Far-ultraviolet optical activity of saccharide derivatives. II. Dextran,amylose, and mycodextran acetes; dextran and amylose xanthates

The ultraviolet ORD and CD spectra of amylose, dextran, and mycodextran acetates and some of thier oligomers were recorded in trifluoroethanol solution in the 300–185nm wavelength range. Similarly, the spectra of amylose and dextran xanthates in water solution were obtained in the 400–200 nm range. In the amylose acetate series, the monomer and dimer both show a normal acetyl n → π* transition in CD, while the trimer and the polymer both exhibit an additional, shorter wavelength peak. The latter is presumed to arise from a helical conformation of the amylose chain. This interpretation is substantiated by a helix–coil type transition of the CD spectra of amylose triacetate at elevated temperatures and a reversion of the anomalous CD to the normal CD upon partial deacetylation. By contrast, neither dextran acetates nor mycodextran acetate exhibit any conformational effects. The CD of dextran acetates is quite sensitive to β-1,6 and branch linkages. The ORD and CD of amylose xanthate are complex, suggesting the presence of organized structure in solution. The dextran xanthate shows only a simple ORD spectrum and no observable CD.     

Synthesis and characterisation of dextran and pullulan sulphate

Dextrans and pullulans of different molar masses in the range of 10(4)-10(5) g/mol were sulphated via a SO3-pyridine complex. The degree of substitution achieved was DS = 2.4 and DS = 1.4 for dextran sulphate and DS = 2.0 and DS = 1.4 for pullulan sulphate, respectively. Confirmation of sulphation was given by FTIR spectroscopy. Asymmetrical S=O and symmetrical C-O-S stretching vibrations were detected at 1260 and 820 cm(-1). Reactivity of the polysaccharide C-atoms was determined by 13C NMR spectroscopy: For dextran this was C-3 > C-2 > C-4, while for pullulan it was C-6 > C-3 > C-2 > C-4.     

Molecular recognition of caffeine in solution and solid state

The molecular recognition of caffeine in both solution and solid state is important to understand different enzymatic reactions i.e., enzyme–substrate interactions, immunological reactions in vivo, selective host–guest complexation and catalytic reactions in bio-mimetic chemistry. The weak intermolecular forces in recognition system direct the molecules toward self-linking in supramolecular engineering in the chemistry of life and material science. In this contribution, it has been illustrated the immense variety of receptors that have been designed for caffeine recognition in both solid and solution phase. The binding studies for the recognition of caffeine are reported by different research groups including our group. It is important to understand the goal of developing artificial molecular receptors, capable of binding very efficiently and very selectively with caffeine which is described elaborately in this context. The modern bioorganic chemistry concerns the design of synthetic molecules that mimic various aspects of enzyme chemistry and to understand their essential roles in biological systems. The stimulating effect of caffeine is not only exploited in nutrient technology but also in cosmetics and pharmaceuticals, which accounts for the economic importance of this particular additive. Although caffeine was first time isolated by Ferdinand Runge from coffee beans almost 200 years ago, it still has some surprise in hoard.     

Synthesis of 2.3-unsaturated polysaccharides from amylose and xylan

Amylose (1) was tritylated at O-6, the ether p-toluenesulfonylated at O-2 and O-3, and the product (3) treated with sodium iodide and zinc dust in N,N-dimethyl-formamide, to give 2,3-dideoxy-6-O-trityl-α-D-erythro-hex-2-enopyranoglycan (4). This 2,3-unsaturated polysaccharide could be converted into a 2,3-dibromo derivative (5), and hydrogenated with concomitant detritylation to the saturated analogue (6), and, on treatment with aqueous acetic acid, it gave 2-(D-glycero-1,2-dihydroxyethyl)-furan (8). The 2,3-bis(p-toluenesulfonate) (10) of β-D-xylan (9) was similarly converted into the 2,3-unsaturated polysaccharide, 2,3-dideoxy-β-D-glycero-pent-2-enopyranoglycan (11), which, with aqueous acetic acid, gave 2-(hydroxymethyl)furan (12a).     

