A new derivation of the GLYCAM06 force field, which removes its previous specificity for carbohydrates, and its dependency on the AMBER force field and parameters, is presented. All pertinent force field terms have been explicitly specified and so no default or generic parameters are employed. The new GLYCAM is no longer limited to any particular class of biomolecules, but is extendible to all molecular classes in the spirit of a small-molecule force field. The torsion terms in the present work were all derived from quantum mechanical data from a collection of minimal molecular fragments and related small molecules. For carbohydrates, there is now a single parameter set applicable to both alpha- and beta-anomers and to all monosaccharide ring sizes and conformations. We demonstrate that deriving dihedral parameters by fitting to QM data for internal rotational energy curves for representative small molecules generally leads to correct rotamer populations in molecular dynamics simulations, and that this approach removes the need for phase corrections in the dihedral terms. However, we note that there are cases where this approach is inadequate. Reported here are the basic components of the new force field as well as an illustration of its extension to carbohydrates. In addition to reproducing the gas-phase properties of an array of small test molecules, condensed-phase simulations employing GLYCAM06 are shown to reproduce rotamer populations for key small molecules and representative biopolymer building blocks in explicit water, as well as crystalline lattice properties, such as unit cell dimensions, and vibrational frequencies.

/pdf/glycam06-a-generalizable-biomolecular-force-field-2f07t7094q.pdf

GLYCAM06: a generalizable biomolecular force field. Carbohydrates.

Experiential phenomena occurring in spontaneous seizures or evoked by brain stimulation were reported by 18 of 29 patients with medically intractable temporal lobe epilepsy who were investigated with chronic, stereotaxically implanted intracerebral electrodes. The phenomena mainly consisted of perceptual (visual or auditory) hallucinations or illusions, memory flashbacks, illusions of familiarity, forced thinking, or emotions. Experiential phenomena did not occur unless a seizure discharge or electrical stimulation involved limbic structures. For such phenomena to occur, seizure discharge or electrical stimulation did not have to implicate temporal neocortex. This was true even for perceptual experiential phenomena. Many experiential responses elicited by electrical stimulation, particularly when applied to the amygdala, were not associated with electrical afterdischarge. Limbic activation by seizure discharge or electrical stimulation may add an affective dimension to perceptual and mnemonic data processed by the temporal neocortex, which may be required for endowing them with experiential immediacy.

The role of the limbic system in experiential phenomena of temporal lobe epilepsy

The relationship between the three-dimensional structures of oligosaccharides and polysaccharides and their biological properties has been the focus of many recent studies. The overall conformation of an oligosaccharide depends primarily on the orientation of the torsion angles (φ, ψ, and ω) between glycosyl residues. Numerous experimental studies have shown that in glucopyranosides the ω-torsion angle (O6-C6-C5-O5) displays a preference for gauche orientations, in disagreement with predictions based on gas-phase quantum mechanics calculations. In contrast, the ω-angle in galactopyranosides displays a high proportion of the anti-orientation. For oligosaccharides containing glycosidic linkages at the 6-position (1→6 linked), variations in rotamer population have a direct effect on the oligosaccharides' structure and function, and yet the physical origin of these conformational preferences remains unclear. Although it is generally recognized that the gauche effect in carbohydrates is a solvent-dependent phenomenon, the mechanism through which solvent induces the gauche preference is not understood. In the present work, quantum mechanics and solvated molecular dynamics calculations were performed on two representative carbohydrates, methyl α-d-glucopyranoside and methyl α-d-galactopyranoside. We show that correct reproduction of the experimental rotamer distributions about the ω-angles is obtained only after explicit water is included in the molecular dynamics simulations. The primary role of the water appears to be to disrupt the hydrogen bonding within the carbohydrate, thereby allowing the rotamer populations to be determined by internal electronic and steric repulsions between the oxygen atoms. The results reported here provide a quantitative explanation of the conformational behavior of (1→6)-linked carbohydrates.

