Determining the crystal structure of cellulose III(I) by modeling

Recently, a one-chain monoclinic unit cell for cellulose III(I) having P2(1) symmetry and a single glucose in the asymmetric unit was proposed, based on high-resolution diffraction patterns. The new work challenged a two-chain structure that was published 25 years earlier, although it did not provide new three-dimensional coordinates. Our goals were to solve the structure by modeling, find whether modeling would reject the previously determined two-chain unit cell, and compare the model with the anticipated experimental structure. Combinations of three rotamers of the O-2, O-3, and O-6 hydroxyl groups produced 27 'up' and 27 'down' starting structures. Clusters ('minicrystals') of 13 cellotetraose chains terminated by methyl groups for each of the 54 starting structures were optimized with MM3(96). Hydroxyl groups on 16 of these 54 structures reoriented to give very similar hydrogen-bonding schemes in the interiors, along with the lowest energies. Hydrogen bonds included the usual intramolecular O-3H...O-5' linkage, with O-6' also accepting from O-3H. Interchain hydrogen bonds form an infinite, cooperative O-6H...O-2H...O-6 network. Direct comparison of total minicrystal energies for the one- and two-chain unit cell was inappropriate because the two-chain cell's alternate chains are shifted 0.9 A along the z-axis. To get comparable energy values, models were built with both cellotetraose and cellohexaose chains. The differences in their energies represent the energies for the central layers of cellobiose units. The one-chain cell models had much lower energy. The eight best 'up' one-chain models agree reasonably well with the structure newly determined by experiment.     

The crystal and molecular structures of cellulose I and II

The paper describes molecular dynamics (MD) simulations on the crystal structures of the Iβ and II phases of cellulose. Structural proposals for each of these were made in the 1970s on the basis of X-ray diffraction data. However, due to the limited resolution of these data some controversies remained and details on hydrogen bonding could not be directly obtained. In contrast to structure factor amplitudes in X-ray diffraction, energies, as obtained from MD simulations, are very sensitive to the positions of the hydroxyl hydrogen atoms. Therefore the latter technique is very suitable for obtaining such structural details. MD simulations of the Iβ phase clearly shows preference for one of the two possible models in which the chains are packed in a parallel orientation. Only the parallel-down mode (in the definition of Gardner and Blackwell (1974) J Biopolym 13: 1975-2001) presents a stable structure. The hydrogen bonding consists of two intramolecular hydrogen bonds parallel to the glycosidic linkage for both chains, and two intralayer hydrogen bonds. The layers are packed hydrophobically. All hydroxymethyl group are positioned in the tg conformation. For the cellulose II form it was found that, in contrast to what seemed to emerge from the X-ray fibre diffraction data, both independent chains had the gt conformation. This idea already existed because of elastic moduli calculations and 13C-solid state NMR data. Recently, the structure of cellotetraose was determined. There appear to be a striking similarity between the structure obtained from the MD simulations and this cellotetraose structure in terms of packing of the two independent molecules, the hydrogen bonding network and the conformations of the hydroxymethyl group, which were also gt for both molecules. The structure forms a 3D hydrogen bonded network, and the contribution from electrostatics to the packing is more pronounced than in case of the Iβ structure. In contrast to what is expected, in view of the irreversible transition of the cellulose I to II form, the energies of the Iβ form is found to be lower than that of II by 1 kcal mol-1 per cellobiose. This revised version was published online in November 2006 with corrections to the Cover Date.     

Supramolecular structure characterization of molecularly thin cellulose I nanoparticles

Unusual fractions of cellulose microfibrils from woody material with dimensions of hundreds of nanometers in length and single digit angstrom thickness were obtained by intensive sonication of TEMPO-oxidized cellulose fibers. These cellulose microfibril fragments, composed of many mono- and bilayer molecular sheets, were analyzed with scattering and spectroscopy techniques to understand the structural changes at the supramolecular level. XRD data indicated that sonication breaks the cellulose microfibrils along its (200) planes, yet some form of the Iβ crystalline structure is still retained with reduced crystallinity. The Raman and FTIR analysis indicated structural changes to the cellulose microfibrils do not occur until after sonication; furthermore, AFM observation indicates that the structural changes began to occur within 5 min of sonication. An altered supramolecular structure is evident after sonication: major features from cellulose I are preserved, although certain spectral features similar to mercerized and ball milled cellulose appeared in its FTIR and Raman spectra. These spectral differences are traced to changes in the methine environment, hydroxymethyl conformations, and skeletal vibrations. By integrating the present findings and previous research, a cellulose molecular sheet delamination scheme is proposed to describe this microfibril fragmentation along its (200) plane.     

