New Crystal Forms of the Motile Major Sperm Protein (MSP) ofAscaris suum

We have obtained two new crystal forms of theAscarismajor sperm protein (MSP) that mediates amoeboid cell motility in nematode sperm. We obtained crystals with C2 symmetry from bacterially expressed α-MSP witha= 216.5 Å,b= 38.6 Å,c= 32.5 Å, γ = 93.1° and also crystals with P2₁symmetry from native β-MSP witha= 63.1 Å,b= 91.7 Å,c= 72.5 Å, γ = 91.3°. A full native data set has been collected for each crystal form using synchrotron radiation. Both crystal forms diffract to 2 Å and are suitable for high-resolution structural investigation.     

Crystallization and Preliminary X-Ray Analysis of Neuropsin, a Serine Protease Expressed in the Limbic System of Mouse Brain

Neuropsin (M_r25 032) is a serine protease expressed in the limbic system of mouse brain. It has been implicated in various neurological processes including formation of memory and may be important as a drug target in the treatment of epilepsy. The recombinant protein was produced using a baculovirus expression system and was purified. Two crystal forms were obtained by a hanging-drop vapor-diffusion method with polyethylene glycol. Preliminary X-ray crystallographic analysis revealed that crystal form I belongs to triclinic space groupP1 with unit cell dimensionsa= 97.16 Å,b= 97.12 Å,c= 46.75 Å and α = 99.17°, β = 99.77°, γ = 117.35°. Self-rotation function analysis of these data of form I indicates the position of a noncrystallographic threefold axis. There are six molecules in the crystallographic asymmetric unit. Crystal form II also belongs to triclinic space groupP1 but has unit cell dimensions ofa= 38.40 Å,b= 55.16 Å,c= 65.37 Å and α = 95.38°, β = 89.98°, γ = 110.46° with two molecules in the crystallographic asymmetric unit. Form II has a noncrystallographic twofold axis. Intensity data to 3.1 Å resolution for form I and to 2.2 Å resolution for form II have been collected.     

An X-ray crystallographic study of α-d-allopyranosyl α-d-allopyranoside · CaCl2 · 5H2O (a pentadentate complex)

Three-dimensional, single-crystal, X-ray diffraction methods were used to determine the structure of the calcium chloride complex of α-d-allopyranosyl α-d-allopyranoside. The crystal is monoclinic with cell dimensions: a = 16.262(5), b = 8.345(5), c = 8.298(5)Å, β = 98.428(5)Å, and z = 2. The space group is P2₁. The structure was solved by three-dimensional Patterson and Fourier methods, and was refined by least-squares techniques to give a conventional discrepancy factor of R = 0.026; 2435 diffractometer-read reflections were used. The cation was found to be in 9-fold co-ordination to O-1, O-2, O-3, O-2′, O-3′, and four water molecules.     

Crystallization and Preliminary X-Ray Analysis of Thermoactinomyces vulgaris R-47 α-Amylase II

Crystals of Thermoactinomyces vulgaris α-amylase II, which is a new type of α-amylase having hydrolysis activities for pullulan and cyclodextrins, have been obtained and diffraction data to 2.9 Å resolution were collected. The crystal belongs to an orthorhombic system with cell dimensions of a = 119.5 Å, b = 120.6 Å, and c = 114.6 Å and a space group of P 2₁2₁2₁. Two or three protein molecules are expected to exist in an asymmetric unit.     

A study of the reactivity and structure of cyclic α,β-unsaturated Fischer-type carbene complexes

