O6-Methylguanine Repair by O6-Alkylguanine-DNA Alkyltransferase

O6-Alkylguanine-DNA alkyltransferase (AGT) repairs O6-methylguanine (O6mG) in DNA that is known to cause Mutation and cancer. On the basis of Calculations performed using density functional theory involving the active site of AGT, a mechanism for catalytic demethylation of O6mG to guanine has been proposed. In this mechanism, roles of six amino acids, i.e., Cys145, His 146, Glu172, Tyr114, Lys165, and Ser159 in catalytic demethylation of O6mG are involved. This mechanism has three steps as follows. At the first step, Cys145 in the Cys145-water-His146-Glu172 tetrad is converted to cysteine thiolate anion while at the second step, abstraction of the Tyr114 proton by the N3 site of O6mG occurs in a barrierless manner. In the third step, abstraction of Lys165 proton by deprotonated Tyr114 and transfer of the methyl group of O6mG to the thiolate group of Cys145 anion Occur simultaneously. As AGT is a major target in cancer therapy, identification of the roles of the different amino acids in demethylation of O6mG is expected to be useful in designing efficient AGT inhibitors.

Search for chaos in neutron star systems: Is Cyg X-3 a black hole?

The accretion disk around a compact object is a nonlinear general relativistic system involving magnetohydrodynamics. Naturally, the question arises whether such a system is chaotic (deterministic) or stochastic (random) which might be related to the associated transport properties whose origin is still not confirmed. Earlier, the black hole system GRS 1915+105 was shown to be low-dimensional chaos in certain temporal classes. However, so far such nonlinear phenomena have not been studied fairly well for neutron stars which are unique for their magnetosphere and kHz quasi-periodic oscillation (QPO). On the other hand, it was argued that the QPO is a result of nonlinear magnetohydrodynamic effects in accretion disks. If a neutron star exhibits chaotic signature, then what is the chaotic/correlation dimension? We analyze RXTE/PCA data of neutron stars Sco X-1 and Cyg X-2, along with the black hole Cyg X-1 and the unknown source Cyg X-3, and show that while Sco X-1 and Cyg X-2 are low dimensional chaotic systems, Cyg X-1 and Cyg X-3 are stochastic sources. Based on our analysis, we argue that Cyg X-3 may be a black hole.

The role of glycodelin as an immune-modulating agent at the feto-maternal interface

Glycodelin A is a progesterone-induced endometrial glycoprotein which has been amply documented to play a role in down-modulation of the maternal immune response to fetal allo-antigens and to be indispensable for the maintenance and progression of pregnancy. Earlier studies from our laboratory have focused on the effect of glycodelin on T cells, key regulators of both the antibody and cell-mediated arms of the acquired immune system. Glycodelin-induced apoptosis inactivated T cells occurs through a caspase-dependant intrinsic mitochondrial pathway. Interestingly, glycodelin inhibited the proliferation of B cells but did not induce apoptosis. More recently, we have studied the effect of glycodelin on the cells of the innate immune system, namely monocytes and NK cells. We have found that glycodelin induced apoptosis in monocytic cells before their differentiation to macrophages, via the mitochondrial pathway, but did not affect their phagocytic capacity after differentiation. Glycodelin induced apoptosis in NK cells but this activity was independent of caspases. In conclusion, glycodelin is observed to affect many cells of the immune system, although the nature of the effect and signaling mechanisms involved in each cell type may be distinct.

Ring Expansion of Oxyglycals. Synthesis and Conformational Analysis of Septanoside-Containing Trisaccharides

Oxyglycals, derived from lactose and maltose, were expanded to trisaccharides through a ring expansion method. Trisaccharides with 6-7-5 and 6-7-6 ring sizes were prepared through the ring expansion method, with high diastereoselectivities, in each step of their synthesis. The NOE and ROESY NMR spectroscopies were used to assess the dipolar Couplings within the trisaccharide. A computational study was undertaken, from which low energy conformations, as well as, dihedral angles that define the glycosidic linkages were identified.

Computational systems approach for drug target discovery

Importance of the field: The shift in focus from ligand based design approaches to target based discovery over the last two to three decades has been a major milestone in drug discovery research. Currently, it is witnessing another major paradigm shift by leaning towards the holistic systems based approaches rather the reductionist single molecule based methods. The effect of this new trend is likely to be felt strongly in terms of new strategies for therapeutic intervention, new targets individually and in combinations, and design of specific and safer drugs. Computational modeling and simulation form important constituents of new-age biology because they are essential to comprehend the large-scale data generated by high-throughput experiments and to generate hypotheses, which are typically iterated with experimental validation. Areas covered in this review: This review focuses on the repertoire of systems-level computational approaches currently available for target identification. The review starts with a discussion on levels of abstraction of biological systems and describes different modeling methodologies that are available for this purpose. The review then focuses on how such modeling and simulations can be applied for drug target discovery. Finally, it discusses methods for studying other important issues such as understanding targetability, identifying target combinations and predicting drug resistance, and considering them during the target identification stage itself. What the reader will gain: The reader will get an account of the various approaches for target discovery and the need for systems approaches, followed by an overview of the different modeling and simulation approaches that have been developed. An idea of the promise and limitations of the various approaches and perspectives for future development will also be obtained. Take home message: Systems thinking has now come of age enabling a `bird's eye view' of the biological systems under study, at the same time allowing us to `zoom in', where necessary, for a detailed description of individual components. A number of different methods available for computational modeling and simulation of biological systems can be used effectively for drug target discovery.

