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Query: UNIPROT:P06889 (Mol)
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The three-dimensional structure of the head-to-tail connecting region of bacteriophage phi 29 has been studied by analysing two-dimensional, hexagonal ordered aggregates of negatively stained viral necks to a resolution of 2 X 2 nm. These necks are composed of two proteins, p10 and p11; p10 being the connector protein. A 12-folded and a 6-folded axially symmetric domain are present in the specimen. The 12-folded domain is the larger part of the structure; it consists of 12 subunits associated in pairs. These subunits appear to be more closely paired towards the centre, where only six subunits are resolved forming the 6-folded domain. The pairs of subunits present an important twist between the 12-folded and the 6-folded areas. A conical hole is formed at the centre of the structure. This hole is more open at the 12-folded domain than at the level of the possible zone of interaction between p10 and p11, where it is almost closed. Protein p11 is very poorly represented in the reconstruction, probably due to lack of staining. The structure described for the phi 29 neck has many of the attributes expected for an active device involved in bacteriophage DNA encapsidation.
J Mol Biol 1985 May 05
PMID:Three-dimensional reconstruction of bacteriophage phi 29 neck particles at 2 X 2 nm resolution. 400 22

The structure of the DNA oligomer d(G-G-G-G-C-C-C-C) has been determined at a resolution of 2.5 A by single-crystal X-ray methods. There are two strands in the asymmetric unit, and these coil about each other to form a right-handed double-helix of the A-type with Watson-Crick hydrogen bonds between base-pairs. The helix has a shallow minor groove and a deep, water-filled major groove; almost all exposed functional groups on the DNA are hydrated, and 106 ordered solvent molecules have been found. The two d(G-G-G-G).d(C-C-C-C) segments in the octamer exhibit similar and uniform structures, but there is a slight discontinuity at the GpC step between them. A recurring feature of the structure is the overlap of adjacent guanine bases in each GpG step, with the five-membered ring of one guanine stacking on the six-membered ring of its neighbour. There is little or no overlap between adjacent cytosine rings. Conformational parameters for these GpG steps are compared with those from other single-crystal X-ray analyses. In general, GpG steps exhibit high slide, low roll and variable twist. Models for poly(dG).poly(dC) were generated by applying a simple rotation and translation to each of the unmodified d(G-G-G-G).d(C-C-C-C) units. Detailed features of these models are shown to be compatible with various assays of poly(dG).poly(dC) in solution, and are useful in understanding the polymorphic behaviour of this sequence under a variety of experimental conditions.
J Mol Biol 1985 Jun 05
PMID:The crystal structure of d(G-G-G-G-C-C-C-C). A model for poly(dG).poly(dC). 402 Aug 65

Recent experimental data of Shore & Baldwin (1983b) and of Horowitz & Wang (1984) for the apparent twisting coefficient K, which determines the breadth of the Gaussian distribution of DNA topoisomers with different linking numbers N, show that the product of K and nbp (the number of base-pairs) is nearly a constant for nbp approximately greater than 2000, but that it increases sharply with decreasing nbp for nbp approximately less than 2000. The main purpose of the present paper is to explain theoretically such behavior of K as a function of nbp. Thus the statistical mechanics of DNA topoisomers in general is developed on the basis of a twisted worm-like chain, i.e. a special case of the helical worm-like chain. The previous treatments of the N-dependent ring-closure probability, i.e. the distribution of N, which are valid only for small chain length L, are extended to the range of larger L. The variance of N is then shown to be exactly the sum of those of the writhe Wr and the twist Tw. For small values of L, the distribution of Wr is not Gaussian, and its variance or moment (Wr2) increases rather steeply with increasing L. With these and known Monte Carlo results for freely jointed chains, an empirical interpolation formula for (Wr2) is also constructed to be valid for all values of L. It predicts that (Wr2)/L increases monotonically, with increasing L to its coil-limiting value. On the other hand, the distribution of N is actually Gaussian in the practical range of N for all values of L. The conditional distribution of Wr with N fixed is also evaluated. Finally, K is expressed in terms of the torsional constant C, the stiffness parameter lambda-1 (which is equal to the Kuhn segment length and twice the persistence length for this special case), and (Wr2). The derived equation predicts that nbpK decreases monotonically to its coil-limiting value with increasing nbp. This decrease arises from the fluctuation in Wr and its neglect leads to an underestimate of C by 7 to 10%, even for short DNA with nbp approximately equal to 200. From an analysis of the experimental data of the two groups, the estimates of C = 3.1 to 3.2 X 10(-19) erg cm and lambda-1 = 1000 to 1200 A are obtained.
J Mol Biol 1985 Jul 20
PMID:Statistical mechanics of DNA topoisomers. The helical worm-like chain. 403 81

