Characterisation, cloning and production of industrially interesting enzymes: gluconolactone oxidase of Penicillium cyaneo-fulvum and gluconate 5-dehydrogenase of Gluconobacter suboxydans

The work covered in this thesis is focused on the development of technology for bioconversion of glucose into D-erythorbic acid (D-EA) and 5-ketogluconic acid (5-KGA). The task was to show on proof-of-concept level the functionality of the enzymatic conversion or one-step bioconversion of glucose to these acids. The feasibility of both studies to be further developed for production processes was also evaluated. The glucose - D-EA bioconversion study was based on the use of a cloned gene encoding a D-EA forming soluble flavoprotein, D-gluconolactone oxidase (GLO). GLO was purified from Penicillium cyaneo-fulvum and partially sequenced. The peptide sequences obtained were used to isolate a cDNA clone encoding the enzyme. The cloned gene (GenBank accession no. AY576053) is homologous to the other known eukaryotic lactone oxidases and also to some putative prokaryotic lactone oxidases. Analysis of the deduced protein sequence of GLO indicated the presence of a typical secretion signal sequence at the N-terminus of the enzyme. No other targeting/anchoring signals were found, suggesting that GLO is the first known lactone oxidase that is secreted rather than targeted to the membranes of the endoplasmic reticulum or mitochondria. Experimental evidence supports this analysis, as near complete secretion of GLO was observed in two different yeast expression systems. Highest expression levels of GLO were obtained using Pichia pastoris as an expression host. Recombinant GLO was characterised and the suitability of purified GLO for the production of D-EA was studied. Immobilised GLO was found to be rapidly inactivated during D-EA production. The feasibility of in vivo glucose - D-EA conversion using a P. pastoris strain co-expressing the genes of GLO and glucose oxidase (GOD, E.C. 1.1.3.4) of A. niger was demonstrated. The glucose - 5-KGA bioconversion study followed a similar strategy to that used in the D-EA production research. The rationale was based on the use of a cloned gene encoding a membrane-bound pyrroloquinoline quinone (PQQ)-dependent gluconate 5-dehydrogenase (GA 5-DH). GA 5-DH was purified to homogeneity from the only source of this enzyme known in literature, Gluconobacter suboxydans, and partially sequenced. Using the amino acid sequence information, the GA 5-DH gene was cloned from a genomic library of G. suboxydans. The cloned gene was sequenced (GenBank accession no. AJ577472) and found to be an operon of two adjacent genes encoding two subunits of GA 5-DH. It turned out that GA 5-DH is a rather close homologue of a sorbitol dehydrogenase from another G. suboxydans strain. It was also found that GA 5-DH has significant polyol dehydrogenase activity. The G. suboxydans GA 5-DH gene was poorly expressed in E. coli. Under optimised conditions maximum expression levels of GA 5-DH did not exceed the levels found in wild-type G. suboxydans. Attempts to increase expression levels resulted in repression of growth and extensive cell lysis. However, the expression levels were sufficient to demonstrate the possibility of bioconversion of glucose and gluconate into 5-KGA using recombinant strains of E. coli. An uncharacterised homologue of GA 5-DH was identified in Xanthomonas campestris using in silico screening. This enzyme encoded by chromosomal locus NP_636946 was found by a sequencing project of X. campestris and named as a hypothetical glucose dehydrogenase. The gene encoding this uncharacterised enzyme was cloned, expressed in E. coli and found to encode a gluconate/polyol dehydrogenase without glucose dehydrogenase activity. Moreover, the X. campestris GA 5-DH gene was expressed in E. coli at nearly 30 times higher levels than the G. suboxydans GA 5-DH gene. Good expressability of the X. campestris GA-5DH gene makes it a valuable tool not only for 5-KGA production in the tartaric acid (TA) bioprocess, but possibly also for other bioprocesses (e.g. oxidation of sorbitol into L-sorbose). In addition to glucose - 5-KGA bioconversion, a preliminary study of the feasibility of enzymatic conversion of 5-KGA into TA was carried out. Here, the efficacy of the first step of a prospective two-step conversion route including a transketolase and a dehydrogenase was confirmed. It was found that transketolase convert 5-KGA into TA semialdehyde. A candidate for the second step was suggested to be succinic dehydrogenase, but this was not tested. The analysis of the two subprojects indicated that bioconversion of glucose to TA using X. campestris GA 5-DH should be prioritised first and the process development efforts in future should be focused on development of more efficient GA 5-DH production strains by screening a more suitable production host and by protein engineering.

