Configurational statistics of polysaccharide chains. Part III. Linear β-(1 → 4′) xylan and mannan

The characteristic ratio C_N = 〈r²〉₀/Nl_v² of the β-D (1 → 4′)-linked polysaccharides xylan and mannan has been computed as a function of the angle τ at the bridge oxygen atom and the degree of polymerization N. The calculated values of the characteristic ratio C_N are very high relative to their free rotational dimensions. The characteristic ratio of these polysaecharides converges to the asymptotic value at low degree of polymerization at higher τ values. The low values of the calculated characteristic ratio of xylan compared to cellulose and mannan for the same τ value indicate that the former is more flexible and assumes a compact configuration. A pronounced difference in the values of the characteristic ratio C_N of cellulose and mannan has also been observed lower τ angles (<120°). On the other hand, nearly the same values of C_N have been obtained at higher τ angles (120°–125°), which suggests that, cellulose and mannan may have similar configuralons in certain solvents.     

Structural changes in microcrystalline cellulose in subcritical water treatment

Subcritical water is a high potential green chemical for the hydrolysis of cellulose. In this study microcrystalline cellulose was treated in subcritical water to study structural changes of the cellulose residues. The alterations in particle size and appearance were studied by scanning electron microscopy (SEM) and those in the degree of polymerization (DP) and molar mass distributions by gel permeation chromatography (GPC). Further, changes in crystallinity and crystallite dimensions were quantified by wide-angle X-ray scattering and (13)C solid-state NMR. The results showed that the crystallinity remained practically unchanged throughout the treatment, whereas the size of the remaining cellulose crystallites increased. Microcrystalline cellulose underwent significant depolymerization in subcritical water. However, depolymerization leveled off at a relatively high degree of polymerization. The molar mass distributions of the residues showed a bimodal form. We infer that cellulose gets dissolved in subcritical water only after extensive depolymerization.     

Cellulose biosynthesis: current views and evolving concepts

* AIMS: To outline the current state of knowledge and discuss the evolution of various viewpoints put forth to explain the mechanism of cellulose biosynthesis. * SCOPE: Understanding the mechanism of cellulose biosynthesis is one of the major challenges in plant biology. The simplicity in the chemical structure of cellulose belies the complexities that are associated with the synthesis and assembly of this polysaccharide. Assembly of cellulose microfibrils in most organisms is visualized as a multi-step process involving a number of proteins with the key protein being the cellulose synthase catalytic sub-unit. Although genes encoding this protein have been identified in almost all cellulose synthesizing organisms, it has been a challenge in general, and more specifically in vascular plants, to demonstrate cellulose synthase activity in vitro. The assembly of glucan chains into cellulose microfibrils of specific dimensions, viewed as a spontaneous process, necessitates the assembly of synthesizing sites unique to most groups of organisms. The steps of polymerization (requiring the specific arrangement and activity of the cellulose synthase catalytic sub-units) and crystallization (directed self-assembly of glucan chains) are certainly interlinked in the formation of cellulose microfibrils. Mutants affected in cellulose biosynthesis have been identified in vascular plants. Studies on these mutants and herbicide-treated plants suggest an interesting link between the steps of polymerization and crystallization during cellulose biosynthesis. * CONCLUSIONS: With the identification of a large number of genes encoding cellulose synthases and cellulose synthase-like proteins in vascular plants and the supposed role of a number of other proteins in cellulose biosynthesis, a complete understanding of this process will necessitate a wider variety of research tools and approaches than was thought to be required a few years back.     

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.     

The conformation of single-strand polynucleotides in solution: sedimentation studies of apurinic acid

To elucidate the role of the bases in single-strand polynucleolide conformation, we have studied apurinic acid, a single-strand polydeoxyribonucleotide from which almost half the bases have been removed. The conformation of apurinic acid in aqueous solution near θ condition has been investigated by sedimentation velocity and sedimentation equilibrium measurements. The unperturbed coil dimensions of apurinic acid are essentially identical to those of poly rU of the same degree of polymerization. The dimensions are also similar to those of poly rA at high temperature, where the adenine residues are not stacked upon one another. We conclude that the considerable rigidity of these polynuclotides is conferred not by residual, undetected base stacking, but by restrictions in rotation about the bonds of the backbone. Furthermore, the rigidity of the ribose-phosphate backbone cannot be attributed to interactions involving the 2'—OH group.     