Light-scattering and specific refractive increment behavior of amylose and dextran in methyl sulfoxide-water

Light-scattering measurements on polysaccharides in methyl sulfoxide or methyl sulfoxide-water are most reliable when made on a dialyzed solution-solvent system and when proper technique is used to remove the “micro gel” that seems unavoidably present when dried polysaccharide is dissolved in solvent. Discrepancies in published molecular weight-intrinsic viscosity relationships for amylose in methyl sulfoxide appear to be caused in part by differences the preparation and treatment of samples and possibly by differences in botanical source. The specific refractive increment of dextran is not a linear function of solvent composition in methyl sulfoxide-water. Measurements at osmotic equilibrium indicate that, over a moderate range of composition in methyl sulfoxide-water, dextran preferentially associates with about 2.5 molecules of water per glucopyranosyl residue of the polymer. Effects of long-term storage, sample treatment, and botanical source upon the specific rotation of amylose are examined.     

Molecular dynamics computations and solid state nuclear magnetic resonance of the gramicidin cation channel.

This paper reports on a coupled approach to determining the structure of the gramicidin A ion channel, utilizing solid state nuclear magnetic resonance (NMR) of isotopically labeled gramicidin channels aligned parallel to the magnetic field direction, and molecular dynamics (MD). MD computations using an idealized right-handed beta-helix as a starting point produce a refined molecular structure that is in excellent agreement with atomic resolution solid state NMR data. The data provided by NMR and MD are complementary to each other. When applied in a coordinated manner they provide a powerful approach to structure determination in molecular systems not readily amenable to x-ray diffraction.     

Study of hydration of cross-linked high amylose starch by solid state 13C NMR spectroscopy

Starch is subjected to chemical treatments such as cross-linking or hydroxypropylation to meet the material requirements for food uses or controlled release in the pharmaceutical industries. In this work, two types of cross-linking formulations have been employed for the preparation of high amylose starch for use as an excipient for sustained drug release. The structural differences and chain dynamics of the modified starches in the dry and hydrated states have been compared by the use of variable contact time cross polarization-magic angle spinning solid state (13)C NMR spectroscopy.     

A 13C NMR study on collagens in the solid state: hydration/dehydration-induced conformational change of collagen and detection of internal motions.

We recorded 13C NMR spectra of type I and IV collagens in the anhydrous and hydrated states, in order to confirm our previous assignment of peaks, and to analyze the mode of partial renaturation of soluble collagens by hydration, as well as rapid intramolecular motions such as ring puckering in proline or hydroxyproline residues. First, we attempted to assign all 13C NMR peaks of collagen fibrils on the basis of computer simulation by utilizing amino-acid composition and chemical shift data from both the solid state and solution. We confirmed that some previously unassigned peaks were not ascribable to a denatured portion but to the minor amino-acid residues. The 13C NMR peaks from soluble collagens were appreciably broadened and some peaks were displaced as compared with those of intact collagen fibrils. This was caused by the presence of a partial conformational disorder and/or denaturation at the time of acid-solubilization and dehydration. Those line broadening and displacements of peaks, however, were partially removed by humidification under an atmosphere of 96% R.H. over 12 h. Furthermore, we found that the 13C spin-lattice relaxation times (T1s) of both the C beta and C gamma carbons of Pro and Hyp in fibrils are substantially reduced as compared with those of some crystalline oligopeptides. It was shown that the presence of rapid ring puckering motion in these residues results in a reduction of the NT1 values, where N stands for the number of protons attached to the carbon under consideration.(ABSTRACT TRUNCATED AT 250 WORDS)     

Molecular organization of cholesterol in polyunsaturated phospholipid membranes: a solid state 2H NMR investigation.

