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Archives of Biochemistry and Biophysics Sep 2015In this contribution, recent developments in the design of biocatalysts are reviewed with particular emphasis in the de novo strategy. Studies based on three different... (Review)
Review
In this contribution, recent developments in the design of biocatalysts are reviewed with particular emphasis in the de novo strategy. Studies based on three different reactions, Kemp elimination, Diels-Alder and Retro-Aldolase, are used to illustrate different success achieved during the last years. Finally, a section is devoted to the particular case of designed metalloenzymes. As a general conclusion, the interplay between new and more sophisticated engineering protocols and computational methods, based on molecular dynamics simulations with Quantum Mechanics/Molecular Mechanics potentials and fully flexible models, seems to constitute the bed rock for present and future successful design strategies.
Topics: Computer-Aided Design; Drug Design; Enzymes; Metalloproteins; Molecular Dynamics Simulation
PubMed: 25797438
DOI: 10.1016/j.abb.2015.03.013 -
Journal of Inorganic Biochemistry Jun 2021Artificial metalloenzymes (ArMs) consist of an unnatural metal or cofactor embedded in a protein scaffold, and are an excellent platform for applying the concepts of... (Review)
Review
Artificial metalloenzymes (ArMs) consist of an unnatural metal or cofactor embedded in a protein scaffold, and are an excellent platform for applying the concepts of protein engineering to catalysis. In this Focused Review, we describe the application of ArMs as simple, tunable artificial models of the active sites of complex natural metalloenzymes for small-molecule activation. In this sense, ArMs expand the strategies of synthetic model chemistry to protein-based supporting ligands with potential for participation from the second coordination sphere. We focus specifically on ArMs that are structural, spectroscopic, and functional models of enzymes for activation of small molecules like CO, CO, O, N, and NO, as well as production/consumption of H. These ArMs give insight into the identities and roles of metalloenzyme structural features within and near the cofactor. We give examples of ArM work relevant to hydrogenases, acetyl-coenzyme A synthase, superoxide dismutase, heme oxygenases, nitric oxide reductase, methyl-coenzyme M reductase, copper-O enzymes, and nitrogenases.
Topics: Catalysis; Catalytic Domain; Coordination Complexes; Hydrogenase; Ligands; Metalloproteins; Metals; Models, Theoretical; Nitrogenase; Oxidoreductases; Protein Engineering
PubMed: 33873051
DOI: 10.1016/j.jinorgbio.2021.111430 -
Chemical Reviews Jun 2020The metallobiochemistry underlying the formation of the inorganic N-N-bond-containing molecules nitrous oxide (NO), dinitrogen (N), and hydrazine (NH) is essential to... (Review)
Review
The metallobiochemistry underlying the formation of the inorganic N-N-bond-containing molecules nitrous oxide (NO), dinitrogen (N), and hydrazine (NH) is essential to the lifestyles of diverse organisms. Similar reactions hold promise as means to use N-based fuels as alternative carbon-free energy sources. This review discusses research efforts to understand the mechanisms underlying biological N-N bond formation in primary metabolism and how the associated reactions are tied to energy transduction and organismal survival. These efforts comprise studies of both natural and engineered metalloenzymes as well as synthetic model complexes.
Topics: Hydrazines; Metalloproteins; Models, Molecular; Nitrogen; Nitrous Oxide
PubMed: 32108471
DOI: 10.1021/acs.chemrev.9b00629 -
Nature Communications Nov 2022Metallohydrolases are ubiquitous in nearly all subclasses of hydrolases, utilizing metal elements to activate a water molecule and facilitate its subsequent dissociation...
Metallohydrolases are ubiquitous in nearly all subclasses of hydrolases, utilizing metal elements to activate a water molecule and facilitate its subsequent dissociation of diverse chemical bonds. However, such a catalytic role of metal ions is rarely found with glycosidases that hydrolyze the glycosidic bonds in sugars. Herein, we design metalloglycosidases by constructing a hydrolytically active Zn-binding site within a barrel-shaped outer membrane protein OmpF. Structure- and mechanism-based redesign and directed evolution have led to the emergence of Zn-dependent glycosidases with catalytic proficiency of 2.8 × 10 and high β-stereoselectivity. Biochemical characterizations suggest that the Zn-binding site constitutes a key catalytic motif along with at least one adjacent acidic residue. This work demonstrates that unprecedented metalloenzymes can be tailor-made, expanding the scope of inorganic reactivities in proteinaceous environments, resetting the structural and functional diversity of metalloenzymes, and providing the potential molecular basis of unidentified metallohydrolases and novel whole-cell biocatalysts.