Supramolecular structure characterization of cellulose II nanowhiskers produced by acid hydrolysis of cellulose I substrates

Cellulose II nanowhiskers (CNW-II) were produced by treatment of microcrystalline cellulose with sulfuric acid by both controlling the amount of H(2)SO(4) introduced and the time of addition during the hydrolysis process. The crystalline structure was confirmed by both XRD and (13)C CP-MAS NMR spectroscopy. When observed between crossed polarizers, the cellulose II suspension displayed flow birefringence and was stable for several months. The CNW-II nanowhiskers were significantly smaller than the cellulose I nanowhiskers (CNW-I) and had a rounded shape at the tip. The CNW-II average length and height were estimated by AFM to be 153 ± 66 and 4.2 ± 1.5 nm, respectively. An average width of 6.3 ± 1.7 nm was found by TEM, suggesting a ribbon-shape morphology for these whiskers. The average dimensions of the CNW-II elementary crystallites were estimated from the XRD data, using Scherrer's equation. A tentative cross-sectional geometry consistent with both XRD and NMR data was then proposed and compared with the geometry of the CNW-I nanowhiskers.     

The crystal structure of samarosporin I at atomic resolution

The atomic resolution structures of samarosporin I have been determined at 100 and 293 K. This is the first crystal structure of a natural 15‐residue peptaibol. The amino acid sequence in samarosporin I is identical to emerimicin IV and stilbellin I. Samarosporin is a peptide antibiotic produced by the ascomycetous fungus Samarospora rostrup and belongs to peptaibol subfamily 2. The structures at both temperatures are very similar to each other adopting mainly a 3₁₀‐helical and a minor fraction of α‐helical conformation. The helices are significantly bent and packed in an antiparallel fashion in the centered monoclinic lattice leaving among them an approximately 10‐Å channel extending along the crystallographic twofold axis. Only two ordered water molecules per peptide molecule were located in the channel. Comparisons have been carried out with crystal structures of subfamily 2 16‐residue peptaibols antiamoebin and cephaibols. The repercussion of the structural analysis of samarosporin on membrane function is discussed. Copyright © 2012 European Peptide Society and John Wiley & Sons, Ltd.     

Molecular dynamics simulations of solvated crystal models of cellulose I(alpha) and III(I)

Swelling behaviors of cellulose I(alpha) and III(I) crystals have been studied using molecular dynamics simulations of the solvated finite-crystal models. The typical crystal models consisted of 48 x 10-mer chains. For the cellulose I(alpha) crystal, models consisting of different numbers of chains and chain lengths were also studied. The structural features of the swollen crystal models, including the cellulose I(beta) crystal model reported previously, were compared. A distinct right-handed twist was observed for models of the native cellulose crystals (cellulose I(alpha) and I(beta)), with a greater amount of twisting observed for the I(alpha) crystal model. Although the amount of twist decreased with increasing dimensions of the cellulose I(alpha) crystal model, the relative changes in twist angle suggest that considerable twist would arise in a crystal model of the actual dimensions. In contrast to the swelling behavior of crystal models of the native cellulose, the cellulose III(I) crystal model exhibited local, gradual disordering at the corner of the reducing end. Comparison of the lattice energies indicated that the cellulose chains of the I(beta) crystal were packed in the most stable fashion, whereas those of the I(alpha) and III(I) crystals were in a metastable state, which is consistent with the crystallization behaviors observed. Upon heating of the native cellulose crystal models, the chain sheets of the I(alpha) model showed a continuous increase in twist angle, suggesting weaker intersheet interactions in this model. The swollen crystal models of cellulose I(alpha) and III(I) reproduce well the representative structural features observed in the corresponding crystal structures. The crystal model twist thus characterizes the swelling behavior of the native cellulose crystal models, which seems to be related to the insolubility of the crystals.     

High resolution crystal structure of domain I of the Saccharomyces cerevisiae homing endonuclease PI-SceI

The homing endonuclease PI-SceI from Saccharo myces cerevisiae consists of two domains. The protein splicing domain I catalyzes the excision of the mature endonuclease (intein) from a precursor protein and the religation of the flanking amino acid sequences (exteins) to a functional protein. Furthermore, domain I is involved in binding and recognition of the specific DNA substrate. Domain II of PI-SceI, the endonuclease domain, which is structurally homologous to other homing endonucleases from the LAGLIDADG family, harbors the endonucleolytic center of PI-SceI, which in vivo initiates the homing process by introducing a double-strand cut in the ~35 bp recognition sequence. At 1.35 Å resolution, the crystal structure of PI-SceI domain I provides a detailed view of the part of the protein that is responsible for tight and specific DNA binding. A geometry-based docking of the 75° bent recognition sequence to the full-length protein implies a conformational change or hinge movement of a subdomain of domain I, the tongs part, that is predicted to reach into the major groove near base pairs +16 to +18.     