Outer Membrane Protease/Adhesin PgtE of Salmonella enterica: Role in Salmonella-Host Interaction

Salmonella enterica serovar Typhimurium is a common cause of gastroenteritis in humans and, occasionally, also causes systemic infection. During systemic infection an important characteristic of Salmonella is its ability to survive and replicate within macrophages. The outer membrane protease PgtE of S. enterica is a member of the omptin family of outer membrane aspartate proteases, which are beta-barrel proteins with five surface-exposed loops. The main goals of this study were to characterize biological substrates and pathogenesis-associated functions of PgtE and to determine the conditions where PgtE is fully active. In this study we found that PgtE requires rough lipopolysaccharide (LPS) to be functional but is sterically inhibited by the long O-antigen side chain in smooth LPS. Salmonella isolates normally are smooth with a long oligosaccharide O-antigen, and PgtE remains functionally cryptic in wild-type Salmonella cultivated in vitro. Interestingly, our results showed that due to increased expression of PgtE and to reduced length of the LPS O-antigen chains, the wild-type Salmonella expresses highly functional PgtE when isolated from mouse macrophage-like J774A.1 cells. Salmonella is thought to be continuously released from macrophages to infect new ones, and our results suggest that PgtE is functional during these transient extracellular growth phases. Six novel host protein substrates were identified for PgtE in this work. PgtE was previously known to activate human plasminogen (Plg) to plasmin, a broad-spectrum serine protease, and in this study PgtE was shown to interfere with the Plg system by inactivating the main inhibitor of plasmin, alpha2-antiplasmin. PgtE also interferes with another important proteolytic system of mammals by activating pro-matrix metalloproteinase-9 to an active gelatinase. PgtE also directly degrades gelatin, a component of extracellular matrices. PgtE also increases bacterial resistance against complement-mediated killing in human serum and enhances survival of Salmonella within murine macrophages as well as in the liver and spleen of intraperitoneally infected mice. Taken together, the results in this study suggest that PgtE is a virulence factor of Salmonella that has adapted to interfere with host proteolytic systems and to modify extracellular matrix; these features likely assist the migration of Salmonella during systemic salmonellosis.

Hydrogel membrane electrolyte for electrochemical capacitors

Polymer electrolytes are known to possess excellent physicochemical properties that are very useful for electrochemical energy systems. The mobility in polymer electrolytes is understood to be mainly due to the segmental motion of polymer chains and the ion transport is generally restricted to the amorphous phase of the polymer. Gel polymer electrolytes (GPE) that are formed using plastizicers and polymers along with ionic salts are known to exhibit liquid-like ionic conductivity while maintaining the dimensional stability of a solid matrix. In the present study, the preparation and characterization of poly(vinyl alcohol)-based hydrogel membranes (PHMEs) as electrolyte for electrochemical capacitors have been reported. VaryingHClO4 dopant concentration leads to different characteristics of the capacitors. The EC comprising PHME doped with 2 M HClO4 and black pearl carbon (BPC) electrodes has been found to exhibit a maximum specific capacitance value of 97 F g(-1), a phase angle value of 78A degrees, and a maximum charge-discharge coulombic efficiency of 88%.

Fluorescent probe studies of biomembranes and model systems. The design and use of anionic site reporters

The fluorescence properties of a homologous series of fluorescent alkylamines are described. The binding of the probes to crythrocyte membranes increases with the length of the alkyl chain. The probes are shown to interact more strongly with membranes than with protein and lipid model systems. The binding of the probes to the membrane is sensitive to the cation concentration of the medium.

Membrane modifying linear polypeptide antibiotics

Peptides Possessing antibiotic activity isolated from microbial sources have been the subject of intensive structural and biological investigation over the past two decades. Perhaps, the discovery and widespread use of penicillin, a molecule biosynthetically derived from a tripeptide precursor, as a strong antibacterial agent, has provided the necessary impetus for the detailed study of microbial peptides. While many of these peptides have not been used clinically, They show unique metal binding properties and often possess the ability to modify the electrical properties or ion permeabilities of artificial lipid membranes. Hence, these peptides have been used extensively to study transmembrane ion transport processes in model and natural systems like mitochondria, chloroplasts and plasma membranes.

