bacteriophage pf1

Summary

Summary: A species of filamentous Pseudomonas phage in the genus INOVIRUS, family INOVIRIDAE.

Top Publications

  1. Sallum C, Martel D, Fournier R, Matousek W, Alexandrescu A. Sensitivity of NMR residual dipolar couplings to perturbations in folded and denatured staphylococcal nuclease. Biochemistry. 2005;44:6392-403 pubmed
    ..By contrast, the invariance of RDCs in denatured states is more consistent with a disruption of cooperative structure than with the retention of a unique long-range folding topology...
  2. Overman S, Kristensen D, Bondre P, Hewitt B, Thomas G. Effects of virion and salt concentrations on the Raman signatures of filamentous phages fd, Pf1, Pf3, and PH75. Biochemistry. 2004;43:13129-36 pubmed
    ..The present results also identify new Raman bands that serve as potential markers of subunit side-chain orientations in filamentous virus assemblies...
  3. Zweckstetter M, Hummer G, Bax A. Prediction of charge-induced molecular alignment of biomolecules dissolved in dilute liquid-crystalline phases. Biophys J. 2004;86:3444-60 pubmed
    ..Inclusion of electrostatic interactions in addition to steric effects makes the extended model applicable to all liquid crystals used in biological NMR to date...
  4. Bucki R, Niemirowicz K, Wnorowska U, WÄ…tek M, Byfield F, Cruz K, et al. Polyelectrolyte-mediated increase of biofilm mass formation. BMC Microbiol. 2015;15:117 pubmed publisher
    ..The bacteriophage Pf1 (1 mg/ml) significantly increased biofilm mass produced by Pseudomonas aeruginosa P14, Escherichia coli ..
  5. Hagens S, Habel A, Blasi U. Augmentation of the antimicrobial efficacy of antibiotics by filamentous phage. Microb Drug Resist. 2006;12:164-8 pubmed
    ..aeruginosa K by concomitant treatment with phage Pf1 and low concentrations of gentamicin, neither of which was able to cure the infection when administered alone...
  6. Zweckstetter M, Bax A. Characterization of molecular alignment in aqueous suspensions of Pf1 bacteriophage. J Biomol NMR. 2001;20:365-77 pubmed
    ..Because ionic strength modulates both the orientation and magnitude of the alignment tensor in Pf1 medium, measurement at two ionic strengths can yield linearly independent alignment tensors...
  7. Wu B, Petersen M, Girard F, Tessari M, Wijmenga S. Prediction of molecular alignment of nucleic acids in aligned media. J Biomol NMR. 2006;35:103-15 pubmed
    ..The procedures are incorporated into MATLAB scripts, which are available on request...
  8. Sonkar K, Purusottam R, Sinha N. Metabonomic study of host-phage interaction by nuclear magnetic resonance- and statistical total correlation spectroscopy-based analysis. Anal Chem. 2012;84:4063-70 pubmed publisher
    ..on (1)H NMR data sets of growth media in planktonic cultures of Pseudomonas aeruginosa infected with bacteriophage pf1. Transient metabolic flux of various important metabolites, identified by STOCSY and PLS-DA analysis applied ..
  9. Park S, Marassi F, Black D, Opella S. Structure and dynamics of the membrane-bound form of Pf1 coat protein: implications of structural rearrangement for virus assembly. Biophys J. 2010;99:1465-74 pubmed publisher
    ..The N-terminal helix and the hinge that connects it to the transmembrane helix are significantly more dynamic than the rest of the protein, thus facilitating structural rearrangement during bacteriophage assembly...

