Enzymes articles within Nature Chemistry

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  • Article
    | Open Access

    Evolution separates complex modern enzymes from their hypothetical simpler early ancestors, which raises the question of how unevolved sequences can develop new functions. Here a library of non-natural protein sequences was subjected to ultrahigh-throughput screens in microfluidic droplets, leading to the isolation of a phosphodiesterase enzyme capable of hydrolysing the biological second messenger, cyclic AMP.

    • J. David Schnettler
    • , Michael S. Wang
    •  & Michael H. Hecht

  • News & Views |

    Cryptic halogenation reactions result in natural products with diverse structural motifs and bioactivities. However, these halogenated species are difficult to detect with current analytical methods because the final products are often not halogenated. An approach to identify products of cryptic halogenation using halide depletion has now been discovered, opening up space for more effective natural product discovery.

    • Ludek Sehnal
    • , Libera Lo Presti
    •  & Nadine Ziemert

  • News & Views |

    Site-specific modification of RNA in cells is crucial for analysis and functional investigations. Natural enzymes that promote RNA methylation using S-adenosyl-l-methionine (SAM) exist, but leveraging these proteins for RNA modification is limited by cell permeability, stability and specificity of their substrates. Now, a de novo ribozyme that acts on a stabilized and cell-permeable SAM analogue enables site-specific RNA modification with a click handle in living cells.

    • Nicolas V. Cornelissen
    •  & Andrea Rentmeister

  • Article |

    The design and improvement of enzymes based on physical principles remain challenging. Now, the vibrational Stark effect has been used to demonstrate how an electrostatic model can unify the catalytic effects of distinct chemical forces in a quantitative manner and guide the design of enzyme variants that outperform their natural counterpart.

    • Chu Zheng
    • , Zhe Ji
    •  & Steven G. Boxer

  • Article
    | Open Access

    Ribosomal incorporation of non-α-amino acid monomers into proteins is largely restricted to in vitro translation. Now, pyrrolysyl-transfer RNA synthetase variants have been shown to acylate tRNAs with α-thio acids, malonic acids, and N-formyl amino acids. This work represents a key step towards the programmed ribosomal synthesis of sequence-defined non-protein polymers in cellulo.

    • Riley Fricke
    • , Cameron V. Swenson
    •  & Alanna Schepartz

  • Article |

    Cellular membranes contain numerous lipids, and efforts to understand the biological functions of individual lipids demand approaches for controlled modulation of membrane composition in situ. Now, click chemistry-based directed evolution of a microbial phospholipase within mammalian cells affords an editor for optogenetic, targeted modification of phospholipids in cell membranes.

    • Reika Tei
    • , Saket R. Bagde
    •  & Jeremy M. Baskin

  • Article |

    Enteropeptins are peptide natural products produced by the gut microbe Enterococcus cecorum. Now, the structure, biosynthesis and function of enteropeptins have been determined. After ribosomal biosynthesis, enteropeptins are post-translationally modified in three reactions carried out by a radical S-adenosylmethionine enzyme, an Mn2+-dependent arginase, and an Fe–S-containing methyltransferase, respectively, to form the N-methylornithine-containing peptide natural products.

    • Kenzie A. Clark
    • , Brett C. Covington
    •  & Mohammad R. Seyedsayamdost

  • Article |

    Oligonucleotide catalysts such as ribozymes and DNAzymes can cleave RNA efficiently and specifically but are typically dependent on high concentrations of divalent cations, limiting their biological applications. A modular XNAzyme catalyst composed of 2′-deoxy-2′-fluoro-β-d-arabino nucleic acid (FANA) has now been developed that can cleave long (>5 kb), highly structured mRNAs under physiological conditions and enables allele-specific catalytic RNA knockdown inside cells.