2(n)-SEMA-a robust solid state nuclear magnetic resonance experiment for measuring heteronuclear dipolar couplings in static oriented systems using effective transverse spin-lock

Separated local field (SLF) spectroscopy is a powerful technique to measure heteronuclear dipolar couplings. The method provides site-specific dipolar couplings for oriented samples such as membrane proteins oriented in lipid bilayers and liquid crystals. A majority of the SLF techniques utilize the well-known Polarization Inversion Spin Exchange at Magic Angle (PISEMA) pulse scheme which employs spin exchange at the magic angle under Hartmann-Hahn match. Though PISEMA provides a relatively large scaling factor for the heteronuclear dipolar coupling and a better resolution along the dipolar dimension, it has a few shortcomings. One of the major problems with PISEMA is that the sequence is very much sensitive to proton carrier offset and the measured dipolar coupling changes dramatically with the change in the carrier frequency. The study presented here focuses on modified PISEMA sequences which are relatively insensitive to proton offsets over a large range. In the proposed sequences, the proton magnetization is cycled through two quadrants while the effective field is cycled through either two or four quadrants. The modified sequences have been named as 2(n)-SEMA where n represents the number of quadrants the effective field is cycled through. Experiments carried out on a liquid crystal and a single crystal of a model peptide demonstrate the usefulness of the modified sequences. A systematic study under various offsets and Hartmann-Hahn mismatch conditions has been carried out and the performance is compared with PISEMA under similar conditions.

Dual-Drug Delivery System Based on In Situ Gel-Forming Nanosuspension of Forskolin to Enhance Antiglaucoma Efficacy

The present study was designed to improve the bioavailability of forskolin by the influence of precorneal residence time and dissolution characteristics. Nanosizing is an advanced approach to overcome the issue of poor aqueous solubility of active pharmaceutical ingredients. Forskolin nanocrystals have been successfully manufactured and stabilized by poloxamer 407. These nanocrystals have been characterized in terms of particle size by scanning electron microscopy and dynamic light scattering. By formulating Noveon AA-1 polycarbophil/poloxamer 407 platforms, at specific concentrations, it was possible to obtain a pH and thermoreversible gel with a pH(gel)/T-gel close to eye pH/temperature. The addition of forskolin nanocrystals did not alter the gelation properties of Noveon AA-1 polycarbophil/poloxamer 407 and nanocrystal properties of forskolin. The formulation was stable over a period of 6 months at room temperature. In vitro release experiments indicated that the optimized platform was able to prolong and control forskolin release for more than 5 h. The in vivo studies on dexamethasone-induced glaucomatous rabbits indicated that the intraocular pressure lowering efficacy for nanosuspension/hydrogel systems was 31% and lasted for 12 h, which is significantly better than the effect of traditional eye suspension (18%, 4-6 h). Hence, our investigations successfully prove that the pH and thermoreversible polymeric in situ gel-forming nanosuspension with ability of controlled drug release exhibits a greater potential for glaucoma therapy.

Stabilization of the bio-membrane by small molecules: interaction of trehalose with the phospholipid bilayer

Anhydrobiotic organisms undergo periods of acute dehydration during their life cycle. It is of interest to understand how the biomembrane remains intact through such stress. A disaccharide, trehalose, which is metabolised during anhydrobiosis is found to prevent disruption of model membrane systems. Molecular modelling techniques are used to investigate the possible mode of interaction of trehalose with a model monolayer. The objective is to maximise hydrogen bonding between the two systems. A phospholipid matrix consisting of 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine (DMPC) is chosen to represent the monolayer. The crystal structure of DMPC reveals that there are two distinct conformers designated as A and B. An expansion of the monolayer, coplanar with its surface, results in the trehalose molecule being accommodated in a pocket formed by four B conformers. One glucose ring of the sugar rests on the hydrophobic patch provided by the choline methyls of an A conformer. Five hydrogen bonds are formed involving the phosphate oxygens of three of the surrounding B conformers. The model will be discussed with reference to relevant experimental data on the interaction.

