Synthesis of Terminal Oligosaccharides from Type Specific Lipooligosaccharide of Mycobacterium Tuberculosis

Abstract

The coupling reaction between 1,3-di-O-acetyl-4-O-benzyl-2-O-methyl-α-L-rhamnopyranose (9) and methyl 4-O-benzyl-2-O-methyl-α-L-rhamno-pyranoside (4) was carried out in the presence of boron trifluoride-etherate followed by deacetylation to give the disaccharide (11) containing a free 3′ position. The second glycosylation reaction with 2,3,4,6-tetra-O-acetyl-α-d-glucopyranosyl bromide in the presence of mercuric salts followed by removal of benzyl and acetyl groups provided the trisaccharide 2. The boron trifluoride catalysed condensation of 1,3,4-tri-O-acetyl-2-O-methyl-L-fucopyranose (14) and methyl 2,4,6-tri-O-benzyl-α-d-glucopyranoside (15) gave the disaccharide (16) from which the protecting groups were removed to form the disaccharide (3).     

Secondary structure sensitivity of hydrogen bond lifetime dynamics in the protein hydration layer

The heterogeneous nature of a protein surface plays an essential role in its biological activity and molecular recognition, and this role is mediated at least partly through the surrounding water molecules. We have performed atomistic molecular dynamics simulations of an aqueous solution of HP-36 to investigate the correlation between the dynamics of the hydration layer water molecules and the lifetimes of protein-water hydrogen bonds. The nonexponential hydrogen bond lifetime correlation functions have been analyzed by using the formalism of Luzar and Chandler, which allowed identification of the quasi-bound states in the surface and quantification of the dynamic equilibrium between quasi-bound and free water molecules in terms of time-dependent rate of interconversion. It is noticed that, irrespective of the structural heterogeneity of different segments of the protein, namely the three alpha-helices, the positively charged amino acid residues form longer-lived hydrogen bonds with water. The overall relaxation behavior of protein-water hydrogen bonds is found to differ significantly among the three helices of the protein. Study of water number density fluctuation reveals that the hydration layer of helix-3 is much less rigid, which can be correlated with faster structural relaxation of the hydrogen bonds between its residues and water. This also agrees excellently with faster translational and rotational motions of water near helix-3, and hence the lower rigidity of its hydration layer. The lower rigidity of the helix-3 hydration layer also correlates well with the biological activity of the protein, as several of the active-site residues of HP-36 are located in helix-3.     

Supersolidity for hard-core-bosons coupled to optical phonons

The coexistence of diagonal long-range order (DLRO) and off-diagonal long-range order (ODLRO), manifested in some systems, is still a theoretical enigma. Here, we present a novel microscopic mechanism for supersolidity or the homogeneous coexistence of charge-density-wave state (an example of DLRO) and superfluidity/superconductivity (a realization of ODLRO). We derive an effective d-dimensional Hamiltonian for a system of hard-core-bosons coupled to optical phonons in a lattice. At non-half-fillings, a superfluid/superconductor to a supersolid transition occurs at intermediate boson–phonon couplings, while at strong-couplings the system phase separates. We demonstrate explicitly that the presence of next-nearest-neighbor hopping and nearest-neighbor repulsion leads to supersolidity.     

Correlation between the dynamics of hydrogen bonds and the local density reorganization in the protein hydration layer

An atomistic molecular dynamics simulation of the protein villin headpiece subdomain or HP-36 has been carried out with explicit water to explore the microscopic inhomogeneity of local density reorganization of the hydration layers of the three alpha-helical segments of the protein. The density reorganization of the hydration layer of helix-3 is found to occur faster than that for the hydration layers of the other two helices. It is noticed that such inhomogeneous density reorganization at the surface of different secondary structures exhibits excellent correlation with the microscopic dynamics of hydrogen bonds between the protein residues and the hydration water. Further, it is observed that the reorientation of water molecules involved in the formation and breaking of protein-water or water-water hydrogen bonds plays an important role in determining the dynamics of local density of the hydration layer. The faster density reorganization of the hydration layer of helix-3 is also consistent with the functionality of HP-36, as helix-3 contains several active site residues.     

