Calculated Structure Factors Research Articles

Interplay between SRPK and Clk/Sty Kinases in Phosphorylation of the Splicing Factor ASF/SF2 Is Regulated by a Docking Motif in ASF/SF2

The arginine-serine (RS)-rich domain of the SR protein ASF/SF2 is phosphorylated by SR protein kinases (SRPKs) and Clk/Sty kinases. However, the mode of phosphorylation by these kinases and their coordination in the biological regulation of ASF/SF2 is unknown. Here, we report the crystal structure of an active fragment of human SRPK1 bound to a peptide derived from an SR protein. This structure led us to identify a docking motif in ASF/SF2. We find that this docking motif restricts phosphorylation of ASF/SF2 by SRPK1 to the N-terminal part of the RS domain - a property essential for its assembly into nuclear speckles. We further show that Clk/Sty causes release of ASF/SF2 from speckles by phosphorylating the C-terminal part of its RS domain. These results suggest that the docking motif of ASF/SF2 is a key regulatory element for sequential phosphorylation by SRPK1 and Clk/Sty and, thus, is essential for its subcellular localization.

Identification of an ITPase/XTPase in Escherichia coli by Structural and Biochemical Analysis

Inosine triphosphate (ITP) and xanthosine triphosphate (XTP) are formed upon deamination of ATP and GTP as a result of exposure to chemical mutagens and oxidative damage. Nucleic acid synthesis requires safeguard mechanisms to minimize undesired lethal incorporation of ITP and XTP. Here, we present the crystal structure of YjjX, a protein of hitherto unknown function. The three-dimensional fold of YjjX is similar to those of Mj0226 from Methanococcus janschii, which possesses nucleotidase activity, and of Maf from Bacillus subtilis, which can bind nucleotides. Biochemical analyses of YjjX revealed it to exhibit specific phosphatase activity for inosine and xanthosine triphosphates and have a possible interaction with elongation factor Tu. The enzymatic activity of YjjX as an inosine/xanthosine triphosphatase provides evidence for a plausible protection mechanism by clearing the noncanonical nucleotides from the cell during oxidative stress in E. coli.

Activation of the Hetero-octameric ATP Phosphoribosyl Transferase through Subunit Interface Rearrangement by a tRNA Synthetase Paralog

ATP phosphoribosyl transferase (ATP-PRT) joins ATP and 5-phosphoribosyl-1-pyrophosphate (PRPP) in a highly regulated reaction that initiates histidine biosynthesis. The unusual hetero-octameric version of ATP-PRT includes four HisG(S) catalytic subunits based on the periplasmic binding protein fold and four HisZ regulatory subunits that resemble histidyl-tRNA synthetases. Here, we present the first structure of a PRPP-bound ATP-PRT at 2.9 A and provide a structural model for allosteric activation based on comparisons with other inhibited and activated ATP-PRTs from both the hetero-octameric and hexameric families. The activated state of the octameric enzyme is characterized by an interstitial phosphate ion in the HisZ-HisG interface and new contacts between the HisZ motif 2 loop and the HisG(S) dimer interface. These contacts restructure the interface to recruit conserved residues to the active site, where they activate pyrophosphate to promote catalysis. Additionally, mutational analysis identifies the histidine binding sites within a region highly conserved between HisZ and the functional HisRS. Through the oligomerization and functional re-assignment of protein domains associated with aminoacylation and phosphate binding, the HisZ-HisG octameric ATP-PRT acquired the ability to initiate the synthesis of a key metabolic intermediate in an allosterically regulated fashion.

Dimensional crossover in Bragg scattering from an optical lattice

We study Bragg scattering at one-dimensional (1D) optical lattices. Cold atoms are confined by the optical dipole force at the antinodes of a standing wave generated inside a laser-driven high-finesse cavity. The atoms arrange themselves into a chain of pancake-shaped layers located at the antinodes of the standing wave. Laser light incident on this chain is partially Bragg reflected. We observe an angular dependence of this Bragg reflection which is different from what is known from crystalline solids. In solids, the scattering layers can be taken to be infinitely spread (three-dimensional limit). This is not generally true for an optical lattice consistent of a 1D linear chain of pointlike scattering sites. By an explicit structure factor calculation, we derive a generalized Bragg condition, which is valid in the intermediate regime. This enables us to determine the aspect ratio of the atomic lattice from the angular dependance of the Bragg scattered light.

