Centre de Recherches sur les Macromolécules Végétales

The amino acid sequences of 301 glycosyl hydrolases and related enzymes have been compared. A total of 291 sequences corresponding to 39 EC entries could be classified into 35 families. Only ten sequences (less than 5% of the sample) could not be assigned to any family. With the sequences available for this analysis, 18 families were found to be monospecific (containing only one EC number) and 17 were found to be polyspecific (containing at least two EC numbers). Implications on the folding characteristics and mechanism of action of these enzymes and on the evolution of carbohydrate metabolism are discussed. With the steady increase in sequence and structural data, it is suggested that the enzyme classification system should perhaps be revised.

The crystal and molecular structure, together with the hydrogen-bonding system in cellulose I(alpha), has been determined using atomic-resolution synchrotron and neutron diffraction data recorded from oriented fibrous samples prepared by aligning cellulose microcrystals from the cell wall of the freshwater alga Glaucocystis nostochinearum. The X-ray data were used to determine the C and O atom positions. The resulting structure is a one-chain triclinic unit cell with all glucosyl linkages and hydroxymethyl groups (tg) identical. However, adjacent sugar rings alternate in conformation giving the chain a cellobiosyl repeat. The chains organize in sheets packed in a "parallel-up" fashion. The positions of hydrogen atoms involved in hydrogen-bonding were determined from a Fourier-difference analysis using neutron diffraction data collected from hydrogenated and deuterated samples. The differences between the structure and hydrogen-bonding reported here for cellulose I(alpha) and previously for cellulose I(beta) provide potential explanations for the solid-state conversion of I(alpha) --> I(beta) and for the occurrence of two crystal phases in naturally occurring cellulose.

Never-dried and once-dried hardwood celluloses were oxidized by a 2,2,6,6-tetramethylpiperidine-1-oxyl radical (TEMPO)-mediated system, and highly crystalline and individualized cellulose nanofibers, dispersed in water, were prepared by mechanical treatment of the oxidized cellulose/water slurries. When carboxylate contents formed from the primary hydroxyl groups of the celluloses reached approximately 1.5 mmol/g, the oxidized cellulose/water slurries were mostly converted to transparent and highly viscous dispersions by mechanical treatment. Transmission electron microscopic observation showed that the dispersions consisted of individualized cellulose nanofibers 3-4 nm in width and a few microns in length. No intrinsic differences between never-dried and once-dried celluloses were found for preparing the dispersion, as long as carboxylate contents in the TEMPO-oxidized celluloses reached approximately 1.5 mmol/g. Changes in viscosity of the dispersions during the mechanical treatment corresponded with those in the dispersed states of the cellulose nanofibers in water.

There are numerous examples where animals or plants synthesize extracellular high-performance skeletal biocomposites consisting of a matrix reinforced by fibrous biopolymers. Cellulose, the world's most abundant natural, renewable, biodegradable polymer, is a classical example of these reinforcing elements, which occur as whisker-like microfibrils that are biosynthesized and deposited in a continuous fashion. In many cases, this mode of biogenesis leads to crystalline microfibrils that are almost defect-free, with the consequence of axial physical properties approaching those of perfect crystals. This quite "primitive" polymer can be used to create high performance nanocomposites presenting outstanding properties. This reinforcing capability results from the intrinsic chemical nature of cellulose and from its hierarchical structure. Aqueous suspensions of cellulose crystallites can be prepared by acid hydrolysis of cellulose. The object of this treatment is to dissolve away regions of low lateral order so that the water-insoluble, highly crystalline residue may be converted into a stable suspension by subsequent vigorous mechanical shearing action. During the past decade, many works have been devoted to mimic biocomposites by blending cellulose whiskers from different sources with polymer matrixes.

301 glycosyl hydrolases and related enzymes corresponding to 39 EC entries of the I.U.B. classification system have been classified into 35 families on the basis of amino-acid-sequence similarities [Henrissat (1991) Biochem. J. 280, 309-316]. Approximately half of the families were found to be monospecific (containing only one EC number), whereas the other half were found to be polyspecific (containing at least two EC numbers). A > 60% increase in sequence data for glycosyl hydrolases (181 additional enzymes or enzyme domains sequences have since become available) allowed us to update the classification not only by the addition of more members to already identified families, but also by the finding of ten new families. On the basis of a comparison of 482 sequences corresponding to 52 EC entries, 45 families, out of which 22 are polyspecific, can now be defined. This classification has been implemented in the SWISS-PROT protein sequence data bank.

