Structural elucidation of transmembrane domain zero (TMD0) of EcdL: A multidrug resistance-associated protein (MRP) family of ATP-binding cassette transporter protein revealed by atomistic simulation

ATP-Binding cassette (ABC) transporters play an extensive role in the translocation of diverse sets of biologically important molecules across membrane. EchnocandinB (antifungal) and EcdL protein of Aspergillus rugulosus are encoded by the same cluster of genes. Co-expression of EcdL and echinocandinB reflects tightly linked biological functions. EcdL belongs to Multidrug Resistance associated Protein (MRP) subfamily of ABC transporters with an extra transmembrane domain zero (TMD0). Complete structure of MRP subfamily comprising of TMD0 domain, at atomic resolution is not known. We hypothesized that the transportation of echonocandinB is mediated via EcdL protein. Henceforth, it is pertinent to know the topological arrangement of TMD0, with other domains of protein and its possible role in transportation of echinocandinB. Absence of effective template for TMD0 domain lead us to model by I-TASSER, further structure has been refined by multiple template modelling using homologous templates of remaining domains (TMD1, NBD1, TMD2, NBD2). The modelled structure has been validated for packing, folding and stereochemical properties. MD simulation for 0.1 μs has been carried out in the biphasic environment for refinement of modelled protein. Non-redundant structures have been excavated by clustering of MD trajectory. The structural alignment of modelled structure has shown Z-score -37.9; 31.6, 31.5 with RMSD; 2.4, 4.2, 4.8 with ABC transporters; PDB ID 4F4C, 4M1 M, 4M2T, respectively, reflecting the correctness of structure. EchinocandinB has been docked to the modelled as well as to the clustered structures, which reveals interaction of echinocandinB with TMD0 and other TM helices in the translocation path build of TMDs.     

Soft and Hard Textured Wheat Differ in Starch Properties as Indicated by Trimodal Distribution,Morphology, Thermal and Crystalline Properties

Starch and proteins are major components in the wheat endosperm that affect its end product quality. Between the two textural classes of wheat i.e. hard and soft, starch granules are loosely bound with the lipids and proteins in soft wheat due to higher expression of interfering grain softness proteins. It might have impact on starch granules properties. In this work for the first time the physiochemical and structural properties of different sized starch granules (A-, B- and C-granules) were studied to understand the differences in starches with respect to soft and hard wheat. A-, B- and C-type granules were separated with >95% purity. Average number and proportion of A-, B-, and C-type granules was 18%, 56%, 26% and 76%, 19%, 5% respectively. All had symmetrical birefringence pattern with varied intensity. All displayed typical A-type crystallites. A-type granules also showed V-type crystallinity that is indicative of starch complexes with lipids and proteins. Granules differing in gelatinization temperature (ΔH) and transition temperature (ΔT), showed different enthalpy changes during heating. Substitution analysis indicated differences in relative substitution pattern of different starch granules. Birefringence, percentage crystallinity, transmittance, gelatinization enthalpy and substitution decreased in order of A>B>C being higher in hard wheat than soft wheat. Amylose content decreased in order of A>B>C being higher in soft wheat than hard wheat. Reconstitution experiment showed that starch properties could be manipulated by changing the composition of starch granules. Addition of A-granules to total starch significantly affected its thermal properties. Effect of A-granule addition was higher than B- and C-granules. Transmittance of the starch granules paste showed that starch granules of hard wheat formed clear paste. These results suggested that in addition to differences in protein concentration, hard and soft wheat lines have differences in starch composition also.     

p38MAPK and MK2 Pathways Are Important for the Differentiation-Dependent Human Papillomavirus Life Cycle

Amplification of human papillomaviruses (HPV) is dependent on the ATM DNA damage pathway. In cells with impaired p53 activity, DNA damage repair requires the activation of p38MAPK along with MAPKAP kinase 2 (MK2). In HPV-positive cells, phosphorylation of p38 and MK2 proteins was induced along with relocalization to the cytoplasm. Treatment with MK2 or p38 inhibitors blocked HPV genome amplification, identifying the p38/MK2 pathway as a key regulator of the HPV life cycle.     

HMCES Maintains Genome Integrity by Shielding Abasic Sites in Single-Strand DNA

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Luminescent inorganic mixed borate phosphors materials for lighting

The need of new materials with desirable optical properties has become important in recent years. In particular, a need has emerged for compounds having better luminescence properties in various practical applications. The introduction of rare earth ions as activators improves the luminescence properties of the compounds considerably. Boron is one of the most abundant elements in nature. It readily combines with almost all other elements. In combination with oxygen; it forms borates comprised of various anions such as BO₃³⁻, B₂O₅⁴⁻, etc. Apart from these simple borates, several complex compositions exist involving mixed anions as well as double metal borates, due to the three-fold, or four-fold coordination of borate atoms. Borates intrinsically possesses characteristics that are advantageous for optical materials, which include a wide transparency range, large electronic band gap, good thermal and chemical stability, low preparative temperature, optical stability with good nonlinear characteristics, and an exceptionally high optical damage threshold. The unique crystal structure of borates determines their enhanced ultraviolet light transparency, good nonlinearity, and relatively high resistance against laser-induced damage. Some of these complex borates have interesting luminescence properties that are covered in this review. These include double borates containing rare earths RM₃(BO₃)₄, pentaborates LaMgB₅O₁₀, M₃R₂(BO₃)₄, where M is an alkaline earth, mixed anion borates such as aluminoborate SrAl₂B₂O₇, silicate-borates such as pekovite, SrB₂Si₂O₈, haloborates, M₂B₅O₉X, where M is an alkaline earth and X is a halogen, phosphate borates, and MBPO₅, where M is an alkaline earth. Phosphors based on these compositions find use in various applications such as fluorescence lamps, colour TVs, plasma display panels, high-intensity discharge lamps based on xenon, optically pumped solid-state lasers, eye-safe lasers, and X-ray imaging.     

