Structure Of HI Research Articles

Vanishing of local cohomology with applications to Hodge theory

Let H=((H,F•),L) be a polarized variation of Hodge structure on a smooth quasi-projective variety U. By M. Saito's theory of mixed Hodge modules, the variation of Hodge structure H can be viewed as a polarized Hodge module M∈HM(U). Let X be a compactification of U, and j:U↪X is the natural map. In this paper, we use local cohomology with mixed Hodge module theory to study j+M∈DbMHM(X). In particular, we study the graded pieces of the de Rham complex GrpFDR(j+M)∈Dcohb(X), and the Hodge structure of Hi(U,L) for i in sufficiently low degrees.

Pivotal role of a conserved histidine in Escherichia coli ribonuclease HI as proposed by X-ray crystallography.

The ribonuclease (RNase) H family of enzymes catalyze the specific cleavage of RNA strands of RNA/DNA hybrid duplexes and play an important role in DNA replication and repair. Since the first report of the crystal structure of RNase HI, its catalytic mechanisms, which require metal ions, have been discussed based on numerous structural and functional analyses, including X-ray crystallography. In contrast, the function of the conserved histidine residue (His124 in Escherichia coli) in the flexible loop around the active site remains poorly understood, although an important role was suggested by NMR analyses. Here, novel high-resolution X-ray crystal structures of E. coli RNase HI are described, with a particular focus on the interactions of divalent cations with His124 oriented towards the active site. The enzyme-Mg2+ complex contains two metal ions in the active site, one of which has previously been observed. The second ion lies alongside the first and binds to His124 in an octahedral coordination scheme. In the enzyme-Zn2+ complex a single metal ionwas found to bind to the active site, showing a tetrahedral coordination geometry with the surrounding atoms, including His124. These results provide structural evidence that His124 plays a crucial role in the catalytic activity of RNase HI by interacting weakly and transiently with metal ions in the catalytic center.

Influence of C-terminal tail deletion on structure and stability of hyperthermophile Sulfolobus tokodaii RNase HI

The C-terminus tail (G144-T149) of the hyperthermophile Sulfolobus tokodaii (Sto-RNase HI) plays an important role in this protein's hyperstabilization and may therefore be a good protein stability tag. Detailed understanding of the structural and dynamic effects of C-terminus tail deletion is required for gaining insights into the thermal stability mechanism of Sto-RNase HI. Focused on Sulfolobus tokodaii RNase HI (Sto-RNase HI) and its derivative lacking the C-terminal tail (ΔC6 Sto-RNase HI) (PDB codes: 2EHG and 3ALY), we applied molecular dynamics (MD) simulations at four different temperatures (300, 375, 475, and 500 K) to examine the effect of the C-terminal tail on the hyperstabilization of Sto-RNase HI and to investigate the unfolding process of Sto-RNase HI and ΔC6 Sto-RNase HI. The simulations suggest that the C-terminal tail has significant impact in hyperstabilization of Sto-RNase HI and the unfolding of these two proteins evolves along dissimilar pathways. Essential dynamics analysis indicates that the essential subspaces of the two proteins at different temperatures are non-overlapping within the trajectories and they exhibit different directions of motion. Our work can give important information to understand the three-state folding mechanism of Sto-RNase HI and to offer alternative strategies to improve the protein stability.

Microwave-Based Structure and Four-Dimensional Morphed Intermolecular Potential for HI−CO2

(Microwave spectra of the four isotopologue/isotopomers, HI-(12)C(16)O(2), HI-(12)C(18)O(2), HI-(12)C(18)O(16)O, and HI-(12)C(16)O(18)O, have been recorded using pulsed-nozzle Fourier transform microwave spectroscopy. In the last two isotopomers, the heavy oxygen atom tilted toward and away from the HI moiety, respectively. Only b-type Ka = 1 <-- 0 transitions were observed. Spectral analysis provided molecular parameters including rotational, centrifugal distortion, and quadrupole constants for each isotopomer. Then, a four-dimensional intermolecular energy surface of a HI-CO2 complex was generated, morphing the results of ab initio calculations to reproduce the experimental data. The morphed potential of HI-(12)C(16)O(2) had two equivalent global minima with a well depth of 457(14) cm(-1) characterized by a planar quasi-T-shaped structure with the hydrogen atom tilted toward the CO2 moiety, separated by a barrier of 181(17) cm(-1). Also, a secondary minimum is present with a well depth of 405(14) cm(-1) with a planar quasi-T-shaped structure with the hydrogen atom tilted away from the CO2 moiety. The ground state structure of HI-(12)C(16)O(2) was determined to have a planar quasi-T-shaped geometry with R = 3.7717(1) A, thetaOCI = 82.30(1) degrees , thetaCIH = 71.55(1) degrees . The morphed potential obtained is now available for future studies of the dynamics of photoinitiated reactions of this complex.