Never-dried native celluloses (bleached sulfite wood pulp, cotton, tunicin, and bacterial cellulose) were disintegrated into individual microfibrils after oxidation mediated by the 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO) radical followed by a homogenizing mechanical treatment. When oxidized with 3.6 mmol of NaClO per gram of cellulose, almost the totality of sulfite wood pulp and cotton were readily disintegrated into long individual microfibrils by a treatment with a Waring Blendor, yielding transparent and highly viscous suspensions. When observed by transmission electron microscopy, the wood pulp and cotton microfibrils exhibited a regular width of 3-5 nm. Tunicin and bacterial cellulose could be disintegrated by sonication. A bulk degree of oxidation of about 0.2 per one anhydroglucose unit of cellulose was necessary for a smooth disintegration of sulfite wood pulp, whereas only small amounts of independent microfibrils were obtained at lower oxidation levels. This limiting degree of oxidation decreased in the following order: sulfite wood pulp > cotton > bacterial cellulose, tunicin.

The crystal and molecular structure, together with the hydrogen-bonding system in cellulose Iα, has been determined using atomic-resolution synchrotron and neutron diffraction data recorded from oriented fibrous samples prepared by aligning cellulose microcrystals from the cell wall of the freshwater alga Glaucocystis nostochinearum. The X-ray data were used to determine the C and O atom positions. The resulting structure is a one-chain triclinic unit cell with all glucosyl linkages and hydroxymethyl groups (tg) identical. However, adjacent sugar rings alternate in conformation giving the chain a cellobiosyl repeat. The chains organize in sheets packed in a “parallel-up” fashion. The positions of hydrogen atoms involved in hydrogen-bonding were determined from a Fourier-difference analysis using neutron diffraction data collected from hydrogenated and deuterated samples. The differences between the structure and hydrogen-bonding reported here for cellulose Iα and previously for cellulose Iβ provide potential explanations for the solid-state conversion of Iα → Iβ and for the occurrence of two crystal phases in naturally occurring cellulose.

Research Article| June 01 1996 Updating the sequence-based classification of glycosyl hydrolases Bernard HENRISSAT; Bernard HENRISSAT ‡ *Centre de Recherches sur les Macromolécules Végétales, France§C.N.R.S., BP 53, 38041 Grenoble Cédex, France ‡To whom correspondence should be addressed. Search for other works by this author on: This Site PubMed Google Scholar Amos BAIROCH Amos BAIROCH †Medical Biochemistry Department, Centre Médical Universitaire, CH-1211 Geneva 4, Switzerland§C.N.R.S., BP 53, 38041 Grenoble Cédex, France Search for other works by this author on: This Site PubMed Google Scholar Biochem J (1996) 316 (2): 695–696. https://doi.org/10.1042/bj3160695 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn MailTo Cite Icon Cite Get Permissions Citation Bernard HENRISSAT, Amos BAIROCH; Updating the sequence-based classification of glycosyl hydrolases. Biochem J 1 June 1996; 316 (2): 695–696. doi: https://doi.org/10.1042/bj3160695 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Journal Search Advanced Search This content is only available as a PDF. The Biochemical Society, London © 19961996 Article PDF first page preview Close Modal You do not currently have access to this content.

The shape and size distribution of crystalline nanoparticles resulting from the sulfuric acid hydrolysis of cellulose from cotton, Avicel, and tunicate were investigated using transmission electron microscopy (TEM) and atomic force microscopy (AFM) as well as small- and wide-angle X-ray scattering (SAXS and WAXS). Images of negatively stained and cryo-TEM specimens showed that the majority of cellulose particles were flat objects constituted by elementary crystallites whose lateral adhesion was resistant against hydrolysis and sonication treatments. Moreover, tunicin whiskers were described as twisted ribbons with an estimated pitch of 2.4-3.2 microm. Length and width distributions of all samples were generally well described by log-normal functions, with the exception of tunicin, which had less lateral aggregation. AFM observation confirmed that the thickness of the nanocrystals was almost constant for a given origin and corresponded to the crystallite size measured from peak broadening in WAXS spectra. Experimental SAXS profiles were numerically simulated, combining the dimensions and size distribution functions determined by the various techniques.