https://www.pnas.org/content/pnas/98/19/10541.full.pdf

Solvent interactions determine carbohydrate conformation

Biosynthesis of polyketides by trans-AT polyketide synthases

Odorant-binding proteins (OBPs) and chemosensory proteins (CSPs) are regarded as carriers of pheromones and odorants in insect chemoreception. These proteins are typically located in antennae, mouth organs and other chemosensory structures; however, members of both classes of proteins have been detected recently in other parts of the body and various functions have been proposed. The best studied of these non-sensory tasks is performed in pheromone glands, where OBPs and CSPs solubilise hydrophobic semiochemicals and assist their controlled release into the environment. In some cases the same proteins are expressed in antennae and pheromone glands, thus performing a dual role in receiving and broadcasting the same chemical message. Several reports have described OBPs and CSPs in reproductive organs. Some of these proteins are male specific and are transferred to females during mating. They likely carry semiochemicals with different proposed roles, from inhibiting other males from approaching mated females, to marking fertilized eggs, but further experimental evidence is still needed. Before being discovered in insects, the presence of binding proteins in pheromone glands and reproductive organs was widely reported in mammals, where vertebrate OBPs, structurally different from OBPs of insects and belonging to the lipocalin superfamily, are abundant in rodent urine, pig saliva and vaginal discharge of the hamster, as well as in the seminal fluid of rabbits. In at least four cases CSPs have been reported to promote development and regeneration: in embryo maturation in the honeybee, limb regeneration in the cockroach, ecdysis in larvae of fire ants and in promoting phase shift in locusts. Both OBPs and CSPs are also important in nutrition as solubilisers of lipids and other essential components of the diet. Particularly interesting is the affinity for carotenoids of CSPs abundantly secreted in the proboscis of moths and butterflies and the occurrence of the same (or very similar CSPs) in the eyes of the same insects. A role as a carrier of visual pigments for these proteins in insects parallels that of retinol-binding protein in vertebrates, a lipocalin structurally related to OBPs of vertebrates. Other functions of OBPs and CSPs include anti-inflammatory action in haematophagous insects, resistance to insecticides and eggshell formation. Such multiplicity of roles and the high success of both classes of proteins in being adapted to different situations is likely related to their stable scaffolding determining excellent stability to temperature, proteolysis and denaturing agents. The wide versatility of both OBPs and CSPs in nature has suggested several different uses for these proteins in biotechnological applications, from biosensors for odours to scavengers for pollutants and controlled releasers of chemicals in the environment.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/brv.12339

Beyond chemoreception: diverse tasks of soluble olfactory proteins in insects.

Chiral Deuteration at C-6 of 1,6-Anhydrohexose Derivatives

Syntheses and 1H-NMR Studies on Mucin-Type Sugars Chirally Deuterated at the C-6 Position

Convenient synthetic routes to 4R- and 4S-γ-lactones from respective d- and l-arabinoses are developed. An application of the routes to the chiral synthesis of a sex pheromone of Japanese beetle is presented.

Syntheses of Chiral γ-Lactones from D- and L-Arabinoses

NMR spectroscopy is a very important and useful method for the structural analysis of oligosaccharides, despite its low sensitivity. We first applied conventional measuring methods, 2D DQF COSY, (1)H-(13)C HSQC, and (1)H-(13)C HMBC, and also the Double Pulsed Field Gradient Spin Echo (DPFGSE)-TOCSY and DPFGSE-NOESY/ROESY techniques to analyze a branched mannose pentasaccharide as a model of high mannose type N-glycans in natural abundance. The NMR spectra of the model compound are very complex and difficult to analyze owing to overlapping signals. The superior selective irradiation capability of the DPFGSE technique is useful for fine structural and conformational analyses of such complex oligosaccharides. We here introduce a novel technique called DPFGSE-Double-Selective Population Transfer (SPT)-Difference and DPFGSE-NOE/ROE-SPT-Difference spectroscopy. The DPFGSE-Double-SPT-Difference method involves irradiation of two peaks from one proton and the subtraction of higher and lower peaks from each spectrum. The DPFGSE-NOE/ROE-SPT-Difference method involves the transfer of the magnetization polarized by NOE/ROE from the nuclei to the spin-coupled nuclei through scalar spin-spin interaction using the SPT method. Even if the signals in the NMR spectra overlap, each signal can be accurately assigned. In particular, DPFGSE-NOE/ROE-SPT-Difference is very useful for identifying sugar connectivity.

Structural analyses of mannose pentasaccharide of high mannose type oligosaccharides by 1D and 2D NMR spectroscopy.

Four stereoisomers of methyl 4,6-di-O-d-glucopyranosyl-β-d-glucopyranosides, in which the H-6proiS proton at the (1→6)-linkage moiety was selectively replaced by a deuterium (2H), were synthesized through the photobromination of 1,6-anhydro-per-O-acetyl-β-d-maltopyranose and β-d-glucose, with subsequent deuteride reduction of the brominated products (C-6exo bromides) by tri-n-butyltin deuteride. The chirally deuterated sugars enabled us to differentiate the H-6proR and H-6proS signals at the (1→6)-linkage moiety and, thereby, to clarify the conformational distributions about the C5-C6 bonds.

https://www.jstage.jst.go.jp/article/bbb1961/52/4/52_4_1003/_pdf

Hiroshi Hori

Papers

Chiral Deuteration at C-6 of 1,6-Anhydrohexose Derivatives

Syntheses and 1H-NMR Studies on Mucin-Type Sugars Chirally Deuterated at the C-6 Position

Syntheses of Chiral γ-Lactones from D- and L-Arabinoses

Structural analyses of mannose pentasaccharide of high mannose type oligosaccharides by 1D and 2D NMR spectroscopy.

Syntheses and 1H-NMR studies of methyl 4,6-di-O-glucopyranosyl-β-D-glucopyranosides chirally deuterated at the (1→6)-linkage moiety