    • Alexander I. Taylor
    • , Christopher J. K. Wan
    •  & Philipp Holliger

  • Article |

    The biosynthesis of fuscimiditide, a ribosomally synthesized post-translationally modified peptide, has now been reported. Heterologous expression and analysis of fuscimiditide showed it contained two side-chain–side-chain ester linkages and an aspartimide in its backbone. The aspartimide moiety is unexpectedly stable, suggesting this structure is the intended natural product.

    • Hader E. Elashal
    • , Joseph D. Koos
    •  & A. James Link

  • News & Views |

    Malleicyprols are highly reactive polyketides responsible for virulence in some pathogenic bacteria. Now, the enzyme that constructs the cyclopropanol warhead of malleicyprols has been identified. This enzyme could represent a useful target for developing new antivirulence therapeutics.

    • Elijah Abraham
    •  & Rebecca A. Butcher

  • Article
    | Open Access

    Burkholderia pseudomallei is a species of bacteria that poses a global health threat and, more generally, bacteria of the Burkholderia pseudomallei group cause severe diseases that are recalcitrant to treatment with antibiotics. Now, it has been shown how these infamous pathogens repurpose the widespread enzyme BurG to produce a reactive cyclopropanol head group found in the virulence-promoting malleicyprol toxins. Interrupting the synthesis of the cyclopropanol warhead is a potential route for developing antivirulence treatments.

    • Felix Trottmann
    • , Keishi Ishida
    •  & Christian Hertweck

  • Article |

    A reduction reaction is usually equated with an electron transfer reaction. Now, ultrafast time-resolved serial femtosecond X-ray crystallography has enabled the visualization of the stepwise structural changes that occur after electron transfers have been observed in the light-triggered reduction of flavin adenine dinucleotide catalysed by DNA photolyase.

    • Manuel Maestre-Reyna
    • , Cheng-Han Yang
    •  & Ming-Daw Tsai

  • Article |

    Carbonic anhydrase enzymatically catalyses CO2 hydration, and its effect on enzymatic and heterogeneous CO2 reduction has now been studied. Through the co-immobilization of carbonic anhydrase, it has been shown that faster CO2 hydration kinetics are beneficial for enzymatic catalysis (using formate dehydrogenase) but detrimental for heterogeneous catalysts, such as gold.

    • Samuel J. Cobb
    • , Vivek M. Badiani
    •  & Erwin Reisner

  • Article |

    A dual cellular-then-heterogeneous catalysis strategy has been used to produce olefins from glucose. 3-Hydroxy acids are made using an engineered microbial host. A hydrolytic step then provides the driving force for fatty acid deoxygenation by simple heterogeneous Lewis acid catalysis. This decarboxylation–dehydration route to olefinic products avoids the need for an additional redox input typically required for deoxygenation of unmodified fatty acids.

    • Zhen Q. Wang
    • , Heng Song
    •  & Michelle C. Y. Chang

  • Article |

    Self-propelled artificial chemical swimmers have previously been developed for chemical sensing. Now, hybrid bioelectrochemical swimmers, capable of translating chiral molecular information into macroscopic motion, have been developed. Diastereomeric interactions between enantiopure oligomers immobilized on the swimmer and a chiral molecule present in solution control the trajectory of the device.

    • Serena Arnaboldi
    • , Gerardo Salinas
    •  & Alexander Kuhn

  • Article |

    Computationally designed enzymes can be substantially improved by directed evolution. Now, it has been shown that evolution can introduce a dynamic network that selectively tightens the transition-state ensemble, giving rise to a negative activation heat capacity. Targeting such transition state conformational dynamics may expedite de novo enzyme creation.

    • H. Adrian Bunzel
    • , J. L. Ross Anderson
    •  & Adrian J. Mulholland

  • Article |

    A de novo designed zinc-binding protein has been converted into a highly active, stereoselective catalyst for a hetero-Diels–Alder reaction. Design and directed evolution were used to effectively harness Lewis acid catalysis and create an enzyme more proficient than other reported Diels–Alderases.