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For many ionic polysaccharides, the ability to form gels in the presence of divalent cations such as calcium is the key to biological functions and technological applications. This is particularly true for alginates and pectins, where the regular occurrence of respectively alpha-L-(1-4)-guluronate residues and alpha-D-galacturonate residues generates ordered templates for polymer chain associations that are involved in physical gels. The molecular basis responsible for the strength and the stereospecificity of calcium interactions for the two polysaccharides were investigated in a previous paper (Braccini; et al. Carbohydr. Res. 1999, 119). In the present work, a novel molecular modeling procedure has been developed; it involves a pairing procedure that evaluates all the possible associations of the ordered polyuronate chains with calcium ions to form dimers. Starting from the stable ordered forms of polygalacturonate and polyguluronate, all possible ways to form Ca(2+)-bridged dimers were computed; the parallel and antiparallel relative arrangements of the chains were also considered. Despite the structural analogy between polyguluronate and polygalacturonate chains, significant differences at the level of chain-chain associations are found. The popular "egg box model" can still be referred to in the case of polyguluronate. However, it cannot be used to describe a pectate junction zone as the unique feature of two consecutive chelation site per repeat, that provides a favorable entropic contribution to the interchain association is not reproduced by this pioneering model. The body of these results corroborates the two-stage process in the mechanism of calcium gelation, where the formation of strongly linked dimer associations is followed by the formation of weak inter-dimer associations mainly governed by electrostatic interactions.

Abstract This review concerns the applications of some polysaccharides in the domain of biomaterials and bioactive polymers. Natural polysaccharides from different sources have been studied for a long time, and their main properties are summarized in this paper; some of their derivatives obtained by chemical modification are also described. The main polysaccharides currently used in the biomedical and pharmaceutical domains are chitin and its derivative chitosan, hyaluronan and alginates. Alginates are well known for their property of forming a physical gel in the presence of divalent counterions (Ca, Ba, Sr) whereas carrageenans form a thermoreversible gel; these seaweed polysaccharides are mainly used to encapsulate different materials (cells, bacteria, fungi). Other promising systems are the electrostatic complexes formed when an anionic polysaccharide is mixed with a cationic polysaccharide (e.g. alginate/chitosan or hyaluronan/chitosan). An important development of the applications of polysaccharides can be predicted for the next few years in relation to their intrinsic properties such as biocompatibility and biodegradability in the human body for some of them; they are also renewable and have interesting physical properties (film‐forming, gelling and thickening properties). In addition, they are easily processed in different forms such as beads, films, capsules and fibres. Copyright © 2007 Society of Chemical Industry

Some simple lipid-water systems have been studied by x-ray scattering techniques, as a function of lipid concentration and temperature. Several liquid-crystalline phases have been found, and their structure has been determined: only one of these is lamellar. In all these phases the hydrocarbon part of the lipid molecules has a disordered, liquid-like structure. One biological phospholipid, a human brain extract, has been studied by the same technique, and two liquid-crystalline phases have been found: a lamellar phase, built up by an ordered sequence of lipid and water planar sheets, and a hexagonal phase, which is a hexagonal array of circular cylinders, each cylinder being a thin water channel covered by the hydrophilic groups of the lipid molecules, the hydrocarbon chains filling the gap between the cylinders. The interpretation of the electron microscope observations of the structure of lipoprotein membranes is discussed, and some possible biological implications are suggested.

The authors have informed us that, in the above paper, several polypeptide GalNAc transferases were listed as part of family 2, i.e. a family of inverting enzymes. However, these enzymes transfer GalNAc from UDP-GalNAc to Ser or Thr residues forming an linkage. They are therefore retaining enzymes and, on this basis, they should be removed from family 2 and grouped in a new family (family 27) of retaining nucleotide-diphosphosugar glycosyltransferases. It is important to point out that the sequences of family 27 members display limited similarities with those of enzymes from family 2. It is therefore possible that these two families share some structural similarities. The composition of family 27 is given in the table below.

