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Query: UNIPROT:P06889 (Mol)
 630,302 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

There is evidence that the Escherichia coli polymerase recognizes and binds to three sites on the promoter DNA: the -10, -35, and -16 regions. Sequence homology was noted among the -10 sites (Pribnow box) and among the -35s with consensus sequences, TATAAT and TTGACA , respectively. Weak nucleotide sequence homology was detected at -16. Since the polymerase recognizes these sites in a multitude of promoters, one expects similarities in the three-dimensional structures. To date, no data directly bearing on such structures exist. Recently, Calladine ( Calladine , C.R. (1982) J. Mol. Biol. 161, 343-352) and, subsequently, Dickerson ( Dickerson , R.E. (1983) J. Mol. Biol. 166, 419-441) suggested "rules" for doublestranded DNA structures which were tested against data from several known crystals. Using these rules, I compare the deviations from "ideal" B-DNA of the twist angles, base pair roll, sideways shift, and propeller suppression in 56 promoters at the three sites. I also appended to these the twist angle computations on additional 77 promoters from the recently published compilation of promoter sequences. For the latter, additional nucleotides from the spacer regions were added. The results display similarities at the -10 site. Equally strong similarities were obtained for the -35 and the -16 contact regions. The existence of structural differences for some sites is likely to account for the different degrees of efficiency of the polymerase recognition and transcriptional regulation.
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PMID:Promoter helical structure variation at the Escherichia coli polymerase interaction sites. 637 66

Using a least-squares fitting procedure, polypeptide backbones of one parallel and seven antiparallel beta-barrels were approximated with various curved surfaces. Although the hyperboloid gave better approximations to all the beta-barrel backbones than the ellipsoid, elliptical cylinder or catenoid, the best approximations were obtained with a novel surface, a twisted hyperboloid (strophoid). The root-mean-square errors between individual beta-barrels and the fitted strophoid surfaces ranged from 0.75 A to 1.64 A. The parameters which determine the strophoid surface allow groups of beta-barrel shapes to be defined according to their barrel twists (i.e. angles subtended by directions of the long axis of cross-section at the top and the bottom of the barrel), course of elliptical cross-sections (either monotonically increasing along the barrel axis, as in cones, or having a middle "waist", as in hyperboloids), and types of backbone curvatures (either convex or concave). The curvatures at individual points of strophoid surface are local, variable quantities related to the local helicity (coil) of the polypeptide backbone, in contrast to values of beta-sheet twist (i.e. dihedral angles subtended by adjacent beta-strands) known to be virtually identical in all the beta-sheets. The variability found in parameters such as barrel shapes and curvatures suggests that simple models (isotropically stressed surfaces, principle of minimal surface tension) proposed in the past to account for beta-barrel shapes are not sufficient. Rather, the complex nature of best-fit theoretical surfaces points to an important role played by a local variability of the forces involved.
J Mol Biol 1984 Aug 15
PMID:Twisted hyperboloid (Strophoid) as a model of beta-barrels in proteins. 647 Nov 5

Fibers of deoxyhemoglobin S undergo spontaneous crystallization by a mechanism involving a variety of intermediate structures. These intermediate structures, in common with the fiber and crystal, consist of Wishner-Love double strands of hemoglobin S molecules arranged in different configurations. The structure of one of the key intermediates linking the fiber and crystal, called a macrofiber, has been studied by a variety of analytical procedures. The results of the analysis indicate that the intermediates involved in the fiber to crystal transition have many common structural features. Fourier analysis of electron micrographs of macrofibers confirms that they are composed of Wishner-Love double strands of hemoglobin molecules. Electron micrographs of macrofiber cross-sections reveal that the arrangement of the double strands in macrofibers resembles that seen in micrographs of the a axis projection of the crystal. This orientation provides an end-on view of the double strands which appear as paired dumb-bell-like masses. The structural detail becomes progressively less distinct towards the edge of the particle due to twisting of the double strands about the particle axis. Serial sections of macrofibers confirm that these particles do indeed rotate about their axes. The twist of the particle is right handed and its average pitch is 10,000 A. The effect of rotation on the appearance of macrofiber cross-sections 300 to 400 A thick can be simulated by a 15 degrees rotation of an a axis crystal projection. The relative polarity of the double strands in macrofibers and crystals can be determined easily by direct inspection of the micrographs. In both macrofibers and crystals they are in an anti-parallel array. On the basis of these observations we conclude that crystallization of macrofibers involves untwisting and alignment of the double strands.
J Mol Biol 1984 Aug 25
PMID:Macrofiber structure and the dynamics of sickle cell hemoglobin crystallization. 648 5

The bundle of actin filaments in the sperm of the horseshoe crab has a polygonal form. This appearance results from regularly spaced, sharp bends (elbows) separated by straight segments (arms). We conclude that the elbows are built into the bundle by a rearrangement of interfilament crossbridges in the arms. The rearrangement, which makes used of the specific bonding properties of the crossbridges, is made possible by the helical symmetry of actin and by the hexagonal packing of the filaments. The angle of the bend (154 degrees) is fixed by the interfilament separation and the axial spacing of actin subunits within a filament. In the arms on either side of an elbow, rows of filaments slip relative to each other. The slippage, and hence the elbow, is locked in by an axial shift of the crossbridges between adjacent rows of filaments. The variable twist of actin filaments may be important in accommodating the strain of crossbridge rearrangement.
J Mol Biol 1984 May 05
PMID:How to build a bend into an actin bundle. 653 79

