Raushan Kumar Singh

From protein engineering to immobilization: promising strategies for the upgrade of industrial enzymes.

Enzymes found in nature have been exploited in industry due to their inherent catalytic properties in complex chemical processes under mild experimental and environmental conditions. The desired industrial goal is often difficult to achieve using the native form of the enzyme. Recent developments in protein engineering have revolutionized the development of commercially available enzymes into better industrial catalysts. Protein engineering aims at modifying the sequence of a protein, and hence its structure, to create enzymes with improved functional properties such as stability, specific activity, inhibition by reaction products, and selectivity towards non-natural substrates. Soluble enzymes are often immobilized onto solid insoluble supports to be reused in continuous processes and to facilitate the economical recovery of the enzyme after the reaction without any significant loss to its biochemical properties. Immobilization confers considerable stability towards temperature variations and organic solvents. Multipoint and multisubunit covalent attachments of enzymes on appropriately functionalized supports via linkers provide rigidity to the immobilized enzyme structure, ultimately resulting in improved enzyme stability. Protein engineering and immobilization techniques are sequential and compatible approaches for the improvement of enzyme properties. The present review highlights and summarizes various studies that have aimed to improve the biochemical properties of industrially significant enzymes.

Role of Conserved Glycine in Zinc-dependent Medium Chain Dehydrogenase/Reductase Superfamily

Background: The function of second-shell residues is not well understood in zinc-dependent medium chain dehydrogenase/reductases (MDRs). Results: The strictly conserved second-shell residue Gly-77 was characterized using a wide variety of methods. Conclusion: Gly-77 maintains the metal binding affinity and electronic state of the catalytic zinc ion. Significance: This study provides the first insights into the role of a conserved glycine in the MDR superfamily. The medium-chain dehydrogenase/reductase (MDR) superfamily consists of a large group of enzymes with a broad range of activities. Members of this superfamily are currently the subject of intensive investigation, but many aspects, including the zinc dependence of MDR superfamily proteins, have not yet have been adequately investigated. Using a density functional theory-based screening strategy, we have identified a strictly conserved glycine residue (Gly) in the zinc-dependent MDR superfamily. To elucidate the role of this conserved Gly in MDR, we carried out a comprehensive structural, functional, and computational analysis of four MDR enzymes through a series of studies including site-directed mutagenesis, isothermal titration calorimetry, electron paramagnetic resonance (EPR), quantum mechanics, and molecular mechanics analysis. Gly substitution by other amino acids posed a significant threat to the metal binding affinity and activity of MDR superfamily enzymes. Mutagenesis at the conserved Gly resulted in alterations in the coordination of the catalytic zinc ion, with concomitant changes in metal-ligand bond length, bond angle, and the affinity (Kd) toward the zinc ion. The Gly mutants also showed different spectroscopic properties in EPR compared with those of the wild type, indicating that the binding geometries of the zinc to the zinc binding ligands were changed by the mutation. The present results demonstrate that the conserved Gly in the GHE motif plays a role in maintaining the metal binding affinity and the electronic state of the catalytic zinc ion during catalysis of the MDR superfamily enzymes.

Photoelectrochemical Reduction of Carbon Dioxide to Methanol through a Highly Efficient Enzyme Cascade

Natural photosynthesis is an effective route for the clean and sustainable conversion of CO2 into high-energy chemicals. Inspired by the natural process, a tandem photoelectrochemical (PEC) cell with an integrated enzyme-cascade (TPIEC) system was designed, which transfers photogenerated electrons to a multienzyme cascade for the biocatalyzed reduction of CO2 to methanol. A hematite photoanode and a bismuth ferrite photocathode were applied to fabricate the iron oxide based tandem PEC cell for visible-light-assisted regeneration of the nicotinamide cofactor (NADH). The cell utilized water as an electron donor and spontaneously regenerated NADH. To complete the TPIEC system, a superior three-dehydrogenase cascade system was employed in the cathodic part of the PEC cell. Under applied bias, the TPIEC system achieved a high methanol conversion output of 220 μm h-1 , 1280 μmol g-1  h-1 using readily available solar energy and water.

Computational approaches for rational design of proteins with novel functionalities

Proteins are the most multifaceted macromolecules in living systems and have various important functions, including structural, catalytic, sensory, and regulatory functions. Rational design of enzymes is a great challenge to our understanding of protein structure and physical chemistry and has numerous potential applications. Protein design algorithms have been applied to design or engineer proteins that fold, fold faster, catalyze, catalyze faster, signal, and adopt preferred conformational states. The field of de novo protein design, although only a few decades old, is beginning to produce exciting results. Developments in this field are already having a significant impact on biotechnology and chemical biology. The application of powerful computational methods for functional protein designing has recently succeeded at engineering target activities. Here, we review recently reported de novo functional proteins that were developed using various protein design approaches, including rational design, computational optimization, and selection from combinatorial libraries, highlighting recent advances and successes.

