The structure of native cellulose

Native cellulose has been shown to consist of a crystalline array of parallel chains, based on the X-ray diffraction data for specimens from the sea alga Valonia ventricosa. The unit cell is monoclinic with dimensions a = 16.34 Å, b = 15.72 Å, c = 10.38 Å (fiber axis), and β = 97.0°. The space group is P2₁ and the cell contains disaccharide segments of eight chains. Models containing chains with the same sense (parallel) or alternating sense (antiparallel) were refined against the intensity data using rigidbody least squares procedures. The results show a preference for a parallel chain structure with specific chain polarity with respect to the c axis. The refinement places the ? CH₂OH side chains approximately 20′ from the so-called tg conformation, with a result that an 02′? H…06 intramolecular bond is formed. The structure also contains an 03? H…05′ intramolecular bond and an 06? H…03 intermolecular bond along the a axis. All these bonds lie in the 020 planes, and the structure is an array of hydrogen-bonded sheets. A major consequence of this work is that regular chain folding can be ruled out and cellulose is seen as extended chain polymer single crystals.     

X-Ray studies on crystalline complexes involving amino acids and peptides. XVII. Chirality and molecular aggregation: The crystal structures of DL-arginine DL-glutamate monohydrate and DL-arginine DL-aspartate

DL -Arginine DL -glutamate monohydrate and DL -arginine DL -aspartate, the first DL -DL amino acid–amino acid complexes to be prepared and x-ray analyzed, crystallize in the space group P1 with a = 5.139(2), b = 10.620(1), c = 14.473(2) Å, α = 101.34(1)°, β = 94.08(2)°, γ = 91.38(2)° and a = 5.402(3), b = 9.933(3), c = 13.881(2) Å, α = 99.24(2)°, β = 99.73(3)°, γ = 97.28(3)°, respectively. The structures were solved using counter data and refined to R values of 0.050 and 0.077 for 1827 and 1739 observed reflections, respectively. The basic element of aggregation in both structures is an infinite chain made up of pairs of molecules. Each pair, consisting of a L - and a D -isomer, is stabilized by two centrosymmetrically or nearly centrosymmetrically related hydrogen bonds involving the α-amino and the α-carboxylate groups. Adjacent pairs in the chain are then connected by specific guanidyl–carboxylate interactions. The infinite chains are interconnected through hydrogen bonds to form molecular sheets. The sheets are then stacked along the shortest cell translation. The interactions between sheets involve two head-to-tail sequences in the glutamate complex and one such sequence in the aspartate complex. However, unlike in the corresponding LL and DL complexes, head-to-tail sequences are not the central feature of molecular aggregation in the DL -DL complexes. Indeed, fundamental differences exist among the aggregation patterns in the LL , the LD , and the DL -DL complexes.     

Crystallization of the bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase domain of the human trifunctional enzyme

Methylenetetrahydrofolate([H₄] folate) dehydrogenase (D) and methenyl[H₄] folate cyclohydrolase (C) coexist as a bifunctional enzyme (DC) or as the amino-terminal domain of a trifunctional enzyme (DCS) where the third activity is 10-formyl[H₄]lfolate synthetase (S). Two crystal forms of the DC domain of the human cytosolic DCS enzyme have been grown from polyethyleneglycol solution. The monoclinic P2₁ crystals diffract to 2.8 Å with a = 72.5 Å, b = 68.5 Å, c = 125.2 Å, and β = 91.8° but were found to be twinned. The orthorhombic P2₁2₁2₁ crystals diffract to 2.5 Å with a = 67.7 Å, b = 135.9 Å, c = 61.6 Å, and contain two molecules per asymmetric unit. Proteins 26:479–480 © 1996 Wiley-Liss, Inc.     

Structural components of alginic acid. I. The crystalline structure of poly-beta-D-mannuronic acid. Results of x-ray diffraction and polarized infrared studies

A Structure determination of the naturally occuring marine algal polysaccharide poly-β-D -mannuronic acid is described. The structure consists of 1e → 4e linked D -mannuronic acid chains with the monosaccharide units in the C1 chair conformation. The X-ray fiber diffraction photograph obtained from bundles of fibers prepared from Fucus vesiculosus has been indexed to an orthorhombic unit cell in which a =7.6 Å, b (fiber axis) = 10.4 Å, c = 8.6 Å, the unit cell containing two disaccharide chain segments with space group P2₁2₁2₁. A sheet-like structure involving one intra-chain, one intra-sheet, and one inter-sheet hydrogen bond per monosaccharide is proposed. Features of the chain-packing arrangement are compared with mannan.     