Polymorphism of cellulose I family: reinvestigation of cellulose IVI

Polymorphs of cellulose I, III(I), and IV(I) have been investigated by X-ray diffraction, FT-IR, and solid-state (13)C NMR spectroscopy. Highly crystalline cellulose III(I) samples were prepared by treating cellulose samples in supercritical ammonia at 140 degrees C for 1 h, and conventional cellulose III(I) samples were prepared by liquid ammonia treatment. The cellulose IV(I) sample of highest crystallinity was that prepared from Cladophora cellulose III(I) in supercritical ammonia, followed by the sample treated in glycerol at 260 degrees C for 0.5 h, whereas the lowest crystallinity was observed in ramie cellulose prepared by conventional liquid ammonia treatment followed by glycerol annealing. In general, the perfection of cellulose IV(I) depends on the crystallinity of the original material: either of the starting cellulose I or of the cellulose III(I) after ammonia treatment. The product thus obtained was analogous to cellulose I(beta), which is what it should be called rather than cellulose IV(I). If the existence of the polymorph cellulose IV(I) is not accepted, the observations on which it has been based may be explained by the fact that the structure termed cellulose IV(I) is cellulose I(beta) which contains lateral disorder.     

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.     

The dependence of pyrolysis behavior on the crystal state of cellulose

Cellulose was dissolved in the ionic liquid 1-butyl-3-methylimidazolium chloride, and then regenerated from the solution by using different methods. Thermogravimetric analysis (TG)-Differential Scanning Calorimetry (DSC), X-ray diffraction (XRD), and Scanning Electron Microscopy (SEM) were used to characterize the structure of the original and regenerated cellulose. Cellulose II or amorphous cellulose was obtained by pouring cellulose solution into de-ioned water or pouring de-ioned water into cellulose solution, respectively. The pyrolysis behavior of original and regenerated cellulose was tested in a fixed bed reactor. The pyrolysis of cellulose I gave high content of furfural and 1,4;3,6-dianhydro-alpha-d-glucopyranose in the liquid products, and cellulose II and amorphous cellulose gave high content of furfural and 5-(hydroxymethyl)-2-furancarboxyaldehyde, with 5-(hydroxymethyl)-2-furancarboxyaldehyde the highest for cellulose II and furfural the highest for amorphous cellulose. And the treatment of the cellulose samples favored the removal of oxygen in the form of CO₂ in the pyrolysis.     

Amine free crystal structure: the crystal structure of d(CGCGCG)2 and methylamine complex crystal

We succeeded in the crystallization of d(CGCGCG)2 and methylamine Complex. The crystal was clear and of sufficient size to collect the X-ray crystallographic data up to 1.0 A resolution using synchrotron radiation. As a result of X-ray crystallographic analysis of 2Fo-Fc map was much clear and easily traced. It is the first time monoamine co-crystallizes with d(CGCGCG)2. However, methylamine was not found from the complex crystal of d(CGCGCG)2 and methylamine. Five Mg ions were found around d(CGCGCG)2 molecules. These Mg ions neutralized the anion of 10 values of the phosphate group of DNA with five Mg2+. DNA stabilized only by a metallic ion and there is no example of analyzing the X-ray crystal structure like this. Mg ion stabilizes the conformation of Z-DNA. To use monoamine for crystallization of DNA, we found that we can get only d(CGCGCG)2 and Mg cation crystal. Only Mg cation can stabilize the conformation of Z-DNA. The method of using the monoamine for the crystallization of DNA can be applied to the crystallization of DNA of long chain of length in the future like this.     

Swelling behavior of the cellulose Ibeta crystal models by molecular dynamics

The various crystal models of cellulose Ibeta, each differing in crystal size, have been studied by computer simulation using the amber molecular-dynamics package and the GLYCAM parameters. The four types of crystal model were constructed by a combination of two base-plane sizes, consisting of either 24 or 48 chains and two chain lengths having either 10 or 20 residues. The base planes of the crystal models were composed by the edges of the [1,1,0], [1,-1,0], and [1,0,0] crystal planes, where the [1,1,0] plane was assigned to the longest edge. The crystal models were soaked in water boxes to investigate their swelling behavior. Unexpectedly, the crystal models twisted quickly to form a slightly right-handed shape during the initial approximately 50 ps and that, in a steady, swollen state, the twisted forms remained for the rest of the simulation time. In spite of such overall deformation, the inner part of the swollen model fairly reproduced the important structural features of the original crystal structure, such as the rotational positions of the substituent groups and the hydrogen-bonding scheme. On heating the crystal model up to 550 K, the twisted shape was conserved in most of the temperature range, while the initial conformations of the substituent groups deviated above approximately 430 K, followed by appreciable disordering in chain sheets at higher temperatures. It is suggested that some internal tensions are involved within a chain sheet of the initial structure. In the course of swelling, some of these tensions were released to introduce a twisted shape in the crystal models.     