Preparation of a thermosensitive highly regioselective cellulose/N-isopropylacrylamide copolymer through atom transfer radical polymerization

Regioselective copolymerization of N-isopropylacrylamide (NIPAM) onto cellulose was achieved by atom transfer radical polymerization (ATRP) using a regioselectively modified 6- O-bromoisobutyryl-2,3-di- O-methyl cellulose macroinitiator. Varying the ratio of NIPAM to macroinitiator to ligand to transition metal in a Cu(I)Br/ N, N, N', N', N'-pentamethyldiethylenetriamine (PMDETA) catalyst system affected graft yield and degree of polymerization. ATRP proceeded to completion without any trace of the macroinitiator, and a degree of polymerization (DP) of polyNIPAM up to 46.3 was obtained. Increasing the DP of the NIPAM component increased both the thermal decomposition temperature and the glass transition temperature of the copolymer. The grafting of NIPAM also affected the solubility properties of the methylcellulose. The 6- O-polyNIPAM-2,3-di- O-methyl cellulose formed a stable suspension in water at room temperature and underwent a hydrophillic-to-hydrophobic transition and copolymer precipitation when the temperature was raised above 30 degrees C.     

Random coil conformations of polynucleotides: a study incorporating long-range correlations due to dynamics of the sugar residue

A novel virtual bond scheme joining the atoms P-C4′ and C4′-P of a nucleotide repeat, consistent with the stereochemistry of polynucleotide chains, has been developed. The scheme, with its inherent feature to account for all the major sources of flexibility, could also consider effectively the short range and long range interactions, thereby simplifying the analysis of random coil and ordered structures. Using this scheme, unperturbed end-to-end dimensions and persistence lengths of polynucleotide chains have been computed incorporating the dynamical aspects of the sugar ring as well as the C4′ C5′ bond and the correlated changes in phosphodiester conformations. Calculated unperturbed dimensions are in excellent agreement with experimental values. Results show that the random coil is characterized by a large proportion of helical segments of the A-form.     

Configurational statistics of 1,6-linked glycans

We have calculated the unperturbed dimensions of some 1,6-linked glycans by regarding the homopolymer as a ‘copolymer’ in which the different ‘comonomers’ are conformers characterized by the dihedral angle about the C5C6 bond.We find that the characteristic ratio is small (e.g. for the α-glucan it is about 3·3 to 3·4). From the results of some model calculations in which the dihedral angle about the C5C6 bond is fixed, we argue that these low values arise from bonding geometry effects, which are at least as important as the additional conformational freedom from rotation about the C5C6 bond.     

Matrix formulation of the transition from a statistical coil to an intramolecular antiparallel beta sheet

A tractible matrix formulation is developed for the formation of intramolecular antiparallel β sheets in a homopolymer chain molecule. The formulation is applicable to chains with a finite degree of polymerization. It can readily be extended to treat specific-sequence heteropolymers. Individual sheets may contain any number of strands, the number of residues per strand can range upward from two, and there is no artificial constraint linking the numbers of residues in adjacent strands. The weighting scheme utilizes two end-effect parameters, denoted by τ and δ. The first parameter is associated with each residue that does not have a partner in a proceding strand, and the latter is associated with each β bend. A third parameter, t, is associated with every residue in the sheet. Conditions are described which lead to the formation of different types of sheets: (1) “sheets” comprised of isolated extended strands; (2) cross-β fibers in which a sheet contains a large number of very short strands; (3) fibers in which a few very long strands run parallel to the fiber axis; (4) sheets comprised of several strands in which the average strand contains five residues. The fourth type of sheet resembles those found in globular proteins. It is formed when τ and δ are both small, with the ratio, τ/δ, being slightly less than one.     

Cellulose biosynthesis and function in bacteria.

