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Clewell D.B. New York: Plenum Press
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Frost LS. Conjugative pili and pilus-specific phages. Clewell DB. Bacterial Conjugation. 1993;189-221 Plenum Press, New York.
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of outstanding interest. B.K. Kay, J. Winter, McCafferty J. Academic Press, New York, An excellent general review, on which we draw extensively here. It includes comprehensive literature references for the 10 years since the last thorough reviews of the field.
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Webster RE. Biology of the filamentous bacteriophage. of outstanding interest Kay BK, Winter J, McCafferty J. Phage Display of Peptides and Proteins. 1996;1-20 Academic Press, New York, An excellent general review, on which we draw extensively here. It includes comprehensive literature references for the 10 years since the last thorough reviews of the field.
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Webster, R.E.1
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of outstanding interest. The latest in a series of excellent reviews of filamentous phage assembly from the Rockefeller group, keeping us up to date on the explosion of knowledge coming from their own and other groups. It includes a helpful diagram summarizing the present understanding of how p1 and p4 are involved in assembly at the membrane, and points out parallels with other protein export systems.
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Russel M, Linderoth NA, Sali A. Filamentous phage assembly: variation on a protein export theme. of outstanding interest Gene. 192:1997;23-32 The latest in a series of excellent reviews of filamentous phage assembly from the Rockefeller group, keeping us up to date on the explosion of knowledge coming from their own and other groups. It includes a helpful diagram summarizing the present understanding of how p1 and p4 are involved in assembly at the membrane, and points out parallels with other protein export systems.
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Gene
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Russel, M.1
Linderoth, N.A.2
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Phage presentation
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of outstanding interest. A useful review of phage display.
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Hill HR, Stockley PG. Phage presentation. of outstanding interest Mol Microbiol. 20:1996;685-692 A useful review of phage display.
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Mol Microbiol
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Hill, H.R.1
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8
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of special interest. A review of phage display for nonspecialists, which also includes references to over 200 papers.
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Smith GP, Petrenko VA. Phage display. of special interest Chem Rev. 97:1997;391-410 A review of phage display for nonspecialists, which also includes references to over 200 papers.
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Smith, G.P.1
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9
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Kuo TT, Chao YS, Lin YH, Lin BY, Liu LF, Feng TY. Integration of the DNA of filamentous bacteriophage Cf1t into the chromosomal DNA of its host. J Virol. 61:1987;60-65.
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Kuo, T.T.1
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10
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0030057090
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of outstanding interest. An exciting new development pointing to the hitherto unsuspected involvement of filamentous phage in the transmission of disease.
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Waldor MK, Mekalanos JJ. Lysogenic conversion by a filamentous phage encoding cholera toxin. of outstanding interest Science. 272:1996;1910-1914 An exciting new development pointing to the hitherto unsuspected involvement of filamentous phage in the transmission of disease.
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Science
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Waldor, M.K.1
Mekalanos, J.J.2
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11
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Characterization of filamentous phages of Vibrio cholerae O139 and O1
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Ehara M, Shimodori S, Kojima F, Ichinose Y, Hirayama T, Albert MJ, Supawat K, Honma Y, Iwanaga M, Amako K. Characterization of filamentous phages of Vibrio cholerae O139 and O1. FEMS Microbiol Lett. 154:1997;293-301.
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Ehara, M.1
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12
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0023123048
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Pf1 Inovirus. Electron density distribution calculated by a maximum entropy algorithm from native fibre diffraction data to 3 Å resolution and single isomorphous replacement data to 5 Å resolution
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Marvin DA, Bryan RK, Nave C. Pf1 Inovirus. Electron density distribution calculated by a maximum entropy algorithm from native fibre diffraction data to 3 Å resolution and single isomorphous replacement data to 5 Å resolution. J Mol Biol. 193:1987;315-343.
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Marvin, D.A.1
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Marvin DA. Model-building studies of Inovirus: genetic variations on a geometric theme. Int J Biol Macromol. 12:1990;125-138.
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Int J Biol Macromol
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Two forms of Pf1 Inovirus: X-ray diffraction studies on a structural phase transition and a calculated libration normal mode of the asymmetric unit
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Marvin DA, Nave C, Bansal M, Hale RD, Salje EKH. Two forms of Pf1 Inovirus: X-ray diffraction studies on a structural phase transition and a calculated libration normal mode of the asymmetric unit. Phase Transit. 39:1992;45-80.