Crystallization and preliminary crystallographic analysis of the N-terminal actin binding domain of human fimbrin

We have crystallized the N-terminal actin binding domain (ABD1) of human fimbrin, a representative member of the largest class of actin crosslinking proteins. Diffraction from these crystals is consistent with the orthorhombic space group P2₁2₁2₁ (a = 50.03 Å, b = 61.24 Å, c = 102.30 Å). These crystals contain one molecule in the asymmetric unit and diffract to at least 1.9 Å resolution. The crystal structure of ABD1 will be the first structure of an actin crosslinking domain. Proteins 28:452–453, 1997. © 1997 Wiley-Liss, Inc.     

Three-dimensional structure of actinoxanthin. III. A 4-Å resolution

The protein actinoxanthin (molecular weight 10,300) crystallizes in space group P2₁2₁2₁, with cell dimensions a = 30.9 Å, b = 48.8 Å, c = 64.1 Å, and z = 4. The three-dimensional structure of actinoxanthin at 4-Å resolution was determined by x-ray methods on the basis of experimental data from the native protein and five isomorphous derivatives. At the stage of solving the phase problem, the heavy atoms in the derivatives were located using direct methods. The actinoxanthin molecule can be described as an oblate ellipsoid with approximate dimensions 20 × 30 × 40 Å and consists of two different sizes of folded units separated by a well-defined cleft. The larger unit, including the N- and C-terminals of the protein chain, is characterized by a significant content of β-sheet structure. The smaller unit, containing two deca- and hexapeptide cycles closed by disulfide bonds, has a mainly irregular structure.     

Crystallization and preliminary X-ray diffraction data of two heparin-binding fragments of human fibronectin

Two different heparin-binding fragments of human fibronectin have been crystallized in forms which are suitable for crystal structure analyses. The 30 kDa hep-2A fragment, consisting of type III domains 12–14, was crystallized from solutions containing ammonium sulfate or polyethylene glycol 6000. The crystals grown in ammonium sulfate solutions were orthorhombic with space group I222 or I2₁2₁2₁ with a = 68.1 Å, b = 88.6 Å, and c = 144.9 Å. The crystals grown in polyethylene glycol solutions are hexagonal with space group P6₁22 or P6₅22 witha a = b = 66.7 Å and c = 245.7 Å. The 40 kDa hep-2B fragment, consisting of type III domains 12–15, was also crystallized from solutions containing ammonium sulfate with the addition of glycerol. Glycerol proved an effective agent for reducing the number of crystals in the crystallization experiments, and thus, increasing the size of the crystals in these experiments. This crystal form is nearly isomorphous to the orthorhombic form of the hep-2A fragment with space group I222 or I2₁2₁2₁ and a = 67.5 Å, b = 87.0 Å, and c = 144.3 Å. All crystal forms diffract to at least 3.5 Å resolution and contain a single molecule in the asymmetric unit. © 1993 Wiley-Liss, Inc.     

Crystallization and preliminary crystallographic studies of 3-deoxy-D-manno-octulosonate-8-phosphate synthase from Escherichia coli

3-Deoxy-D-manno-octulosonate-8-phosphate (KDOP) synthase catalyzes the production of KDOP from phosphoenolpyruvate (PEP) and arabinose-5-phosphate (A5P). In gram-negative bacteria KDOP is subsequently dephosphorylated, cytidylylated, and linked to lipid A and is required for lipid A incorporation into the outer membrane (Raetz, Annu. Rev. Biochem. 59:129–170, 1990). We have crystallized two forms of KDOP synthase belonging to space groups I23 or I2₁3, one with a = b = c = 118.0 Å and the other with a = b = c = 233 Å.     