Topics: Metalloproteins; Binding Sites; Catalytic Domain; Catalysis; Glycoside Hydrolases; Metals
PubMed: 36369431
DOI: 10.1038/s41467-022-34713-8 -
Journal of Inorganic Biochemistry Aug 2022Nitrogenase is a versatile metalloenzyme that reduces N, CO and CO at its cofactor site. Designated the M-cluster, this complex cofactor has a composition of... (Review)
Review
Nitrogenase is a versatile metalloenzyme that reduces N, CO and CO at its cofactor site. Designated the M-cluster, this complex cofactor has a composition of [(R-homocitrate)MoFeSC], and it is assembled through the generation of a unique [FeSC] core prior to the insertion of Mo and homocitrate. NifB is a radical S-adenosyl-L-methionine (SAM) enzyme that is essential for nitrogenase cofactor assembly. This review focuses on the recent work that sheds light on the role of NifB in the formation of the [FeSC] core of the nitrogenase cofactor, highlighting the structure, function and mechanism of this unique radical SAM methyltransferase.
Topics: Metalloproteins; Methyltransferases; Molybdoferredoxin; Nitrogenase; S-Adenosylmethionine
PubMed: 35550498
DOI: 10.1016/j.jinorgbio.2022.111837 -
Chemical Communications (Cambridge,... Mar 2021Cluster complexes have attracted interest for decades due to their promise of drawing analogies to metallic surfaces and metalloenzyme active sites, but only recently... (Review)
Review
Cluster complexes have attracted interest for decades due to their promise of drawing analogies to metallic surfaces and metalloenzyme active sites, but only recently have chemists started to develop ligand scaffolds that are specifically designed to support multinuclear transition metal cores. Such ligands not only hold multiple metal centers in close proximity but also allow for fine-tuning of their electronic structures and surrounding steric environments. This Feature Article highlights ligand designs that allow for cooperative small molecule activation at cluster complexes, with a particular focus on complexes that contain metal-metal bonds. Two useful ligand-design elements have emerged from this work: a degree of geometric flexibility, which allows for novel small molecule activation modes, and the use of redox-active ligands to provide electronic flexibility to the cluster core. The authors have incorporated these factors into a unique class of dinucleating macrocycles (PDI). Redox-active fragments in PDI mimic the weak-overlap covalent bonding that is characteristic of M-M interactions, and aliphatic linkers in the ligand backbone provide geometric flexibility, allowing for interconversion between a range of geometries as the dinuclear core responds to the requirements of various small molecule substrates. The union of these design elements appears to be a powerful combination for analogizing critical aspects of heterogeneous and metalloenzyme catalysts.
Topics: Biomimetic Materials; Catalysis; Catalytic Domain; Coordination Complexes; Ligands; Macrocyclic Compounds; Metalloproteins; Metals; Molecular Structure; Oxidation-Reduction; Structure-Activity Relationship; Transition Elements
PubMed: 33624638
DOI: 10.1039/d0cc07721f -
Molecules (Basel, Switzerland) Oct 2023In prokaryotes, the role of Mo/W enzymes in physiology and bioenergetics is widely recognized. It is worth noting that the most diverse family of Mo/W enzymes is... (Review)
Review
In prokaryotes, the role of Mo/W enzymes in physiology and bioenergetics is widely recognized. It is worth noting that the most diverse family of Mo/W enzymes is exclusive to prokaryotes, with the probable existence of several of them from the earliest forms of life on Earth. The structural organization of these enzymes, which often include additional redox centers, is as diverse as ever, as is their cellular localization. The most notable observation is the involvement of dedicated chaperones assisting with the assembly and acquisition of the metal centers, including Mo/W-bisPGD, one of the largest organic cofactors in nature. This review seeks to provide a new understanding and a unified model of Mo/W enzyme maturation.