Cycloaddition reactions with α,β-unsaturated carbene complexes of the Fischer-type bearing the carbene carbon atom and the double bond incorporated in the same ring are described. Pentacarbonyl(2H-benzopyran-2- ylidene)chromium(0) complexes (2a-c) and pentacarbonyl(4-methoxy-3,3-dimethyl-2-oxacyclopentylidene)- chromium(0) (3) show a rather low reactivity towards 1,3-dipoles and 1,3-dienes. The reactions with diazomethane are regioselective but not chemoselective; compounds 2 and 3 show two sites of attack: the α,β carbon-carbon and the carbon-metal double bond. The crystal and molecular structures of 2a and 3 have been elucidated by single crystal X-ray analysis. Crystals of 2a are monoclinic, space group P2₁/c, a=7.614(3), b=14.033(3), c=12.766(3) Å, β=95.24°, V=1358.3(7) Å Z=4; crystals of 3 are triclinic, space group P , a=6.553(1), b=9.408(1), c=10.620(1) Å α=92.70(1), β=92.30(1), γ=92.12(1)°, V=653.0(1), ų, Z=2. Final agreement indices for 2a and 3 are R=0.034 and 0.033, respectively. Vibrational properties of the Cr(CO)₅ moiety were interpreted by FT-IR and FT-Raman spectroscopy. Electronic spectra and π electron distribution were interpreted by resonance Raman spectroscopy.     

Three-Dimensional Structure of the Porcine Gastric H,K-ATPase from Negatively Stained Crystals

A low-resolution three-dimensional model of membrane-bound H,K-ATPase from pig gastric mucosa has been reconstructed by electron microscopy and image processing of two-dimensional crystals in negative stain. The crystal formation is induced by magnesium and vanadate, which stabilize the E₂conformation of the enzyme. The unit cell, with a size ofa=b= 123 Å, γ = 90°, has tetragonal p4 symmetry. There are four separate αβ protomers within each unit cell. The high-contrast region is limited to the cytoplasmic part of the protein. The total volume of the observed asymmetric protein domain corresponds to a molecular mass of 80–90 kDa. It consists mainly of a large pear-shaped domain measuring 60 × 45 Ų, with a height of 50 Å as measured perpendicular to the membrane plane. A small stalk segment, 20 Å in length, forms a connection to the transmembrane region.     

β-Sheet Models for the Ordered Filamentous Structure Formed by a Peptide That Enhances the Action of Insulin

Certain peptides with sequences related to part of the major histocompatibility complex class I antigen enhance the action of insulin. These peptides also aggregate into fibrous structures that seem to be related to their biological activity. In the current study, the 17-residue peptide with amino acid sequence Gly-Asn-Glu-Gln-Ser-Phe-Arg-Val-Asp-Leu-Arg-Thr-Leu-Leu-Arg-Tyr-Ala is used as a representative example of these bioactive molecules. As seen by electron microscopy, the peptide associates into gently twisted ribbons, 50 Å thick, in which the amount of twist decreases as the ribbons become wider. X-ray diffraction analysis suggests that the peptides are arranged as in an antiparallel β-sheet extending essentially endlessly along the fiber axis. The amino acid sequence of the peptide is such that one side of the β-sheet is predominantly polar while the opposite side is nonpolar. This allows the β-sheets to form multilayers with alternating hydrophobic and hydrophilic interfaces. The length of the extended peptide (≈54 Å) determines the thickness of the ribbon and the tendency of individual β-sheets to twist accounts for the twisting of the ribbons. An alternative model is also discussed, again based on antiparallel β-sheets, but with adjacent sheets interdigitated in a “side-by-side” fashion rather than forming stacked layers. Comparable inactive peptides such as Gly-Asn-Glu-Gln-Ser- A_l_a_-Arg-Val-Asp-Leu-Arg-Thr-Leu-Leu-Arg-Tyr-T_y_r_ (changed amino acids underlined) do not form ordered filamentous structures.     

Cryo-EM structure of SNAP-SNARE assembly in 20S particle

N-ethylmaleimide-sensitive factor (NSF) and α soluble NSF attachment proteins (α-SNAPs) work together within a 20S particle to disassemble and recycle the SNAP receptor (SNARE) complex after intracellular membrane fusion. To understand the disassembly mechanism of the SNARE complex by NSF and α-SNAP, we performed single-particle cryo-electron microscopy analysis of 20S particles and determined the structure of the α-SNAP-SNARE assembly portion at a resolution of 7.35 Å. The structure illustrates that four α-SNAPs wrap around the single left-handed SNARE helical bundle as a right-handed cylindrical assembly within a 20S particle. A conserved hydrophobic patch connecting helices 9 and 10 of each α-SNAP forms a chock protruding into the groove of the SNARE four-helix bundle. Biochemical studies proved that this structural element was critical for SNARE complex disassembly. Our study suggests how four α-SNAPs may coordinate with the NSF to tear the SNARE complex into individual proteins.     