Structural Basis for Autoinhibition and Mutational Activation of Eukaryotic Initiation Factor 2α Protein Kinase GCN2*[boxs

The GCN2 protein kinase coordinates protein synthesis with levels of amino acid stores by phosphorylating eukaryotic translation initiation factor 2. The autoinhibited form of GCN2 is activated in cells starved of amino acids by binding of uncharged tRNA to a histidyl-tRNA synthetase-like domain. Replacement of Arg-794 with Gly in the PK domain (R794G) activates GCN2 independently of tRNA binding. Crystal structures of the GCN2 protein kinase domain have been determined for wild-type and R794G mutant forms in the apo state and bound to ATP/AMPPNP. These structures reveal that GCN2 autoinhibition results from stabilization of a closed conformation that restricts ATP binding. The R794G mutant shows increased flexibility in the hinge region connecting the N- and C-lobes, resulting from loss of multiple interactions involving Arg794. This conformational change is associated with intradomain movement that enhances ATP binding and hydrolysis. We propose that intramolecular interactions following tRNA binding remodel the hinge region in a manner similar to the mechanism of enzyme activation elicited by the R794G mutation.

High Energy-Resolution Inelastic Neutron Scattering Experiments on Triplet Bound State Excitations in SrCu2(BO3)2

In this letter we report on the high energy-resolution neutron scattering studies on the dynamic structure factor of the two-triplet bound states in the two-dimensional S ¼ 1=2 Shastry–Sutherland system, SrCu2(BO3)2, in the energy transfer range of 4 to 7 meV. In contrast to the earlier interpretation of the low energy-resolution results, these bound state excitations show hardly any dispersion, but do show a strong wave-vector-dependent structure factor. Although these findings are in overall agreement with the recent theoretical calculation of the 2-triplon dynamic structure factor by Knetter and Uhrig [Phys. Rev. Lett. 92 (2004) 027204], they also show distinct differences, which may be due to some symmetry-breaking terms in the Hamiltonian that are not included in the theory, such as the interdimer Dzyaloshinski–Moriya interactions recently discovered in this compound.

On the sensitivity of electron and X-ray scattering factors to valence charge distributions

The sensitivity of atomic scattering factors to valence charge distributions has been compared quantitatively for X-ray and electron diffraction. It is found that below a critical scattering vector,s(|s| = sinθ/λ), ranging typically from 0.2 to 0.6 Å−1depending on the atomic number, electron diffraction is more sensitive to valence charge densities than X-ray diffraction. Thus, electron diffraction provides crucial electronic structure informationviathe low-order structure factors, which are relatively insensitive to thermal vibrations, but sensitive to the charge distribution that characterizes the chemical bonding properties of the materials. On the other hand, the high-order structure factors, which are mainly influenced by atomic position and core charge, in many cases can be replaced by structure factors of a procrystal (superposition of neutral atoms), or by calculated structure factors from modern density functional theory (DFT), without losing significant accuracy. This is demonstrated by detailed analyses of an MgB2superconductor. The work reveals the importance of accurate determination of a very few low-order structure factors in valence electron density studies, and suggests the merit of the combined use of electron diffraction and DFT calculations for solids, especially those with large unit cells and nanocrystalline grains, unsuitable for X-ray studies.