    • Sophie Basler
    • , Sabine Studer
    •  & Donald Hilvert

  • News & Views |

    Enzymes that methylate using S-adenosyl-l-methionine — nature’s methyliodide — are abundant and often promiscuous; however, a preference for alkylation over methylation has been neither observed in nature nor engineered. Now, carboxymethylation has been demonstrated using engineered methyltransferases.

    • Jennifer N. Andexer
    •  & Andrea Rentmeister

  • News & Views |

    Tailor-made reverse transcriptases are used in molecular biology and synthetic genetics. However, re-engineering these enzymes to work with non-natural nucleic acids is difficult and requires powerful directed evolution strategies. Now, an adaptable selection approach has been demonstrated for the evolution of new reverse transcriptases.

    • Melanie Henkel
    •  & Andreas Marx

  • Article |

    Single-molecule nanopore measurements have revealed ligand-induced conformational changes in the catalytic cycle of dihydrofolate reductase, and showed that the enzyme adopts distinctive conformers, which have different affinities for substrates and products. Crossing the transition state facilitates conformer exchange, suggesting that the chemical step catalyses the switch between conformers to obtain a more efficient product release.

    • Nicole Stéphanie Galenkamp
    • , Annemie Biesemans
    •  & Giovanni Maglia

  • Article |

    Enacyloxin IIa is an antibiotic, assembled by a modular polyketide synthase, with promising activity against the Gram-negative bacterium Acinetobacter baumannii. Now, it has been shown that the enacyloxin IIa polyketide chain is released via transfer to a separately encoded carrier protein by a non-elongating ketosynthase domain, followed by condensation with 3,4-dihydroxycyclohexane carboxylic acid by a non-ribosomal peptide synthetase condensation domain.

    • Joleen Masschelein
    • , Paulina K. Sydor
    •  & Gregory L. Challis

  • Article |

    Natural hydrogenases exclusively utilize Ni and/or Fe to activate or produce hydrogen. Now, a catalytically active [Mn]-hydrogenase has been prepared by incorporating a synthetic Mn complex into the apoenzyme of [Fe]-Hydrogenase. The semi-synthetic [Mn]-hydrogenase shows higher activity than the corresponding Fe analogue.

    • Hui-Jie Pan
    • , Gangfeng Huang
    •  & Xile Hu

  • Article |

    An automated platform that can synthesize a wide range of complex glycans could greatly facilitate progress in glycoscience. Now, a fully automated process for enzyme-mediated oligosaccharide synthesis has been developed. This process uses glycosyltransferase-catalysed reactions performed in solution, with product purification being accomplished by solid phase extraction using a sulfonate tag.

    • Tiehai Li
    • , Lin Liu
    •  & Geert-Jan Boons

  • Article |

    Preparation of well-defined N-glycans is very demanding, which hampers progress in glycoscience. Now, a biomimetic synthetic approach has been developed in which a readily available bi-antennary glycan can be converted in ten or fewer steps into multi-antennary N-glycans. This approach enables each arm to be uniquely extended by glycosyltransferases to give complex branched N-glycans.

    • Lin Liu
    • , Anthony R. Prudden
    •  & Geert-Jan Boons

  • Article |

    A chemical proteomic strategy has now been developed for profiling pyridoxal-phosphate dependent enzymes (PLP-DEs) in cells. Pyridoxal-based probes are phosphorylated in situ and bind to cellular PLP-DEs as cofactor mimics. The method accessed 73% of the Staphylococcus aureus PLP-dependent proteome and annotated uncharacterized proteins as novel PLP-DEs.

    • Annabelle Hoegl
    • , Matthew B. Nodwell
    •  & Stephan A. Sieber

  • Article |

    The construction of dynamic protein–DNA nano-assemblies suitable for modulating protein proximities and activities has now been demonstrated. This approach uses DNA strand displacement and can enable control of enzyme activity to be programmed using logic gates. As a demonstration, a split enzyme capable of activating a prodrug is triggered is by cancer-specific miRNAs.

