Analysis of Alpha CA Genes in Early Vertebrates and ; High-Invertebrates

Carbonic anhydrases are enzymes that are ubiquitously found in all organisms that are engaged in catalyzing the hydration of carbon dioxide to form bicarbonate and proton and vice versa. They are crucial in the process of respiration, bone resorption, pH regulation, ion transport, and photosynthesis in plants. Out of the five classes of carbonic anhydrase α, β, γ, δ, ζ this study focused in the α carbonic anhydrases. This class of CAs constitute of 16 subfamilies in mammals that include 3 non-active enzymes known as Carbonic Anhydrase Related Proteins. The inactiveness of these enzymes is due to the loss of one or more Histidine residues in the active site. This thesis was conducted based on the aim of studying evolutionary analysis of carbonic anhydrase sequences from organisms spanning from the Cambrian age. It was carried out in two phases. The first phase was the sequence collection, which involved many biological sequence databases as a source. The scope of this segment included sequence alignments and analysis of the sequence manually and in an automated form incorporating few analysis tools. The second Phase was phylogenetic analysis and exploring the subcellular location of the proteins, which was key for the evolutionary analysis. Through the medium of the methods conducted with respect to the phases mentioned above, it was possible to accomplish the desired result. Certain thought-provoking sequences were come across and analyzed thoroughly. Whereas, Phylogenetics showed interesting results to bolster previous findings and new findings as well which lay bedrock for future intensified studies.

New biomass derived carbon catalysts for biomass valorization

Due to diminishing petroleum reserves, unsteady market situation and the environmental concerns associated with utilization of fossil resources, the utilization of renewables for production of energy and chemicals (biorefining) has gained considerable attention. Biomass is the only sustainable source of organic compounds that has been proposed as petroleum equivalent for the production of fuels, chemicals and materials. In fact, it would not be wrong to say that the only viable answer to sustainably convene our future energy and material requirements remain with a bio-based economy with biomass based industries and products. This has prompted biomass valorization (biorefining) to become an important area of industrial research. While many disciplines of science are involved in the realization of this effort, catalysis and knowledge of chemical technology are considered to be particularly important to eventually render this dream to come true. Traditionally, the catalyst research for biomass conversion has been focused primarily on commercially available catalysts like zeolites, silica and various metals (Pt, Pd, Au, Ni) supported on zeolites, silica etc. Nevertheless, the main drawbacks of these catalysts are coupled with high material cost, low activity, limited reusability etc. – all facts that render them less attractive in industrial scale applications (poor activity for the price). Thus, there is a particular need to develop active, robust and cost efficient catalytic systems capable of converting complex biomass molecules. Saccharification, esterification, transesterification and acetylation are important chemical processes in the valorization chain of biomasses (and several biomass components) for production of platform chemicals, transportation fuels, food additives and materials. In the current work, various novel acidic carbons were synthesized from wastes generated from biodiesel and allied industries, and employed as catalysts in the aforementioned reactions. The structure and surface properties of the novel materials were investigated by XRD, XPS, elemental analysis, SEM, TEM, TPD and N2-physisorption techniques. The agro-industrial waste derived sulfonic acid functionalized novel carbons exhibit excellent catalytic activity in the aforementioned reactions and easily outperformed liquid H2SO4 and conventional solid acids (zeolites, ion-exchange resins etc). The experimental results indicated strong influence of catalyst pore-structure (pore size, pore-volume), concentration of –SO3H groups and surface properties in terms of the activity and selectivity of these catalysts. Here, a large pore catalyst with high –SO3H density exhibited the highest esterification and transesterification activity, and was successfully employed in biodiesel production from fatty acids and low grade acidic oils. Also, a catalyst decay model was proposed upon biodiesel production and could explain that the catalyst loses its activity mainly due to active site blocking by adsorption of impurities and by-products. The large pore sulfonated catalyst also exhibited good catalytic performance in the selective synthesis of triacetin via acetylation of glycerol with acetic anhydride and out-performed the best zeolite H-Y with respect to reusability. It also demonstrated equally good activity in acetylation of cellulose to soluble cellulose acetates, with the possibility to control cellulose acetate yield and quality (degree of substitution, DS) by a simple adjustment of reaction time and acetic anhydride concentration. In contrast, the small pore and highly functionalized catalysts obtained by hydrothermal method and from protein rich waste (Jatropha de-oiled waste cake, DOWC), were active and selective in the esterification of glycerol with fatty acids to monoglycerides and saccharification of cellulosic materials, respectively. The operational stability and reusability of the catalyst was found to depend on the stability of –SO3H function (leaching) as well as active site blocking due to adsorption of impurities during the reaction. Thus, our results corroborate the potential of DOWC derived sulfated mesoporous active carbons as efficient integrated solid acid catalysts for valorization of biomass to platform chemicals, biofuel, bio-additive, surfactants and celluloseesters.