The structure of proteolytically modified fibrin and a closely related modified fibrinogen aggregate have been studied by analysis of electron microscope images. For both structures, we propose a model that consists of double-stranded, 2-fold helical protofibrils, which are associated laterally to form ordered fibrils, with a C222 space group: a = 44.0 nm, b = c = 9.4 nm. Each fibril is 80 nm or less in diameter, and twists along its length in a right-handed sense, with a pitch from 7 to 12 times the molecular length. The fibrils associate laterally to form bundles, which tend to twist in a left-handed sense, with a pitch of the order of 40 times the molecular length. The specific volume of modified fibrin calculated from this model is 3.9 A3 per dalton, which is comparable to the specific volume of 3.6 A3 per dalton for modified fibrinogen crystals but is lower than the 6 A3 per dalton determined for fibrin from light-scattering experiments. Comparison of our electron microscope results with X-ray and neutron diffraction data suggest a similar, but less well-ordered, structure for native fibrin, with a smaller fibril, approximately 18.4 nm wide, consisting of eight protofibrils.
J Mol Biol 1983 Oct 15
PMID:Electron microscope structural study of modified fibrin and a related modified fibrinogen aggregate. 663 61

The structure of complexes between double-stranded DNA and oligopeptide dansyl hydrazide trivaline was studied by linear dichroism, electron microscopy and hydrodynamical methods. The results show that the binding of the oligopeptide to DNA is a cooperative process that leads to the formation of particles significantly differing in the structure from free DNA. The linear dichroism studies were carried out in a wide range of flow-speed gradients. From the theoretical analysis of these data a conclusion can be drawn that the DNA-oligopeptide complexes possesses a higher rigidity as compared with that of free DNA. The hydrodynamical behaviour of these particles is consistent with the rigid rod-like structure of the particles with a long axis nearly parallel to the DNA helix axis in the complexes. The sedimentation patterns of the complexes suggest the existence of the fast and slow sedimenting species. The sedimentation coefficient measured for a fast sedimenting species is about 3 times higher than that of free DNA. The linear dichroism spectra obtained for the floworiented DNA-oligopeptide complexes correlate with the existence of a superhelical organization of DNA in the complex. This offers a possibility for the determining of the angle of the DNA local axis inclination with respect to the superhelix axis. On electron micrographs the DNA-oligopeptide complexes look like rod-shaped structures with the thickness of about 180 A and 80 A on the rotatory-shadowed preparations and on the uranylacetate stained preparations, respectively. The rod-shaped structures are formed by two interwound DNA molecules. The superhelix has a pitch of about 150 A with an angle of twist inclination of about 40 degrees. These values are in good agreement with the optical anisotropic data. It is suggested that the complex structure is stabilized by periodically spaced hydrophobic contacts between the dimeric oligopeptide species bound to the DNA molecules.
Mol Biol (Mosk)
PMID:[Spatial structure of DNA complex with the oligopeptide dansyl hydrazide trivaline]. 663 29

A gel electrophoresis method has been developed for resolving small (approximately equal to 250 bp DNA topoisomers. In this size range only one major topoisomer band is observed, except for ligase closure conditions in which the probabilities are nearly equal for circularization by untwisting and overtwisting the corresponding linear DNA. The two probabilities are nearly equal when delta Tw is close to 0.5, if the mean helical twist of the linear DNA is n + delta Tw, where n is an integer and delta Tw is the fractional twist. We determine delta Tw of the linear DNA in standard conditions (20 degrees C, no ethidium) by titration experiments in which delta Tw is varied at the time of ligase closure, either by changing temperature or ethidium concentration. The endpoint (delta Tw = 0.5) is found when the two topoisomers formed by untwisting and overtwisting are present at equal concentrations. This analysis assumes that the net writhe is zero and the DNA helix is isotropically bendable. The results confirm the analysis of cyclization probabilities given in the preceding paper: delta Tw = 0 at the two maxima in the curve of j-factor versus DNA length and delta Tw = 0.5 at the minimum. Consequently, we can determine the DNA lengths at which Tw takes on integral values and use them to measure precisely the average helix repeat. From the difference between the delta Tw values of DNAs with 237 and 247 bp, we obtain an approximate value for the helix repeat of h = 10.4 +/- 0.1 bp/turn, in good agreement with earlier values found by the band-shift and nuclease-cutting methods. The twist is integral at 250.8 +/- 0.4 bp and from h = 10.4 +/- 0.1 we find n = 24; then 250.8/24 gives h = 10.45 +/- 0.02 bp/turn. The mean linking number (Lk) changes in a stepwise manner as delta Tw is varied for 250 bp DNAs. This result is expected when the free energy of twisting half a turn becomes large compared to thermal fluctuations. In these experiments, it is possible to obtain the mean Tw value from the mean Lk value only when delta Tw = 0.5, and consequently the mean Lk value is not simply related to DNA length for 250 bp DNAs except when delta Tw = 0.5.(ABSTRACT TRUNCATED AT 400 WORDS)
J Mol Biol 1983 Nov 15
PMID:Energetics of DNA twisting. II. Topoisomer analysis. 664 17