The X-ray crystal structure of beta-ketoacyl [acyl carrier protein] synthase I

The crystal structure of the fatty acid elongating enzyme beta-ketoacyl [acyl carrier protein] synthase I (KAS I) from Escherichia coli has been determined to 2.3 A resolution by molecular replacement using the recently solved crystal structure of KAS II as a search model. The crystal contains two independent dimers in the asymmetric unit. KAS I assumes the thiolase alpha(beta)alpha(beta)alpha fold. Electrostatic potential distribution reveals an acyl carrier protein docking site and a presumed substrate binding pocket was detected extending the active site. Both subunits contribute to each substrate binding site in the dimer.     

New insight into cellulose structure by atomic force microscopy shows the i(alpha) crystal phase at near-atomic resolution

The organization of the surface of cellulose is important in cell structure, as well as in industrial processing and modification. Using atomic force microscopy, we show that the I(alpha) phase of native cellulose first proposed in 1984 and subsequently characterized by a triclinic unit cell exists over large areas of the surface of microcrystals from Valonia, one of the most highly crystalline celluloses. There is startling agreement between the observed structure and crystal models, and it is possible to identify the specific crystal face being imaged. The near-atomic resolution images also offer an insight into structural reconstructions at the surface compared to the interior. We are able to assign features in the images to particular side groups attached to the glucose ring and find indications of subtle modifications of the position of surface hydroxyls due to changes in hydrogen bonding.     

Respiratory complex I: mechanistic and structural insights provided by the crystal structure of the hydrophilic domain

Complex I of respiratory chains plays a central role in cellular energy production. Mutations in its subunits lead to many human neurodegenerative diseases. Recently, a first atomic structure of the hydrophilic domain of complex I from Thermus thermophilus was determined. This domain represents a catalytic core of the enzyme. It consists of eight different subunits, contains all the redox centers, and comprises more than half of the entire complex. In this review, novel mechanistic implications of the structure are discussed, and the effects of many known mutations of complex I subunits are interpreted in a structural context.     

Geometry of proline and hydroxyproline I: An analysis of X-ray crystal structure data

We have carried out an analysis of crystal structure data on prolyl and hydroxyprolyl moieties in small molecules. The flexibility of the pyrrolidine ring due to the pyramidal character of nitrogen has been defined in terms of two projection angles delta 1 and delta 2. The distribution of these parameters in the crystal structures is found to be consistent with results of the energy calculations carried out on prolyl moieties in our laboratory.     

The crystal structure of pyroglutamyl peptidase I from Bacillus amyloliquefaciens reveals a new structure for a cysteine protease

BACKGROUND: The N-terminal pyroglutamyl (pGlu) residue of peptide hormones, such as thyrotropin-releasing hormone (TRH) and luteinizing hormone releasing hormone (LH-RH), confers resistance to proteolysis by conventional aminopeptidases. Specialized pyroglutamyl peptidases (PGPs) are able to cleave an N-terminal pyroglutamyl residue and thus control hormonal signals. Until now, no direct or homology-based three-dimensional structure was available for any PGP. RESULTS: The crystal structure of pyroglutamyl peptidase I (PGP-I) from Bacillus amyloliquefaciens has been determined to 1.6 A resolution. The crystallographic asymmetric unit of PGP-I is a tetramer of four identical monomers related by noncrystallographic 222 symmetry. The protein folds into an alpha/beta globular domain with a hydrophobic core consisting of a twisted beta sheet surrounded by five alpha helices. The structure allows the function of most of the conserved residues in the PGP-I family to be identified. The catalytic triad comprises Cys144, His168 and Glu81. CONCLUSIONS: The catalytic site does not have a conventional oxyanion hole, although Cys144, the sidechain of Arg91 and the dipole of an alpha helix could all stabilize a negative charge. The catalytic site has an S1 pocket lined with conserved hydrophobic residues to accommodate the pyroglutamyl residue. Aside from the S1 pocket, there is no clearly defined mainchain substrate-binding region, consistent with the lack of substrate specificity. Although the overall structure of PGP-I resembles some other alpha/beta twisted open-sheet structures, such as purine nucleoside phosphorylase and cutinase, there are important differences in the location and organization of the active-site residues. Thus, PGP-I belongs to a new family of cysteine proteases.     

Synthesis and crystal structure of tetrameric silver(I) 3,5-di-tert-butyl-pyrazolate

A tetrameric [Ag(μ-3,5-^tBu₂pz)]₄ · CH₂Cl₂ (1 · CH₂Cl₂) has been prepared and structurally characterized. The four Ag-atoms are in an approximate rhombic arrangement with pyrazolato bridges alternating on either side of the Ag₄-plane. A ¹H NMR study shows partial decomposition of 1 to the mononuclear [Ag(3,5-^tBu₂pzH)₂]⁺ in solution.