Search for fucose binding domains in recently sequenced hypothetical proteins using molecular modeling techniques and structural analysis.

The crystal structure of a fucose-binding lectin from the bacteria Pseudomonas aeruginosa in complex with alpha-L-fucose has been recently determined. It is a tetramer; each monomer displays a nine-stranded, antiparallel, beta-sandwiched arrangement and contains two calcium ions that mediate the binding of fucose in a recognition mode unique among protein-carbohydrate interactions. In search of this type of unique interactions in other newly discovered protein sequences, we have used molecular modeling techniques to predict and analyze the 3-D structures of some proteins, which exhibited reasonable degree of homology with the amino acid sequence of the bacterial protein.

Structural studies on mannose-selective glycoprotein receptors using molecular modeling techniques.

Glycoproteins play important roles in various cellular events and their presence in appropriate locations in proper active conformations is essential for many biochemical functions. Recent evidences suggest that some glycoproteins may require sorting receptors for efficient exit from the endoplasmic reticulum. These receptors need the presence of calcium or other metal ions for their native activity.

Simulation of grafted polymers on nanopatterned surfaces.

Structural properties of polymer brushes on nanopatterned surfaces in good solvent have been determined by computer simulations. Scaling relations for the brush height and brush width are proposed. The properties of the central part of the patterned brush remain constant as long as the pattern is wider than a few times the brush height.

Under the influence of alcohol: the effect of ethanol and methanol on lipid bilayers.

Extensive microscopic molecular dynamics simulations have been performed to study the effects of short-chain alcohols, methanol and ethanol, on two different fully hydrated lipid bilayer systems (POPC and DPPC) in the fluid phase at 323 K. It is found that ethanol has a stronger effect on the structural properties of the membranes. In particular, the bilayers become more fluid and permeable: ethanol molecules are able to penetrate through the membrane in typical timescales of approximately 200 ns, whereas for methanol that timescale is considerably longer, at least of the order of microseconds.

Influence of spatial correlations on the lasing threshold of random lasers.

The lasing threshold of a random laser is computed numerically from a generic model. It is shown that spatial correlations of the disorder in the medium (i.e.

Lateral pressure profiles in cholesterol-DPPC bilayers.

By means of atomistic molecular dynamics simulations, we study cholesterol-DPPC (dipalmitoyl phosphatidylcholine) bilayers of different composition, from pure DPPC bilayers to a 1:1 mixture of DPPC and cholesterol. The lateral pressure profiles through the bilayers are computed and separated into contributions from the different components. We find that the pressure inside the bilayer changes qualitatively for cholesterol concentrations of about 20% or higher.

Evaluation of mercury toxicity by some cytological indices in leucocyte cultures.

The genotoxicity induced by different levels of inorganic mercury was evaluated by chromosome metaphase analysis in human leucocytes, treated in vitro for 72 hr. Mitotic index gradually decreased with an increase in concentration of mercury but the reverse phenomenon was observed with respect to chromosomal aberration due to its probable interaction with protein and DNA.

Use of black tea in modulating clastogenic effects of arsenic in mice in vivo.

The concentration of arsenic in drinking water has far exceeded the permissible limit of 0.001 mg/L and has reached epidemic proportions, with a maximum of 3.7 mg/L in several districts of West Bengal and in the adjoining Bangladesh.

Response to comment by Almeida et al.: free area theories for lipid bilayers--predictive or not?

Free area theories for lateral diffusion in lipid bilayers are reviewed and discussed. It has been suggested by Almeida et al. that free area theories yield quantitative predictions for lateral diffusion coefficients of lipids.

Role of sulfur compounds in the detection of amino acids by ninhydrin on TLC plate.

Three new sulfur reagents for specific identification of amino acids on thin-layer chromatography plates have been introduced. These three sulfur containing reagents are capable of developing various distinguishable colors with many of them. A probable mechanism for such color formation is proposed.

Impact of cholesterol on voids in phospholipid membranes.

Free volume pockets or voids are important to many biological processes in cell membranes. Free volume fluctuations are a prerequisite for diffusion of lipids and other macromolecules in lipid bilayers. Permeation of small solutes across a membrane, as well as diffusion of solutes in the membrane interior are further examples of phenomena where voids and their properties play a central role.