One-dimensional nuclear Overhauser effect (NOE) in nuclear magnetic resonance spectroscopy along with stereochemically sound model building was employed to derive the structure of the hybrid poly(rA).poly(dT) in solution. Extremely strong NOE was observed at AH2' when AH8 was presaturated; strong NOEs were observed at TH2'TH2'' when TH6 was presaturated; in addition the observed NOEs at TH2' and TH2'' were nearly equal when TH6 was presaturated. There was no NOE transfer to AH3' from AH8 ruling out the possibility of (C-3'-endo, low anti chi approximately equal to 200 degrees to 220 degrees) conformation for the A residues. The observed NOE data suggest that the nucleotidyl units in both rA and dT strands have equivalent conformations: C-2'-endo/C-1'-exo, anti chi approximately equal to 240 degrees to 260 degrees. Such a nucleotide geometry for rA/dT is consistent with a right-handed B-DNA model for poly(rA).poly(dT) in solution in which the rA and dT strands are conformationally equivalent. Molecular models were generated for poly(rA).poly(dT) in the B-form based upon the geometrical constraints as obtained from the NOE data. Incorporation of (C-2'-endo pucker, chi congruent to 240 degrees to 260 degrees) into the classical B-form resulted in severe close contacts in the rA chain. By introducing base-displacement, tilt and twist along with concomitant changes in the backbone torsion angles, we were able to generate a B-form for the hybrid poly(rA).poly(dT) fully consistent with the observed NOE data. In the derived model the sugar pucker is C-1'-exo, a minor variant of C-2'-endo and the sugar base torsion is 243 degrees, the remaining torsion angles being: epsilon = 198 degrees, xi = 260 degrees, alpha = 286 degrees, beta = 161 degrees and gamma = 72 degrees; this structure is free of any steric compression and indicates that it is not necessary to switch to C-3'-endo pucker for rA residues in order to accommodate the 2'-OH group. The structure that we have proposed for the polynucleotide RNA-DNA hybrid in solution is in complete agreement with that proposed for a hexamer hybrid in solution from NOE data and is inconsistent with the heteronomous model proposed for the fibrous state.
J Mol Biol 1985 Nov 20
PMID:Secondary structure of the hybrid poly(rA).poly(dT) in solution. Studies involving NOE at 500 MHz and stereochemical modelling within the constraints of NOE data. 408 99

Helical-twist, roll and torsion-angle variations calculated by the Calladine (1982)-Dickerson (1983) rules were scanned along several nucleotide sequences for which DNAase I cleavage data are available. It has been shown that for short synthetic oligomers DNAase I cuts preferentially at positions of high helical twist (Dickerson & Drew, 1981; Lomonossoff et al., 1981). Our calculations indicate that DNAase I sensitive and hypersensitive sites in chromatin are correlated with regions of successive, large, helical-twist angle variations from regular B-DNA. In many cases these regions exhibit large variations in base-pair roll and backbone torsion angles as well. It has been suggested that DNAase I cuts in the vicinity of cruciforms. However, it was recently demonstrated by Courey & Wang (1983) and Gellert et al. (1983) that such cruciform formation in a negatively supercoiled DNA is kinetically forbidden under physiological conditions. We thus propose that clustering of large twist-angle (and/or roll and backbone torsion angle) variations may be among the conformational features recognized by the enzyme. Specific cuts can then preferentially occur at base-pair steps with high helical twists.
J Mol Biol 1984 Aug 25
PMID:DNAase I hypersensitive sites may be correlated with genomic regions of large structural variation. 609 Jun 73

