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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, Marvin DA
Acta Crystallogr D Biol Crystallogr 51 792-804 (1995)
Related entries: 2ifm, 2ifn, 4ifm

Cited: 21 times
EuropePMC logo PMID: 15299811

Abstract

The filamentous bacteriophage Pf1 is structurally similar to the well known Ff (fd, fl, M13) strains, but it gives much better X-ray diffraction patterns, enabling a more detailed analysis of the molecular structure. The 46-residue protein subunit can be closely approximated by a single gently curved stretch of alpha-helix. The axes of the subunits are at a small angle to the virion axis, and several thousand subunits form an overlapping inter-digitated helical array surrounding a DNA core. We have derived a detailed model of the virion based on X-ray data and stereochemical constraints. We have considered potential sources of error in the diffraction data, and used the improved data to study regions where the protein subunit of Pf1 may deviate from a continuous alpha-helix. We use simulated annealing to escape from local minima, and various kinds of electron-density maps to guide the model building. Refinement of the model shows that the first few residues at the N terminus are non-helical, and there is a slight discontinuity in the alpha-helix near the middle of the sequence. The model is consistent both with general structural principles derived from high-resolution analysis of other proteins, and with specific chemical and spectroscopic data about Pf1. We apply the same refinement techniques to an alternative model with a non-helical surface loop between residues 13 and 19. Comparative analysis of models with and without a loop shows that the loop model is not supported by 3.3 A resolution X-ray diffraction data.

Reviews citing this publication (5)

  1. Filamentous phage structure, infection and assembly. Marvin DA. Curr. Opin. Struct. Biol. 8 150-158 (1998)
  2. Stress, order and survival. Minsky A, Shimoni E, Frenkiel-Krispin D. Nat. Rev. Mol. Cell Biol. 3 50-60 (2002)
  3. Structure, dynamics, and assembly of filamentous bacteriophages by nuclear magnetic resonance spectroscopy. Opella SJ, Zeri AC, Park SH. Annu Rev Phys Chem 59 635-657 (2008)
  4. New strategies for protein crystal growth. Wiencek JM. Annu Rev Biomed Eng 1 505-534 (1999)
  5. Developments in fiber diffraction. Stubbs G. Curr. Opin. Struct. Biol. 9 615-619 (1999)

Articles citing this publication (16)

  1. Structure of the coat protein in Pf1 bacteriophage determined by solid-state NMR spectroscopy. Thiriot DS, Nevzorov AA, Zagyanskiy L, Wu CH, Opella SJ. J. Mol. Biol. 341 869-879 (2004)
  2. Structure of the capsid of Pf3 filamentous phage determined from X-ray fibre diffraction data at 3.1 A resolution. Welsh LC, Symmons MF, Sturtevant JM, Marvin DA, Perham RN. J. Mol. Biol. 283 155-177 (1998)
  3. The protein capsid of filamentous bacteriophage PH75 from Thermus thermophilus. Pederson DM, Welsh LC, Marvin DA, Sampson M, Perham RN, Yu M, Slater MR. J. Mol. Biol. 309 401-421 (2001)
  4. Fungal prion HET-s as a model for structural complexity and self-propagation in prions. Wan W, Stubbs G. Proc. Natl. Acad. Sci. U.S.A. 111 5201-5206 (2014)
  5. On the structures of filamentous bacteriophage Ff (fd, f1, M13). Straus SK, Scott WR, Symmons MF, Marvin DA. Eur Biophys J 37 521-527 (2008)
  6. Heterogeneous seeding of a prion structure by a generic amyloid form of the fungal prion-forming domain HET-s(218-289). Wan W, Bian W, McDonald M, Kijac A, Wemmer DE, Stubbs G. J. Biol. Chem. 288 29604-29612 (2013)
  7. Intersubunit hydrophobic interactions in Pf1 filamentous phage. Goldbourt A, Day LA, McDermott AE. J. Biol. Chem. 285 37051-37059 (2010)
  8. Consensus structure of Pf1 filamentous bacteriophage from X-ray fibre diffraction and solid-state NMR. Straus SK, Scott WR, Schwieters CD, Marvin DA. Eur. Biophys. J. 40 221-234 (2011)
  9. A structural model for the single-stranded DNA genome of filamentous bacteriophage Pf1. Tsuboi M, Tsunoda M, Overman SA, Benevides JM, Thomas GJ. Biochemistry 49 1737-1743 (2010)
  10. Raman optical activity of filamentous bacteriophages: hydration of alpha-helices. Blanch EW, Bell AF, Hecht L, Day LA, Barron LD. J. Mol. Biol. 290 1-7 (1999)
  11. Magic-angle spinning NMR of intact bacteriophages: insights into the capsid, DNA and their interface. Abramov G, Morag O, Goldbourt A. J. Magn. Reson. 253 80-90 (2015)
  12. Fiber diffraction of the prion-forming domain HET-s(218-289) shows dehydration-induced deformation of a complex amyloid structure. Wan W, Stubbs G. Biochemistry 53 2366-2370 (2014)
  13. The hand of the filamentous bacteriophage helix. Straus SK, Scott WR, Marvin DA. Eur Biophys J 37 1077-1082 (2008)
  14. Raman spectroscopy of proteins and nucleoproteins. Nemecek D, Stepanek J, Thomas GJ. Curr Protoc Protein Sci Chapter 17 Unit17.8 (2013)
  15. Automated determination of fibrillar structures by simultaneous model building and fiber diffraction refinement. Potrzebowski W, André I. Nat. Methods 12 679-684 (2015)
  16. Sensitivity enhancement for membrane proteins reconstituted in parallel and perpendicular oriented bicelles obtained by using repetitive cross-polarization and membrane-incorporated free radicals. Koroloff SN, Tesch DM, Awosanya EO, Nevzorov AA. J. Biomol. NMR 67 135-144 (2017)


Related citations provided by authors (3)

  1. Two Forms of Pf1 Inovirus: X-Ray Diffraction Studies on a Structural Phase Transition and a Calculated Libration Normal Mode of the Asymmetric Unit. Marvin DA, Nave C, Bansal M, Hale RD, Salje EKH Phase Transitions 39 45- (1992)
  2. Model-Building Studies of Inovirus: Genetic Variations on a Geometric Theme. Marvin DA Int. J. Biol. Macromol. 12 125- (1990)
  3. Dynamics of Telescoping Inovirus: A Mechanism for Assembly at Membrane Adhesions. Marvin DA Int. J. Biol. Macromol. 11 159- (1989)

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