More Information

Publications49

  1. Hagens S, Habel A, von Ahsen U, von Gabain A, Blasi U. Therapy of experimental pseudomonas infections with a nonreplicating genetically modified phage. Antimicrob Agents Chemother. 2004;48:3817-22 pubmed
    ..Thus, the use of a nonreplicating modified phage for the delivery of genes encoding proteins toxic to bacterial pathogens may open up a new avenue in antimicrobial therapy...
  2. Thiriot D, Nevzorov A, Zagyanskiy L, Wu C, Opella S. Structure of the coat protein in Pf1 bacteriophage determined by solid-state NMR spectroscopy. J Mol Biol. 2004;341:869-79 pubmed publisher
    ..0 A. The symmetry and distance constraints determined by X-ray fiber and neutron diffraction enable the construction of an accurate model of the bacteriophage particle from the coordinates of the coat protein monomers...
  3. Goldbourt A, Gross B, Day L, McDermott A. Filamentous phage studied by magic-angle spinning NMR: resonance assignment and secondary structure of the coat protein in Pf1. J Am Chem Soc. 2007;129:2338-44 pubmed
    ..in the magic-angle spinning solid-state NMR spectra of the major coat protein subunit of the filamentous bacteriophage Pf1. NMR spectra were collected on uniformly 13C and 15N isotopically enriched, polyethylene glycol precipitated ..
  4. Lorieau J, Yao L, Bax A. Liquid crystalline phase of G-tetrad DNA for NMR study of detergent-solubilized proteins. J Am Chem Soc. 2008;130:7536-7 pubmed publisher
    ..Alignment of the detergent-solubilized fusion domain of hemagglutinin is demonstrated to be homogeneous and stable, resulting in high quality NMR spectra suitable for the measurement of residual dipolar couplings...
  5. Straus S, Scott W, Schwieters C, Marvin D. Consensus structure of Pf1 filamentous bacteriophage from X-ray fibre diffraction and solid-state NMR. Eur Biophys J. 2011;40:221-34 pubmed publisher
  6. Sergeyev I, Day L, Goldbourt A, McDermott A. Chemical shifts for the unusual DNA structure in Pf1 bacteriophage from dynamic-nuclear-polarization-enhanced solid-state NMR spectroscopy. J Am Chem Soc. 2011;133:20208-17 pubmed publisher
    ..Overall, these observations characterize and support the DNA model proposed by Liu and Day and refined by Tsuboi et al., which calls for the most highly stretched and twisted naturally occurring DNA yet encountered...
  7. Ward J, Skrynnikov N. Very large residual dipolar couplings from deuterated ubiquitin. J Biomol NMR. 2012;54:53-67 pubmed publisher
    ..The technical ability to measure RDCs under moderately strong alignment conditions may open the door for development of alternative alignment media, including new types of media that mimic biologically relevant systems...
  8. Webb J, Thompson L, James S, Charlton T, Tolker Nielsen T, Koch B, et al. Cell death in Pseudomonas aeruginosa biofilm development. J Bacteriol. 2003;185:4585-92 pubmed
    ..aeruginosa. We propose that prophage-mediated cell death is an important mechanism of differentiation inside microcolonies that facilitates dispersal of a subpopulation of surviving cells...
  9. Tsuboi M, Kubo Y, Ikeda T, Overman S, Osman O, Thomas G. Protein and DNA residue orientations in the filamentous virus Pf1 determined by polarized Raman and polarized FTIR spectroscopy. Biochemistry. 2003;42:940-50 pubmed
    The Pseudomonas bacteriophage Pf1 is a long ( approximately 2000 nm) and thin ( approximately 6...
  10. Trempe J, Morin F, Xia Z, Marchessault R, Gehring K. Characterization of polyacrylamide-stabilized Pfl phage liquid crystals for protein NMR spectroscopy. J Biomol NMR. 2002;22:83-7 pubmed
    ..We show that the quadrupolar splitting and RDCs are zero in media in which the Pf1 phage particles are aligned at the magic angle. This allows measurement of J and dipolar couplings in a single sample...
  11. Evgeny N, Jerschow A. Quadrupole sensitive pulse for signal filtering. J Magn Reson. 2016;265:153-63 pubmed publisher
  12. Lin E, Opella S. 1H assisted 13C/15N heteronuclear correlation spectroscopy in oriented sample solid-state NMR of single crystal and magnetically aligned samples. J Magn Reson. 2011;211:37-44 pubmed publisher
  13. Tang W, Nevzorov A. Repetitive cross-polarization contacts via equilibration-re-equilibration of the proton bath: Sensitivity enhancement for NMR of membrane proteins reconstituted in magnetically aligned bicelles. J Magn Reson. 2011;212:245-8 pubmed publisher
    ..The new technique is applicable to systems with short T1?'s, and speeds up acquisition of the multidimensional solid-state NMR spectra of oriented membrane proteins for their subsequent structural and dynamic studies...