The current model of cellulose biogenesis in plants, as well as bacteria, holds that the membranous cellulose synthase complex polymerizes glucose moieties from UDP-Glc into beta-1,4-glucan chains which give rise to rigid crystalline fibrils upon extrusion at the outer surface of the cell. The distinct arrangement and degree of association of the polymerizing enzyme units presumably govern extracellular chain assembly in addition to the pattern and width of cellulose fibril deposition. Most evident for Acetobacter xylinum, polymerization and assembly appear to be tightly coupled. To date, only bacteria have been effectively studied at the biochemical and genetic levels. In A. xylinum, the cellulose synthase, composed of at least two structurally similar but functionally distinct subunits, is subject to a multicomponent regulatory system. Regulation is based on the novel nucleotide cyclic diguanylic acid, a positive allosteric effector, and the regulatory enzymes maintaining its intracellular turnover: diguanylate cyclase and Ca2(+)-sensitive bis-(3',5')-cyclic diguanylic acid (c-di-GMP) phosphodiesterase. Four genes have been isolated from A. xylinum which constitute the operon for cellulose synthesis. The second gene encodes the catalytic subunit of cellulose synthase; the functions of the other three gene products are still unknown. Exclusively an extracellular product, bacterial cellulose appears to fulfill diverse biological roles within the natural habitat, conferring mechanical, chemical, and physiological protection in A. xylinum and Sarcina ventriculi or facilitating cell adhesion during symbiotic or infectious interactions in Rhizobium and Agrobacterium species. A. xylinum is proving to be most amenable for industrial purposes, allowing the unique features of bacterial cellulose to be exploited for novel product applications.     

Ionic polysaccharides. IV. Free-rotation dimensions for disaccharide polymers. Comparison with experiment for hyaluronic acid

The root-mean-square end-to-end distance has been calculated for a model allowing free rotation about glycoside bonds for the general case of polysaccharides having a disaccharide repeating unit. Numerical estimates are given for several naturally occurring structures based on an idealized pyranose unit in the C1 chair conformation. Extrapolation procedures which make use of the intrinsic viscosity [η] in good solvents to obtain unperturbed dimensions do not represent, data for hyaluronic acid very well, especially at low molecular weights. However, order-of-magnitude estimates suggest that this polymer behaves similarly to other polysaccharides, and probably has stiffer local structure than typical non-ionic synthetic polymers. A double logarithmic plot of the product of [η] and M?_w, the weight-average molecular weight, against the degree of polymerization in the range for M?_w of 10⁴ to 2 × 10⁴ permits a straight-line fit of available data for all the glycosaminoglycans, including heparin and the chondroitin sulfates, as well as sodium carboxymethyl cellulose. This result suggests similarity of short-chain hydrodynamic behavior of these polymers.     

Hydration of amino acid side chains: dependence on secondary structure.

Energy calculations have been used to study the hydration sites around the polar groups of serine, threonine and tyrosine side chains. These hydration sites depend not only on the hybridization of the polar group but also on the local secondary structure, the chi 1 side chain torsion angle and the position of the hydroxyl hydrogen atom. For tyrosine side chains, two solvent sites are found approximately in the plane of the ring. Even for serine and threonine side chains only two minimum energy sites are found in general of which one is in an expected position within hydrogen bonding of the hydroxyl hydrogen atom (unless this is blocked from interaction with solvent molecules by, for example, Oi-4 or Oi-3. The position of the second of these sites depends not only on the position of the hydroxyl oxygen but also on neighbouring main chain atoms to which it can also hydrogen bond. There is good agreement with the solvent distributions obtained from crystallographic data.     

Antibacterial cellulose fiber via RAFT surface graft polymerization

2-(dimethylamino)ethyl methacrylate (DMAEMA) was polymerized from cellulosic filter paper via reversible addition-fragmentation chain transfer (RAFT) polymerization. The tertiary amino groups of the grafted PDMAEMA chains were subsequently quaternized with alkyl bromides of different chain lengths (C8-C16) to provide a large concentration of quaternary ammonium groups on the cellulose surface. The antibacterial activity of the quaternized and nonquaternized PDMAEMA-grafted cellulosic fibers was tested against Escherichia coli. The antibacterial activity was found to depend on the alkyl chain length and on the degree of quaternization, i.e., the amount of quaternary amino groups present in the cellulose graft copolymers. The PDMAEMA-grafted cellulose fiber with the highest degree of quaternization and quaternized with the shortest alkyl chains was found to exhibit particularly high activity against E. coli.     