Physical and chemical microstructure of spider dragline: A study by analytical transmission electron microscopy

We report the first direct observations of the physical and chemical microstructure of spider dragline, revealed by analytical transmission electron microscopy. Individual crystallites were imaged within the amorphous matrix. They are irregularly shaped, approximately 70–100 nm in diameter, and uniformly distributed throughout the matrix. Electron diffraction determined their space group to be P2₁. The corresponding orthogonal cell has lattice parameters of a = 13.31 Å (β-sheet repeat), b = 9.44 Å (interchain repeat within β-sheets), and c = 20.88 Å (repeat along polypeptide chain). Electron energy loss spectroscopy indicated compositional variations within the matrix, and between the crystallites and matrix. Most notably, calcium was found exclusively in the crystallites. Attempts to produce synthetic analogues of dragline, which exhibits an unparalleled combination of strength, stiffness, and toughness, cannot depend solely on duplicating the constituent proteins. The complex hierarchical microstructure of the natural material must be taken into account. © 1994 John Wiley & Sons, Inc.     

Crystallization and preliminary x-ray analysis of the flavoenzyme vanillyl-alcohol oxidase from Penicillium Simplicissimum

Vanillyl-alcohol oxidase catalyses the oxidation of several 4-hydroxybenzyl alcohols by using 8-α-(N³-histidyl)-FAD as a covalently bound prosthetic group. Crystals of vanillyl-alcohol oxidase from Penicillium simplicissimum have been grown by using the vapor diffusion technique. The space group was found to be I4, with cell dimensions a = b = 140.5 Å, c = 132.9 Å. Diffraction data have been recorded to 3.2 Å resolution by using a laboratory source and to 2.5 Å resolution on flash freezing the crystal at the ELETTRA Synchrotron X-ray diffraction beam line. Proteins 27:601–603, 1997. © 1997 Wiley-Liss Inc.     

Expression,crystallization and preliminary X-ray diffraction study of FtsY,the docking protein of the signal recognition particle of E. coli

FtsY is the docking protein or SRα homologue in E. coli. It is involved in targeting secretory proteins to the cytoplasmic membrane by interacting with the signal recognition particle, controlled by guanosine 5′-triphosphate. Two different constructs have been used in crystallization studies: the full-length protein and a truncated fragment with a his-tag at the C terminus. Only the second construct resulted in crystals suitable for x-ray diffraction. The crystals belong to the monoclinic space group P2₁ with cell dimensions a = 32.20 Å, b = 79.57 Å, c = 59.21 Å, and β = 94.45, and contain one molecule per asymmetric unit. At cryogenic temperatures the crystals diffract to a resolution limit of 2.5 Å by using a rotating anode, and beyond 1.8 Å by using synchrotron radiation. Proteins 28:285–288, 1997. © 1997 Wiley-Liss Inc.     

Disordered Single Crystal Evidence for a Quadruple Helix Formed by Guanosine 5′-Monophosphate

Abstract

The disodium salt of guanosine 5′-monophosphate (5′-GMP) has been crystallized earlier in an orthorhombic array. We have obtained a new crystal form of 5′-GMP at pH 8 which reveals a clear helical nature, with guanine bases stacked perpendicular to the helix axis. Although the X-ray pictures show partial disorder, they can be indexed on a hexagonal net with a = b = 28.6 Å,c = 9.8 Å, V= 6942ų(1Å = 0.1 nm). The probable space group is P6₄, and past experience with ca. 600 ų per base in oligonucleotide crystals suggests that the cell contains 12 GMP molecules. The crystal packing parameters and the intensity distribution agree with a model of three hydrogen-bonded guanine tetrads in the unit cell, stacked so as to build a quadruple helix similar to that proposed earlier from fiber studies (Zimmerman, S.B., J. Mol. Biol. 106, 663–672 (1976)).     