  14. Knox R, Lu G, Opella S, Nevzorov A. A resonance assignment method for oriented-sample solid-state NMR of proteins. J Am Chem Soc. 2010;132:8255-7 pubmed publisher
    ..This method is applicable to proteins with arbitrary topology and will find use in assigning solid-state NMR spectra of oriented membrane proteins for their subsequent structure determination...
  15. Lorieau J, Day L, McDermott A. Conformational dynamics of an intact virus: order parameters for the coat protein of Pf1 bacteriophage. Proc Natl Acad Sci U S A. 2008;105:10366-71 pubmed publisher
    ..The large-amplitude dynamic motion of these positively charged side chains in their interactions with the DNA were not previously expected. The results reveal a highly dynamic aspect of a DNA-protein interface within a virus...
  16. Platt M, Schurr M, Sauer K, Vazquez G, Kukavica Ibrulj I, Potvin E, et al. Proteomic, microarray, and signature-tagged mutagenesis analyses of anaerobic Pseudomonas aeruginosa at pH 6.5, likely representing chronic, late-stage cystic fibrosis airway conditions. J Bacteriol. 2008;190:2739-58 pubmed publisher
    ..aeruginosa to limit the growth of this important CF pathogen when it is either limited or completely restricted in its oxygen supply...
  17. Mao X, Cui W, Gmeiner W. Line shape analyses for water 17O NMR quintet observed in a bacteriophage Pf1 solution at different temperatures. Biophys Chem. 2004;107:255-62 pubmed
    Partially resolved 17O NMR quintet was observed in a filamentous bacteriophage Pf1 solution at 70 degrees C with a quadrupole splitting approximately 100 Hz...
  18. Burton R, Tjandra N. Determination of the residue-specific 15N CSA tensor principal components using multiple alignment media. J Biomol NMR. 2006;35:249-59 pubmed
    ..Am. Chem. Soc. 122, 10143-10154]. Significant deviations from the averages coincide with residues in beta-strand or extended regions, while alpha-helical residue tensor components cluster close to the average values...
  19. Kaadige M, Ayer D. The polybasic region that follows the plant homeodomain zinc finger 1 of Pf1 is necessary and sufficient for specific phosphoinositide binding. J Biol Chem. 2006;281:28831-6 pubmed
  20. Purusottam R, Rai R, Sinha N. Mechanistic insights into water-protein interactions of filamentous bacteriophage. J Phys Chem B. 2013;117:2837-40 pubmed publisher
    ..The results obtained also suggest the first evidence of a water-mediated interface cluster formed at the site of Arg44 with the single-stranded DNA genome of the filamentous phage supramolecular assembly...
  21. Trempe J, Denisov A, Gehring K. Recoupling of residual dipolar couplings in single-domain polymer-stabilized liquid crystals undergoing magic-angle spinning. J Magn Reson. 2003;164:329-37 pubmed
    ..The effectiveness of the technique is demonstrated both theoretically and experimentally, using the recently developed polyacrylamide-stabilized Pf1 phage medium and 15N-labeled benzamide as the aligned molecule...
  22. Ding K, Gronenborn A. Protein Backbone 1H(N)-13Calpha and 15N-13Calpha residual dipolar and J couplings: new constraints for NMR structure determination. J Am Chem Soc. 2004;126:6232-3 pubmed
    ..A Karplus-type relationship between the one-bond 1JNCA couplings and the backbone dihedral psi angles holds, and on the basis of the two-bond 2JNCA couplings a secondary structure index can be established...
  23. Denisov A, Ritter B, McPherson P, Gehring K. 1H, 15N and 13C resonance assignments and 15N-1H residual dipolar couplings for the alpha-adaptin ear-domain. J Biomol NMR. 2004;29:441-2 pubmed
  24. Jaroniec C, Boisbouvier J, Tworowska I, Nikonowicz E, Bax A. Accurate measurement of 15N-13C residual dipolar couplings in nucleic acids. J Biomol NMR. 2005;31:231-41 pubmed
  25. Velicer G. Evolution of cooperation: the benefits of ridesharing. Heredity (Edinb). 2005;95:116-7 pubmed
  26. Lee J, Regatte R, Jerschow A. Optimal excitation of (23)Na nuclear spins in the presence of residual quadrupolar coupling and quadrupolar relaxation. J Chem Phys. 2009;131:174501 pubmed publisher
    ..The optimized pulses are tested with (23)Na NMR, and their performance is compared with that of pulses optimized in the absence of relaxation...
  27. Lee J, Regatte R, Jerschow A. Selective detection of ordered sodium signals by a jump-and-return pulse sequence. J Magn Reson. 2009;200:126-9 pubmed publisher