Synthesis, redox and electrochemical properties of new anthraquinone-attached micelle- and vesicle-forming cationic amphiphiles

Three new cationic amphiphiles bearing anthraquinone moieties at the polar headgroup region were synthesized, The single-chain amphiphile, N,N-dimethyl-N-octadecyl-N-(9,10-dihydro dioxoanthracen-2-ylmethyl)ammonium bromide 1, in the presence of cetyltrimethylammonium bromide upon dispersion in water gave co-micellar aggregates containing covalently attached anthraquinone residues at the polar aqueous interfaces. The other two double-chain amphiphiles, N,N-dioctadecyl-N-methyl-N-(9,10-dihydro-9,10-dioxoanthracen-2-ylmethyl)ammonium bromide 2 and N,N-dimethyl-N-(1,2-bispalmitoyloxypropanyl)-N-(9,10-dihydro-9,10-dioxanthracen-2-ylmethyl)ammonium bromide 3, however, on dispersion in aqueous media produced vesicular aggregates. The critical temperatures for the gel to liquid-crystalline-like phase transition processes for the vesicular systems were determined by following temperature-dependent changes in the ratios of keto-enol tautomeric forms of benzoylacetanilide doped within respective. vesicular assemblies. The redox chemistry of the these supramolecular assemblies was also studied by following the time-dependent changes in the ITV-VIS absorption spectroscopy in the presence of exogenous reducing or oxidizing agents, Electrochemical studies using glassy carbon electrodes reveal that redox-active amphiphiles adsorb on to the glassy carbon surfaces to form electroactive deposits when dipped into aqueous suspensions of either of these aggregates irrespective of the micellar or vesicular nature of the dispersions.

Characterization of the dynamics of glass-forming liquids from the properties of the potential energy landscape

We develop a framework for understanding the difference between strong and fragile behavior in the dynamics of glass-forming liquids from the properties of the potential energy landscape. Our approach is based on a master equation description of the activated jump dynamics among the local minima of the potential energy (the so-called inherent structures) that characterize the potential energy landscape of the system. We study the dynamics of a small atomic cluster using this description as well as molecular dynamics simulations and demonstrate the usefulness of our approach for this system. Many of the remarkable features of the complex dynamics of glassy systems emerge from the activated dynamics in the potential energy landscape of the atomic cluster. The dynamics of the system exhibits typical characteristics of a strong supercooled liquid when the system is allowed to explore the full configuration space. This behavior arises because the dynamics is dominated by a few lowest-lying minima of the potential energy and the potential energy barriers between these minima. When the system is constrained to explore only a limited region of the potential energy landscape that excludes the basins of attraction of a few lowest-lying minima, the dynamics is found to exhibit the characteristics of a fragile liquid.

Adam-Gibbs Relation for Glass-Forming Liquids in Two, Three, and Four Dimensions

The Adam-Gibbs relation between relaxation times and the configurational entropy has been tested extensively for glass formers using experimental data and computer simulation results. Although the form of the relation contains no dependence on the spatial dimensionality in the original formulation, subsequent derivations of the Adam-Gibbs relation allow for such a possibility. We test the Adam-Gibbs relation in two, three, and four spatial dimensions using computer simulations of model glass formers. We find that the relation is valid in three and four dimensions. But in two dimensions, the relation does not hold, and interestingly, no single alternate relation describes the results for the different model systems we study.

Biogenic nanosilver incorporated reverse osmosis membrane for antibacterial and antifungal activities against selected pathogenic strains: An enhanced eco-friendly water disinfection approach