Phytohemagglutinin and transmembrane proteins in agglutinated sheep erythrocyte ghost membranes

Oriented and periodically stacked sheep erythrocyte ghost membrane specimens were prepared by agglutination of the ghosts with phytohemagglutinin M and sedimentation, and were studied by X-ray diffraction. The spatial orientation of the planes of the membranes in the diffracting stack was determined from the lamellar reflections of the periodic stacking. Equatorial diffraction at (10.5 Å)⁻¹ and a (1.5 Å)⁻¹ reflection were recorded which correlate with side-to-side packed transmembrane α-helices in the agglutinated membrane. A broad (4.6 Å)⁻¹ ring with strong equatorial accentuation and broad maxima at about (2.2 Å)⁻¹ and (1.2 Å)⁻¹ were observed which are attributed to the hydrocarbon chain arrangement in lipid phases of the agglutinated ghost membrane.     

Type IIβ Regulatory Subunit of cAMP-Dependent Protein Kinase: Purification Strategies to Optimize Crystallization

To elucidate the structural basis for important differences between types I and II regulatory subunit isoforms (RI and RII) of adenosine 3′,5′-cyclic monophosphate (cAMP)-dependent protein kinase, the full-length RIIβ isoform and five RIIβ deletion mutants were constructed, expressed, purified, and screened for crystallization. Only one of these six proteins yielded diffraction quality crystals. Crystals were grown of the RIIβ deletion mutant (Δ1–111) monomer potentially in complex with two cAMP molecules. X-ray diffraction quality data were obtained only after significant modification to existing purification procedures. Modifications required a Sepharose, not agarose, support for cAMP affinity chromatography followed by rapid, quantitative removal of free cAMP by size-exclusion chromatography under reducing conditions. Data to 2.4 Å resolution were collected at 29°C using synchrotron radiation on a single crystal measuring 0.2 × 0.3 × 1.2 mm³. Data were 99% complete. The hexagonal crystal belonged to space group P6₍₁₎ or P6₍₅₎ with unit cell dimensions a = b = 161.62 Å and c = 39.66 Å.     

Structural investigations of lipid, polypeptide and protein multilayers

Langmuir-Blodgett multilayers of lipids, polypeptides and proteins have been examined by X-ray diffraction and infrared spectroscopic methods. The complex polymorphism exhibited by multilayers of glycerides and various phospholipids of different chain length mirror those shown in other three-dimensional structures and suggest that multilayers of lipids can be considered as oriented “crystals”. Both the α and β types of hdyrocarbon chain packing are adopted by different classes of lipids in multilayers.Stable multilayers of the synthetic polypeptide poly-γ-benzyl-l-glutamate consist of α-helical rods stacked in an hexagonal array with a rod axis separation of 14.2 Å. Poly-γ-methyl-l-glutamate behaves similarly but little structural information could be derived from potentially non-helical or sheet-like structures formed by other homopolypeptides. The observation of a single, invariant diffraction line at 9.3 Å for multilayers of a number of water-soluble proteins is consistent with the occurrence of extensive structural reorganization (uncoiling, denaturation) at the air-water interface.     

Preparation and characterization of some uranyl complexes of amino acids. The crystal structure of [UO2(γ-aminobutanoic acid)3] (NO3)2

Uranyl complexes of glycine, β-alanine and γ-aminobutanoic acid were prepared and characterized. All those studied or examined contain the aminoacids in the zwitterionic form binding the metal through the ionized carboxyl group. The structure of the title compound was determined by X-ray crystallography and refined to R=6.6%. The crystals are triclinic, space group P1, Z = 2, with a = 11.966(5), b = 12.054(5), c = 10.581(5) Å, α = 70.88(3)°, β = 109.89(3)°, and γ = 120.72(3)°. The uranyl group is equatorially bonded to the bidentate carboxylate of three molecules of the organic ligand forming a distorted hexagonal bipyramidal coordination geometry around the metal. U---O(equatorial) distances are in the range 2.24–2.48 Å.     

