Immobilized biocatalytic process development and potential application in membrane separation: a review

Biocatalytic membrane reactors have been widely used in different industries including food, fine chemicals, biological, biomedical, pharmaceuticals, environmental treatment and so on. This article gives an overview of the different immobilized enzymatic processes and their advantages over the conventional chemical catalysts. The application of a membrane bioreactor (MBR) reduces the energy consumption, and system size, in line with process intensification. The performances of MBR are considerably influenced by substrate concentration, immobilized matrix material, types of immobilization and the type of reactor. Advantages of a membrane associated bioreactor over a free-enzyme biochemical reaction, and a packed bed reactor are, large surface area of immobilization matrix, reuse of enzymes, better product recovery along with heterogeneous reactions, and continuous operation of the reactor. The present research work highlights immobilization techniques, reactor setup, enzyme stability under immobilized conditions, the hydrodynamics of MBR, and its application, particularly, in the field of sugar, starch, drinks, milk, pharmaceutical industries and energy generation.     

Coevolutionary constraints in the sequence‐space of macromolecular complexes reflect their self‐assembly pathways

Is the order in which biomolecular subunits self‐assemble into functional macromolecular complexes imprinted in their sequence‐space? Here, we demonstrate that the temporal order of macromolecular complex self‐assembly can be efficiently captured using the landscape of residue‐level coevolutionary constraints. This predictive power of coevolutionary constraints is irrespective of the structural, functional, and phylogenetic classification of the complex and of the stoichiometry and quaternary arrangement of the constituent monomers. Combining this result with a number of structural attributes estimated from the crystal structure data, we find indications that stronger coevolutionary constraints at interfaces formed early in the assembly hierarchy probably promotes coordinated fixation of mutations that leads to high‐affinity binding with higher surface area, increased surface complementarity and elevated number of molecular contacts, compared to those that form late in the assembly. Proteins 2017; 85:1183–1189. © 2017 Wiley Periodicals, Inc.     

SHW1, a common regulator of abscisic acid (ABA) and light signaling pathways

In our recent paper in Plant Physiology, we have reported the identification and functional characterization of a unique regulator, SHW1, a serine-arginine-aspartate rich protein in Arabidopsis seedling development.¹ Genetic and molecular analyses have revealed that SHW1 functions in an independent and interdependent manner with COP1, and differentially regulates photomorphogenic growth and light regulated gene expression. Here, we show the involvement of photoreceptors in the function of SHW1. Our results have further revealed that SHW1 is a common regulator of light and ABA signaling pathways. These results along with some data described in Plant Physiology paper have been discussed here in a broader perspective.Key words: light signaling, photomorphogenesis, SHW1, COP1, ABA responsePlants are exposed to various intensities and wavelengths of light with a specific wavelength of light being predominant at a particular daytime. For example, plants are exposed to varied intensities of light in the morning and noon, or far-red light being predominant in the twilight. However, plants have also evolved to respond to and subsequently tackle such variations in light quality or quantity by multiple modes of actions. One such mode of action might be to employ multiple negative regulatory proteins that function as filtering units to light intensity. These negative regulators could be operative in a specific wavelength of light or in a broad spectrum of light². Identification and functional characterization of several negative regulators, including SHW1, of photomorphogenic growth support such notion. SHW1 does not seem to have a homologue in animal system or in lower eukaryotes, and thereby has evolved as a plant specific gene. When seedlings are exposed to light after reaching the soil surface, it is important to protect the emerging cotyledons from high intensity light that otherwise might get bleached and subsequently die. SHW1 is expressed in germinating seeds to flowering plants, and it is predominantly expressed in the photosynthetically active tissues.¹ Therefore, SHW1 might function as a filtering unit not only in the case of emerging seedlings in the soil but also in the adult plants during dark to light transition.     

Design,synthesis and bioactivity of catechin/epicatechin and 2-azetidinone derived chimeric molecules

A new class of chimeric molecules have been developed. These are based on polyphenols like catechin and epicatechin and monocyclic β-lactams. The two units are joined via a triazole linker using the ‘Click Chemistry’ conditions. The compounds showed good to weak antibacterial activity against Escherichia coli as well as moderate inhibition of RNase A.     

Carbon nanotubes-polymer-redox mediator hybrid thin film for electrocatalytic sensing

Electrocatalytic sensing of NADH using a hybrid thin film derived from multi-wall carbon nanotubes (CNTs), Nafion (Nf) polymer and electrogenerated redox mediator is described. The redox mediator was electrochemically generated by the oxidation of serotonin on the hybrid thin film modified glassy carbon electrode (GC/Nf-CNT). Controlled potential electrolysis of serotonin at 0.1 V in neutral solution results in the generation of the redox mediator 5,5'-dihydroxy-4,4'-bitryptamine (DHB) on the hybrid thin film. The electrogenerated DHB has redox active quinone-imine structure and was electrochemically characterized by studying the pH dependent redox response. DHB on the hybrid thin film exhibits reversible redox peak at -0.05 V and the formal potential shifts by -55 mV while increasing the solution pH by 1 unit. The quinone-imine structure of DHB efficiently catalyzes the oxidation of NADH with a decrease in the overpotential of about 500 mV compared to the unmodified electrode. The CNTs of the hybrid thin film facilitates the mediated electrocatalytic oxidation of NADH. The hybrid thin film modified electrode exhibits stable amperometric response and it linearly responds to NADH (0.5-400 microM). This hybrid thin film modified electrode could detect NADH as low as 0.1 microM at -0.05 V with a sensitivity of 11.1 nA/microM in physiological pH.     