    • Rebecca P. Chen
    • , Daniel Blackstock
    •  & Wilfred Chen

  • Article |

    Nonribosomal peptide synthetases (NRPSs) produce vital natural products but have proven recalcitrant to biosynthetic engineering. Now, a combination of yeast surface display and fluorescence-activated cell sorting (FACS) has been used to reprogram an L-Phe-incorporating module for β-Phe. The resulting module is highly selective and functions efficiently in NRPS pathways.

    • David L. Niquille
    • , Douglas A. Hansen
    •  & Donald Hilvert

  • Article |

    The intermolecular amination of C–H bonds is an enabling transformation for the synthesis of nitrogen-containing molecules; however, developing catalysts for this class of reactions is very challenging. Now, an iron-based enzyme for this reaction has been engineered, demonstrating that a protein can confer a difficult new function upon an otherwise unreactive base metal.

    • Christopher K. Prier
    • , Ruijie K. Zhang
    •  & Frances H. Arnold

  • Article |

    Despite decades of research into heme-copper oxidases, the advantages provided by copper over iron as the non-heme metal has remained unclear. Now, the preference of copper over iron has finally been explained. Copper favours faster electron transfer and higher O–O bond activation, which results in much higher oxidase activity than would be achieved by an iron equivalent.

    • Ambika Bhagi-Damodaran
    • , Matthew A. Michael
    •  & Yi Lu

  • Article |

    A chemical proteomic strategy is described for the discovery of protein-bound electrophilic groups in human cells. Using this approach, the dynamic regulation of the pyruvoyl catalytic cofactor in S-adenosyl-L-methionine decarboxylase was characterized and an N-terminal glyoxylyl modification on secernin proteins was discovered.

    • Megan L. Matthews
    • , Lin He
    •  & Benjamin F. Cravatt

  • Article |

    A generally applicable small-molecule switch for protein function in live cells has been developed based on selective protein protection using unnatural amino acid mutagenesis and a bioorthogonal deprotection via Staudinger reduction.

    • Ji Luo
    • , Qingyang Liu
    •  & Alexander Deiters

  • Article |

    Functional catalytic triads have been designed into a hyperstable heptameric α-helical barrel protein. Twenty-one mutations were introduced to form seven Cys-His-Glu catalytic triads. The resulting protein hydrolyses p-nitrophenyl acetate with activities matching the most-efficient redesigned hydrolases based on natural protein scaffolds. This is the first example of a functional catalytic triad being engineered into a fully de novo protein.

    • Antony J. Burton
    • , Andrew R. Thomson
    •  & Derek N. Woolfson

  • Article |

    NO participates in numerous physiological processes of which many involve the reaction of NO with metalloenzymes to form a metal–nitrosyl (M–NO). Now, addition of NO to models of type 1 Cu sites has provided a fully characterized S-nitrosothiol adduct, [CuI](κ1-N(O)SR), that reversibly loses NO upon purging with an inert gas. These findings suggest a new motif for reversible binding of nitric oxide at bioinorganic metal centres.

    • Shiyu Zhang
    • , Marie M. Melzer
    •  & Timothy H. Warren

  • Article |

    Naturally occurring DNA polymerases can amplify DNA efficiently via PCR, but they cannot utilize C2′-modified substrates to make non-natural nucleic acids. Such C2′-modified nucleic acids are of interest as they are resistant to nucleases. Now, a Stoffel fragment DNA polymerase has been evolved to transcribe C2′-modified DNA from a DNA template, reverse transcribe C2′-modified DNA back into DNA, and PCR-amplify C2′-modified DNA.

    • Tingjian Chen
    • , Narupat Hongdilokkul
    •  & Floyd E. Romesberg

  • Article |

    A collaborative approach between experiment and simulation has revealed a single mutation in the F/G loop of the newly described nitrating cytochrome P450 TxtE that controls loop dynamics and, more surprisingly, the regioselectivity of the reaction. This mutation is present in a subset of homologous nitrating P450s that produce a previously unidentified biosynthetic intermediate, 5-nitro-L-tryptophan.