    ..This QJR sequence is tested with a phantom made of sodium ions in bacteriophage and in aqueous solution and its feasibility for contrast modification based on the quadrupolar coupling is demonstrated...
  28. Ruan K, Tolman J. Composite alignment media for the measurement of independent sets of NMR residual dipolar couplings. J Am Chem Soc. 2005;127:15032-3 pubmed
    ..sets of RDCs can be measured for ubiquitin using just a single alignment medium composed of aligned bacteriophage Pf1 particles embedded in a strained polyacrylamide gel matrix...
  29. Goldbourt A, Day L, McDermott A. Assignment of congested NMR spectra: carbonyl backbone enrichment via the Entner-Doudoroff pathway. J Magn Reson. 2007;189:157-65 pubmed
  30. Wu C, Das B, Opella S. (1)H-(13)C Hetero-nuclear dipole-dipole couplings of methyl groups in stationary and magic angle spinning solid-state NMR experiments of peptides and proteins. J Magn Reson. 2010;202:127-34 pubmed publisher
  31. Goldbourt A, Day L, McDermott A. Intersubunit hydrophobic interactions in Pf1 filamentous phage. J Biol Chem. 2010;285:37051-9 pubmed publisher
    ..These contacts are important constraints for structure modeling...
  32. Park S, Loudet C, Marassi F, Dufourc E, Opella S. Solid-state NMR spectroscopy of a membrane protein in biphenyl phospholipid bicelles with the bilayer normal parallel to the magnetic field. J Magn Reson. 2008;193:133-8 pubmed publisher
    ..In addition, the large temperature range of these samples is advantageous for the studies of membrane proteins that are unstable at elevated temperatures and for experiments requiring measurements as a function of temperature...
  33. Vögeli B, Kovacs H, Pervushin K. Measurements of side-chain 13C-13C residual dipolar couplings in uniformly deuterated proteins. J Am Chem Soc. 2004;126:2414-20 pubmed
    ..An excellent correlation between measured RDCs and the 3D structure of the protein was observed, indicating a potential use of the (13)C-(13)C RDCs in the structure determination of perdeuterated proteins...
  34. Nevzorov A. Orientational and motional narrowing of solid-state NMR lineshapes of uniaxially aligned membrane proteins. J Phys Chem B. 2011;115:15406-14 pubmed publisher
    ..The static disorder dominates the (15)N NMR spectra of Pf1 aligned on a phage, while fast uniaxial diffusion provides a line narrowing mechanism for the Pf1 protein reconstituted in magnetically aligned bicelles...
  35. Sobieski D, Krueger N, Vyas S, Augustine M. Nuclear spin relaxation of sodium cations in bacteriophage Pf1 solutions. J Chem Phys. 2006;125:244509 pubmed
    The nuclear magnetic resonance (NMR) spectra for the I=3/2 23Na cation dissolved into filamentous bacteriophage Pf1 solutions display line splittings and relaxation times consistent with an interaction between the 23Na nuclear quadrupole ..
  36. Fu Y, Wand A. Partial alignment and measurement of residual dipolar couplings of proteins under high hydrostatic pressure. J Biomol NMR. 2013;56:353-7 pubmed publisher
    ..However, DMPC/DHPC bicelles and collagen gel are found to be unsuitable. Evidence is presented to demonstrate that pressure-induced structural changes can be identified using the residual dipolar coupling. ..
  37. Park S, Yang C, Opella S, Mueller L. Resolution and measurement of heteronuclear dipolar couplings of a noncrystalline protein immobilized in a biological supramolecular assembly by proton-detected MAS solid-state NMR spectroscopy. J Magn Reson. 2013;237:164-8 pubmed publisher
    ..coupling/(15)N chemical shift/(1)H chemical shift MAS solid-state NMR correlation spectra of the filamentous bacteriophage Pf1 major coat protein show single-site resolution in noncrystalline, intact-phage preparations...
  38. Pervushin K, Vögeli B. Observation of individual transitions in magnetically equivalent spin systems. J Am Chem Soc. 2003;125:9566-7 pubmed
    ..The use of the experiments for the measurement of RDCs is demonstrated with two proteins, one weakly aligned by means of Pf1 phages and the other using a naturally present paramagnetic heme group...
  39. Riley S, Giuliani J, Augustine M. Capture and manipulation of magnetically aligned Pf1 with an aqueous polymer gel. J Magn Reson. 2002;159:82-6 pubmed
    The magnetic alignment of the Pseudomonas bacteriophage Pf1 is captured indefinitely in a gel of the aqueous triblock copolymer Pluronic F-127...
  40. Gebel E, Ruan K, Tolman J, Shortle D. Multiple alignment tensors from a denatured protein. J Am Chem Soc. 2006;128:9310-1 pubmed