The biological and structural characterization of Mycobacterium tuberculosis UvrA provides novel insights into its mechanism of action

Mycobacterium tuberculosis is an extremely well adapted intracellular human pathogen that is exposed to multiple DNA damaging chemical assaults originating from the host defence mechanisms. As a consequence, this bacterium is thought to possess highly efficient DNA repair machineries, the nucleotide excision repair (NER) system amongst these. Although NER is of central importance to DNA repair in M. tuberculosis, our understanding of the processes in this species is limited. The conserved UvrABC endonuclease represents the multi-enzymatic core in bacterial NER, where the UvrA ATPase provides the DNA lesion-sensing function. The herein reported genetic analysis demonstrates that M. tuberculosis UvrA is important for the repair of nitrosative and oxidative DNA damage. Moreover, our biochemical and structural characterization of recombinant M. tuberculosis UvrA contributes new insights into its mechanism of action. In particular, the structural investigation reveals an unprecedented conformation of the UvrB-binding domain that we propose to be of functional relevance. Taken together, our data suggest UvrA as a potential target for the development of novel anti-tubercular agents and provide a biochemical framework for the identification of small-molecule inhibitors interfering with the NER activity in M. tuberculosis.

Revisiting the Mechanism of the Triosephosphate Isomerase Reaction: The Role of the Fully Conserved Glutamic Acid 97 Residue

An analysis of 503 available triosephosphate isomerase sequences revealed nine fully conserved residues. Of these, four residues-K12, H95, E97 and E165-are capable of proton transfer and are all arrayed around the dihydroxyacetone phosphate substrate in the three-dimensional structure. Specific roles have been assigned to the residues K12, H95 and E165, but the nature of the involvement of E97 has not been established. Kinetic and structural characterization is reported for the E97Q and E97D mutants of Plasmodium falciparum triosephosphate isomerase (Pf TIM). A 4000-fold reduction in k(cat) is observed for E97Q, whereas the E97D mutant shows a 100-fold reduction. The control mutant, E165A, which lacks the key catalytic base, shows an approximately 9000-fold drop in activity. The integrity of the overall fold and stability of the dimeric structure have been demonstrated by biophysical studies. Crystal structures of E97Q and E97D mutants have been determined at 2.0 angstrom resolution. In the case of the isosteric replacement of glutamic acid by glutamine in the E97Q mutant a large conformational change for the critical K12 side chain is observed, corresponding to a trans-to-gauche transition about the C gamma-C delta (chi(3)) bond. In the E97D mutant, the K12 side chain maintains the wild-type orientation, but the hydrogen bond between K12 and D97 is lost. The results are interpreted as a direct role for E97 in the catalytic proton transfer cycle. The proposed mechanism eliminates the need to invoke the formation of the energetically unfavourable imidazolate anion at H95, a key feature of the classical mechanism.

Synthesis from zinc oxalate, growth mechanism and optical properties of ZnO nano/micro structures

We report the synthesis of various morphological micro to nano structured zinc oxide crystals via simple precipitation technique. The growth mechanisms of the zinc oxide nanostructures such as snowflake, rose, platelets, porous pyramid and rectangular shapes were studied in detail under various growth conditions. The precursor powders were prepared using several zinc counter ions such as chloride, nitrate and sulphate along with oxalic acid as a precipitating agent. The precursors were decomposed by heating in air resulting in the formation of different shapes of zinc oxide crystals. Variations in ZnO nanostructural shapes were possibly due to the counter ion effect. Sulphate counter ion led to unusual rose-shape morphology. Strong ultrasonic treatment on ZnO rose shows that it was formed by irregular arrangement of micro to nano size hexagonal zinc oxide platelets. The X-ray diffraction studies confirmed the wurzite structure of all zinc oxide samples synthesized using different zinc counter ions. Functional groups of the zinc oxalate precursor and zinc oxide were identified using micro Raman studies. The blue light emission spectra of the various morphologies were recorded using luminescence spectrometer. (C) 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

Mechanism of enhanced corrosion of alumina graphite refractories near slag/metal interface

All refractories show enhanced corrosion near the slag/metal interface due to Marangoni and convective flows. However, in the case of oxide refractories containing graphite flakes, corrosion is severe due to periodic oscillations in the contact angle at the slag/metal interface, resulting in cyclic dissolution of oxide and graphite into the slag and metal, respectively. Alumina--graphite (AG) refractories should be used only where they are not in simultaneous contact with slag (flux) and low carbon steel.

A Mechanism for the Occurrence of Ions in Distilled Water

Solar distillation can be used to produce potable water from contaminated water. However, studies show that ions such as F(-) and NO(3)(-) occur in distillates from solar stills. In order to understand the reasons for this behavior, imaging and distillation experiments were conducted. White dots were seen in the vapor space above the interface of hot water poured into containers. The concentrations of various ions such as F(-) and SO(4)(2-) in the distillates from thermal and solar distillation experiments were roughly comparable when the feed consisted of deionized water and also solutions having fluoride concentrations of 100 and 10 000 mg/L. These observations suggest that aerosols enter the distillation setup through leaks and provide nuclei for the condensation of water vapor. The water-soluble component of aerosols dissolves in the drops formed, and some of the drops are transferred to the distillate by buoyancy-driven convection.

A compliant mechanism kit with flexible beams and connectors along with analysis and optimal synthesis procedures

We present a compliant mechanism kit as a parallel to the kits available for rigid-body mechanisms. The kit consists of flexible beams and connectors that can be easily hand-assembled using snap fits. The mechanisms assembled using the kit accurately capture the aspects of the topology, shape, and size of joint-free compliant mechanisms. Thus, the kit enables designers to conceive and design new, practicable, single-piece compliant mechanisms that do not require assembly. The concept of the kit also resolves a discrepancy in the finite element (FE) modeling of beam-based compliant mechanisms. The discrepancy arises when two or more beams are joined at one point and thus leading to increased stiffness. After resolving this discrepancy, this work extends the topology optimization to automatically generate designs that can be assembled with the kit for quick and easy validation instead of time-consuming prototyping. Thus, the kit and the accompanying analysis and optimal synthesis procedures comprise a self-contained educational as well as a research and practice toolset for compliant mechanisms. The paper also illustrates how human creativity finds new ways of using the kit beyond the original intended use and how it enables even a novice to design compliant mechanisms. (C) 2011 Elsevier Ltd. All rights reserved.