Molecular Basis of Intramolecular Electron Transfer in Sulfite-oxidizing Enzymes Is Revealed by High Resolution Structure of a Heterodimeric Complex of the Catalytic Molybdopterin Subunit and a c-Type Cytochrome Subunit

Sulfite-oxidizing molybdoenzymes convert the highly reactive and therefore toxic sulfite to sulfate and have been identified in insects, animals, plants, and bacteria. Although the well studied enzymes from higher animals serve to detoxify sulfite that arises from the catabolism of sulfur-containing amino acids, the bacterial enzymes have a central role in converting sulfite formed during dissimilatory oxidation of reduced sulfur compounds. Here we describe the structure of the Starkeya novella sulfite dehydrogenase, a heterodimeric complex of the catalytic molybdopterin subunit and a c-type cytochrome subunit, that reveals the molecular mechanism of intramolecular electron transfer in sulfite-oxidizing enzymes. The close approach of the two redox centers in the protein complex (Mo-Fe distance 16.6 A) allows for rapid electron transfer via tunnelling or aided by the protein environment. The high resolution structure of the complex has allowed the identification of potential through-bond pathways for electron transfer including a direct link via Arg-55A and/or an aromatic-mediated pathway. A potential site of electron transfer to an external acceptor cytochrome c was also identified on the SorB subunit on the opposite side to the interaction with the catalytic SorA subunit.

The liquidlike ordering of lipid A-diphosphate colloidal crystals: The influence of Ca2+, Mg2+, Na+, and K+ on the ordering of colloidal suspensions of lipid A-diphosphate in aqueous solutions

A comprehensive study was performed on electrostatically stabilized aqueous dispersion of lipid A-diphosphate in the presence of bound Ca2+, Mg2+, K+, and Na+ ions at low ionic strength (0.10-10.0-mM NaCl, 25 degrees C) over a range of volume fraction of 1.0 x 10(-4)< or =phi< or =4.95 x 10(-4). These suspensions were characterized by light scattering (LS), quasielastic light scattering, small-angle x-ray scattering, transmission electron microscopy, scanning electron microscopy, conductivity measurements, and acid-base titrations. LS and electron microscopy yielded similar values for particle sizes, particle size distributions, and polydispersity. The measured static structure factor, S(Q), of lipid A-diphosphate was seen to be heavily dependent on the nature and concentration of the counterions, e.g., Ca2+ at 5.0 nM, Mg2+ at 15.0 microM, and K+ at 100.0 microM (25 degrees C). The magnitude and position of the S(Q) peaks depend not only on the divalent ion concentration (Ca2+ and Mg2+) but also on the order of addition of the counterions to the lipid A-diphosphate suspension in the presence of 0.1-microM NaCl. Significant changes in the rms radii of gyration (R2G) 1/2 of the lipid A-diphosphate particles were observed in the presence of Ca2+ (24.8+/-0.8 nm), Mg2+ (28.5+/-0.7 nm), and K+ (25.2+/-0.6 nm), whereas the Na+ salt (29.1+/-0.8 nm) has a value similar to the one found for the de-ionized lipid A-diphosphate suspensions (29.2+/-0.8 nm). Effective particle charges were determined by fits of the integral equation calculations of the polydisperse static structure factor, S(Q), to the light-scattering data and they were found to be in the range of Z*=700-750 for the lipid A-diphosphate salts under investigation. The light-scattering data indicated that only a small fraction of the ionizable surface sites (phosphate) of the lipid A-diphosphate was partly dissociated (approximately 30%). It was also discovered that a given amount of Ca2+ (1.0-5.0 nM) or K+ (100 microM) influenced the structure much more than Na+ (0.1-10.0-mM NaCl) or Mg2+ (50 microM). By comparing the heights and positions of the structure factor peaks S(Q) for lipid A-diphosphate-Na+ and lipid A-diphosphate-Ca2+, it was concluded that the structure factor does not depend simply on ionic strength but more importantly on the internal structural arrangements of the lipid A-diphosphate assembly in the presence of the bound cations. The liquidlike interactions revealed a considerable degree of ordering in solution accounting for the primary S(Q) peak and also the secondary minimum at large particle separation. The ordering of lipid A-diphosphate-Ca2+ colloidal crystals in suspension showed six to seven discrete diffraction peaks and revealed a face-centered-cubic (fcc) lattice type (a=56.3 nm) at a volume fraction of 3.2 x 10(-4)< or =phi< or =3.9 x 10(-4). The K+ salt also exhibited a fcc lattice (a=55.92 nm) at the same volume fractions, but reveals a different peak intensity distribution, as seen for the lipid A-diphosphate-Ca2+ salt. However, the Mg2+ and the Na+ salts of lipid A-diphosphate showed body-centered-cubic (bcc) lattices with a=45.50 nm and a=41.50 nm, respectively (3.2 x 10(-4)< or =phi< or =3.9 x 10(-4)), displaying the same intensity distribution with the exception of the (220) diffraction peaks, which differ in intensity for both salts of lipid A-diphosphate.