Topics: Metalloproteins; Prokaryotic Cells; Oxidation-Reduction; Energy Metabolism; Molecular Chaperones; Molybdenum
PubMed: 37894674
DOI: 10.3390/molecules28207195 -
Molecules (Basel, Switzerland) Aug 2023Laccase, one of the metalloproteins, belongs to the multicopper oxidase family. It oxidizes a wide range of substrates and generates water as a sole by-product. The... (Review)
Review
Laccase, one of the metalloproteins, belongs to the multicopper oxidase family. It oxidizes a wide range of substrates and generates water as a sole by-product. The engineering of laccase is important to broaden their industrial and environmental applications. The general assumption is that the low redox potential of laccases is the principal obstacle, as evidenced by their low activity towards certain substrates. Therefore, the primary goal of engineering laccases is to improve their oxidation capability, thereby increasing their redox potential. Even though some of the determinants of laccase are known, it is still not entirely clear how to enhance its redox potential. However, the laccase active site has additional characteristics that regulate the enzymes' activity and specificity. These include the electrostatic and hydrophobic environment of the substrate binding pocket, the steric effect at the substrate binding site, and the orientation of the binding substrate with respect to the T1 site of the laccase. In this review, these features of the substrate binding site will be discussed to highlight their importance as a target for future laccase engineering.
Topics: Laccase; Metalloproteins; Binding Sites; Engineering; Industry
PubMed: 37687038
DOI: 10.3390/molecules28176209 -
Molecules (Basel, Switzerland) Jun 2020Artificial metalloenzymes (ArMs) comprise a synthetic metal complex in a protein scaffold. ArMs display performances combining those of both homogeneous catalysts and... (Review)
Review
Artificial metalloenzymes (ArMs) comprise a synthetic metal complex in a protein scaffold. ArMs display performances combining those of both homogeneous catalysts and biocatalysts. Specifically, ArMs selectively catalyze non-natural reactions and reactions inspired by nature in water under mild conditions. In the past few years, the construction of ArMs that possess a genetically incorporated unnatural amino acid and the directed evolution of ArMs have become of great interest in the field. Additionally, biochemical applications of ArMs have steadily increased, owing to the fact that compartmentalization within a protein scaffold allows the synthetic metal complex to remain functional in a sea of inactivating biomolecules. In this review, we present updates on: 1) the newly reported ArMs, according to their type of reaction, and 2) the unique biochemical applications of ArMs, including chemoenzymatic cascades and intracellular/ catalysis. We believe that ArMs have great potential as catalysts for organic synthesis and as chemical biology tools for pharmaceutical applications.
Topics: Catalysis; Chemistry Techniques, Synthetic; Coordination Complexes; Metalloproteins; Protein Engineering
PubMed: 32629938
DOI: 10.3390/molecules25132989 -
Journal of Biological Inorganic... Apr 2017Nature uses dioxygen as a key oxidant in the transformation of biomolecules. Among the enzymes that are utilized for these reactions are copper-containing... (Review)
Review
Nature uses dioxygen as a key oxidant in the transformation of biomolecules. Among the enzymes that are utilized for these reactions are copper-containing metalloenzymes, which are responsible for important biological functions such as the regulation of neurotransmitters, dioxygen transport, and cellular respiration. Enzymatic and model system studies work in tandem in order to gain an understanding of the fundamental reductive activation of dioxygen by copper complexes. This review covers the most recent advancements in the structures, spectroscopy, and reaction mechanisms for dioxygen-activating copper proteins and relevant synthetic models thereof. An emphasis has also been placed on cofactor biogenesis, a fundamentally important process whereby biomolecules are post-translationally modified by the pro-enzyme active site to generate cofactors which are essential for the catalytic enzymatic reaction. Significant questions remaining in copper-ion-mediated O-activation in copper proteins are addressed.
Topics: Animals; Catalytic Domain; Copper; Humans; Metalloproteins; Oxygen
PubMed: 27921179
DOI: 10.1007/s00775-016-1415-2