Crystallization and preliminary X-ray analysis of the cytoplasmic domain of human erythrocyte band 3

A cytoplasmic domain of the human erythrocyte membrane protein band 3 (M_r = 42,500), residues 1–379, expressed in and purified from E. coli, has been crystallized by the method of vapor diffusion in sitting drops with subsequent streak-seeding at room temperature. Initial crystals were grown from solutions containing 65–68% saturated ammonium sulfate at pH 4.9 and 2 mg/ml protein. Subsequent streak-seeding into solutions of 50–53% ammonium sulfate at pH 4.9 and 7 mg/ml protein produced single crystals suitable fur X-ray analysis, which contained pure protein as revealed by gel electrophoresis. The crystals belong to the monoclinic space group C2 with cell dimensions of a = 178.8 Å, b = 90.5 Å, c = 122.1 Å, and β = 131.3° and diffract at least to 2.7 Å resolution (at 100 K). A self-rotation function shows the presence of approximate 222 local symmetry. © 1995 Wiley-Liss, Inc.     

Crystallization and preliminary x-ray diffraction studies of a monoclonal antibody fab fragment against foot-and-mouth disease virus and of its complex with the main antigenic site peptide

The Fab fragment of the neutralizing monoclonal antibody SD6 elicited against foot-and-mouth disease virus (FMDV) C-SBcl and its complex with a peptide, corresponding to the major antigenic site of FMDV (VPl residues 136–150, YTASARGDLAHLTTT), have been crystallized using the hanging drop vapor diffusion techniques. For the isolated Fab, crystals diffracting to 2.5 Å resolution were obtained at room temperature using ammonium sulfate as precipitant. These crystals are monoclinic, space group C2, and unit cell parameters a = 109.53 Å, b = 89.12 Å, c = 64.04 Å, and β = 112.9° and contain one Fab molecule per asymmetric unit. Crystals from the complex diffract, at least, to 2.8 Å resolution and were obtained, at room temperature, using PEG as precipitant. These crystals are monoclinic, space group P2, and unit cell parameters a = 56.11 Å, b = 60.67 Å, c = 143.45 Å, and β = 95.4°, Density packing considerations indicate that there are two Fab molecules in the asymmetric unit. © 1994 John Wiley & Sons, Inc.     

Crystallization and preliminary x-ray studies of I-CreI: a group I intron-encoded endonuclease from C. reinhardtii

Group I intron endonuclease I-CreI is encoded by an open reading frame contained within a self-splicing intron in the Chlamydomonas reinhardtii chloroplast 23S rRNA gene. I-CreI initiates the lateral transfer or homing of this intron by specifically recognizing and cleaving a pseudopalindromic 19–24 bp homing site in chloroplast 23S rRNA genes that lack the intron. The gene encoding this enzyme has been subcloned, and the protein product has been purified and crystallized. The crystals belong to space group P321, with unit cell dimensions a = b = 78.2 Å, c = 67.4 Å. The crystal unit cell is consistent with an asymmetric unit consisting of the enzyme monomer. The specific volume of this unit cell is 3.3 ų/Da. The crystals diffract to at least 3.0 Å resolution after flash-cooling, when using a rotating anode x-ray source and an RAXIS image plate detector. © 1997 Wiley-Liss Inc.     

Side-chain conformation in poly(γ-phenethyl-L-glutamate)

X-ray diffraction and energy-minimization results are reported for poly(γ-phenethyl-L -glutamate). Orthorhombic unit-cell parameters of drawn fibers are a = 15.4 Å, b = 26.6 Å, c = 54.4 Å. Atomic coordinates are derived for an α-helix peptide conformation that corresponds to a calculated side-chain internal energy minimum. The side-chain conformation correlates well with the electron density projection; the side chains wrap around the α-helical main chain with the phenethyl ester group directed toward the N-terminus. The para-axis of the benzene ring is inclined at an angle nearly nearly normal to the helix axis. The x-ray structure factors calculated for this model, when compared to the 10 observed structure factors, yield a crystallographic reliability index of R = 0.23.     