Phosphorus: First principle simulation of a liquid–liquid phase transition

We report a Car-Parrinello molecular dynamics study of the liquid-liquid phase transition in phosphorus. We employed a gradient corrected density functional (B-LYP) to describe the electronic structure and performed simulations at constant pressure. Upon increasing pressure we observed, along the 1500 K isotherm, a structural transition converting the molecular P4 liquid into an atomic liquid with a network structure. Our calculations suggest this transition to be first order with a discontinuous density increase accompanied by an insulator into metal transition. The transition pressure is significantly higher than obtained by employing the less accurate local density functional (LDA) [Morishita, Phys. Rev. Lett. 87, 105701 (2001)], which matches the experimental value for the pressure. We argue why the LDA result should be considered fortuitous. The change of the calculated structure factor upon the transition shows the same trend as experimentally observed. Analysis of the structural changes during the phase transition revealed that a chain of linked and opened up ("butterfly") P4 molecules may serve as a seed triggering the transition from the molecular to the network phase.

Crystal Structure of Baculovirus RNA Triphosphatase Complexed with Phosphate

Baculovirus RNA 5'-triphosphatase (BVP) exemplifies a family of RNA-specific cysteine phosphatases that includes the RNA triphosphatase domains of metazoan and plant mRNA capping enzymes. Here we report the crystal structure of BVP in a phosphate-bound state at 1.5 A resolution. BVP adopts the characteristic cysteine-phosphatase alpha/beta fold and binds two phosphate ions in the active site region, one of which is proposed to mimic the phosphate of the product complex after hydrolysis of the covalent phosphoenzyme intermediate. The crystal structure highlights the role of backbone amides and side chains of the P-loop motif (118)HCTHGXNRT(126) in binding the cleavable phosphate and stabilizing the transition state. Comparison of the BVP structure to the apoenzyme of mammalian RNA triphosphatase reveals a concerted movement of the Arg-125 side chain (to engage the phosphate directly) and closure of an associated surface loop over the phosphate in the active site. The structure highlights a direct catalytic role of Asn-124, which is the signature P-loop residue of the RNA triphosphatase family and a likely determinant of the specificity of BVP for hydrolysis of phosphoanhydride linkages.

The partial structure with errors: a probabilistic treatment

The method of the joint probability distribution functions has been applied to the case in which observed (with errors) and calculated structure factors are available, the latter referred to a part of the structure with finite errors in the coordinates, the thermal parameters and the scattering factors. Results obtained by other authors are confirmed and generalized. A new relationship is found to estimate the parameter sigmaA, affecting the reliability of the estimates of cos(varphi-varphip). Some practical applications are described.

Long-range disorder effects on the GaAs(0 0 1) β2(2 × 4) surface

We first summarise previous work on long-range disorder effects occurring on the GaAs(0 0 1) β2(2 × 4) surface, as determined by reflection high energy electron diffraction (RHEED), grazing incidence X-ray diffraction and scanning tunnelling microscopy (STM). Models which have been deduced are related to the assembly of β2(2 × 4) and c(2 × 8) unit cells and involve the presence of antiphase domains and one-dimensional disorder boundaries. We ignore kinks produced by cooperative shifts of whole (2 × 4) units in the [1 1 0] direction, since they are only present in significant numbers on surfaces formed in the presence of a large excess of arsenic. We show from a combination of multi-azimuthal RHEED data and structure factor calculations that none of the existing models is consistent with all of the diffraction information. In particular, STM images show that the surface has a non-ideal c(2 × 8) structure made up of a distribution of β2(2 × 4) cells having equal but irregular occupancy of the two possible phase positions. The equal occupancy means that certain reflections should be forbidden, but in practice some of these appear strongly. We have suggested possible structural effects which might produce these results, such as a change in atom positions in the boundary region where two cells conjoin, so that they are no longer identical entities. We have been unable to obtain confirmation, however, since the precise atom locations are not known.

