2.9 A resolution by X-ray fiber diffraction
    • Namba K, Pattanayek R, Stubbs G (1989) Visualization of protein-nucleic acid interactions in a virus. Refined structure of intact tobacco mosaic virus at 2.9 A resolution by X-ray fiber diffraction. J Mol Biol 208:307-325.
    • (1989) J Mol Biol , vol.208 , pp. 307-325
    • Namba, K.1    Pattanayek, R.2    Stubbs, G.3
  • 29
    • 0027518457 scopus 로고
    • Ordered duplex RNA controls capsid architecture in an icosahedral animal virus
    • Fisher AJ, Johnson JE (1993) Ordered duplex RNA controls capsid architecture in an icosahedral animal virus. Nature 361:176-179.
    • (1993) Nature , vol.361 , pp. 176-179
    • Fisher, A.J.1    Johnson, J.E.2
  • 30
    • 0027497651 scopus 로고
    • Double-helical RNA in satellite tobacco mosaic virus
    • Larson SB, et al. (1993) Double-helical RNA in satellite tobacco mosaic virus. Nature 361:179-182.
    • (1993) Nature , vol.361 , pp. 179-182
    • Larson, S.B.1
  • 31
    • 34250839422 scopus 로고    scopus 로고
    • Long-range structural and dynamical changes induced by cofactor binding in DNA methyltransferase M.HhaI
    • Zhou HJ, et al. (2007) Long-range structural and dynamical changes induced by cofactor binding in DNA methyltransferase M.HhaI. Biochemistry 46:7261-7268.
    • (2007) Biochemistry , vol.46 , pp. 7261-7268
    • Zhou, H.J.1
  • 32
    • 31144473532 scopus 로고    scopus 로고
    • Time-resolved fluorescence of 2-aminopurine as a probe of base flipping in M.HhaI-DNA complexes
    • Neely RK, et al. (2005) Time-resolved fluorescence of 2-aminopurine as a probe of base flipping in M.HhaI-DNA complexes. Nucleic Acids Res 33:6953-6960.
    • (2005) Nucleic Acids Res , vol.33 , pp. 6953-6960
    • Neely, R.K.1
  • 33
    • 33644851082 scopus 로고    scopus 로고
    • DNA nicking by HinP1I endonuclease: Bending, base flipping and minor groove expansion
    • Horton JR, et al. (2006) DNA nicking by HinP1I endonuclease: Bending, base flipping and minor groove expansion. Nucleic Acids Res 34:939-948.
    • (2006) Nucleic Acids Res , vol.34 , pp. 939-948
    • Horton, J.R.1
  • 34
    • 19444373245 scopus 로고    scopus 로고
    • C-13 NMR relaxation studies of RNA base and ribose nuclei reveal a complex pattern of motions in the RNA binding site for human U1A protein
    • Shajani Z, Varani G (2005) C-13 NMR relaxation studies of RNA base and ribose nuclei reveal a complex pattern of motions in the RNA binding site for human U1A protein. J Mol Biol 349:699-715.
    • (2005) J Mol Biol , vol.349 , pp. 699-715
    • Shajani, Z.1    Varani, G.2
  • 35
    • 0037461028 scopus 로고    scopus 로고
    • Multiple-spin effects in fast magic angle spinning Lee-Goldburg cross-polarization experiments in uniformly labeled compounds
    • Ladizhansky V, Vinogradov E, Van Rossum BJ, De Groot HJM, Vega S (2003) Multiple-spin effects in fast magic angle spinning Lee-Goldburg cross-polarization experiments in uniformly labeled compounds. J Chem Phys 118:5547-5557.
    • (2003) J Chem Phys , vol.118 , pp. 5547-5557
    • Ladizhansky, V.1    Vinogradov, E.2    Van Rossum, B.J.3    De Groot, H.J.M.4    Vega, S.5
  • 36
    • 0030217514 scopus 로고    scopus 로고
    • Nuclear magnetic resonance studies of biopolymer dynamics
    • Palmer AG, Williams J, McDermott A (1996) Nuclear magnetic resonance studies of biopolymer dynamics. J Phys Chem 100:13293-13310.