Crystal Structure of Type 1 Ribonuclease H from Hyperthermophilic ArchaeonSulfolobus tokodaii: Role of Arginine 118 and C-Terminal Anchoring,

The crystal structure of ribonuclease HI from the hyperthermophilic archaeon Sulfolobus tokodaii (Sto-RNase HI) was determined at 1.6 A resolution. Sto-RNase HI exhibits not only RNase H activity but also double-stranded RNA-dependent ribonuclease (dsRNase) activity. The main-chain fold and steric configurations of the four acidic active-site residues of Sto-RNase HI are very similar to those of other type 1 RNases H. However, Arg118 of Sto-RNase HI is located at the position in which His124 of E. coli RNase HI, His539 of HIV-1 RNase H, and Glu188 of Bacillus halodurans RNase H are located. The mutation of this residue to Ala considerably reduced both the RNase H and dsRNase activities without seriously affecting substrate binding, suggesting that Arg118 is involved in catalytic function. This residue may promote product release by perturbing the coordination of the metal ion A as proposed for Glu188 of B. halodurans RNase H. In addition, the extreme C-terminal region of Sto-RNase HI is anchored to its core region by one disulfide bond and several hydrogen bonds. Differential scanning calorimetry measurements indicated that Sto-RNase HI is a hyperstable protein with a melting temperature of 102 degrees C. The mutations of the cysteine residues forming disulfide bond or elimination of the extreme C-terminal region greatly destabilized the protein, indicating that anchoring of the C-terminal tail is responsible for hyperstabilization of Sto-RNase HI.

Structural, Thermodynamic, and Mutational Analyses of a Psychrotrophic RNase HI,

Ribonuclease (RNase) HI from the psychrotrophic bacterium Shewanella oneidensis MR-1 was overproduced in Escherichia coli, purified, and structurally and biochemically characterized. The amino acid sequence of MR-1 RNase HI is 67% identical to that of E. coli RNase HI. The crystal structure of MR-1 RNase HI determined at 2.0 A resolution was highly similar to that of E. coli RNase HI, except that the number of intramolecular ion pairs and the fraction of polar surface area of MR-1 RNase HI were reduced compared to those of E. coli RNase HI. The enzymatic properties of MR-1 RNase HI were similar to those of E. coli RNase HI. However, MR-1 RNase HI was much less stable than E. coli RNase HI. The stability of MR-1 RNase HI against heat inactivation was lower than that of E. coli RNase HI by 19 degrees C. The conformational stability of MR-1 RNase HI was thermodynamically analyzed by monitoring the CD values at 220 nm. MR-1 RNase HI was less stable than E. coli RNase HI by 22.4 degrees C in Tm and 12.5 kJ/mol in DeltaG(H2O). The thermodynamic stability curve of MR-1 RNase HI was characterized by a downward shift and increased curvature, which results in an increased DeltaCp value, compared to that of E. coli RNase HI. Site-directed mutagenesis studies suggest that the difference in the number of intramolecular ion pairs partly accounts for the difference in stability between MR-1 and E. coli RNases HI.

Organic solvents effect on the secondary structure of araujiain hI, in different media

The aim of this work was to carry out a comparative study of the secondary structure of araujiain hI (cystein plant protease) in aqueous–organic media ( N, N-dimethylformamide (50%) and hexane (50%)) and in Tris–HCl buffer (0.1 M, pH 8), using FT-IR spectroscopy. The changes in the enzyme structure were correlated with the changes in the preferences and enzyme activities in such media. The enzyme activity observed in the organic media was higher than those obtained in buffer. Although, the substrate preferences of araujiain hI exhibit different patterns in each medium, the enzyme always showed a high preference for glutamine derivative. According to the study of the secondary structure, it was possible to conclude that a secondary structure with a high α-helical character was responsible for the highest activity of araujiain hI in the studied organic media. Although, the correlation between enzyme structure and catalytic activity requires direct measurement of active-site structure and of the effect of the reaction medium on the transition state of the reaction, it is clear that the non-covalent forces which maintain the native secondary structure of enzyme were modified when araujiain hI was suspended in such aqueous–organic media.