The Role of PME-1 in Cancer: Therapeutic Implication

Protein phosphatase 2A (PP2A) plays a major role in maintaining cellular signaling homeostasis in human cells by reversibly affecting the phosphorylation of a variety of proteins. Protein phosphatase methylesterase-1 (PME-1) negatively regulates PP2A activity by reversible demethylation and active site binding. Thus far, it is known that overexpression of PME-1 in human gliomas contributes to ERK pathway signaling, cell proliferation, and malignant progression. Whether PME-1-mediated PP2A inhibition promotes therapy resistance in gliomas is unknown. Specific PP2A targets regulated by PME-1 in cancers also remain elusive. Additionally, whether oncogenic function of PME-1 can be generalized to various human cancers needs to be investigated. This study demonstrated that PME-1 expression promotes kinase inhibitor resistance in glioblastoma (GBM). PME-1 silencing sensitized GBM cells to a group of clinically used indolocarbazole multikinase inhibitors (MKIs). To facilitate the quantitative evaluation of MKIs by cancer-cell specific colony formation assay, Image-J software-plugin ‘ColonyArea’ was developed. PME-1-silencing was found to reactivate specific PP2A complexes and affect PP2A-target histone deacetylase HDAC4 activity. The HDAC4 inhibition induced synthetic lethality with MKIs similar to PME-1 depletion. However, synthetic lethality by both approaches required co-expression of a pro-apoptotic protein BAD. In gliomas, PME-1 and HDAC4 expression was associated with malignant progression. Using tumor PME-1, HDAC4 and BAD expression based stratification signatures this study defined patient subgroups that are likely to respond to MKI alone or in combination with HDAC4 inhibitor therapies. In contrast to the oncogenic role of PME-1 in certain cancer types, this study established that colorectal cancer (CRC) patients with high tumor PME-1 expression display favorable prognosis. Interestingly, PME-1 regulated survival signaling did not operate in CRC cells. Summarily, this study potentiates the candidacy of PME-1 as a therapy target in gliomas, but argues against generalization of these findings to other cancers, especially CRC.

Glutathione Transferases as Detoxification Agents: Structural and Functional Studies

Glutathione transferases (GSTs) are a diverse family of enzymes that catalyze the glutathione-dependent detoxification of toxic compounds. GSTs are responsible for the conjugation of the tripeptide glutathione (GSH) to a wide range of electrophilic substrates. These include industrial pollutants, drugs, genotoxic carcinogen metabolites, antibiotics, insecticides and herbicides. In light of applications in biomedicine and biotechnology as cellular detoxification agents, detailed structural and functional studies of GSTs are required. Plant tau class GSTs play crucial catalytic and non-catalytic roles in cellular xenobiotic detoxification process in agronomically important crops. The abundant existence of GSTs in Glycine max and their ability to provide resistance to abiotic and biotic stresses such as herbicide tolerance is of great interest in agriculture because they provide effective and suitable tools for selective weed control. Structural and catalytic studies on tau class GST isoenzymes from Glycine max (GmGSTU10-10, GmGSTU chimeric clone 14 (Sh14), and GmGSTU2-2) were performed. Crystal structures of GmGSTU10-10 in complex with glutathione sulfenic acid (GSOH) and Sh14 in complex with S-(p-nitrobenzyl)-glutathione (Nb-GSH) were determined by molecular replacement at 1.6 Å and 1.75 Å, respectively. Major structural variations that affect substrate recognition and catalytic mechanism were revealed in the upper part of helix H4 and helix H9 of GmGSTU10-10. Structural analysis of Sh14 showed that the Trp114Cys point mutation is responsible for the enhanced catalytic activity of the enzyme. Furthermore, two salt bridges that trigger an allosteric effect between the H-sites were identified at the dimer interface between Glu66 and Lys104. The 3D structure of GmGSTU2-2 was predicted using homology modeling. Structural and phylogenetic analysis suggested GmGSTU2-2 shares residues that are crucial for the catalytic activity of other tau class GSTs–Phe10, Trp11, Ser13, Arg20, Tyr30, Leu37, Lys40, Lys53, Ile54, Glu66 and Ser67. This indicates that the catalytic and ligand binding site in GmGSTU2-2 are well-conserved. Nevertheless, at the ligandin binding site a significant variation was observed. Tyr32 is replaced by Ser32 in GmGSTU2-2 and thismay affect the ligand recognition and binding properties of GmGSTU2-2. Moreover, docking studies revealed important amino acid residues in the hydrophobic binding site that can affect the substrate specificity of the enzyme. Phe10, Pro12, Phe15, Leu37, Phe107, Trp114, Trp163, Phe208, Ile212, and Phe216 could form the hydrophobic ligand binding site and bind fluorodifen. Additionally, side chains of Arg111 and Lys215 could stabilize the binding through hydrogen bonds with the –NO2 groups of fluorodifen. GST gene family from the pathogenic soil bacterium Agrobacterium tumefaciens C58 was characterized and eight GST-like proteins in A. tumefaciens (AtuGSTs) were identified. Phylogenetic analysis revealed that four members of AtuGSTs belong to a previously recognized bacterial beta GST class and one member to theta class. Nevertheless, three AtuGSTs do not belong to any previously known GST classes. The 3D structures of AtuGSTs were predicted using homology modeling. Comparative structural and sequence analysis of the AtuGSTs showed local sequence and structural characteristics between different GST isoenzymes and classes. Interactions at the G-site are conserved, however, significant variations were seen at the active site and the H5b helix at the C-terminal domain. H5b contributes to the formation of the hydrophobic ligand binding site and is responsible for recognition of the electrophilic moiety of the xenobiotic. It is noted that the position of H5b varies among models, thus providing different specificities. Moreover, AtuGSTs appear to form functional dimers through diverse modes. AtuGST1, AtuGST3, AtuGST4 and AtuGST8 use hydrophobic ‘lock–and–key’-like motifs whereas the dimer interface of AtuGST2, AtuGST5, AtuGST6 and AtuGST7 is dominated by polar interactions. These results suggested that AtuGSTs could be involved in a broad range of biological functions including stress tolerance and detoxification of toxic compounds.