Uptake of 26-Al and 67-Ga into brain and other tissues of normal and hypotransferrinaemic mice

Aluminium uptake from blood into tissues of control and homozygous hypotransferrinaemic (hpx/hpx) mice, following continuous intravenous infusion of Al and Ga, has been compared with that of gallium, a proposed tracer for aluminium. Al uptake into tissues of control (hpx/+ and +/+) mice occurred in the order (expressed as a space): bone 464.7ml 100g; renal cortex 102.9ml 100g; liver 13.0ml 100g; spleen 8.4ml 100g and brain 0.8ml 100g. Ga uptakes were similar in liver, spleen and brain, but smaller in the renal cortex and bone, at one-third and one-fifth of the values for Al, respectively. In the hypotransferrinaemic mice, uptake of Ga into all tissues was increased, especially in renal cortex (ninefold) and bone (twentyfold) as compared with the controls. Increases in Ga uptakes into cerebral hemisphere, cerebellum and brain stem of the hypotransferrinaemic mice were 3.8, 4.2 and 2.8 fold, respectively. Al uptake into tissues of the hypotransferrinaemic mice was similar to control values except in bone where it was three times greater. Pre-treatment of control animals with the anti-transferrin receptor antibody, RI7 208, enhanced Ga uptake in all tissues, the effect being greatest in renal cortex (tenfold) and bone (ninefold). Ga uptakes into cerebral hemisphere, cerebellum and brain stem in the mice pre-treated with RI7 208 were 6.4, 6 and 10 times greater than in untreated mice, respectively. No influence of antibody on Al uptake into mouse tissues was observed except in spleen where it was three times greater than in untreated mice. Hence, transport of aluminium and gallium into mouse tissues is not similar under all conditions. Non-transferrin mediated transport of each metal can occur into all tissues, especially in renal cortex and bone, where gallium may be a suitable marker for aluminium.     

Methyl directed DNA mismatch repair inVibrio cholerae

Mismatches in DNA occur either due to replication error or during recombination between homologous but non-identical DNA sequences or due to chemical modification of bases. The mismatch in DNA, if not repaired, result in high spontaneous mutation frequency. The repair has to be in the newly synthesized strand of the DNA molecule, otherwise the error will be fixed permanently. Three distinct mechanisms have been proposed for the repair of mismatches in DNA in prokaryotic cells and gene functions involved in these repair processes have been identified. The methyl-directed DNA mismatch repair has been examined inVibrio cholerae, a highly pathogenic gram negative bacterium and the causative agent of the diarrhoeal disease cholera. The DNA adenine methyltransferase encoding gene (dam) of this organism which is involved in strand discrimination during the repair process has been cloned and the complete nucleotide sequence has been determined.Vibrio cholerae dam gene codes for a 21.5 kDa protein and can substitute for theEscherichia coli enzyme. Overproduction ofVibrio cholerae Dam protein is neither hypermutable nor lethal both in Escherichia coli andVibrio cholerae. WhileEscherichia coli dam mutants are sensitive to 2-aminopurine,Vibrio cholerae 2-aminopurine sensitive mutants have been isolated with intact GATC methylation activity. The mutator genesmutS andmutL involved in the recognition of mismatch have been cloned, nucleotide sequence determined and their products characterized. Mutants ofmutS andmutL ofVibrio cholerae have been isolated and show high rate of spontaneous mutation frequency. ThemutU gene ofVibrio cholerae, the product of which is a DNA helicase II, codes for a 70 kDa protein. The deduced amino acid sequence of themutU gene hs all the consensus helicase motifs. The DNA cytosine methyltransferase encoding gene (dam) ofVibrio cholerae has also been cloned. Thedcm gene codes for a 53 kDa protein. This gene product might be involved in very short patch (VSP) repair of DNA mismatches. The vsr gene which is directly involved in VSP repair process codes for a 23 kDa protein. Using these information, the status of DNA mismatch repair inVibrio cholerae will be discussed.     

Heterochromatin: On the ADAR Radar?

Vigilin proteins, the absence of which is known to cause abnormalities in heterochromatin, have been found to bind edited RNAs. Molecular complexes including vigilin comprise proteins involved with RNA editing and with DNA repair, making connections between these processes and RNA-based silencing mechanisms.     

Role of lipid and lipoprotein metabolizing enzymes in the development of atherosclerosis

Cardiovascular disease is the primary cause of mortality in developed and developing nations. With an increase in the aging population, there is a surge in the incidence of atheroscleortic cardiovascular diseases. One of the most common and lethal manifestations of atherosclerosis is coronary heart disease, accounting for 50% of the atherosclerotic cardiovascular diseases in men and women younger than 75 years. Peripheral arterial diseases, manifested mainly as intermittent claudication constitute approximately 10% of the atherosclerotic cardiovascular events. According to the American Heart Association 2001 Heart and Stroke Statistical Update, atherosclerosis accounts for 75% of all deaths due to cardiovascular diseases. Therefore, atherosclerosis continues to remain the primary cause of health concern for the population at large. The aim of this review is to discuss the role of enzymes that are involved in the metabolism of lipid and lipoproteins in the development of atherosclerosis.