The sensitivity of the ColE1 cruciform to four enzyme and chemical probes of secondary structure has been studied as a function of plasmid topology. Purified topoisomers of pColIR515 have been probed with S1 nuclease, Bal31 nuclease, phage T4 endonuclease VII or osmium tetroxide, and site-specific reaction quantified. Closely similar profiles of reactivity as a function of linking difference were obtained for each probe. Electrophoresis of the pure topoisomers on polyacrylamide/agarose gels revealed a discontinuity in migration as a function of linking difference. Above a threshold linking difference, topoisomers exhibit pronounced reduction in mobility. The linking difference at which this band shift is found correlates precisely with that required for site-specific reaction with the four probes. We conclude that both probing and topological methods are valuable in the study of cruciform structure in supercoiled DNA. The band shift has been measured with accuracy to allow the calculation of the twist change that accompanies the transition, corresponding to delta Tw = -3.2 +/- 0.1. Using this value together with the critical linking difference we calculate a free energy of formation for this structure delta G = 18.4 +/- 0.5 kcal mol-1 (1 kcal = 4.184 kJ).
J Mol Biol 1984 Nov 25
PMID:Thermodynamics of the ColE1 cruciform. Comparisons between probing and topological experiments using single topoisomers. 609 58

The twisting potential of DNA has been determined directly by a method that measures the cyclization probability or j-factor of EcoRI restriction fragments as a function of DNA twist. The cyclization probability is proportional to Kc, the equilibrium constant for cyclization of the restriction fragment via its cohesive ends (Shore et al., 1981). Here we vary the twist of the DNA by making small internal additions to or deletions from a 242 bp EcoRI restriction fragment. A series of 12 DNA molecules has been studied, which range in length from 237 to 254 bp. The cyclization probability is measured from the rates of covalent closure by phage T4 DNA ligase of two systems: (1) a linear restriction fragment in equilibrium with its cyclized form and (2) half molecules (cut by a blunt-end endonuclease) in equilibrium with joined half molecules. The striking result is that, in this DNA size range, the j-factor depends strongly on the fractional twist: the difference between the total helical twist and the nearest integer. Thus j depends in an oscillatory manner on DNA length between 237 and 254 bp with a period of about 10 bp. These data give the free energy of DNA twisting as a function of twist. The curve of j versus DNA length can be fitted to a harmonic twisting potential with a torsional constant of C = 2.4 X 10(-19) erg cm. This value is in reasonable agreement with different estimates of C made by Barkley & Zimm (1979: C = 1.8 X 10(-19) to 4.1 X 10(-19) erg cm) and is somewhat larger than the value obtained resulting from the kinetics of DNA twisting measured by fluorescence depolarization of ethidium intercalated into DNA (C = 1.4 X 10(-19) erg cm; Millar et al., 1982; Thomas et al., 1980) or from spin label studies (Hurley et al., 1982). Our experiments provide a direct measurement of the torsional free energy and they show that the DNA twisting potential is symmetric. Our experiments also indicate that the DNA helix is continuous, or nearly so, in a nicked circle; presumably this happens because the DNA stacking interaction maintains the double helix in register across a single-strand nick. As a consequence, the twist of a singly nicked DNA circle is integral for small (approximately equal to 250 bp) planar DNA circles and there is a change in twist upon cyclization.(ABSTRACT TRUNCATED AT 400 WORDS)
J Mol Biol 1983 Nov 15
PMID:Energetics of DNA twisting. I. Relation between twist and cyclization probability. 631 55