Structural study of immunoaffinity-purified DNA polymerase α-DNA primase complex from calf thymus

The DNA polymerase α-DNA primase complex was purified over 17 000-fold to near homogeneity from calf thymus using an immunoaffinity column. Sodium dodecyl sulfate gel electrophoresis revealed three polypeptides with molecular weights of 140, 50 and 47 kDa, in a ratio of 1:2:0.25. The complex showed a sedimentation coefficient of 9.7 S, a Stokes radius of 56 Å and a native molecular weight of 250–260 kDa. Taken together, the data suggest that the calf thymus dNA polymerase α-DNA primase complex is essentially a heterotrimer of large (140 kDa) and small (50 kDa) subunits in a ratio of 1:2, with a globular conformation. Electron-microscopic studies of the complex revealed a spherical particle of 120 Å in diameter, in agreement with the physicochemical results. The binding of the complex to DNA was also demonstrated.     

Heterocyclic compounds containing antimony 1. Synthesis, physicochemical properties, crystal and molecular structure of 2-(β-hydroxyethylthio) 1,3,2-oxathiastibolane

The compound (HOCH₂CH₂S) ) (1) has been prepared by the reaction of antimony(III) isopropoxide and 2-mercaptoethanol in a 1:2 molar ratio. Reaction of 1 with MOCH₃ (where M = Li, Na and K) yields bimetallic products of the type, M[(OCH₂CH₂S) )]. All these derivatives have been characterized by elemental analysis, IR, NMR (¹H and ¹³C) spectra and molar conductivity measurements. Crystals of 1 are triclinic, space group P , with a = 6.449(2), b = 10.285(2), c = 13.494(1) Å, α = 78.08(1), β = 75.99(1), γ = 71.54(2)°, V = 815.48 ų, Z = 4, D_calc = 2.239 g cm⁻³, (Mo Kα) λ = 0.7107 Å, μ = 3.55 mm₋₁, F(000) = 528, T = 295 K, final R = 0.0189 for 2344 reflections. One of the two mercaptoethanol moieties in 1 forms a five-membered chelate ring with antimony, Sb(1)---O(11) = 2.023(2) Å and Sb(1)---S(11) = 2.434(1) Å, while the other is bonded through the S atom only, Sb(1)---S(12) = 2.434(1) Å. The angles between these primary bonds with a mean value of 90.2° suggest a basically pyramidal, or pseudo tetrahedral structure if the stereochemically active lone pair is included in the coordination sphere. Two molecules are linked by intermolecular hydrogen bridges. The presence of weak intermolecular secondary bonding, Sb(1)---O(12) = 2.567(3) Å, in the complex indicates that the overall coordination polyhedron is best described in terms of a distorted trigonal bipyramidal arrangement.     

Crystallization and Characterization of Pumilio: A Novel RNA Binding Protein

Axis determination in early Drosophila embryos is controlled, in part, by regulation of translation of mRNAs transcribed in maternal cells during oogenesis. The Pumilio protein is essential in posterior determination, binding to hunchback mRNA in complex with Nanos to suppress hunchback translation. In order to understand the structural basis of RNA binding, Nanos recruitment, and translational control, we have crystallized a domain of the Drosophila Pumilio protein that binds RNA. The crystals belong to the space group P6₃ with unit cell dimensions of a = b = 94.5 Å, c = 228.9 Å, α = β = 90°, γ = 120° and diffract to 2.6 Å with synchrotron radiation. We show that the purified protein actively binds RNA and is likely to have a novel RNA binding fold due to a very high content of α-helical secondary structure.     

Protein farnesyltransferase

In the past year, the crystal structure of αβ heterodimeric protein farnesyltransferase from rat was reported to a resolution of 2.25 Å. Farnesyltransferase catalyzes the essential post-transduction proteins. The structure provides a foundation for understanding the specificity and mechanism of protein prenylation and may aid in the design of new anticancer therapeutics.     