Biological methanol production by immobilized Methylocella tundrae using simulated biohythane as a feed

Biohythane may be used as an alternative feed for methanol production instead of costly pure methane. In this study, methanol production potential of Methylocella tundrae immobilized through covalent immobilization, adsorption, and encapsulation was evaluated. Cells covalently immobilized on groundnut shells and chitosan showed a relative methanol production potential of 83.9 and 91.6%, respectively, compared to that of free cells. The maximum methanol production by free cells and cells covalently immobilized on groundnut shells and chitosan was 6.73, 6.20, and 7.23mM, respectively, using simulated biohythane as a feed. Under repeated batch conditions of eight cycles, cells covalently immobilized on chitosan and groundnut shells, and cells encapsulated in sodium-alginate resulted in significantly higher cumulative methanol production of 37.76, 31.80, and 25.58mM, respectively, than free cells (18.57mM). This is the first report on immobilization of methanotrophs on groundnut shells and its application in methanol production using biohythane as a feed.

pH-rate profiles of L-arabinitol 4-dehydrogenase from Hypocrea jecorina and its application in L-xylulose production.

l-Arabinitol 4-dehydrogenase (LAD) from Hypocrea jecorina (HjLAD) was cloned and overexpressed in Escherichia coli BL21 (DE3). The kinetics of l-arabinitol oxidation by NAD(+), catalyzed by HjLAD, was studied within the pH range of 7.0-9.5 at 25°C. The turnover number (kcat) and the catalytic efficiency (kcat/Km) were 4200min(-1) and 290mM(-1)min(-1), respectively. HjLAD showed the highest turnover number and catalytic efficiency among all previously characterized LADs. In further application of HjLAD, rare l-sugar l-xylulose was produced by the enzymatic oxidation of arabinitol to give a yield of approximately 86%.

An artificial synthetic pathway for acetoin, 2,3-butanediol, and 2-butanol production from ethanol using cell free multi-enzyme catalysis

Upgrading ethanol to higher order alcohols is desired but difficult using current biotechnological methods. In this study, we designed a completely artificial reaction pathway for upgrading ethanol to acetoin, 2,3-butanediol, and 2-butanol in a cell-free bio-system composed of ethanol dehydrogenase, formolase, 2,3-butanediol dehydrogenase, diol dehydratase, and NADH oxidase. Under optimized conditions, acetoin, 2,3-butanediol, and 2-butanol were produced at 88.78%, 88.28%, and 27.25% of the theoretical yield from 100 mM ethanol, respectively. These results demonstrate that this artificial synthetic pathway is an environmentally-friendly novel approach for upgrading bio-ethanol to acetoin, 2,3-butanediol, and 2-butanol.

Structure-based studies on the metal binding of two-metal-dependent sugar isomerases

Two‐metal‐dependent sugar isomerases are important in the synthesis of rare sugars. Many of their properties, specifically their metal dependency, have not been sufficiently explored. Here we used X‐ray crystallography, site‐directed mutagenesis, isothermal titration calorimetry and electron paramagnetic resonance spectroscopy to investigate the molecular determinants of the metal‐binding affinity of l‐rhamnose isomerase, a two‐Mn2+‐dependent isomerase from Bacillus halodurans (BHRI). The crystal structure of BHRI confirmed the presence of two metal ion‐binding sites: a structural metal ion‐binding site for substrate binding, and a catalytic metal ion‐binding site that catalyzes a hydride shift. One conserved amino acid, W38, in wild‐type BHRI was identified as a critical residue for structural Mn2+ binding and thus the catalytic efficiency of BHRI. This function of W38 was explored by replacing it with other amino acids. Substitution by Phe, His, Lys, Ile or Ala caused complete loss of catalytic activity. The role of W38 was further examined by analyzing the crystal structure of wild‐type BHRI and two inactive mutants of BHRI (W38F and W38A) in complex with Mn2+. A structural comparison of the mutants and the wild‐type revealed differences in their coordination of Mn2+, including changes in metal–ligand bond length and affinity for Mn2+. The role of W38 was further confirmed in another two‐metal‐dependent enzyme: xylose isomerase from Bacillus licheniformis. These data suggest that W38 stabilizes protein–metal complexes and in turn assists ligand binding during catalysis in two‐metal‐dependent isomerases.

Probing the Role of Sigma π Interaction and Energetics in the Catalytic Efficiency of Endo-1,4-β-Xylanase

ABSTRACT Chaetomium globosum endo-1,4-β-xylanase (XylCg) is distinguished from other xylanases by its high turnover rate (1,860 s−1), the highest ever reported for fungal xylanases. One conserved amino acid, W48, in the substrate binding pocket of wild-type XylCg was identified as an important residue affecting XylCgs catalytic efficiency.

An efficient ribitol-specific dehydrogenase from Enterobacter aerogenes

An NAD(+)-dependent ribitol dehydrogenase from Enterobacter aerogenes KCTC 2190 (EaRDH) was cloned and successfully expressed in Escherichia coli. The complete 729-bp gene was amplified, cloned, expressed, and subsequently purified in an active soluble form using nickel affinity chromatography. The enzyme had an optimal pH and temperature of 11.0 and 45°C, respectively. Among various polyols, EaRDH exhibited activity only toward ribitol, with Km, Vmax, and kcat/Km values of 10.3mM, 185Umg(-1), and 30.9s(-1)mM(-1), respectively. The enzyme showed strong preference for NAD(+) and displayed no detectable activity with NADP(+). Homology modeling and sequence analysis of EaRDH, along with its biochemical properties, confirmed that EaRDH belongs to the family of NAD(+)-dependent ribitol dehydrogenases, a member of short-chain dehydrogenase/reductase (SCOR) family. EaRDH showed the highest activity and unique substrate specificity among all known RDHs. Homology modeling and docking analysis shed light on the molecular basis of its unusually high activity and substrate specificity.