The DNA oligomer of sequence IC-C-G-G has been synthesized, and its X-ray crystal structure solved at a resolution of 2.0 A, using anomalous scattering from iodines in phase analysis: 48 cycles of Jack-Levitt restrained least-squares refinement resulted in a residual error of 19.9% over all data, or 16.5% for two-sigma data. Two double-helical tetramers stack in the crystal to form a continuous octamer, except for the two missing phosphate connections across the center. The octamer has a mean helix rotation of 33.7 degrees (10.7 base-pairs per turn), rise of 2.87 A, mean inclination angle of base-pairs of 14 degrees, and mean base-pair propeller twist of +16.3 degrees. Local variations in both helix rotation and base plane roll angles, including those across the center of the octamer, are as predicted from base sequence by sum functions sigma 1 and sigma 2. The three known DNA octamers: IC-C-G-G/IC-C-G-G, G-G-T-A-T-A-C-C and G-G-C-C-G-G-C-C, make up a graded series in this order, with monotonically changing structural parameters. An exhaustive comparison of torsion angle correlations among the known A helices confirms some structural expectations and reveals some new features. 86 water molecules have been located per double-helical IC-C-G-G tetramer (the asymmetric unit), of which 451/2 per tetramer lie within a first hydrogen-bonded shell of hydration. No ordered water structure is observed comparable to the minor groove spine of hydration in B-DNA.
J Mol Biol 1984 Apr 25
PMID:Helix geometry and hydration in an A-DNA tetramer: IC-C-G-G. 672 97

Catabolite activator protein (CAP) is a dimeric molecule (M(r) = 2 x 22,500) involved in transcription initiation of several catabolite-sensitive genes of Escherichia coli. The present communication proposes a model for the interaction of CAP with DNA. The model is based upon known geometrical features of the CAP molecule [McKay, D. B. & Steitz, T. A. (1981) Nature (London) 290, 744-749], which allow interaction between dyad-related alpha-helices of the dimeric protein and major grooves in adjacently aligned sections of right-handed B-DNA. These geometrical features suggest that in vivo CAP binding to closed-circular DNA involves CAP bridging adjacent loops of a DNA solenoidal coil. This interaction pattern is shown to be consistent with the geometrical and stoichiometric properties of nonspecifically bound CAP complexes observed by Chang et al. [Chang, J. J., Dubochet, J., Baudras, A., Blazy, B. & Takahashi, M. (1981) J. Mol. Biol. 150, 435-439]. CAP-induced coil formation is related to in vivo CAP potentiation of RNA polymerase activity in underwound closedcircular DNA. Specifically, it is proposed that CAP binding to the right-interwound form of supercoiled DNA effects a local redistribution of DNA twist-strain energy, thus resulting in the formation of a left-handed solenoidal loop. The production of this localized solenoidal loop, which reflects compensatory alterations in DNA twist and writhe, may provide a conformationally unique site for RNA polymerase binding where the DNA is partially unwound. The proposed interaction pattern is consistent with both recent DNA unwinding experiments and various nuclease protection data. Moreover, features of the model suggest that the repetitive and symmetric character of many promoter sequences may provide the structural basis for a switching mechanism operative in the differential control of gene transcription.
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PMID:A model for catabolite activator protein binding to supercoiled DNA. 675 42

The observed propeller twist in base-pairs of crystalline double-helical DNA oligomers improves the stacking overlap along each individual helix strand. But, as proposed by Calladine, it also leads to clash or steric hindrance between purines at adjacent base-pairs on opposite strands of the helix. This clash can be relieved by: (1) decreasing the local helix twist angle between base-pairs; (2) opening up the roll angle between base-pairs on the side on which the clash occurs; (3) separating purines by sliding base-pairs along their long axes so that the purines are partially pulled out of the stack (leading to equal but opposite alterations in main-chain torsion angle delta at the two ends of the base-pair); and (4) flattening the propeller twist of the offending base-pairs. Simple sum functions, sigma 1 through sigma 4, are defined, by which the expected local variation in helix twist, base roll angle, torsion angle delta and propeller twist may be calculated from base sequence. All four functions are quite successful in predicting the behavior of B DNA. Only the helix twist and base roll functions are applicable to A DNA, and the helix twist function begins to fail for an A helical RNA/DNA hybrid. Within these limits, the sequence-derived sum functions match the observed helix parameter variation quite closely, with correlation coefficients greater than 0.900 in nearly all cases. Implications of this sequence-derived helix parameter variation for repressor-operator interactions are considered.
J Mol Biol 1983 May 25
PMID:Base sequence and helix structure variation in B and A DNA. 685 50


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