Pim-1 Ligand-bound Structures Reveal the Mechanism of Serine/Threonine Kinase Inhibition by LY294002

Pim-1 is an oncogene-encoded serine/threonine kinase primarily expressed in hematopoietic and germ cell lines. Pim-1 kinase was originally identified in Maloney murine leukemia virus-induced T-cell lymphomas and is associated with multiple cellular functions such as proliferation, survival, differentiation, apoptosis, and tumorigenesis (Wang, Z., Bhattacharya, N., Weaver, M., Petersen, K., Meyer, M., Gapter, L., and Magnuson, N. S. (2001) J. Vet. Sci. 2, 167-179). The crystal structures of Pim-1 complexed with staurosporine and adenosine were determined. Although a typical two-domain serine/threonine protein kinase fold is observed, the inter-domain hinge region is unusual in both sequence and conformation; a two-residue insertion causes the hinge to bulge away from the ATP-binding pocket, and a proline residue in the hinge removes a conserved main chain hydrogen bond donor. Without this hydrogen bond, van der Waals interactions with the hinge serve to position the ligand. The hinge region of Pim-1 resembles that of phosphatidylinositol 3-kinase more closely than it does other protein kinases. Although the phosphatidylinositol 3-kinase inhibitor LY294002 also inhibits Pim-1, the structure of the LY294002.Pim-1 complex reveals a new binding mode that may be general for Ser/Thr kinases.

Crystal Structure of Vinorine Synthase, the First Representative of the BAHD Superfamily

Vinorine synthase is an acetyltransferase that occupies a central role in the biosynthesis of the antiarrhythmic monoterpenoid indole alkaloid ajmaline in the plant Rauvolfia. Vinorine synthase belongs to the benzylalcohol acetyl-, anthocyanin-O-hydroxy-cinnamoyl-, anthranilate-N-hydroxy-cinnamoyl/benzoyl-, deacetylvindoline acetyltransferase (BAHD) enzyme superfamily, members of which are involved in the biosynthesis of several important drugs, such as morphine, Taxol, or vindoline, a precursor of the anti-cancer drugs vincaleucoblastine and vincristine. The x-ray structure of vinorine synthase is described at 2.6-angstrom resolution. Despite low sequence identity, the two-domain structure of vinorine synthase shows surprising similarity with structures of several CoA-dependent acyltransferases such as dihydrolipoyl transacetylase, polyketide-associated protein A5, and carnitine acetyltransferase. All conserved residues typical for the BAHD family are found in domain 1. His160 of the HXXXD motif functions as a general base during catalysis. It is located in the center of the reaction channel at the interface of both domains and is accessible from both sides. The channel runs through the entire molecule, allowing the substrate and co-substrate to bind independently. Asp164 points away from the catalytic site and seems to be of structural rather than catalytic importance. Surprisingly, the DFGWG motif, which is indispensable for the catalyzed reaction and unique to the BAHD family, is located far away from the active site and seems to play only a structural role. Vinorine synthase represents the first solved protein structure of the BAHD superfamily.

Ab initiomolecular-dynamics simulations of liquid GaSb and InSb

We report results for the structural, dynamical, and electronic properties of liquid GaSb $(l\text{\ensuremath{-}}\mathrm{Ga}\mathrm{Sb})$ and liquid InSb $(l\text{\ensuremath{-}}\mathrm{In}\mathrm{Sb})$ simulated by using ab initio molecular dynamics. Our calculated structure factors and pair correlation functions for $l\text{\ensuremath{-}}\mathrm{Ga}\mathrm{Sb}$ and $l\text{\ensuremath{-}}\mathrm{In}\mathrm{Sb}$ are in good agreement with available experimental data. The calculated results indicate that covalent heteroatomic bonds similar to those of the crystalline phase are preserved in the liquid state, and the local structures of Ga (In) and Sb atoms in $l\text{\ensuremath{-}}\mathrm{Ga}\mathrm{Sb}$ and $l\text{\ensuremath{-}}\mathrm{In}\mathrm{Sb}$ are analogous with those in pure-element liquids.