A simple,efficient and green procedure for Michael addition catalyzed by [C_4dabco]OH ionic liquid

A dabco-based basic ionic liquid,1-butyl-4-aza-1-azaniabicyclo[2.2.2]octane hydroxide,has been developed as a catalyst for a convenient and rapid method for the Michael addition of active methylene compounds to a b-unsaturated carboxylic esters and nitriles.The method is very simple,and the yields are very high.The catalyst can be recycled several times without much loss of activity.     

Perturbation of phospholipid bilayer properties by ethanol at a high concentration

Atomistic molecular dynamics (MD) simulations have been carried out at 30 degrees C on a fully hydrated liquid crystalline lamellar phase of dimyrystoylphosphatidylcholine (DMPC) lipid bilayer with embedded ethanol molecules at 1:1 composition, as well as on the pure bilayer phase. The ethanol molecules are found to exhibit a preference to occupy regions near the upper part of the lipid acyl chains and the phosphocholine headgroups. The calculations revealed that the phosphocholine headgroup dipoles (P- --> N+) of the lipids prefer to orient more toward the aqueous layer in the presence of ethanol. It is noticed that the ethanol molecules modify the dynamic properties of both lipids as well as the water molecules in the hydration layer of the lipid headgroups. Both the in-plane "rattling" and out-of-plane "protrusion" motions of the lipids have been found to increase in the presence of ethanol. Most importantly, it is observed that the water molecules within the hydration layer of the lipid headgroups exhibit faster translational and rotational motions in the presence of ethanol. This arises due to faster dynamics of hydrogen bonds between lipid headgroups and water in the presence of ethanol.     

Low-frequency vibrational spectrum of water in the hydration layer of a protein: a molecular dynamics simulation study

An atomistic molecular dynamics simulation has been carried out to understand the low-frequency intermolecular vibrational spectrum of water present in the hydration layer of the protein villin headpiece subdomain or HP-36. An attempt is made to explore how the heterogeneous rigidity of the hydration layers of different segments (three alpha helices) of the protein, strength of the protein-water hydrogen bonds, and their differential relaxation behavior influence the distribution of the intermolecular vibrational density of states of water in the hydration layers. The calculations revealed that compared to bulk water these bands are nonuniformly blue-shifted for water near the helices, the extent of shifts being more pronounced for water molecules hydrogen bonded to the protein residues. It is further noticed that the larger blue shift observed for the water molecules hydrogen bonded to helix 2 residues correlates excellently with the slowest structural relaxation of these hydrogen bonds. These results can be verified by suitable experimental measurements.     

A retention‐time‐shift‐tolerant background subtraction and noise reduction algorithm (BgS‐NoRA) for extraction of drug metabolites in liquid chromatography/mass spectrometry data from biological matrices

A retention‐time‐shift‐tolerant background subtraction and noise reduction algorithm (BgS‐NoRA) is implemented using the statistical programming language R to remove non‐drug‐related ion signals from accurate mass liquid chromatography/mass spectrometry (LC/MS) data. The background‐subtraction part of the algorithm is similar to a previously published procedure (Zhang H and Yang Y. J. Mass Spectrom. 2008, 43: 1181–1190). The noise reduction algorithm (NoRA) is an add‐on feature to help further clean up the residual matrix ion noises after background subtraction. It functions by removing ion signals that are not consistent across many adjacent scans. The effectiveness of BgS‐NoRA was examined in biological matrices by spiking blank plasma extract, bile and urine with diclofenac and ibuprofen that have been pre‐metabolized by microsomal incubation. Efficient removal of background ions permitted the detection of drug‐related ions in in vivo samples (plasma, bile, urine and feces) obtained from rats orally dosed with ¹⁴C‐loratadine with minimal interference. Results from these experiments demonstrate that BgS‐NoRA is more effective in removing analyte‐unrelated ions than background subtraction alone. NoRA is shown to be particularly effective in the early retention region for urine samples and middle retention region for bile samples, where the matrix ion signals still dominate the total ion chromatograms (TICs) after background subtraction. In most cases, the TICs after BgS‐NoRA are in excellent qualitative correlation to the radiochromatograms. BgS‐NoRA will be a very useful tool in metabolite detection and identification work, especially in first‐in‐human (FIH) studies and multiple dose toxicology studies where non‐radio‐labeled drugs are administered. Data from these types of studies are critical to meet the latest FDA guidance on Metabolite in Safety Testing (MIST). Copyright © 2009 John Wiley & Sons, Ltd.