Cyrstal structure of a complex of α-cyclodextrin with 2-fluoro-4-nitrophenol · 3H2O

The crystal structure of a complex of α-cyclodextrin (α-CD) with 2-fluoro-4-nitrophenol · 3H₂O has been determined by the X-ray diffraction technique. The complex crystallizes in space group P2₁2₁2₁ with cell dimensions: a = 13.431(3), b = 15.299(4), c = 24.780(5) Å. The structure was solved by direct methods and refined to R = 6.7% for 4483 reflections. The crystal structure is isomorphous to the α-CD-4-nitrophneol · 3H₂O complex. The phenyl group is inside the cavity, so that the O-4 hexagon of the α-CD is distorted in a systematic manner: the longest diagonal [O-4(G2) O-4(G5)] is in the direction of the benzene ring. The phenolic OH group protrudes from the secondary OH side of the cavity and the NO₂ group is situated on the primary OH side. The hydrophobic F atom is statitically disordered over two sites and is located in the hydrophilic space, just beyond the rim of the secondary OH side of the cavity.     

Achievable resolution from images of biological specimens acquired from a 4k x 4k CCD camera in a 300-kV electron cryomicroscope

Bacteriorhodopsin and ε 15 bacteriophage were used as biological test specimens to evaluate the potential structural resolution with images captured from a 4k × 4k charge-coupled device (CCD) camera in a 300-kV electron cryomicroscope. The phase residuals computed from the bacteriorhodopsin CCD images taken at 84,000× effective magnification averaged 15.7° out to 5.8-Å resolution relative to Henderson’s published values. Using a single-particle reconstruction technique, we obtained an 8.2-Å icosahedral structure of ε 15 bacteriophage with the CCD images collected at an effective magnification of 56,000×. These results demonstrate that it is feasible to retrieve biological structures to a resolution close to 2/3 of the Nyquist frequency from the CCD images recorded in a 300-kV electron cryomicroscope at a moderately high but practically acceptable microscope magnification.     

Crystal structures of cyclomaltohexaose (α-cyclodextrin) complexes with p-chlorophenol and p-cresol

Crystal structures of cyclomaltohexaose (α-cyclodextrin) complexes with p-chlorophenol and p-cresol have been determined by single-crystal X-ray diffraction studies. The space group of the α-cyclodextrin–p-chlorophenol complex is P2₁2₁2₁ with unit cell dimensions of a=15.299(3), b=24.795(5), c=13.447(5) Å, and that of the α-cyclodextrin–p-cresol complex is P2₁ with unit cell dimensions of a=7.927(7), b=13.568(7), c=24.54(1) Å, β=90.41(8)°. In spite of the similar structures of guest molecules, both complexes have different inclusion modes and packing structures.     

A Model of the Reactive Form of Plasminogen Activator Inhibitor-1

A model of the reactive form of plasminogen activator inhibitor-1 (PAI-1) has been constructed using molecular graphics and starting from the known crystal structure of latent PAI-1. The residues P16 to P10′, of which P16-P4 form strand 4 of the β-sheet A (s4A) and P3-P10′ form an extended loop in the latent form, have been removed and remodeled into this structure, based on the structures of ovalbumin and cleaved α1-proteinase inhibitor. Residues P4′-P10′ were remodeled as a β-strand s1C, located on the surface of the molecule and the N-terminal end (P16-P14) of the eliminated loop was rebuilt using appropriate backbone dihedrals. Subsequently, a secondary structure prediction program was applied and further optimization of the model was performed by several molecular dynamics runs. Apparently the β-strand was stabilized by only two hydrogen bonds. Further analysis revealed that, although s4A was removed, s3A and s5A did not approach each other. In this current model it was also found that the large gap between the loop connecting s4C-s3C and the loop connecting s3B-hG remained 11 Å in contrast to the small gap (4Å) at a similar position in other serpins. These observations may explain the ease of a conformational change of the reactive site loop of PAI-1 during transition to the latent and the preinserted form. In addition the current model can be used for the design of stable, functional, PAI-1 mutants. Detailed structural analysis of the latter may facilitate studies on the structure-function relationship in PAI-1 in particular and in other serpins in general.