Timescales of merger, starburst and AGN activity in radio galaxy B2 0648+27

In this paper we use neutral hydrogen HI and optical spectroscopic observations to compare the timescales of a merger event, starburst episode and radio-AGN activity in the radio galaxy B2 0648+27. We detect a large ring-like structure of HI in emission around the early-type host galaxy of B2 0648+27 (M_HI = 8.5 x 10^9 Msun, diameter = 190 kpc). We interpret this as the result of a major merger that occurred > 1.5 Gyr ago. From modelling optical long-slit spectra we find that a young stellar population of 0.3 Gyr, indicative of a past starburst event, dominates the stellar light throughout the galaxy. The off-set in time between the merger event and the starburst activity in B2 0648+27 suggests that the starburst was triggered in an advanced stage of the merger, which can be explained if the gas-rich progenitor galaxies contained a bulge. Although the exact age of the radio source remains uncertain, there appears to be a significant time-delay between the merger/starburst event and the current episode of radio-AGN activity. We also observe an outflow of emission-line gas in this system, which is likely related to superwinds driven by the stars that formed during the starburst event. We argue that the radio galaxy B2 0648+27 is a link in the evolutionary sequence between Ultra-Luminous Infrared Galaxies (ULIRGs) and genuine early-type galaxies.

Single-molecule Forster resonance energy transfer study of protein dynamics under denaturing conditions.

Proteins are highly complex systems, exhibiting a substantial degree of structural variability in their folded state. In the presence of denaturants, the heterogeneity is greatly enhanced, and fluctuations among vast numbers of folded and unfolded conformations occur via many different pathways. Here, we have studied the structure and dynamics of the small enzyme ribonuclease HI (RNase H) in the presence of the chemical denaturant guanidinium chloride (GdmCl) using single-molecule fluorescence microscopy, with a particular focus on the characterization of the unfolded-state ensemble. A dye pair was specifically attached to the enzyme to measure structural changes through Förster resonance energy transfer (FRET). Enzyme immobilization on star-polymer surfaces that were specially developed for negligible interaction with folded and unfolded proteins enabled us to monitor conformational changes of individual proteins for several hundred seconds. FRET efficiency histograms were calculated from confocal scan images. They showed an expansion of the unfolded proteins with increasing GdmCl concentration. Cross-correlation analysis of donor and acceptor fluorescence intensity time traces from single molecules revealed reconfiguration of the polypeptide chain on a timescale of approximately equal to 20 micros at 1.7 M GdmCl. Slow conformational dynamics gave rise to characteristic, stepwise FRET efficiency changes. Transitions between folded and unfolded enzyme molecules occurred on the 100-s timescale, in excellent agreement with bulk denaturation experiments. Transitions between unfolded conformations were more frequent, with characteristic times of approximately equal to 2 s. These data were analyzed to obtain information on the free energy landscape of RNase H in the presence of chemical denaturants.

Theoretical and experimental evaluation of the radial function for electric dipole moment of hydrogen iodide

From relativistic quantum-chemical calculations of the molecular electronic structure of hydrogen iodide HI in electronic state X 1Σ+ or 0+ using the Dirac–Coulomb coupled-cluster method with singles, doubles and non-iterative triples (DC-CCSD(T)), we have evaluated the electric dipole moment p at 17 values of internuclear distance R. On this basis we have calculated the pure vibrational expectation value in the vibrational ground state and matrix elements of p(R) for transitions from that ground state to the first seven vibrationally excited states within the electronic ground state. For comparison with these theoretical results, we have undertaken a re-analysis of all experimental data of intensities of vibration-rotational transitions in infrared spectra, combined with a value of the expectation value of p(R) in the ground state from the Stark effect, to generate a radial function for electric dipole moment. The agreement between calculated and experimental values of vibrational matrix elements of the electric dipole moment is satisfactory, resolving outstanding questions about experimental and computational accuracy in the literature. We predict matrix elements for intensities of vibration-rotational bands 6–0 and 7–0, not yet measured.