Configuration-dependent properties of randomly coiling polynucleotide chains. I. A comparison of theoretical energy estimates

Various theoretical estimates of the conformational energy associated with polynucleotides in solution have been compared with each other and also with the experimentally observed conformations found in X-ray crystallographic investigations of low-molecular-weight nucleic acid analogs. In view of the disparities between these data, certain configuration-dependent properties (i.e., the mean-square unperturbed end-to-end distance 〈r²〉₀ and the average vicinal nmr coupling constant 〈J〉) appropriate to randomly coiling polynucleotides described by either the energy estimates or by the crystallographically preferred conformations have also been calculated and compared with the known solution behavior of polynucleotide chains. Both the theoretical energy surfaces and the X-ray data show good agreement with the nmr coupling constant indications of the preferred rotations about the O-C and C-C bonds of the chain backbone. The principal discrepancies between the theoretical methods and X-ray data arise in their ability to predict successfully the preferred rotations about the two phosphodiester bonds of the chain backbone and the unperturbed dimensions of randomly coiling polynucleotide chains.     

A priori crystal structure prediction of native celluloses

The packing of beta-1,4-glucopyranose chains has been modeled to further elaborate the molecular structures of native cellulose microfibrils. A chain pairing procedure was implemented that evaluates the optimal interchain distance and energy for all possible settings of the two chains. Starting with a rigid model of an isolated chain, its interaction with a second chain was studied at various helix-axis translations and mutual rotational orientations while keeping the chains at van der Waals separation. For each setting, the sum of the van der Waals and hydrogen-bonding energy was calculated. No energy minimization was performed during the initial screening, but the energy and interchain distances were mapped to a three-dimensional grid, with evaluation of parallel settings of the cellulose chains. The emergence of several energy minima suggests that parallel chains of cellulose can be paired in a variety of stable orientations. A further analysis considered all possible parallel arrangements occurring between a cellulose chain pair and a further cellulose chain. Among all the low-energy three-chain models, only a few of them yield closely packed three-dimensional arrangements. From these, unit-cell dimensions as well as lattice symmetry were derived; interestingly two of them correspond closely to the observed allomorphs of crystalline native cellulose. The most favorable structural models were then optimized using a minicrystal procedure in conjunction with the MM3 force field. The two best crystal lattice predictions were for a triclinic (P(1)) and a monoclinic (P2(1)) arrangement with unit cell dimensions a = 0.63, b = 0.69, c = 1.036 nm, alpha = 113.0, beta = 121.1, gamma = 76.0 degrees, and a = 0.87, b = 0.75, c = 1.036 nm, gamma = 94.1 degrees, respectively. They correspond closely to the respective lattice symmetry and unit-cell dimensions that have been reported for cellulose Ialpha and cellulose Ibeta allomorphs. The suitability of the modeling protocol is endorsed by the agreement between the predicted and experimental unit-cell dimensions. The results provide pertinent information toward the construction of macromolecular models of microfibrils.     

Structure of yeast hexokinase. II. A 6 angstrom resolution electron density map showing molecular shape and heterologous interaction of subunits

An electron density map of yeast hexokinase has been calculated at 6 Å resolution using six heavy atom derivatives. The map shows each of the enzyme's two 51,000 molecular weight subunits to consist of two separate lobes connected by a narrow bridge of density. Furthermore, these two subunits are related to each other in the asymmetric unit of the crystal by a quasi-2-fold rather than a true 2-fold axis. That is, they are related by a rotation of 180 ° plus a relative translation of 3.6 Å along the symmetry axis. This gives rise to a heterologous subunit interaction and a possibility of non-identical structure and function for these chemically identical subunits. The molecule is quite asymmetric, having dimensions of 150 Å × 45 Å × 55 Å. Each subunit is about 80 Å × 40 Å × 50 Å.A portion of an electron density map at 3 Å resolution has been also calculated, based on phases from two heavy atom derivatives. Polypeptide backbone and side chains are visible in this map.     