Properties of the amino acid sequence of the nematode myosin rod region, deduced from cloned DNA, are analysed. The rod sequence of 1117 residues contains a regular region of 1094 residues, which has features typical of an alpha-helical coiled coil, followed by a short non-helical tailpiece at the carboxyl end. The hydrophobic amino acids show the expected seven-residue pattern a, b, c, d, e, f, g, which is modulated by a longer repeat of 28-residue zones. In addition, there are four one-residue insertions, or skip residues, at the ends of zones, at positions 351, 548, 745 and 970. Myosin is considerably less hydrophobic than tropomyosin or alpha-keratin and the outer surface of the coiled coil is covered by clusters of positive and negatively charged amino acid side-chains. Molecular models suggest that the coiled coil is continuous throughout the rod, with an approximately uniform left-handed twist, except for a few turns of helix near each skip region, where the twist flattens out to accommodate the extra residue. Fourier transforms of the amino acid profiles show strong periodicities based on repeats of seven residues (7/2 and 7/3) and 28 residues (especially 28/3 and 28/9). The positive and negative charges each have strong 28/3-residue periodicities that are out of phase with one another. The negative charges also show a 196/9-residue modulation frequency, which may reflect the presence of a 196-residue structural unit in muscle, approximately 2 X 143 A long. The distribution of charged amino acids suggests that electrostatic forces are dominant in forming the thick filament structure. Models that allow regular patterns of interacting charges are restricted and the simplest types are discussed.
J Mol Biol 1983 Mar 15
PMID:Periodic features in the amino acid sequence of nematode myosin rod. 634 6

Caulobacter crescentus flagellar filaments were examined for their shape and handedness. Contour length, wavelength and height of the helical filaments were 1.34 +/- 0.14 micron, 1.08 +/- 0.05 micron and 0.27 +/- 0.04 micron, respectively. Together with the value of the filament diameter, 14 +/- 1.5 nm, the parameters of the curvature (alpha) and twist (phi) were calculated as 3.9(%) for alpha and 0.026 (rad) for phi, which are similar to those of the curly I filament of Salmonella typhimurium. Dark-field light microscopic analysis revealed that the C. crescentus wild-type filament possesses a right-handed helical form. Given the result that C. crescentus cells normally swim forward, in the opposite direction to a polar flagellum, it is likely that C. crescentus swims by rotation of a right-handed curly shaped flagellum in a clockwise sense, whereas S. typhimurium and Escherichia coli swim by rotation of left-handed normal type flagella in a counterclockwise sense.
J Mol Biol 1984 Feb 15
PMID:Caulobacter crescentus flagellar filament has a right-handed helical form. 636 38

Bacterial flagellar polyhook fibers were reversibly transformed into a set of helical forms depending on pH, ionic strength and temperature. Electron microscopy with formalin fixation and freeze-drying was useful for observing three-dimensional shapes of various polyhook helices and determining their helical handedness. A Cartesian plot of curvature against twist for these polyhook helices gave a sinusoidal curve as in the case of the polymorphic forms of flagellar filament. In the study on the polymorphism of flagellar filaments. Calladine (1976, 1978) and Kamiya et al. (1979) pointed out that such a relation in the polymorphic forms could be derived from the assumption that the subunits on the near-longitudinal (11-start) helical lines should work as elastic fibers (protofilaments) having two distinct states of conformation. In contrast, the observed twist for the polyhook helices is too large to be explained by the same assumption. Instead, we must assume that subunits on the strongly twisted, 16-start helical line should work as the co-operative protofilament.
J Mol Biol 1984 Mar 15
PMID:Polymorphic transition of the flagellar polyhook from Escherichia coli and Salmonella typhimurium. 636 39


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