We compared the molecular organization of equimolar [3alpha-2H1]cholesterol in 18:0-18:1PC (1-stearoyl-2-oleoylphosphatidylcholine), 18:0-22:6PC (1-stearoyl-2-docosahexaenoylphosphatidylcholine), 18:0-20:4PC (1-stearoyl-2-arachidonylphosphatidylcholine) and 20:4-20:4PC (1,2-diarachidonylphosphatidylcholine) bilayers by solid state 2H NMR. Essentially identical quadrupolar splittings (delta v(r) = 45 +/- 1 kHz) corresponding to the same molecular orientation characterized by tilt angle alpha0 = 16 +/- 1 degrees were measured in 18:0-18:1PC, 18:0-22:6PC and 18:0-20:4PC. A profound difference in molecular interaction with dipolyunsaturated 20:4-20:4PC, in contrast, is indicated for the sterol. Specifically, the tilt angle alpha0 = 22 +/- 1 degrees (derived from delta v(r) = 37 +/- 1 kHz) is greater and its membrane intercalation is only 15 mol%.     

Influence of anomeric configuration on mechanochemical degradation of polysaccharides: cellulose versus amylose

Cellulose and amylose are (1-->4)-linked polysaccharides that are used extensively in the textiles, paper, and food and feed industries and are finding increasing use as alternative fuels and so forth. At the molecular level, cellulose and amylose differ only in their anomeric configuration: beta in cellulose, alpha in amylose. During processing and end use, these polymers experience a variety of mechanochemical stresses, many through contact with transient elongational flow fields. Here, we subject solutions of both polysaccharides to extended periods of ultrasonic irradiation, as the cavitational bubble collapse characteristic of ultrasound experiments creates flow fields strictly analogous to those encountered in other transient elongational flow scenarios. With the use of multidetector size-exclusion chromatography, the effects of anomeric configuration on both the limiting molar mass, beyond which polymers do not degrade in transient elongation flow ( M lim), and the rate of degradation have been isolated in these (1-->4)-linked polysaccharides. This effect was found to be pronounced; for example, M lim (cellulose) = 5( M lim (amylose)). Also, while extensive change was observed in molar mass averages, distribution, polydispersity, and size of the analytes during degradation, their structure was found to remain invariant. A modified "path theory" of transient elongational flow degradation was proposed, with the persistence length identified as a parameter which embodies the minimum continuous path length and flexibility requirements of the theory.     

Crystallography of polysaccharides: Current state and challenges

Polysaccharides are the most abundant class of biopolymers, holding an important place in biological systems and sustainable material development. Their spatial organization and intra- and intermolecular interactions are thus of great interest. However, conventional single crystal crystallography is not applicable since polysaccharides crystallize only into tiny crystals. Several crystallographic methods have been developed to extract atomic-resolution structural information from polysaccharide crystals. Small-probe single crystal diffractometry, high-resolution fiber diffraction and powder diffraction combined with molecular modeling brought new insights from various types of polysaccharide crystals, and led to many high-resolution crystal structures over the past two decades. Current challenges lie in the analysis of disorder and defects by further integrating molecular modeling methods for low-resolution diffraction data.     

Molecular motions within the pore of voltage-dependent sodium channels.

The pores of ion channel proteins are often modeled as static structures. In this view, selectivity reflects rigidly constrained backbone orientations. Such a picture is at variance with the generalization that biological proteins are flexible, capable of major internal motions on biologically relevant time scales. We tested for motions in the sodium channel pore by systematically introducing pairs of cysteine residues throughout the pore-lining segments. Two distinct pairs of residues spontaneously formed disulfide bonds bridging domains I and II. Nine other permutations, involving all four domains, were capable of disulfide bonding in the presence of a redox catalyst. The results are inconsistent with a single fixed backbone structure for the pore; instead, the segments that line the permeation pathway appear capable of sizable motions.     

Molecular dynamics simulations of heme reorientational motions in myoglobin.

