Pf1 filamentous bacterial virus

Nave, C.; Brown, Robert S.; Fowler, Allan; Ladner, Jane E.; Marvin, D.A.; Provencher, Stephen W.; Tsugita, A; Armstrong, J. T.; Perham, Richard N.

doi:10.1016/0022-2836(81)90353-3

Cited by 61 publications

(32 citation statements)

References 42 publications

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“…Therefore, most of the separation between the two iodines must be in the axial and azimuthal directions. On layer lines 1 = 6, 12, and 18 of the diffraction patterns, there are large differences between the native and derivative intensities, suggesting that the iodines lie along the helical direction (n,l) = (5,6) defined by these layer lines.…”

Section: Pf1 Structurementioning

confidence: 99%

“…To start the calculation, we chose either a completely flat featureless map or various trial maps with roughly axial rods of density. Irrespective of the starting map, all solutions showed rods of electron density similar to those found from model building (17)(18)(19) and earlier heavy-atom methods (5). A solution at 7 A resolution was then used as the starting point for a refinement process that included successively more diffraction data and refined iodine coordinates until 4 A resolution was reached (Fig.…”

Section: Pf1 Structurementioning

confidence: 99%

“…To calculate a Pfl electron-density map, we used data from the native virion and from the iodine derivative (5). The radial coordinates of the two iodines attached to tyrosine-25 are both within ±1.5 A of 27 A.…”

Section: Pf1 Structurementioning

confidence: 99%

“…This analysis showed that the 46-residue coat-protein subunits can be approximated by rods of electron density whose long axes are tilted slightly with respect to the axis of the virion, forming an overlapping interdigitating helical array. Experimental advances have now made possible true three-dimensional x-ray fiber data to 4 A resolution, in spite of the cylindrical averaging inherent in fiber patterns (4,5). We have used these data from native Pfl and a single isomorphous heavy-atom derivative to calculate an electron-density map by the maximum-entropy method.…”

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confidence: 99%

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Maximum-entropy calculation of the electron density at 4 A resolution of Pf1 filamentous bacteriophage.

Bryan¹,

Bansal²,

Folkhard³

et al. 1983

Proc. Natl. Acad. Sci. U.S.A.

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A 4 A electron-density map of Pf1 filamentous bacterial virus has been calculated from x-ray fiber diffraction data by using the maximum-entropy method. This method produces a map that is free of features due to noise in the data and enables incomplete isomorphous-derivative phase information to be supplemented by information about the nature of the solution. The map shows gently curved (banana-shaped) rods of density about 70 A long, oriented roughly parallel to the virion axis but slewing by about 1/6th turn while running from a radius of 28 A to one of 13 A. Within these rods, there is a helical periodicity with a pitch of 5 to 6 A. We interpret these rods to be the helical subunits of the virion. The position of strongly diffracted intensity on the x-ray fiber pattern shows that the basic helix of the virion is right handed and that neighboring nearly parallel protein helices cross one another in an unusual negative sense.Two structural classes of filamentous bacterial viruses have been identified (1). Class 1, exemplified by the fd (= fl = M 13) species, has been extensively studied by biochemical and genetic techniques whereas class 2, exemplified by the Pfl species, gives higher resolution x-ray fiber diffraction data and has been intensively studied by structural techniques (reviewed in refs. 2 and 3). Both classes of virion have a cylindrical protein coat of 60 A average outer diameter and 20 A average inner diameter encapsulating a single-stranded circular DNA molecule that stretches down the length of the central hole. The protein coat is essentially a helical array of several thousand identical protein units, although there are minor proteins at the ends of the virion that make up about 1% by weight of the coat.

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Section: Pf1 Structurementioning

confidence: 99%

Section: Pf1 Structurementioning

confidence: 99%

Section: Pf1 Structurementioning

confidence: 99%

mentioning

confidence: 99%

See 2 more Smart Citations

Maximum-entropy calculation of the electron density at 4 A resolution of Pf1 filamentous bacteriophage.

Bryan¹,

Bansal²,

Folkhard³

et al. 1983

Proc. Natl. Acad. Sci. U.S.A.

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“…2, the ratio of the Cotton- (23), Pf1 and fd, whose structures are well characterized (24)(25)(26). The ratio of the specific CMs is 8.0 x 10-4 (fibrinogen/Pfl) and 16.2 X 10-4 (fibrinogen/fd), whereas the ratios of the molecular weights are, respectively, 9.07 x 10-3 and 2 x 10-2.…”

mentioning

confidence: 97%

Fibrinogen and fibrin structure and fibrin formation measured by using magnetic orientation.

Freyssinet¹,

Torbet²,

Hudry-Clergeon³

et al. 1983

Proc. Natl. Acad. Sci. U.S.A.

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Accurate birefringence measurements show that fibrinogen orients to a small degree in high magnetic fields. This effect can be explained as due to the molecule having about 30% (by weight) a-helix oriented relatively parallel to the long axis. Birefringence measurements on fully oriented fibrin suggest that aligned a-helical content is less than that estimated for fibrinogen. But because of limitations in the analysis this difference must be viewed with caution. Highly oriented fibrin results when polymerization takes place slowly in a strong magnetic field. Low-angle neutron diffraction patterns from oriented fibrin made in the presence of EDTA, made in the presence of calcium, or stabilized with factor XIIIa are very similar, showing that the packing of the molecules within the fibers is the same or very similar in these different preparations. The induced magnetic birefringence was used to follow fibrin formation under conditions in which thrombin was rate limiting. The fiber network formed by approximately the gelation point constitutes a kind of matrix or frame that is largely built upon during the remaining ==85% of the reaction. After gelation the reaction is pseudo-first order.The arrest of blood loss from an injured vessel, hemostasis, requires the participation of several plasma proteins and also platelets, cells that form occlusive aggregates at the site of the rupture. The last stage of the blood clotting process is the enzyme-catalyzed activation of a soluble plasma protein, fibrinogen, which then undergoes polymerization to form an insoluble fibrin gel, thus mechanically reinforcing the platelet plug. The limited cleavage of fibrinogen by thrombin, a serine proteinase, is the result of a series of steps involving many other clotting factors; much is known about this sequence of highly regulated events (for a recent and exhaustive review see ref. 1). Thrombin also converts factor XIII into factor XIIIa, the plasma transglutaminase which, in the presence of calcium, crosslinks adjacent fibrin monomers of a fiber by forming E-(y-glutamyl)lysyl pseudo peptide bonds (2).The trinodular elongated (450-A-long) structure for the fibrinogen molecule proposed by Hall and Slayter (3) is the most widely accepted model, and it has obtained additional support from recent work on native fibrinogen (4-8) or slightly modified fibrinogen (9-11). Fibrin monomers are produced by thrombin, which releases the small negatively charged fibrinopeptides A and B. The monomers associate in a longitudinal half-staggered arrangement to generate the two-stranded fibrin protofibril (12, 13), then these protofibrils associate laterally to form the thicker fibrin fibers (12). In a recent study, we have shown that when polymerization of fibrin takes place slowly in a high magnetic field one ends up with a highly oriented gel on which neutron low-angle diffraction studies demonstrate that the protofibrils pack with three-dimensional order, probably in a tetragonal unit cell with a = b = 185 A and c = 446 A and containing eigh...

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