    • (1996) J Phys Chem , vol.100 , pp. 13293-13310
    • Palmer, A.G.1    Williams, J.2    McDermott, A.3
  • 37
    • 0023660998 scopus 로고
    • Molecular dynamics of collagen side chains in hard and soft tissues. A multinuclear magnetic resonance study
    • Sarkar SK, et al. (1987) Molecular dynamics of collagen side chains in hard and soft tissues. A multinuclear magnetic resonance study. Biochemistry 26:6793-6800.
    • (1987) Biochemistry , vol.26 , pp. 6793-6800
    • Sarkar, S.K.1
  • 38
    • 0018982584 scopus 로고
    • Lipid conformation in model membranes and biological membranes
    • Seelig J, Seelig A (1980) Lipid conformation in model membranes and biological membranes. Q Rev Biophys 13:19-61.
    • (1980) Q Rev Biophys , vol.13 , pp. 19-61
    • Seelig, J.1    Seelig, A.2
  • 39
    • 0032581942 scopus 로고    scopus 로고
    • A solid-state deuterium NMR study of the localized dynamics at the C9pG10 step in the DNA dodecamer [d(CGCCAATTCGCG)](2)
    • Hatcher ME, Mattiello DL, Meints GA, Orban J, Drobny GP (1998) A solid-state deuterium NMR study of the localized dynamics at the C9pG10 step in the DNA dodecamer [d(CGCCAATTCGCG)](2). J Am Chem Soc 120:9850-9862.
    • (1998) J Am Chem Soc , vol.120 , pp. 9850-9862
    • Hatcher, M.E.1    Mattiello, D.L.2    Meints, G.A.3    Orban, J.4    Drobny, G.P.5
  • 40
    • 0035789518 scopus 로고    scopus 로고
    • GROMACS 3.0: A package for molecular simulation and trajectory analysis
    • Lindahl E, Hess B, van der Spoel D (2001) GROMACS 3.0: A package for molecular simulation and trajectory analysis. J Mol Mod 7:306-317.
    • (2001) J Mol Mod , vol.7 , pp. 306-317
    • Lindahl, E.1    Hess, B.2    van der Spoel, D.3
  • 41
    • 0037202183 scopus 로고    scopus 로고
    • Contact model for the prediction of NMR N-H order parameters in globular proteins
    • Zhang FL, Bruschweiler R (2002) Contact model for the prediction of NMR N-H order parameters in globular proteins. J Am Chem Soc 124:12654-12655.
    • (2002) J Am Chem Soc , vol.124 , pp. 12654-12655
    • Zhang, F.L.1    Bruschweiler, R.2
  • 43
    • 0001437779 scopus 로고
    • Structure and thermal vibrations of adenosine from neutron diffraction data at 123 K
    • Klooster WT, Ruble JR, Craven BM, McMullan RK (1991) Structure and thermal vibrations of adenosine from neutron diffraction data at 123 K. Acta Crystallogr B 47:376-383.
    • (1991) Acta Crystallogr B , vol.47 , pp. 376-383
    • Klooster, W.T.1    Ruble, J.R.2    Craven, B.M.3    McMullan, R.K.4
  • 44
    • 0000607964 scopus 로고    scopus 로고
    • Homonuclear radio frequency-driven recoupling in rotating solids
    • Bennett AE, et al. (1998) Homonuclear radio frequency-driven recoupling in rotating solids. J Chem Phys 108:9463-9479.
    • (1998) J Chem Phys , vol.108 , pp. 9463-9479
    • Bennett, A.E.1
  • 46
    • 48749090962 scopus 로고    scopus 로고
    • DeLano WL, Lam JW (2005) PyMOL: A communications tool for computational models. Abstr Pap Am Chem Soc 230:U1371-U1372. 10372-10377
    • DeLano WL, Lam JW (2005) PyMOL: A communications tool for computational models. Abstr Pap Am Chem Soc 230:U1371-U1372. 10372-10377


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