Crystal structure of archaeal RNase HII: a homologue of human major RNase H

Background: RNases H are present in all organisms and cleave RNAs in RNA/DNA hybrids. There are two major types of RNases H that have little similarity in sequence, size and specificity. The structure of RNase HI, the smaller enzyme and most abundant in bacteria, has been extensively studied. However, no structural information is available for the larger RNase H, which is most abundant in eukaryotes and archaea. Mammalian RNase H participates in DNA replication, removal of the Okazaki fragments and possibly DNA repair. Results: The crystal structure of RNase HII from the hypothermophile Methanococcus jannaschii, which is homologous to mammalian RNase H, was solved using a multiwavelength anomalous dispersion (MAD) phasing method at 2 Å resolution. The structure contains two compact domains. Despite the absence of sequence similarity, the large N-terminal domain shares a similar fold with the RNase HI of bacteria. The active site of RNase HII contains three aspartates: Asp7, Asp112 and Asp149. The nucleotide-binding site is located in the cleft between the N-terminal and C-terminal domains. Conclusions: Despite a lack of any detectable similarity in primary structure, RNase HII shares a similar structural domain with RNase HI, suggesting that the two classes of RNases H have a common catalytic mechanism and possibly a common evolutionary origin. The involvement of the unique C-terminal domain in substrate recognition explains the different reaction specificity observed between the two classes of RNase H.

NMR structure of ribonuclease HI from Escherichia coli.

The solution structure of ribonuclease HI (RNase HI) from Escherichia coli (E. coli), a protein of 155 residues, was determined. Three-dimensional nuclear Overhauser enhancement spectroscopy (NOESY) was used to obtain 1,424 distance constraints between individually assigned polypeptide chain hydrogen atoms. Supplemental geometric constraints of 90phi angles and 12chi1 angles, and the distance constraints of 66 hydrogen bonds were experimentally derived. Using the DADAS90 program that calculates structures in dihedral angle space, 15 structures satisfying almost all constraints were obtained. The average root mean square deviation (RMSD) from the mean structure was 0.75 A for backbone atoms. The RMSD for backbone atoms between the representative NMR structure with the smallest constraint violation and crystal structures was within 1.2 A. Although the NMR and crystal structures thus resemble one another, a significant discrepancy was observed in a region termed 'basic protrusion.' The discrepancy observed in NMR experiments is explained by fluctuation in this region.

HI Observations of NGC 1068

Neutral hydrogen is an important tracer of galactic dynamics. Hence, observations of the detailed structure and kinematics of HI are vital in order to determine the relationship between AGN and their host galaxy.

Structure of Bam HI Endonuclease Bound to DNA: Partial Folding and Unfolding on DNA Binding

The crystal structure of restriction endonuclease Bam HI complexed to DNA has been determined at 2.2 angstrom resolution. The DNA binds in the cleft and retains a B-DNA type of conformation. The enzyme, however, undergoes a series of conformational changes, including rotation of subunits and folding of disordered regions. The most striking conformational change is the unraveling of carboxyl-terminal alpha helices to form partially disordered "arms." The arm from one subunit fits into the minor groove while the arm from the symmetry related subunit follows the DNA sugar-phosphate backbone. Recognition of DNA base pairs occurs primarily in the major groove, with a few interactions occurring in the minor groove. Tightly bound water molecules play an equally important role as side chain and main chain atoms in the recognition of base pairs. The complex also provides new insights into the mechanism by which the enzyme catalyzes the hydrolysis of DNA phosphodiester groups.

Two-photon spectroscopy of HI in the 69 600–73 600 cm−1 region

Several new electronic states in HI have been identified from resonance-enhanced multiphoton ionization (REMPI) spectra in the 69 600–73 600 cm−1 region. These results have been combined with previously unpublished single-photon absorption data and, in selected wavelength regions, with REMPI spectra of DI to provide a more complete description of the excited electronic structure of HI up to ∼9.2 eV above the ground state.