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Marvin, D.A.1
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Pf1 filamentous bacteriophage: Refinement of a molecular model by simulated annealing using 3.3 Å resolution X-ray fibre diffraction data
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Gonzalez A, Nave C, Marvin DA. Pf1 filamentous bacteriophage: refinement of a molecular model by simulated annealing using 3.3 Å resolution X-ray fibre diffraction data. Acta Crystallogr D. 51:1995;792-804.
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Overman SA, Tsuboi M, Thomas GJ Jr. Subunit orientation in the filamentous virus Ff(fd, f1, M13). J Mol Biol. 259:1996;331-336.
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Overman, S.A.1
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Packing of coat protein amphipathic and transmembrane helices in filamentous bacteriophage M13: Role of small residues in protein oligomerization
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Williams KA, Glibowicka M, Li Z, Li H, Khan AR, Chen YMY, Wang J, Marvin DA, Deber CM. Packing of coat protein amphipathic and transmembrane helices in filamentous bacteriophage M13: role of small residues in protein oligomerization. J Mol Biol. 252:1995;6-14.
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Williams, K.A.1
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Biophysical characterization of wild-type and mutant bacteriophage IKe major coat protein in the virion and in detergent micelles
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Williams KA, Deber CM. Biophysical characterization of wild-type and mutant bacteriophage IKe major coat protein in the virion and in detergent micelles. Biochemistry. 35:1996;10472-10483.
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Williams, K.A.1
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Accessibility and dynamics of Cys residues in bacteriophage IKe and M13 major coat protein mutants
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Khan AR, Williams KA, Boggs JM, Deber CM. Accessibility and dynamics of Cys residues in bacteriophage IKe and M13 major coat protein mutants. Biochemistry. 34:1995;1388-12397.
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Khan, A.R.1
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20
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0028999261
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Raman spectroscopy of the filamentous virus Ff(fd, f1, M13); Structural interpretation for coat protein aromatics
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Overman SA, Thomas GJ Jr. Raman spectroscopy of the filamentous virus Ff(fd, f1, M13); structural interpretation for coat protein aromatics. Biochemistry. 34:1995;5440-5451.
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Structure and interactions of the single-stranded DNA genome of filamentous virus fd: Investigation by ultraviolet resonance Raman spectroscopy
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Wen ZQ, Overman SA, Thomas GJ Jr. Structure and interactions of the single-stranded DNA genome of filamentous virus fd: investigation by ultraviolet resonance Raman spectroscopy. Biochemistry. 36:1997;7810-7820.
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22
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Raman linear intensity difference of flow-oriented macromolecules: Orientation of the indole ring of tryptophan-26 in filamentous virus fd
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Takeuchi H, Matsuno M, Overman SA, Thomas GJ Jr. Raman linear intensity difference of flow-oriented macromolecules: orientation of the indole ring of tryptophan-26 in filamentous virus fd. J Am Chem Soc. 118:1996;3498-3507.
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Takeuchi, H.1
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23
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0029824276
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Orientation of tryptophan-26 in coat protein subunits of the filamentous virus Ff by polarized Raman microspectroscopy
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of special interest. Polarized Raman microspectroscopy of fibres can give a value for the orientation of the tryptophan sidechain with respect to the fibre axis. This important new technique will become even more powerful when it is applied to highly aligned fibres of the kind used for X-ray fibre diffraction, where the virion axes are all parallel (within 1°) to the fibre axis, so the orientation with respect to the fibre axis is essentially the same as the orientation with respect to the virion axis.
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Tsuboi M, Overman SA, Thomas GJ Jr. Orientation of tryptophan-26 in coat protein subunits of the filamentous virus Ff by polarized Raman microspectroscopy. of special interest Biochemistry. 35:1996;10403-10410 Polarized Raman microspectroscopy of fibres can give a value for the orientation of the tryptophan sidechain with respect to the fibre axis. This important new technique will become even more powerful when it is applied to highly aligned fibres of the kind used for X-ray fibre diffraction, where the virion axes are all parallel (within 1°) to the fibre axis, so the orientation with respect to the fibre axis is essentially the same as the orientation with respect to the virion axis.