Abstract A multiordering parameter model for glass‐transition phenomena has been developed on the basis of nonequilibrium thermodynamics. In this treatment the state of the glass is determined by the values of N ordering parameters in addition to T and P ; the departure from equilibrium is partitioned among the various ordering parameters, each of which is associated with a unique retardation time. These times are assumed to depend on T, P , and on the instantaneous state of the system characterized by its overall departure from equilibrium, giving rise to the well‐known nonlinear effects observed in volume and enthalpy recovery. The contribution of each ordering parameter to the departure and the associated retardation times define the fundamental distribution function (the structural retardation spectrum) of the system or, equivalently, its fundamental material response function. These, together with a few experimentally measurable material constants, completely define the recovery behavior of the system when subjected to any thermal treatment. The behavior of the model is explored for various classes of thermal histories of increasing complexity, in order to simulate real experimental situations. The relevant calculations are based on a discrete retardation spectrum, extending over four time decades, and on reasonable values of the relevant material constants in order to imitate the behavior of polymer glasses. The model clearly separates the contribution of the retardation spectrum from the temperature‐structure dependence of the retardation times which controls its shifts along the experimental time scale. This is achieved by using the natural time scale of the system which eliminates all the nonlinear effects, thus reducing the response function to the Boltzmann superposition equation, similar to that encountered in the linear viscoelasticity. As a consequence, the system obeys a rate (time) ‐temperature reduction rule which provides for generalization within each class of thermal treatment. Thus the model establishes a rational basis for comparing theory with experiment, and also various kinds of experiments between themselves. The analysis further predicts interesting features, some of which have often been overlooked. Among these are the impossibility of extraction of the spectrum (or response function) from experiments involving cooling from high temperatures at finite rate; and the appearance of two peaks in the expansion coefficient, or heat capacity, during the heating stage of three‐step thermal cycles starting at high temperatures. Finally, the theory also provides a rationale for interpreting the time dependence of mechanical or other structure‐sensitive properties of glasses as well as for predicting their long‐range behavior.

A new catalytic oxidation using 2,2,6,6-tetramethylpiperidinyl-1-oxyl (TEMPO) and NaClO is applied to hardwood cellulose in water at 60 °C and pH 6.8 with NaClO(2) used as a primary oxidant. The oxidized celluloses with carboxylate content of approximately 0.8 mmol/g were convertible to highly crystalline and individual fibrils 5 nm in width and at least 2 μm in length by disintegration in water. The oxidized celluloses had no aldehyde groups, and high degrees of polymerization of more than 900. Solid-state (13)C NMR and X-ray analyses revealed that the C6 carboxylate groups formed are selectively present on the crystalline fibril surfaces at high densities. Films prepared from the dispersions were transparent and flexible, and exhibited a high tensile strength of 312 MPa even at a low density of 1.47 g/cm(3).

Correct expression of the genetic code at translation is directly correlated with tRNA identity. This survey describes the molecular signals in tRNAs that trigger specific aminoacylations. For most tRNAs, determinants are located at the two distal extremities: the anticodon loop and the amino acid accepting stem. In a few tRNAs, however, major identity signals are found in the core of the molecule. Identity elements have different strengths, often depend more on k cat effects than on K m effects and exhibit additive, cooperative or anti-cooperative interplay. Most determinants are in direct contact with cognate synthetases, and chemical groups on bases or ribose moieties that make functional interactions have been identified in several systems. Major determinants are conserved in evolution; however, the mechanisms by which they are expressed are species dependent. Recent studies show that alternate identity sets can be recognized by a single synthetase, and emphasize the importance of tRNA architecture and anti-determinants preventing false recognition. Identity rules apply to tRNA-like molecules and to minimalist tRNAs. Knowledge of these rules allows the manipulation of identity elements and engineering of tRNAs with switched, altered or multiple specificities.

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Glycosyltransferases (GTs) catalyze the transfer of a sugar moiety from an activated donor sugar onto saccharide and nonsaccharide acceptors. A sequence-based classification spreads GTs in many families thus reflecting the variety of molecules that can be used as acceptors. In contrast, this enzyme family is characterized by a more conserved three-dimensional architecture. Until recently, only two different folds (GT-A and GT-B) have been identified for solved crystal structures. The recent report of a structure for a bacterial sialyltransferase allows the definition of a new fold family. Progress in the elucidation of the structures and mechanisms of GTs are discussed in this review. To accommodate the growing number of crystal structures, we created the 3D-Glycosyltransferase database to gather structural information concerning this class of enzymes.

Nanocomposite materials were obtained using glycerol plasticized starch as the matrix and a colloidal suspension of cellulose whiskers as the reinforcing phase. The cellulose whiskers, prepared from tunicin, consisted of slender parallelepiped rods with a high aspect ratio. After mixing the raw materials and gelatinization of starch, the resulting suspension was cast and evaporated under vacuum. The composites were conditioned at various moisture contents in order to evaluate the effect of this parameter on the composite structure. The resulting films were characterized using scanning electron microscopy, differential scanning calorimetry, water absorption experiments, and wide-angle X-ray scattering. An accumulation of plasticizer in the cellulose/amylopectin interfacial zones was evidenced. The specific behavior of amylopectin chains located near the interface in the presence of cellulose probably led to a transcrystallization phenomenon of amylopectin on cellulose whiskers surface.