Dynamics of loop formation in a semiflexible polymer

The dynamics of loop formation by linear polymer chains has been a topic of several theoretical and experimental studies. Formation of loops and their opening are key processes in many important biological processes. Loop formation in flexible chains has been extensively studied by many groups. However, in the more realistic case of semiflexible polymers, not much results are available. In a recent study [K. P. Santo and K. L. Sebastian, Phys. Rev. E 73, 031923 (2006)], we investigated opening dynamics of semiflexible loops in the short chain limit and presented results for opening rates as a function of the length of the chain. We presented an approximate model for a semiflexible polymer in the rod limit based on a semiclassical expansion of the bending energy of the chain. The model provided an easy way to describe the dynamics. In this paper, using this model, we investigate the reverse process, i.e., the loop formation dynamics of a semiflexible polymer chain by describing the process as a diffusion-controlled reaction. We make use of the ``closure approximation'' of Wilemski and Fixman [G. Wilemski and M. Fixman, J. Chem. Phys. 60, 878 (1974)], in which a sink function is used to represent the reaction. We perform a detailed multidimensional analysis of the problem and calculate closing times for a semiflexible chain. We show that for short chains, the loop formation time tau decreases with the contour length of the polymer. But for longer chains, it increases with length obeying a power law and so it has a minimum at an intermediate length. In terms of dimensionless variables, the closing time is found to be given by tau similar to L-n exp(const/L), where n=4.5-6. The minimum loop formation time occurs at a length L-m of about 2.2-2.4. These are, indeed, the results that are physically expected, but a multidimensional analysis leading to these results does not seem to exist in the literature so far.

Are Metallocene-Acetylene (M = Ti, Zr, Hf) Complexes Aromatic Metallacyclopropenes?

The bonding nature of metallocene acetylene complexes Cp2M(eta(2)-H3SiC2SiH3) 1M and CP2M (eta(2)- HC2H) 1M' (M = Ti, Zr, Hf) wits studied by density functional theory method. It is found that this acetylene complex has indeed it metallacyclopropene moiety with two in-plane M-C sigma-bonds and one out-of-plane pi-bond interacting with the metal center, resulting in the formation of it delocalized three-center and two-electron (3c-2e) system. Along with its delocalized out-of-plane bonding, this complex has been characterized its aromatic on the basis of the computed stabilizing energy and negative nucleus-independent chemical shifts (NICS). The aromatic stabilization increases from Ti to Zr and Hf, and this is because of the increased charge separation between the CP2M fragment and the H3SiC2SiH3 (also HC2H) unit. The decrease of the M-C bond length from Zr to Hf is ttributed to the increased s character of both M and C hybridization of the M-C a-bonds.

Solubilities of Some Chlorophenols in Supercritical CO2 in the Presence and Absence of Cosolvents

The solubilities of three chlorophenols, namely, 4-chlorophenol, 2,4-dichlorophenol, and 2,4,6-trichlorophenol, in supercritical carbon dioxide were determined at temperatures from (308 to 3 18) K in the pressure range of (8.8 to 15.6) MPa. The Solubilities were determined both in the absence of cosolvents and in the presence of two cosolvents, methanol and acetone. The solubilities (in the absence of cosolvents) in mole fraction of 4-chlorophenol, 2,4-dichlorophenol, and 2,4,6-trichlorophenol at 308 K were in the range of (0.0113 to 0.0215), (0.0312 to 0.0645), and (0.008 to 0.0173), respectively. The Solubilities of the chlorophenols followed the order 2,4-dichlorophenol & 4-chlorophenol & phenol & 2,4,6-trichlorophenol & pentachlorophenol. The solubility data were correlated with the Charstil model and with the Mendez-Santiago and Teja model. The overall deviation between the experimental data and the correlated results Was less than 6 % in averaged absolute relative deviation (AARD) for both of the models.

[B4O9H2] Cyclic Borate Units as the Building Unit in a Family of Zinc Borate Structures

A solvothermal reaction of ZnO, boric acid (B(OH)(3)), and aliphatic airlines in a water-pyridine mixture gave four zinc borate phases of different dimensionalities: [Zn(B4O8H2)(C3H10N2)], I (one-dimensional); [Zn(B4O8H2)(C3H10N2)] H2O, II (two-dimensional); [Zn(B5O10H3)(C10H24N4)]center dot H2O, III (two-dimensional): and [Zn-2(B8O15H2)(C3H10N2)(2)], IV (three-dimensional). The structures are formed by the connectivity involving polyborate chains and layers with Zn2+ species. In all the compounds, the amine molecules act its file ligand binding either the same or different zn centers. The formation of two different structures, II and IV, from the same amine by varying the reaction time is noteworthy. Transformation studies on II indicate that the formation of IV. from II, is facile and has been investigated for the first time. Two of file compounds, I and III, exhibit activity for second-order nonlinear optical behavior. The UV exposure of the sample indicates the absorption of all the UV radiation suggesting that the zinc borate compounds could be exploited for UV-blocking applications. The compounds have been characterized by powder X-ray diffraction, infrared spectroscopy, thermogravimetric analysis, UV-vis, photoluminescence, and NMR studies.