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Biochemistry
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Tsuboi, M.1
Overman, S.A.2
Thomas G.J., Jr.3
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24
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Kishchenko G, Makowski L. Shuffling of structural elements in filamentous bacteriophages. Proteins. 27:1997;405-409.
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Overman SA, Thomas GJ Jr. Novel vibrational assignments for proteins from Raman spectra of viruses. J Raman Spectrosc. 29:1998;23-29.
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Kramer H, Deggelmann M, Graf C, Hagenbüchle M, Johner C, Weber R. Electric birefringence measurements in aqueous fd virus solutions. Macromolecules. 25:1992;4325-4328.
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Tang J, Fraden S. Nonmonotonic temperature dependence of the flexibility of bacteriophage fd. Biopolymers. 39:1996;13-22.
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Welsh LC, Symmons MF, Nave C, Perham RN, Marseglia EA, Marvin DA. Evidence for tilted smectic liquid crystalline packing of Inovirus from X-ray fiber diffraction. Macromolecules. 29:1996;7075-7083.
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Endemann H, Model P. Location of filamentous phage minor coat proteins in phage and in infected cells. J Mol Biol. 250:1995;496-506.
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Kremser A, Rasched I. The adsorption protein of filamentous phage fd: assignment of its disulfide bridges and identification of the domain incorporated in the coat. Biochemistry. 33:1994;13954-13958.
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32
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0031568809
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A conserved infection pathway for filamentous bacteriophages is suggested by the structure of the membrane penetration domain of the minor coat protein g3p from phage fd
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of outstanding interest. Take an interesting small domain of a protein, clone and express the domain in large amounts, and solve the structure using solution NMR. The application to D1 of p3 of this approach has yielded beautiful results.
-
Holliger P, Riechmann L. A conserved infection pathway for filamentous bacteriophages is suggested by the structure of the membrane penetration domain of the minor coat protein g3p from phage fd. of outstanding interest Structure. 5:1997;265-275 Take an interesting small domain of a protein, clone and express the domain in large amounts, and solve the structure using solution NMR. The application to D1 of p3 of this approach has yielded beautiful results.
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(1997)
Structure
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Holliger, P.1
Riechmann, L.2
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33
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0030797114
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The C-terminal domain of TolA is the coreceptor for filamentous phage infection of E. coli
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of special interest. Heteronuclear NMR spectroscopy on purified protein domains shows that domain D1 of p3 interacts specifically with the C-terminal periplasmic domain of the bacterial TolA protein, and domain D2 of p3 competes with this interaction.
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Riechmann L, Holliger P. The C-terminal domain of TolA is the coreceptor for filamentous phage infection of E. coli. of special interest Cell. 90:1997;351-360 Heteronuclear NMR spectroscopy on purified protein domains shows that domain D1 of p3 interacts specifically with the C-terminal periplasmic domain of the bacterial TolA protein, and domain D2 of p3 competes with this interaction.
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Cell
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Riechmann, L.1
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Gailus V, Rasched I. The adsorption protein of bacteriophage fd and its neighbour minor coat protein build a structural entity. Eur J Biochem. 222:1994;927-931.
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Marvin DA. Dynamics of telescoping Inovirus: a mechanism for assembly at membrane adhesions. Int J Biol Macromol. 11:1989;159-164.
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Marvin, D.A.1
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36
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Marvin DA, Hale RD, Nave C, Helmer Citterich M. Molecular models and structural comparisons of native and mutant class I filamentous bacteriophages Ff (fd,f1,M13), If1 and IKe. J Mol Biol. 235:1994;260-286.
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Marvin, D.A.1
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37
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Selective phage infection mediated by epitope expression on F pilus
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of special interest. If a peptide is fused to the C terminus of F-pilin, the decorated F-pili no longer adsorb Ff. But if an antibody against this peptide is displayed on p3, the modified virions do infect the bacteria.
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Malmborg A-C, Söderlind E, Frost L, Borrebaeck CAK. Selective phage infection mediated by epitope expression on F pilus. of special interest J Mol Biol. 273:1997;544-551 If a peptide is fused to the C terminus of F-pilin, the decorated F-pili no longer adsorb Ff. But if an antibody against this peptide is displayed on p3, the modified virions do infect the bacteria.