Structure refinement of large-pore aluminophosphate molecular sieve, H1, by Rietveld methods

The structure of HI, a large-pore molecular sieve, is analyzed using X-ray powder diffraction data collected on two samples from separate preparations. Data for one of the samples, H1-A, prepared using a combination of tributylamine and dipentylamine was collected using a synchrotron source, whereas for the other sample prepared using dipropylamine (H1-B), radiation from a rotating anode was used. The space group for these crystals is P6 3 cm with a = 18.9702(3) and c = 8.1163(2) Å for H1-A and a = 18.9923(4) and c = 8.1206(3) Å for H1-B. Final agreement indices were Rp = 0.086 and Rwp = 0.122 for Hl-A and Rp = 0.087 and Rp = 0.112 for Hl-B. The framework structure of Hl in these two samples is similar to that of VPI-5 except that the 6-membered rings in HI contain disordered phosphate groups. The structure is described on the basis of two partially occupied models: The first one is a regular VPI-5 framework with an occupancy of about 0.75, and the other is a different orientation of the groups in the 6-membered ring with occupancy of about 0.25. The Al atom of the 4-ring is 6-coordinated by four framework oxygens and two water molecules. The large channel is occupied by a network of hydrogen-bonded water molecules. These studies together with our earlier results on dehydrated samples show that HI has two partially occupied structures, but that their populations vary from one preparation to the other. The disorder model for HI clearly distinguishes it from VPI-5, which does not display this disorder.

Large scale Structure of HI in other Galaxies

In this paper we discuss the large-scale structures (&gt; 500 pc) of the neutral atomic hydrogen in the disk of nearby galaxies, with an emphasis on finding evidence for neutral gas features in the disk - halo interface. Most nearby galaxies studied in detail appear to have hole and shell type structures in their HI disks and several show evidence for gas at peculiar velocities, probably examples of gas streaming out of the disk into the halo. Not all of the observed phenomena can be explained by stellar winds and supernova explosions and other explanations will briefly be discussed.

Microwave spectra and structure of HI–HF complexes

Microwave spectra for the HI–HF, HI–DF, DI–HF, and DI–DF complexes were measured using a pulsed-beam, Fourier-transform microwave spectrometer. Rotational transitional transitions were measured over the 4–18 GHz range to an accuracy of 5 kHz. The spectroscopic constants obtained by fitting the observed transitions for the series HI–HF, HI–DF, DI–HF, and DI–DF are, respectively: (B+C)/2=2220.7482(8), 2173.236(2), 2209.623(4), and 2162.884(6) MHz; eQq(I)=687.01(2), 693.63(5), 725.96(4), and 727.8(1) MHz; ΔeQq(I)=−42(2), −50(6), −210(14), and −141(25) kHz; DJ =8.86(3), 8.25(6), 8.1(6), and 8.6(5) kHz. This complex has an interesting triangular structure with the H–I and H–F bonds making an acute angle of 70.1 (2.8)°. The iodine atom is coaxial with HF with a heavy atom separation R0(I–F)=3.660(8) Å. Hyperfine structure due to deuterium quadrupole coupling and H–F spin–spin interactions was resolved and measured.

The structure of galactic HI in directions of low total column density

A detailed 21 cm study of areas of that have the smallest known amount of HI in the northern sky was performed. These observations were corrected for stray radiation. The region of main interest, around alpha = 10(h)45(m), delta = 57 deg 20', has a minimium N(HI) of 4.5 x 10 to the 19th power/sq cm. Spectra taken at 21' resolution over a field 4 x 3 deg in this direction show up to four HI line components. Two, near 0 and -50 km/s, are ubiquitous. There is also a narrow component at -10 km/s attributable to a diffuse cloud covering half of the field, and scattered patches of HI at v -100 km/s. the low and intermediate velocity components have a broad line width and are so smoothly distributed across the region that it is unlikely that they contain significant unresolved angular structure. Eight other low column density directions were also observed. Their spectra typically have several components, but the total column density is always 7 x 10 to the 19th power/sq cm and changes smoothly along a 2 deg strip. Half of the directions show narrow lines arising from weak diffuse HI clouds that contain 0.5 to 3.0 x 10 to the 19th power/sq cm.

Spiral structure and kinematics of HI and HII in external galaxies

Compression of the interstellar gas by a passing density-wave is thought to be responsible for triggering the presently observable star formation processes in the arms of spiral galaxies. We present new observations of the distribution and kinematics of the Hβ emission in the spiral arms of M83, obtained with the TAURUS imaging Fabry-Pérot system. These results, when combined with observations of the neutral and molecular components with sufficiently high resolution, should contribute to our understanding of the time sequence by which stars form out of the interstellar gas.