Structural basis for the hyperthermostability of an archaeal enzyme induced by succinimide formation

Stability of proteins from hyperthermophiles (organisms existing under boiling water conditions) enabled by a reduction of conformational flexibility is realized through various mechanisms. A succinimide (SNN) arising from the post-translational cyclization of the side chains of aspartyl/asparaginyl residues with the backbone amide -NH of the succeeding residue would restrain the torsion angle Ψ and can serve as a new route for hyperthermostability. However, such a succinimide is typically prone to hydrolysis, transforming to either an aspartyl or β-isoaspartyl residue. Here, we present the crystal structure of Methanocaldococcus jannaschii glutamine amidotransferase and, using enhanced sampling molecular dynamics simulations, address the mechanism of its increased thermostability, up to 100°C, imparted by an unexpectedly stable succinimidyl residue at position 109. The stability of SNN109 to hydrolysis is seen to arise from its electrostatic shielding by the side-chain carboxylate group of its succeeding residue Asp110, as well as through n → π¹ interactions between SNN109 and its preceding residue Glu108, both of which prevent water access to SNN. The stable succinimidyl residue induces the formation of an α-turn structure involving 13-atom hydrogen bonding, which locks the local conformation, reducing protein flexibility. The destabilization of the protein upon replacement of SNN with a Φ-restricted prolyl residue highlights the specificity of the succinimidyl residue in imparting hyperthermostability to the enzyme. The conservation of the succinimide-forming tripeptide sequence (E(N/D)(E/D)) in several archaeal GATases strongly suggests an adaptation of this otherwise detrimental post-translational modification as a harbinger of thermostability.     

The ESAT-6 Protein of Mycobacterium tuberculosis Interacts with Beta-2-Microglobulin (β2M) Affecting Antigen Presentation Function of Macrophage

ESAT-6, an abundantly secreted protein of Mycobacterium tuberculosis (M. tuberculosis) is an important virulence factor, inactivation of which leads to reduced virulence of M. tuberculosis. ESAT-6 alone, or in complex with its chaperone CFP-10 (ESAT-6:CFP-10), is known to modulate host immune responses; however, the detailed mechanisms are not well understood. The structure of ESAT-6 or ESAT-6:CFP-10 complex does not suggest presence of enzymatic or DNA-binding activities. Therefore, we hypothesized that the crucial role played by ESAT-6 in the virulence of mycobacteria could be due to its interaction with some host cellular factors. Using a yeast two-hybrid screening, we identified that ESAT-6 interacts with the host protein beta-2-microglobulin (β2M), which was further confirmed by other assays, like GST pull down, co-immunoprecipitation and surface plasmon resonance. The C-terminal six amino acid residues (90–95) of ESAT-6 were found to be essential for this interaction. ESAT-6, in complex with CFP-10, also interacts with β2M. We found that ESAT-6/ESAT-6:CFP-10 can enter into the endoplasmic reticulum where it sequesters β2M to inhibit cell surface expression of MHC-I-β2M complexes, resulting in downregulation of class I-mediated antigen presentation. Interestingly, the ESAT-6:β2M complex could be detected in pleural biopsies of individuals suffering from pleural tuberculosis. Our data highlight a novel mechanism by which M. tuberculosis may undermine the host adaptive immune responses to establish a successful infection. Identification of such novel interactions may help us in designing small molecule inhibitors as well as effective vaccine design against tuberculosis.     

Analysis of phylogeny and codon usage bias and relationship of GC content,amino acid composition with expression of the structural nif genes

Bacteria and archaea have evolved with the ability to fix atmospheric dinitrogen in the form of ammonia, catalyzed by the nitrogenase enzyme complex which comprises three structural genes nifK, nifD and nifH. The nifK and nifD encodes for the beta and alpha subunits, respectively, of component 1, while nifH encodes for component 2 of nitrogenase. Phylogeny based on nifDHK have indicated that Cyanobacteria is closer to Proteobacteria alpha and gamma but not supported by the tree based on 16SrRNA. The evolutionary ancestor for the different trees was also different. The GC1 and GC2% analysis showed more consistency than GC3% which appeared to below for Firmicutes, Cyanobacteria and Euarchaeota while highest in Proteobacteria beta and clearly showed the proportional effect on the codon usage with a few exceptions. Few genes from Firmicutes, Euryarchaeota, Proteobacteria alpha and delta were found under mutational pressure. These nif genes with low and high GC3% from different classes of organisms showed similar expected number of codons. Distribution of the genes and codons, based on codon usage demonstrated opposite pattern for different orientation of mirror plane when compared with each other. Overall our results provide a comprehensive analysis on the evolutionary relationship of the three structural nif genes, nifK, nifD and nifH, respectively, in the context of codon usage bias, GC content relationship and amino acid composition of the encoded proteins and exploration of crucial statistical method for the analysis of positive data with non-constant variance to identify the shape factors of codon adaptation index.