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J Mol Biol
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Malmborg A-C1
Söderlind, E.2
Frost, L.3
Borrebaeck, C.A.K.4
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38
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Marzari R, Sblattero D, Righi M, Bradbury A. Extending filamentous phage host range by the grafting of a heterologous receptor binding domain. Gene. 185:1997;27-33.
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The A protein of the filamentous bacteriophage Cf of Xanthomonas campestris pv. citri
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Yang MK, Yang YC. The A protein of the filamentous bacteriophage Cf of Xanthomonas campestris pv. citri. J Bacteriol. 179:1997;2840-2844.
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of special interest. The bacterial TolA protein is necessary for Ff infection. The protein has three domains: an N-terminal membrane anchor domain, a linker domain and a C-terminal periplasmic domain. Deletion analysis shows that the linker domain helps but is not essential for infection; it appears to form an α helix (based on sequence analysis). The periplasmic domain appears to be the site of interaction with the Ff p3 protein.
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Click EM, Webster RE. Filamentous phage infection: required interactions with the TolA protein. of special interest J Bacteriol. 179:1997;6464-6471 The bacterial TolA protein is necessary for Ff infection. The protein has three domains: an N-terminal membrane anchor domain, a linker domain and a C-terminal periplasmic domain. Deletion analysis shows that the linker domain helps but is not essential for infection; it appears to form an α helix (based on sequence analysis). The periplasmic domain appears to be the site of interaction with the Ff p3 protein.
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Click, E.M.1
Webster, R.E.2
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Three-dimensional structure of the single-stranded DNA-binding protein encoded by gene V of the filamentous bacteriophage M13 and a model of its complex with single-stranded DNA
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Konings RNH, Folmer RHA, Folkers PJM, Nilges M, Hilbers CW. Three-dimensional structure of the single-stranded DNA-binding protein encoded by gene V of the filamentous bacteriophage M13 and a model of its complex with single-stranded DNA. FEMS Microbiol Rev. 17:1995;57-72.
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Guan Y, Zhang H, Wang AHJ. Electrostatic potential distribution of the gene V protein from Ff phage facilitates cooperative DNA binding: a model of the GVP-ssDNA complex. Protein Sci. 4:1995;187-197.
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Mark BL, Terwilliger TC, Vaughan MR, Gray DM. Circular dichroism spectroscopy of three tyrosine-to-phenylalanine substitutions of fd gene 5 protein. Biochemistry. 34:1995;12854-12865.
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Direct measurement of oligonucleotide binding stoichiometry of gene V protein by mass spectrometry
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47
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0029777441
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Raman spectroscopy of the Ff gene V protein and complexes with poly(dA): Nonspecific DNA recognition and binding
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49
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0030872558
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Refined structure, DNA binding studies, and dynamics of the bacteriophage Pf3 encoded single-stranded DNA binding protein
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of special interest. The structure of the p5 protein of Pf3 is quite similar to that of Ff. despite relatively little sequence homology, and a plausible model of the nucleoprotein complex similar to that of Ff can be constructed.
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Folmer RHA, Nilges M, Papavoine CHM, Harmsen BJM, Konings RNH, Hilbers CW. Refined structure, DNA binding studies, and dynamics of the bacteriophage Pf3 encoded single-stranded DNA binding protein. of special interest Biochemistry. 36:1997;9120-9135 The structure of the p5 protein of Pf3 is quite similar to that of Ff. despite relatively little sequence homology, and a plausible model of the nucleoprotein complex similar to that of Ff can be constructed.
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Folmer, R.H.A.1
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Hilbers, C.W.6
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50
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51
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52
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53
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Kiefer D, Hu X, Dalbey R, Kuhn A. Negatively charged amino acid residues play an active role in orienting the Sec-independent Pf3 coat protein in the Escherichia coli inner membrane. EMBO J. 16:1997;2197-2204.
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54
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Structural characterization of membrane insertion of M13 procoat, M13 coat and Pf3 coat proteins
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Vogel, H.5
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55
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Sanders JC, Haris PI, Chapman D, Otto C, Hemminga MA. Secondary structure of M13 coat protein in phospholipids studied by circular dichroism, Raman, and Fourier transform infrared spectroscopy. Biochemistry. 32:1993;12446-12454.