    • Sheel C. Dodani
    • , Gert Kiss
    •  & Frances H. Arnold

  • Article |

    The development of cells requires a mechanism to support homeostasis—the maintenance of constant internal conditions—as cellular growth results in internal dilution. Now, a simple physical process is described in which short oligonucleotide inhibitors enable dilution-driven activation of encapsulated ribozymes via membrane growth, suggesting homeostatic mechanisms could have existed in the earliest cells.

    • Aaron E. Engelhart
    • , Katarzyna P. Adamala
    •  & Jack W. Szostak

  • Article |

    [Fe]-hydrogenase has an iron-guanylylpyridinol cofactor and catalyses the reversible hydrogenation of a methenyl-tetrahydromethanopterin. Now, [Fe]-hydrogenase has been reconstituted using synthetic cofactor mimics. The enzyme containing a mimic with a 2-hydroxy-pyridine group was active, whereas one containing a 2-methoxy-pyridine group was inactive. This result, together with DFT computations, supports a catalytic mechanism involving the deprotonated pyridinol hydroxy group as a proton acceptor.

    • Seigo Shima
    • , Dafa Chen
    •  & Xile Hu

  • News & Views |

    A supramolecular polymer comprising stacked artificial chromophores to which zinc(II) complexes are appended is able to respond to enzymatic hydrolysis in aqueous solution. The assembly of molecules can twist reversibly and quickly in response to changes in the type of adenosine phosphate present.

    • David B. Amabilino

  • News & Views |

    Supramolecular assembly has been used to design and create new proteins capable of performing biomimetic functions in complex environments such as membranes and inside living cells.

    • Arnold J. Boersma
    •  & Gerard Roelfes

  • Research Highlights |

    • Leonie Mueck

  • News & Views |

    ATP synthase is an important enzyme for the storage and release of energy in cells. Ion-mobility mass spectrometry has now been used to study its structure, revealing important mechanistic details about its operation and regulation.

    • Jianhua Zhao
    •  & John L. Rubinstein

  • News & Views |

    An RNA replicase ribozyme has long been sought by chemists interested in the origin of life. Now, a selection strategy employing a low-temperature water–ice mixture as the medium has led to discovery of a ribozyme that can catalyse polymerization of an RNA chain greater than its own length.

    • Niles Lehman

  • Article |

    Molecular self-replication through ribozyme-catalysed RNA synthesis could shed light on the origins of life. Here, a polymerase ribozyme capable of synthesizing an RNA sequence longer than itself is described, based on a cold-adapted ribozyme variant evolved in ice. This process demonstrates the potential for the emergence of novel ribozyme phenotypes in altered reaction environments.

    • James Attwater
    • , Aniela Wochner
    •  & Philipp Holliger

  • News & Views |

    Protein drugs are important therapies for many different diseases, but very few can be administered orally. Now, a cationic dendronized polymer has been shown to stabilize a therapeutic protein for delivery to the gut.

    • Heather D. Maynard

  • Article |

    Methods for stabilizing enzymatic activity in the gastrointestinal tract are rarely investigated because of the difficulty in protecting proteins from an environment that promotes their digestion. Now, functionally diverse polymers have been conjugated to therapeutic enzymes, which lead to a substantial enhancement of their in vivo activity in the gastrointestinal tract.

    • Gregor Fuhrmann
    • , Andrea Grotzky
    •  & Jean-Christophe Leroux

  • Article |

    The influence of protein motions on the chemical step of enzyme reactions is a contentious issue. Now, by constructing free-energy surfaces using an explicit solvent coordinate, it is shown that, although some structural flexibility is required, protein motions can be described as equilibrium fluctuations.

    • Rafael García-Meseguer
    • , Sergio Martí
    •  & Iñaki Tuñón

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