Temperature and Stress Controlled Surface Manipulation in Ni-Al Nano-Layers

In the present paper the effects of temperature and high strain rate loading on the formation of various surface patterns in Ni-Al nano-layers are discussed. Effects of boundary conditions on the B2 -> BCT phase transformation in the nano-layer are also discussed. This study is aimed at developing several interesting patterned surface structures in Ni-Al nanolayer by controlling the phase transformation temperature and mechanical loading.

High Resolution Surface Imaging Using a Carbon Nanotube Array with Pointed Height distribution

In this paper we discuss a new technique to image the surfaces of metallic substrates using field emission from a pointed array of carbon nanotubes (CNTs). We consider a pointed height distribution of the CNT array under a diode configuration with two side gates maintained at a negative potential to obtain a highly intense beam of electrons localized at the center of the array. The CNT array on a metallic substrate is considered as the cathode and the test substrate as the anode. Scanning the test Substrate with the cathode reveals that the field emission current is highly sensitive to the surface features with nanometer resolution. Surface features of semi-circular, triangular and rectangular geometries (projections and grooves) are considered for simulation. This surface scanning/mapping technique can be applied for surface roughness measurements with nanoscale accuracy. micro/nano damage detection, high precision displacement sensors, vibrometers and accelerometers. among other applications.

Photocytotoxic Oxovanadium(IV) Complexes Showing Light-Induced DNA and Protein Cleavage Activity

Oxovanadium(IV) complexes [VO(L)(B)]Cl-2 (1-3), where L is bis(2-benzimidazolylmethyl)amine and B is 1,10-phenanthroline(phen),dipyrido[3,2-d:2',3'-f]quinoxaline(dpq) or dipyrido[3,2-a:2',3'-c]phenazine (dppz), have been prepared, characterized, and their photo-induced DNA and protein cleavage activity studied. The photocytotoxicity of complex 3 has been studied using adenocarcinoma A549 cells, The phen complex 1, structurally characterized by single-crystal X-ray crystallography, shows the presence of a vanadyl group in six-coordinate VON5 coordination geometry. The ligands L and phen display tridentate and bidentate N-donor chelating binding modes, respectively. The complexes exhibit a d-d band near 740 nm in 15% DMF-Tris-HCl buffer (pH 7.2). The phen and dpq complexes display an irreversible cathodic cyclic voltammetric response near -0.8 V in 20% DMF-Tris-HCl buffer having 0.1 M KCl as supporting electrolyte. The dppz complex 3 exhibits a quasi-reversible voltammogram near -0.6 V (vs SCE) that is assignable to the V(IV)-V(III)couple. The complexes bind to calf thymus DNA giving binding constant values in the range of 6.6 x 10(4)-2.9 x 10(5) M-1. The binding site size, thermal melting and viscosity binding data suggest DNA surface and/or groove binding nature of the complexes. The complexes show poor ``chemical nuclease'' activity in dark in the presence of 3-mercaptopropionic acid or hydrogen peroxide. The dpq and dppz complexes are efficient photocleavers of plasmid DNA in UV-A light of 365 nm via a mechanistic pathway that involves formation of both singlet oxygen and hydroxyl radicals. The complexes show significant photocleavage of DNA in near-IR light (>750 nm) via hydroxyl radical pathway. Among the three complexes, the dppz complex 3 shows significant BSA and lysozyme protein cleavage activity in UV-A light of 365 nm via hydroxyl radical pathway. The dppz complex 3 also exhibits photocytotoxicity in non-small cell lung carcinoma/human lung adenocarcinoma A549 cells giving IC50 value of 17 mu M in visible light(IC50 = 175 mu M in dark).

Vertex-Fused Metallaborane Clusters: Synthesis, Characterization and Electronic Structure of [(eta(5)-C5Me5Mo)(3)MoB9H18]

The reaction of the [(eta(5)-C5Me5)MoCl4] complex with [LiBH4 - TH F] in toluene at - 70 degrees C, followed by pyrolysis at 110 degrees C, afforded dark brown [(eta(5)-C5Me5Mo)(3)MoB9H18], 2, in parallel with the known [(eta(5)-C5Me5Mo)(2)B5H9], 1. Compound 2 has been characterized in solution by H-1, B-11, and C-13 NMR spectroscopy and elemental analysis, and the structural types were unequivocally established by crystallographic studies. The title compound represents a novel class of vertex-fused clusters in which a Mo atom has been fused in a perpendicular fashion between two molybdaborane clusters. Electronic structure calculations employing density functional theory yield geometries in agreement with the structure determinations, and on grounds of density functional theory calculations, we have analyzed the bonding patterns in the structure,