Crystal structure of a Cbtx–AChBP complex reveals essential interactions between snake α-neurotoxins and nicotinic receptors

The crystal structure of the snake long alpha-neurotoxin, alpha-cobratoxin, bound to the pentameric acetylcholine-binding protein (AChBP) from Lymnaea stagnalis, was solved from good quality density maps despite a 4.2 A overall resolution. The structure unambiguously reveals the positions and orientations of all five three-fingered toxin molecules inserted at the AChBP subunit interfaces and the conformational changes associated with toxin binding. AChBP loops C and F that border the ligand-binding pocket move markedly from their original positions to wrap around the tips of the toxin first and second fingers and part of its C-terminus, while rearrangements also occur in the toxin fingers. At the interface of the complex, major interactions involve aromatic and aliphatic side chains within the AChBP binding pocket and, at the buried tip of the toxin second finger, conserved Phe and Arg residues that partially mimic a bound agonist molecule. Hence this structure, in revealing a distinctive and unpredicted conformation of the toxin-bound AChBP molecule, provides a lead template resembling a resting state conformation of the nicotinic receptor and for understanding selectivity of curaremimetic alpha-neurotoxins for the various receptor species.

Improved quantitative CBED structure-factor measurement by refinement of nonlinear geometric distortion corrections

A new method that accounts for small but significant geometric distortions in quantitative convergent beam electron diffraction (QCBED) is briefly introduced. A summary of preliminary results obtained with this method shows an average three- to fourfold improvement in structure-factor measurement precision by QCBED. In the present work this method is applied to α-\rm Al_{2}O_{3}, a benchmark compound for charge density studies. Experimental uncertainty is reduced to a level three times smaller than differences between density functional theory and periodic Hartree–Fock calculated structure factors.

The effects of Lowe–Andersen temperature controlling method on the polymer properties in mesoscopic simulations

Lowe-Andersen (LA) temperature controlling method [C. P. Lowe, Europhys. Lett. 47, 145 (1999)] is applied in a series of mesoscopic polymer simulations to test its validity and efficiency. The method is an alternative for dissipative particle dynamics simulation (DPD) technique which is also Galilean invariant. It shows excellent temperature control and gives correct radial distribution function as that from DPD simulation. The efficiency of LA method is compared with other typical DPD integration schemes and is proved to be moderately efficient. Moreover, we apply this approach to diblock copolymer microphase separation simulations. With LA method, we are able to reproduce all the results from the conventional DPD simulations. The calculated structure factors of the microphases are consistent with the experiments. We also study the microphase evolution dynamics with increasing chiN and find that the bath collision frequency Gamma does not affect the order of appearing phases. Although the thermostat does not affect the surface tension, the order-disorder transition (ODT) is somewhat sensitive to the values of Gamma, i.e., the ODT is nonmonotonic with increasing Gamma. The dynamic scaling law is also tested, showing that the relation obeys the Rouse theory with various Gamma.

The Molecular Architecture of the Mammalian DNA Repair Enzyme, Polynucleotide Kinase

Mammalian polynucleotide kinase (PNK) is a key component of both the base excision repair (BER) and nonhomologous end-joining (NHEJ) DNA repair pathways. PNK acts as a 5'-kinase/3'-phosphatase to create 5'-phosphate/3'-hydroxyl termini, which are a necessary prerequisite for ligation during repair. PNK is recruited to repair complexes through interactions between its N-terminal FHA domain and phosphorylated components of either pathway. Here, we describe the crystal structure of intact mammalian PNK and a structure of the PNK FHA bound to a cognate phosphopeptide. The kinase domain has a broad substrate binding pocket, which preferentially recognizes double-stranded substrates with recessed 5' termini. In contrast, the phosphatase domain efficiently dephosphorylates single-stranded 3'-phospho termini as well as double-stranded substrates. The FHA domain is linked to the kinase/phosphatase catalytic domain by a flexible tether, and it exhibits a mode of target selection based on electrostatic complementarity between the binding surface and the phosphothreonine peptide.