Structure of the protein and DNA in fd filamentous bacterial virus

Abstract

The virion of filamentous bacterial viruses comprises a cylindrical protein shell of o.d. approximately 60 A and i.d. 20A, containing a single-stranded circular DNA molecule which has two oppositely directed but not base-paired strands extending the length of the virion. The assembly of the virion involves an intracellular prepackaging of the DNA with a viral DNA-binding protein which is then displaced by the coat protein as the growing virion crosses the bacterial membrane. Studies of the virion by X-ray fibre diffraction show that the protein coat consists largely of alpha-helices oriented roughly parallel to the axis of the virion. As the normal to a planar peptide tends to align normal to a magnetic field, it is possible to improve significantly the orientation of virions in fibres using a strong magnet. The success of this technique with the Pf1 strain of virus led us to apply it to the better-known fd (f1, M13) strain. We report here new information about the arrangement of protein and DNA in the fd virion obtained from the improved diffraction pattern (Fig. 1).

The NMR–Rosetta capsid model of M13 bacteriophage reveals a quadrupled hydrophobic packing epitope

“…In this manner, we modeled 7 concentric rings, consisting of 35 subunits in total. As the C5 symmetry was observed before by fiber diffraction in several studies (15,18), no attempt has been made to fit our model to other symmetries. The relative orientation of neighboring subunits is defined by three rigid-body DOF on a local coordinate system, the distance of each subunit from the center of the (identical) fivefold and helical axes and two helical parameters (rise and rotation per pentamer, respectively).…”

“…Pure, intact, infectious M13 phage particles were obtained as described before (32,33) and detailed in SI Appendix. Sparsely labeled samples were grown using 15 NH 4 Cl as a nitrogen source and on either [1,3-13 C]-glycerol and NaH 12 CO 3 or on [2-13 C]-glycerol and NaH 13 CO 3 , as the sole carbon sources (37).…”

“…Previous structural models for a small number of phages have been obtained by means of X-ray fiber diffraction (15)(16)(17)(18)(19), static solid-state NMR (20,21), and cryo-EM (22). Structural models for the Ff family have been proposed based on the three methods; however, satisfactory resolution was only obtained for the Y21M mutant of the fd phage (17,18,21) (wt fd is related to M13 by one additional mutation, N12D).…”

FT-IR spectroscopy of the major coat protein of M13 and Pf1 in the phage and reconstituted into phospholipid systems

“…M l3 coat protein when associated with DNA in the virion is almost completely a-helical, as judged by X-ray diffraction techniques (Banner et al, 1981;Glucksman et al, 1992), circular dichroism (Fodor et al, 1981;Clack & Gray, 1989;Arnold et al, 1992), and laser Raman spectroscopy (Thomas et al, 1983;Williams et al, 1984). The results found here for the coat protein in M13 phage correspond well with these studies, indicating that for the M 13 coat protein in the phage, similar to P fl, two a-helical regions are observed separated by a loop structure.…”

Raman spectroscopic study on the conformation of a peptide fragment representing the DNA‐binding domain of filamentous virus Pf3 coat protein

“…Each subunit consists of acidic N-terminal, basic Cterminal, and middle hydrophobic regions [1][2][3][4][5]. In the best-studied filamentous bacteriophages, M 13 and Pfl, the secondary structure of the coat subunit is predominantly ~-helical and the helix is oriented roughly parallel to the axis of the filamellt with the positively charged C-terminal region abutting on the encapsulated DNA [6][7][8][9][10]. ~-Helical interaction of coat protein with nucleic acid has also been suggested for the cylindrical tobacco mosaic virus [11] and for an icosahedral plant virus, cowpea chlorotic mottle virus [12].…”