Molecular dynamics simulations of 2-ns duration were performed on carbonmonoxymyoglobin and deoxymyoglobin in vacuo to study the reorientational dynamics of the heme group. The heme in both simulations undergoes reorientations of approximately 5 degrees amplitude on a subpicosecond time scale, which produce a rapid initial decay in the reorientational correlation function to about 0.99. The heme also experiences infrequent changes in average orientation of approximately 10 degrees amplitude, which lead to a larger slow decay of the reorientational correlation function over a period of hundreds of picoseconds. The simulations have not converged with respect to these infrequent transitions. However, an estimate of the order parameter for rapid internal motions of the heme from those orientations which are sampled by the simulations suggests that the subnanosecond orientational dynamics of the heme accounts for at least 30% of the unresolved initial anisotropy decay observed in the nanosecond time-resolved optical absorption experiments on myoglobin reported by Ansari et al. in a companion paper (Ansari, A., C.M. Jones, E.R. Henry, J. Hofrichter, and W.A. Eaton. 1992. Biophys. J. 64:852-868.). A more complete sampling of the accessible heme orientations would most likely increase this fraction further. The simulation of the liganded molecule also suggests that the conformational dynamics of the CO ligand may contribute significantly to discrepancies between the ligand conformation as probed by x-ray diffraction and by infrared-optical photoselection experiments. The protein back-bone explores multiple conformations during the simulations, with the largest structural changes appearing in the E and F helices, which are in contact with the heme. The variations in the heme orientation correlate with the conformational dynamics of the protein on a time scale of hundreds of picoseconds, suggesting that the heme orientation may provide a useful probe of dynamical processes in the protein.     

Study of polysaccharides by the fluorescence method. III. Chain length dependence of the micro-Brownian motion of amylose in an aqueous solution

The fluorescence polarization method was applied to the investigation of the micro-Brownian motion of amylose chains having a wide range of degree of polymerization (DP). We prepared two types of fluorescent conjugates of amylose: amylose conjugated with fluorescein randomly throughout the chain (F-amylose) and amylose conjugated locally on a terminal segment (t-F-amylose). The degree of fluorescence polarization of these conjugates was measured by changing the solvent viscosity at a constant temperature (25°C). The data obtained were analyzed by a Perrin-type equation to calculate the mean rotational relaxation time, 〈ρ〉. By examination of the plots of 〈ρ〉 vs DP, and by comparison of 〈ρ〉 with the theoretical rotational relaxation time of the whole molecule at a given DP, it was found that 〈ρ〉 mainly reflects the segmental motion of the amylose chain in the high-DP range. Thus, the fact that 〈ρ〉 for t-F-amylose is much smaller than that for F-amylose at a sufficiently high DP shows that a terminal segment undergoes a more rapid micro-Brownian motion than interior segments. In the low-DP range, we felt that the rotational diffusion of the whole molecule contributes significantly to the relaxation process. We also examined, for comparison, the segmental motion of dextran and pullulan in a similar manner and found that these segmental motions are more rapid than those of amylose. Based on the results obtained, the segmental mobility and conformation of the amylose molecule are discussed in relation to its chain length.     

Molecular motions and conformational changes of HPPK

6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) belongs to a class of catalytic enzymes involved in phosphoryl transfer and is a new target for the development of novel antimicrobial agents. In the present study, the fundamental consideration is to view the overall structure of HPPK as a network of interacting residues and to extract the most cooperative collective motions that define its global dynamics. A coarse-grained model, harmonically constrained according to HPPK's crystal structure is used. Four crystal structures of HPPK (one apo and three holo forms with different nucleotide and pterin analogs) are studied with the goal of providing insights about the function-dynamic correlation and ligand induced conformational changes. The dynamic differences are examined between HPPK's apo- and holo-forms, because they are involved in the catalytic reaction steps. Our results indicate that the palm-like structure of HPPK is nearly rigid, whereas the two flexible loops: L2 (residues 43-53) and L3 (residues 82-92) exhibit the most concerted motions for ligand recognition and presumably, catalysis. These two flexible loops are involved in the recognition of HPPKs nucleotide and pterin ligands, whereas the rigid palm region is associated with binding of these cognate ligands. Six domains of collective motions are identified, comprised of structurally close but not necessarily sequential residues. Two of these domains correspond to the flexible loops (L2 and L3), whereas the remaining domains correspond to the rigid part of the molecule.