SciCombinator

Discover the most talked about and latest scientific content & concepts.

Concept: Ribozyme

166

Platinum-nanoparticle-based catalysts are widely used in many important chemical processes and automobile industries. Downsizing catalyst nanoparticles to single atoms is highly desirable to maximize their use efficiency, however, very challenging. Here we report a practical synthesis for isolated single Pt atoms anchored to graphene nanosheet using the atomic layer deposition (ALD) technique. ALD offers the capability of precise control of catalyst size span from single atom, subnanometer cluster to nanoparticle. The single-atom catalysts exhibit significantly improved catalytic activity (up to 10 times) over that of the state-of-the-art commercial Pt/C catalyst. X-ray absorption fine structure (XAFS) analyses reveal that the low-coordination and partially unoccupied densities of states of 5d orbital of Pt atoms are responsible for the excellent performance. This work is anticipated to form the basis for the exploration of a next generation of highly efficient single-atom catalysts for various applications.

Concepts: Chemical reaction, Hydrogen, Catalysis, Atom, Ribozyme, Catalytic converter, Solid, Enzyme catalysis

163

The specificity for the α-1,4- and α-1,6-glucosidic linkages varies among glycoside hydrolase family 31 α-glucosidases. This difference in substrate specificity has been considered to be due to the difference in an aromatic residue on β→α loop 1 in the catalytic domain with a (β/α)8 barrel fold; i.e., the enzymes having Tyr and Trp on β→α loop 1 were respectively described as α-1,4-specific and α-1,6-specific α-glucosidases. Schwanniomyces occidentalis α-glucosidase, however, prefers the α-1,4-glucosidic linkage, although the enzyme possesses Trp324 at the corresponding position. The mutation of Trp324 to Tyr decreased the ability for hydrolysis of the α-1,6-glucosidic linkage and formation of the α-1,6-glucosidic linkage in transglycosylation, indicating Trp324 to be closely associated with α-1,6 specificity, even if the enzyme preferred the α-1,4-glucosidic linkage. The mutant enzyme was found to catalyze the production of the branched oligosaccharide, 2,4-di-O-(α-D-glucopyranosyl)-D-glucopyranose, more efficiently than the wild-type enzyme.

Concepts: Protein, Metabolism, Enzyme, Enzyme substrate, Product, Catalysis, Ribozyme, Hydrolysis

142

Biological systems use compartmentalisation as a general strategy to control enzymatic reactions by precisely regulating enzyme-substrate interactions. With the advent of DNA nanotechnology, it has become possible to rationally design DNA-based nano-containers with programmable structural and dynamic properties. These DNA nanostructures have been used to cage enzymes, but control over enzyme-substrate interactions using a dynamic DNA nanostructure has not been achieved yet. Here we introduce a DNA origami device that functions as a nanoscale vault: an enzyme is loaded in an isolated cavity and the access to free substrate molecules is controlled by a multi-lock mechanism. The DNA vault is characterised for features such as reversible opening/closing, cargo loading and wall porosity, and is shown to control the enzymatic reaction catalysed by an encapsulated protease. The DNA vault represents a general concept to control enzyme-substrate interactions by inducing conformational changes in a rationally designed DNA nanodevice.

Concepts: DNA, Enzyme, Catalysis, Ribozyme, Nanotechnology, Enzymes, DNA nanotechnology, Active site

40

Amides are ubiquitous and abundant in nature and our society, but are very stable and reluctant to salt-free, catalytic chemical transformations. Through the activation of a “sterically confined bipyridine-ruthenium (Ru) framework (molecularly well-designed site to confine adsorbed H2 in)” of a precatalyst, catalytic hydrogenation of formamides through polyamide is achieved under a wide range of reaction conditions. Both C=O bond and C-N bond cleavage of a lactam became also possible using a single precatalyst. That is, catalyst diversity is induced by activation and stepwise multiple hydrogenation of a single precatalyst when the conditions are varied. The versatile catalysts have different structures and different resting states for multifaceted amide hydrogenation, but the common structure produced upon reaction with H2, which catalyzes hydrogenation, seems to be “H-Ru-N-H.”

Concepts: Chemical reaction, Hydrogen, Catalysis, Hydrogenation, Ribozyme, Nitrogen, Adsorption

38

Enzymes that catalyze carbon-silicon bond formation are unknown in nature, despite the natural abundance of both elements. Such enzymes would expand the catalytic repertoire of biology, enabling living systems to access chemical space previously only open to synthetic chemistry. We have discovered that heme proteins catalyze the formation of organosilicon compounds under physiological conditions via carbene insertion into silicon-hydrogen bonds. The reaction proceeds both in vitro and in vivo, accommodating a broad range of substrates with high chemo- and enantioselectivity. Using directed evolution, we enhanced the catalytic function of cytochrome c from Rhodothermus marinus to achieve more than 15-fold higher turnover than state-of-the-art synthetic catalysts. This carbon-silicon bond-forming biocatalyst offers an environmentally friendly and highly efficient route to producing enantiopure organosilicon molecules.