Reverse osmosis (RO) membranes have been used extensively in water desalination plants, waste water treatment in industries, agricultural farms and drinking water production applications. The objective of this work is to impart antibacterial and antifungal activities to commercially available RO membrane used in water purification systems by incorporating biogenic silver nanoparticles (AgNPs) synthesized using Rosa indica wichuriana hybrid leaf extract. The morphology and surface topography of uncoated and AgNPs-coated RO membrane were studied using Scanning Electron Microscopy (SEM) and Atomic Force Microscopy (AFM). Elemental composition of the AgNPs-coated RO membrane was analyzed by energy-dispersive X-ray spectroscopy (EDAX). The functional groups were identified by Fourier Transform Infrared spectroscopy (FT-IR). Hydrophilicity of the uncoated and AgNPs-coated RO membrane was analyzed using water contact angle measurements. The thermal properties were studied by thermogravimetric analysis (TGA). The AgNPs incorporated RO membrane exhibited good antibacterial and antifungal activities against pathogenic bacterial strains such as E. coli, S. aureus, M. luteus, K. pneumoniae, and P. aeruginosa and fungal strains such as Candida tropicalis, C. krusei, C. glabrata, and C. albicans.

Sequence and conformational preferences at termini of alpha-helices in membrane proteins: Role of the helix environment

-helices are amongst the most common secondary structural elements seen in membrane proteins and are packed in the form of helix bundles. These -helices encounter varying external environments (hydrophobic, hydrophilic) that may influence the sequence preferences at their N and C-termini. The role of the external environment in stabilization of the helix termini in membrane proteins is still unknown. Here we analyze -helices in a high-resolution dataset of integral -helical membrane proteins and establish that their sequence and conformational preferences differ from those in globular proteins. We specifically examine these preferences at the N and C-termini in helices initiating/terminating inside the membrane core as well as in linkers connecting these transmembrane helices. We find that the sequence preferences and structural motifs at capping (Ncap and Ccap) and near-helical (N' and C') positions are influenced by a combination of features including the membrane environment and the innate helix initiation and termination property of residues forming structural motifs. We also find that a large number of helix termini which do not form any particular capping motif are stabilized by formation of hydrogen bonds and hydrophobic interactions contributed from the neighboring helices in the membrane protein. We further validate the sequence preferences obtained from our analysis with data from an ultradeep sequencing study that identifies evolutionarily conserved amino acids in the rat neurotensin receptor. The results from our analysis provide insights for the secondary structure prediction, modeling and design of membrane proteins. Proteins 2014; 82:3420-3436. (c) 2014 Wiley Periodicals, Inc.

Fragility correlates thermodynamic and kinetic properties of glass forming liquids

In our earlier communication we proposed a simple fragility determining function, (NBO]/(VmTg)-T-3), which we have now used to analyze several glass systems using available thermal data. A comparison with similar fragility determining function, Delta C-p/C-p(1), introduced by Chryssikos et al. in their investigation of lithium borate glasses has also been performed and found to be more convenient quantity for discussing fragilities. We now propose a new function which uses both Delta C-p and Delta T and which gives a numerical fragility parameter, F whose value lies between 0 and 1 for glass forming liquids. F can be calculated through the use of measured thermal parameters Delta C-p, C-p(1), T-g and T-m. Use of the new fragility values in reduced viscosity equation reproduces the whole range of viscosity curves of the Angell plot. The reduced viscosity equation can be directly compared with the Adam-Gibbs viscosity equation and a heat capacity function can be formulated which reproduces satisfactorily the Delta C-p versus In(T-r) curves and hence the configurational entropy. (C) 2014 Elsevier Ltd. All rights reserved.

Fragility correlates thermodynamic and kinetic properties of glass forming liquids

In our earlier communication we proposed a simple fragility determining function, (NBO]/(VmTg)-T-3), which we have now used to analyze several glass systems using available thermal data. A comparison with similar fragility determining function, Delta C-p/C-p(1), introduced by Chryssikos et al. in their investigation of lithium borate glasses has also been performed and found to be more convenient quantity for discussing fragilities. We now propose a new function which uses both Delta C-p and Delta T and which gives a numerical fragility parameter, F whose value lies between 0 and 1 for glass forming liquids. F can be calculated through the use of measured thermal parameters Delta C-p, C-p(1), T-g and T-m. Use of the new fragility values in reduced viscosity equation reproduces the whole range of viscosity curves of the Angell plot. The reduced viscosity equation can be directly compared with the Adam-Gibbs viscosity equation and a heat capacity function can be formulated which reproduces satisfactorily the Delta C-p versus In(T-r) curves and hence the configurational entropy. (C) 2014 Elsevier Ltd. All rights reserved.