Coarse-grained model for phospholipid/cholesterol bilayer.

We construct a coarse-grained (CG) model for dipalmitoylphosphatidylcholine (DPPC)/cholesterol bilayers and apply it to large-scale simulation studies of lipid membranes. Our CG model is a two-dimensional representation of the membrane, where the individual lipid and sterol molecules are described by pointlike particles. The effective intermolecular interactions used in the model are systematically derived from detailed atomic-scale molecular dynamics simulations using the Inverse Monte Carlo technique, which guarantees that the radial distribution properties of the CG model are consistent with those given by the corresponding atomistic system.

Lessons of slicing membranes: interplay of packing, free area, and lateral diffusion in phospholipid/cholesterol bilayers.

We employ 100-ns molecular dynamics simulations to study the influence of cholesterol on structural and dynamic properties of dipalmitoylphosphatidylcholine bilayers in the fluid phase. The effects of the cholesterol content on the bilayer structure are considered by varying the cholesterol concentration between 0 and 50%. We concentrate on the free area in the membrane and investigate quantities that are likely to be affected by changes in the free area and free volume properties.

Cationic DMPC/DMTAP lipid bilayers: molecular dynamics study.

Cationic lipid membranes are known to form compact complexes with DNA and to be effective as gene delivery agents both in vitro and in vivo. Here we employ molecular dynamics simulations for a detailed atomistic study of lipid bilayers consisting of a mixture of cationic dimyristoyltrimethylammonium propane (DMTAP) and zwitterionic dimyristoylphosphatidylcholine (DMPC). Our main objective is to examine how the composition of the DMPC/DMTAP bilayers affects their structural and electrostatic properties in the liquid-crystalline phase.

Systematic comparison of force fields for microscopic simulations of NaCl in aqueous solutions: diffusion, free energy of hydration, and structural properties.

In this article we compare different force fields that are widely used (Gromacs, Charmm-22/x-Plor, Charmm-27, Amber-1999, OPLS-AA) in biophysical simulations containing aqueous NaCl. We show that the uncertainties of the microscopic parameters of, in particular, sodium, and, to a lesser extent, chloride, translate into large differences in the computed radial-distribution functions. This uncertainty reflect the incomplete experimental knowledge of the structural properties of ionic aqueous solutions at finite molarity.

Molecular dynamics simulations of lipid bilayers: major artifacts due to truncating electrostatic interactions.

We study the influence of truncating the electrostatic interactions in a fully hydrated pure dipalmitoylphosphatidylcholine (DPPC) bilayer through 20 ns molecular dynamics simulations. The computations in which the electrostatic interactions were truncated are compared to similar simulations using the particle-mesh Ewald (PME) technique. All examined truncation distances (1.

Parmelia cirrhatum: a potential source of broad spectrum natural antifungal.

During antifungal screening of some plants, the water extract of lichen, Parmelia cirrhatum was found to be most effective against tested pathogenic fungi at the range of 60-80 microL/mL concentrations. The extract showed heavy doses of inoculum potential at 80 microL/mL and the antifungal activity of the extract did not expire up to 24 months of storage. The extract did not showed any irritation on mammalian skin up to 10% concentration.

Stability of charge inversion, Thomson problem, and application to electrophoresis.

We analyze charge inversion in colloidal systems at zero temperature using stability concepts, and connect this to the classical Thomson problem of arranging electrons on sphere. We show that for a finite microion charge, the globally stable, lowest-energy state of the complex formed by the colloid and the oppositely charged microions is always overcharged. This effect disappears in the continuous limit.

Decay rate distributions of disordered slabs and application to random lasers.

We compute the distribution of the decay rates (also referred to as residues) of the eigenstates of a disordered slab from a numerical model. From the results of the numerical simulations, we are able to find simple analytical formulas which describe these results well. This is possible for samples both in the diffusive and in the localized regimes.

A non-Newtonian fluid model for blood flow through arteries under stenotic conditions.

This paper presents an analytical study on the behaviour of blood flow through an arterial segment having a mild stenosis. The artery has been treated as a thin-walled initially stressed orthotropic non-linear viscoelastic cylindrical tube filled with a non-Newtonian fluid representing blood. The analysis is restricted to propagation of small-amplitude harmonic waves, generated due to blood flow whose wave length is large compared to the radius of the arterial segment.