Concepts: Metabolism, Enzyme, Chemical reaction, Hydrogen, Catalysis, Chemistry, Ribozyme, Activation energy

35

The origins of life on Earth required the establishment of self-replicating chemical systems capable of maintaining and evolving biological information. In an RNA world, single self-replicating RNAs would have faced the extreme challenge of possessing a mutation rate low enough both to sustain their own information and to compete successfully against molecular parasites with limited evolvability. Thus theoretical analyses suggest that networks of interacting molecules were more likely to develop and sustain life-like behaviour. Here we show that mixtures of RNA fragments that self-assemble into self-replicating ribozymes spontaneously form cooperative catalytic cycles and networks. We find that a specific three-membered network has highly cooperative growth dynamics. When such cooperative networks are competed directly against selfish autocatalytic cycles, the former grow faster, indicating an intrinsic ability of RNA populations to evolve greater complexity through cooperation. We can observe the evolvability of networks through in vitro selection. Our experiments highlight the advantages of cooperative behaviour even at the molecular stages of nascent life.

Concepts: DNA, Gene, Bacteria, Evolution, Life, Ribozyme, RNA world hypothesis, Evolutionary biology

32

Transition metal-catalyzed transfers of carbenes, nitrenes and oxenes are powerful methods for functionalizing C=C and C-H bonds. Nature has evolved a diverse toolbox for oxene transfers, as exemplified by the myriad monooxygenation reactions catalyzed by cytochrome P450 enzymes. The isoelectronic carbene transfer to olefins, a widely used C-C bond forming reaction in organic synthesis, has no biological counterpart. Here, we report engineered variants of cytochrome P450(BM3) that catalyze highly diastereo- and enantioselective cyclopropanation of styrenes from diazoester reagents via putative carbene transfer. This work highlights the capacity to adapt existing enzymes for catalysis of synthetically important reactions not previously observed in Nature.

Concepts: Metabolism, Enzyme, Chemical reaction, Catalysis, Hydrogenation, Ribozyme, Cytochrome P450, Olefin metathesis

30

RNA performs important cellular functions in contemporary life forms. Its ability to act both as a catalyst and a storage mechanism for genetic information is also an important part of the RNA world hypothesis. Compartmentalization within modern cells allows the local concentration of RNA to be controlled and it has been suggested that this was also important in early life forms. Here, we mimic intracellular compartmentalization and macromolecular crowding by partitioning RNA in an aqueous two-phase system (ATPS). We show that the concentration of RNA is enriched by up to 3,000-fold in the dextran-rich phase of a polyethylene glycol/dextran ATPS and demonstrate that this can lead to approximately 70-fold increase in the rate of ribozyme cleavage. This rate enhancement can be tuned by the relative volumes of the two phases in the ATPS. Our observations support the importance of compartmentalization in the attainment of function in an RNA World as well as in modern biology.

Concepts: DNA, Genetics, Enzyme, Biology, Life, RNA, Ribozyme, RNA world hypothesis

29

Enzymes fold into unique three-dimensional structures, which underlie their remarkable catalytic properties. The requirement to adopt a stable, folded conformation is likely to contribute to their relatively large size (>10,000 Da). However, much shorter peptides can achieve well-defined conformations through the formation of amyloid fibrils. To test whether short amyloid-forming peptides might in fact be capable of enzyme-like catalysis, we designed a series of seven-residue peptides that act as Zn(2+)-dependent esterases. Zn(2+) helps stabilize the fibril formation, while also acting as a cofactor to catalyse acyl ester hydrolysis. These results indicate that prion-like fibrils are able to not only catalyse their own formation, but they can also catalyse chemical reactions. Thus, they might have served as intermediates in the evolution of modern-day enzymes. These results also have implications for the design of self-assembling nanostructured catalysts including ones containing a variety of biological and non-biological metal ions.

Concepts: Metabolism, Enzyme, Chemical reaction, Hydrogen, Catalysis, Ribozyme, Enzyme catalysis, Activation energy

28

A series of anthracene and acridine derivatives were hydrogenated under mild reaction conditions (80 °C, 3 bar of H(2)) using the bis(dihydrogen) complex [RuH(2)(η(2)-H(2))(2){P(C(6)H(11))(3)}(2)] (1) as a catalyst precursor. The influence of a methyl substituent on the substrate was studied. In all our systems, hydrogenation was only observed at the external rings leading to the corresponding 4H- or 8H-derivatives of anthracene and acridine. Three complexes resulting from the η(4)(C,C)-coordination of the substrate to the unsaturated fragment [RuH(2){P(C(6)H(11))(3)}(2)] were characterized. In the case of 9-methyl acridine, the corresponding complex [RuH(2)(η(4)-C(14)H(11)N){P(C(6)H(11))(3)}(2)] (4) turned out to be an active catalyst precursor leading to 1,2,3,4,5,6,7,8-octahydro-9-methylacridine as the sole product after 24 h. Regeneration of 1 from 4 supports the role of complex 4 in the catalytic cycle. Three hydrogenated products, 1,2,3,4-tetrahydroanthracene (4H-Anth), 1,2,3,4-tetrahydro-9-methylanthracene (4H-9-Me-Anth) and 1,2,3,4-tetrahydroacridine (4H-Acr), were characterized by X-ray diffraction.

Concepts: Enzyme, X-ray, Chemical reaction, Hydrogen, Catalysis, Hydrogenation, Ribozyme, Olefin metathesis