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57
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59
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of special interest. The authors determine, for Ff coat protein with and without the leader sequence, the standard free energy change for in vitro partition from water to the lipid bilayer, based on measurements of fluorescence energy transfer between the tryptophan of the protein and labelled lipids. They conclude that "it is the final energy gain of the interaction of the hydrophobic portions of the folded pre-protein with the lipid chains that drives the transmembrane insertion", and that hydrophobic interactions are more important than electrostatic effects.
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Soekarjo M, Eisenhawer M, Kuhn A, Vogel H. Thermodynamics of the membrane insertion process of the M13 procoat protein, a lipid bilayer traversing protein containing a leader sequence. of special interest Biochemistry. 35:1996;1232-1241 The authors determine, for Ff coat protein with and without the leader sequence, the standard free energy change for in vitro partition from water to the lipid bilayer, based on measurements of fluorescence energy transfer between the tryptophan of the protein and labelled lipids. They conclude that "it is the final energy gain of the interaction of the hydrophobic portions of the folded pre-protein with the lipid chains that drives the transmembrane insertion", and that hydrophobic interactions are more important than electrostatic effects.
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60
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Spruijt RB, Wolfs CJAM, Verver JWG, Hemminga MA. Accessibility and environment probing using cysteine residues introduced along the putative transmembrane domain of the major coat protein of bacteriophage M13. Biochemistry. 35:1996;10383-10391.
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Spruijt, R.B.1
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Hemminga, M.A.4
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61
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63
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65
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0030933301
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A permeabilized cell system that assembles filamentous bacteriophage
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of special interest. Wouldn't it be nice to have an in vitro system for membrane transport? This is probably the closest ye1: a system in which the membrane is still intact but purified goodies, including proteins, can be introduced into the cell from outside, resulting in phage assembly. We expect great things as this system is developed further.
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Feng JN, Russel M, Model P. A permeabilized cell system that assembles filamentous bacteriophage. of special interest Proc Natl Acad Sci USA. 94:1997;4068-4073 Wouldn't it be nice to have an in vitro system for membrane transport? This is probably the closest ye1: a system in which the membrane is still intact but purified goodies, including proteins, can be introduced into the cell from outside, resulting in phage assembly. We expect great things as this system is developed further.
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67
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The Escherichia coli phage-shock-protein (psp) operon
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of outstanding interest. The E. coli phage-shock protein (psp) operon is induced after infection by Ff, apparently as a result of the process of p4 insertion into the outer membrane. It is also induced by expression of (nonphage) homologs of p4, and by diverse other challenges, whose common feature may be that they damage the membrane proton gradient. The sequence of PspA predicts a coiled-coil motif, and PspB, C and D all contain leucine zipper motifs.
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Model P, Jovanovic G, Dworkin J. The Escherichia coli phage-shock-protein (psp) operon. of outstanding interest Mol Microbiol. 24:1997;255-261 The E. coli phage-shock protein (psp) operon is induced after infection by Ff, apparently as a result of the process of p4 insertion into the outer membrane. It is also induced by expression of (nonphage) homologs of p4, and by diverse other challenges, whose common feature may be that they damage the membrane proton gradient. The sequence of PspA predicts a coiled-coil motif, and PspB, C and D all contain leucine zipper motifs.
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Model, P.1
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68
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Model, P.4
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Essential role of a sodium dodecyl sulfate-resistant protein IV multimer in assembly - Export of filamentous phage
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71
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Symmons MF, Welsh LC, Nave C, Marvin DA, Perham RN. Matching electrostatic charge between DNA and coat protein in filamentous bacteriophage. Fibre diffraction of charge-deletion mutants. J Mol Biol. 245:1995;86-91.
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W. Neupert, Lill R. Amsterdam: Elsevier
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Kuhn A. Major coat proteins of bacteriophage Pf3 and M13 as model systems for Sec-independent protein transport. FEMS Microbiol Rev. 17:1995;185-190.
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Structural changes accompanying chloroform-induced contraction of the filamentous phage fd
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Roberts LM, Dunker AK. Structural changes accompanying chloroform-induced contraction of the filamentous phage fd. Biochemistry. 32:1993;10479-10488.
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