Stereochemistry of Schellman motifs in peptides: Crystal structure of a hexapeptide with a C‐terminus 6 → 1 hydrogen bond

The Schellman motif is a widely observed helix terminating structural motif in proteins, which is generated when the C‐terminus residue adopts a left‐handed helical (α_L) conformation. The resulting hydrogen‐bonding pattern involves the formation of an intramolecular 6 → 1 interaction. This helix terminating motif is readily mimicked in synthetic helical peptides by placing an achiral residue at the penultimate position of the sequence. Thus far, the Schellman motif has been characterized crystallographically only in peptide helices of length 7 residues or greater. The structure of the hexapeptide Boc–Pro–Aib–Gly–Leu–Aib–Leu–OMe in crystals reveal a short helical stretch terminated by a Schellman motif, with the formation of 6 → 1 C‐terminus hydrogen bond. The crystals are in the space group P2₁2₁2₁ with a = 18.155(3) Å, b = 18.864(8) Å, c = 11.834(4) Å, and Z = 4 . The final R₁ and wR₂ values are 7.68 and 14.6%, respectively , for 1524 observed reflections [F_o ≥ 3ς(F_o)]. A 6 → 1 hydrogen bond between Pro(1)CO · · · Leu(6)NH and a 5 → 2 hydrogen bond between Aib(2)CO · · · Aib(5)NH are observed. An analysis of the available oligopeptides having an achiral Aib residue at the penultimate position suggests that chain length and sequence effects may be the other determining factors in formation of Schellman motifs. © 1999 John Wiley & Sons, Inc. Biopoly 50: 13–22, 1999     

Characterization of crystals of Penicillium purpurogenum acetyl xylan esterase from high-resolution X-ray diffraction

Acetyl xylan esterase from Penicillium purpurogenum, a single-chain 23 kDa member of a newly characterized family of esterases that cleaves side chain ester linkages in xylan, has been crystallized. The crystals diffract to better than 1 Å resolution at the Cornell High Energy Synchrotron Source (CHESS) and are highly stable in the synchrotron radiation. The space group is P2₁2₁2₁ and cell dimensions are a = 34.9 Å, b = 61.0 Å, c = 72.5 Å.     

An X-Ray diffraction study of poly-L-ornithine hydrobromide

An X-ray study has been made of the synthetic polypeptide poly-L -ornithine hydrobromide to investigate whether, like the chemically related polypeptides poly-L -lysine and poly-L -arginine hydrochlorides, it can undergo conformational changes merely from variations in its degree of hydration. X-ray powder and fiber photographs of specimens with from half up to about three molecules of water per ornithine residue show features that suggest a “cross-β-pleated-sheet” structure. Each pleated sheet is formed from parallel chains and the sheets are piled up along the b axis. The spacings, which do not vary appreciably with hydration, can be satisfactorily indexed in terms of an orthogonal unit cell with a = 4.60 Å, b = 30.2 Å, and c = 6.64 Å. These dimensions are shown by models to be compatible with the proposed structure. Removal of the last half molecule of water results in a very diffuse pattern but on rehydration the sharp pattern reappears. Specimens containing four to nine molecules of water per residue show a quite different pattern. Reflections other than equatorial are absent in oriented diagrams except for a 5.4 Å diffuse streak across the meridian which is suggestive of an α-helical structure. Increasing the relative humidity from 86% to about 100% causes the a axis of the hexagonal unit cell to increase from 14.7 Å to 15.3 Å. On drying, the β structure reappears once again. These conformational changes are very similar to those observed in poly-L -lysine hydrochloride except that the latter shows a more stable α-helical form. This difference may be explained in terms of stabilizing hydrophobic interactions between side chains, since ornithine has a shorter side chain than lysine.     

Structure of a cellulose I–ethylenediamine complex

The structure of a crystalline cellulose I–ethylenediamine complex has been determined by x-ray diffraction methods as part of an investigation of cellulose–solvent interaction. The complex studied is that formed when native ramie fibers are swollen in ethylenediamine and then vacuum-dried. The unit cell is monoclinic with dimensions a = 12.87 Å, b = 9.52 Å, c = 10.35 Å, and γ = 118.8°, and it contains disaccharide segments of two chains, with one ethylenediamine per glucose residue. The refined model contains parallel cellulose chains that are linked by hydrogen-bonded ethylenediamine molecules. The chains along the b-axis are packed in register, leading to stacks of chains analogous to those in chitin. All the hydroxyl groups are satisfactorily hydrogen-bonded and each ethylenediamine forms four donor and two acceptor hydrogen bonds. From this work it can be seen that the interaction of cellulose I with ethylenediamine involves scission of the intermolecular hydrogen bonds followed by disruption of the stacks of quarter-staggered chains.