Conformational energy calculations on alginic acid I. Helix parameters and flexibility of the homopolymers

Conformational energy maps have been calculated for the 1-4-linked dimers of β-D -mannuronic acid and α-L -guluronic acid. Helix parameters have been calculated for poly(mannuronic acid) and for poly(guluronic acid), which are in reasonable agreement with data from x-ray fiber diffraction studies of these polysaccharides. The flexibility of the homopolymers was investigated by calculating the characteristic ratios, i.e., the ratio of the mean-square end-to-end lengths of the unperturbed chains to the product of the number of residues in the chains and the virtual bond lengths. The general conclusions are that both polymers are very stiff and extended, but that poly(mannuronic acid) is less extended than poly(guluronic acid).     

酶促聚合：绿色的高分子材料合成技术

以酶促聚合为代表的绿色高分子合成途径，以其反应条件温和、产物多分散性低、无金属催化剂残留、高度立体和区位选择性等优势，成为医用高分子材料合成领域中的研究热点。目前，氧化还原酶、水解酶、转移酶均成功应用于聚合反应，其中脂肪酶催化的缩聚反应及开环聚合反应研究最为广泛，同时，以可逆加成-断裂链转移聚合和原子转移自由基聚合为代表的酶促可逆失活自由基聚合得到了快速发展。针对酶促聚合中单体及合成产物结构与性能单一、应用范围有限等缺陷，基于酶促聚合与原子转移自由基聚合、开环易位聚合等反应的偶联，制备了多种不同结构与性能的聚合物材料，推动了上述材料在药物与基因递送领域中的应用。本文综述了脂肪酶催化聚合、酶促可逆失活自由基聚合、酶促化学偶联催化等方面的研究进展，并探讨了目前研究的局限性和未来研究方向。     

Combination of SEC/MALS experimental procedures and theoretical analysis for studying the solution properties of macromolecules

Size-exclusion chromatography (SEC) with dual detection, i.e., employing refractive index (RI) and multiangle light-scattering (MALS) detectors, has been applied to study the solution properties of two very different polymer-solvent systems at 25 degrees C: poly(N-vinylcarbazole) (PVCz) in an organic solvent THF that is a very good solvent and a system under theta conditions that is formed by polyvinylpyrrolidone (PVP) in water containing a 0.1 M concentration of NaNO(3). In both cases, the analysis of a single highly polydisperse sample obtained by free radical polymerization is enough for obtaining molecular weight and radius of gyration calibration curves, molecular weight distributions (MWD) (and thus, molecular weight averages), molecular dimensions, scaling laws coefficients and unperturbed dimensions. Extrapolation to theta conditions produces values of the characteristic ratio of the unperturbed dimensions C(n)=(o)/nl(2)=15.9 and 14, respectively, for PVCz and PVP. Unperturbed dimensions are also theoretically calculated with different models such as Kuhn equivalent chain, worm-like chain and rotational isomeric states model. Conformational parameters required for this last model were taken from the literature in the case of PVCz; however, they are calculated by molecular dynamics simulations in the case of PVP. Theoretical values obtained with the RIS model are in good agreement with the experimental results.     

Intramolecular steric effects and hydrogen bonding in regular conformations of polyamino acids

A survey has been made, by using computer methods, of the types of helices which polypeptide chains can form, taking into account steric requirements and intramolecular hydrogen-bonding interactions. The influence on these two requirements, of small variations in the bond angles of the peptide residues, or of small changes in the overall dimensions of the helix (pitch and residues per turn), have been assessed for the special case of the α-helix. Criteria for the formation of acceptable hydrogen bonds have also been applied to helices of other types, viz., the 3, γ^?, ω^?, and π-helices. It was shown that the N? H … O and H … O? C angles in hydrogen bonds are sensitive to changes in either the NC^αC′ bond angle or in the rotational angles about the N? C^α and C^α? C′ bonds. However, the variants of the α-helix observed experimentally in myoglobin can all be constructed without distortion of the hydrogen bonds. For α-helices, the steric and hydrogen bonding requirements are more easily fulfilled with an NC^αC′ bond angle of 111°, rather than 109.5°. The decreased stability observed for the left-handed α-helix relative to the right-handed one for L -amino acids is due essentially only to interactions of the C^β atom of the side chains with atoms in adjacent peptide units in the backbone, and interactions with atoms in adjacent turns of the helical backbone are not significantly different in the two helices. Restrictions in the freedom of rotation of bulky side chains may have significant kinetic effects during the formation of the α-helix from the “random coil” state.