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Current Opinion in Chemical Biology Oct 2020Combining organometallics and biology has generated broad interest from scientists working on applications from in situ drug release to biocatalysis. Engineered enzymes... (Review)
Review
Combining organometallics and biology has generated broad interest from scientists working on applications from in situ drug release to biocatalysis. Engineered enzymes and biohybrid catalysts (also referred to as artificial enzymes) have introduced a wide range of abiotic chemistry into biocatalysis. Predominantly, this work has concentrated on using these catalysts for single step in vitro reactions. However, the promise of using these hybrid catalysts in vivo and combining them with synthetic biology and metabolic engineering is vast. This report will briefly review recent advances in artificial metalloenzyme design, followed by summarising recent studies that have looked at the use of these hybrid catalysts in vivo and in enzymatic cascades, therefore exploring their potential for synthetic biology.
Topics: Biocatalysis; Enzymes; Metalloproteins; Synthetic Biology
PubMed: 32768658
DOI: 10.1016/j.cbpa.2020.06.004 -
Methods in Enzymology 2022Electron paramagnetic resonance spectroscopy encompasses a versatile set of techniques that allow detailed insight into intrinsically occurring paramagnetic centers in...
Electron paramagnetic resonance spectroscopy encompasses a versatile set of techniques that allow detailed insight into intrinsically occurring paramagnetic centers in metalloproteins and enzymes that undergo oxidation-reduction reactions. In this chapter, we discuss the process from isolating the protein to acquiring and analyzing pulse EPR spectra, adopting a practical perspective. We start with considerations when preparing the protein sample, explain techniques and procedures available for determining the reduction potential of the redox-active center of interest and provide details on methodologies to trap a given paramagnetic state for detailed pulse EPR studies, with an emphasis on biochemical and spectroscopic tools available when multiple EPR-active species are present. We elaborate on some of the most commonly used pulse EPR techniques and the choices the user has to make, considering advantages and disadvantages and how to avoid pitfalls. Examples are provided throughout.
Topics: Electron Spin Resonance Spectroscopy; Electrons; Metalloproteins; Oxidation-Reduction
PubMed: 35465921
DOI: 10.1016/bs.mie.2022.02.014 -
Journal of Inorganic Biochemistry Sep 2022Metalloproteins represent a substantial fraction of the proteome where they have an outsized contribution to enzymology. This stems from the reactivity of transition... (Review)
Review
Metalloproteins represent a substantial fraction of the proteome where they have an outsized contribution to enzymology. This stems from the reactivity of transition metals found in the active sites of numerous classes of enzymes that undergo redox and/or spin-state transitions. Notwithstanding, NMR structures of metalloproteins deposited in the PDB are under-represented and NMR studies exploring paramagnetic states are a minute fraction of the overall database content. This state of affairs contrasts with the early recognition that paramagnetic proteins offer unique opportunities for structure-function studies which are not available for diamagnetic proteins. Recent development of novel pulse sequences that minimize quenching of signal intensity that arises from the presence of a paramagnetic center in metalloproteins is extending even further the range of systems which can be studied by solution-state NMR. In this manuscript we review solution-state NMR applications to paramagnetic proteins, highlighting the developments in both methodologies and data interpretation, laying bare the vast range of opportunities for paramagnetic NMR to contribute to the understanding of structure and function of metalloenzymes and biomimetic metallocatalysts.
Topics: Magnetic Resonance Imaging; Magnetic Resonance Spectroscopy; Metalloproteins
PubMed: 35636014
DOI: 10.1016/j.jinorgbio.2022.111871 -
Proceedings of the Japan Academy.... 2020In order to harness the functionality of metals, nature has evolved over billions of years to utilize metalloproteins as key components in numerous cellular processes.... (Review)
Review
In order to harness the functionality of metals, nature has evolved over billions of years to utilize metalloproteins as key components in numerous cellular processes. Despite this, transition metals such as ruthenium, palladium, iridium, and gold are largely absent from naturally occurring metalloproteins, likely due to their scarcity as precious metals. To mimic the evolutionary process of nature, the field of artificial metalloenzymes (ArMs) was born as a way to benefit from the unique chemoselectivity and orthogonality of transition metals in a biological setting. In its current state, numerous examples have successfully incorporated transition metals into a variety of protein scaffolds. Using these ArMs, many examples of new-to-nature reactions have been carried out, some of which have shown substantial biocompatibility. Given the rapid rate at which this field is growing, this review aims to highlight some important studies that have begun to take the next step within this field; namely the development of ArM-centered drug therapies or biotechnological tools.
Topics: Biocatalysis; Biomimetic Materials; Biosensing Techniques; Coenzymes; Metalloproteins; Metals; Models, Molecular; Protein Conformation; Protein Engineering; Stereoisomerism
PubMed: 32161212
DOI: 10.2183/pjab.96.007 -
World Journal of Microbiology &... Aug 2022Ferredoxin (Fd) is a small metalloprotein holding one or two Fe-S clusters in its inner shell. Like many other metalloproteins, Fd is redox active and involved in... (Review)
Review
Ferredoxin (Fd) is a small metalloprotein holding one or two Fe-S clusters in its inner shell. Like many other metalloproteins, Fd is redox active and involved in electron transfer during cellular metabolism. The electrons from reduced Fd are mostly used to regenerate NADPH under physiological conditions. Increasing number of attempts have been reported, however, where Fd delivers electrons to enable biosynthesis of valuable compounds. Various compounds ranging from H to vitamin D have been synthesized successfully using electrons mediated by Fd molecules. In this review, we provide an overview of the engineering studies utilizing Fd for biosynthesis of targeted molecules. The emphasis is on the role and activity of Fd as well as the methods used to improve the rate of electron transfer. Both microbial and electrochemical biosynthesis technologies are described and compared with respect to productivity and the compound being produced. In addition to the ferredoxins from the microbial organisms, artificially designed de novo types are described, highlighting the potential of the emerging computational methods used in metabolic and protein engineering. We believe that the recent advances in utilization of Fd for biosynthesis can result in breakthrough innovation across the biotechnology industry.
Topics: Electron Transport; Electrons; Ferredoxins; Oxidation-Reduction; Photosynthesis
PubMed: 35941298
DOI: 10.1007/s11274-022-03371-9 -
Advances in Microbial Physiology 2017The metals manganese, iron, cobalt, nickel, copper and zinc are essential for almost all bacteria, but their precise metal requirements vary by species, by ecological... (Review)
Review
The metals manganese, iron, cobalt, nickel, copper and zinc are essential for almost all bacteria, but their precise metal requirements vary by species, by ecological niche and by growth condition. Bacteria thus must acquire each of these essential elements in sufficient quantity to satisfy their cellular demand, but in excess these same elements are toxic. Metal toxicity has been exploited by humanity for centuries, and by the mammalian immune system for far longer, yet the mechanisms by which these elements cause toxicity to bacteria are not fully understood. There has been a resurgence of interest in metal toxicity in recent decades due to the problematic spread of antibiotic resistance amongst bacterial pathogens, which has led to an increased research effort to understand these toxicity mechanisms at the molecular level. A recurring theme from these studies is the role of intermetal competition in bacterial metal toxicity. In this review, we first survey biological metal usage and introduce some fundamental chemical concepts that are important for understanding bacterial metal usage and toxicity. Then we introduce a simple model by which to understand bacterial metal homeostasis in terms of the distribution of each essential metal ion within cellular 'pools', and dissect how these pools interact with each other and with key proteins of bacterial metal homeostasis. Finally, using a number of key examples from the recent literature, we look at specific metal toxicity mechanisms in model bacteria, demonstrating the role of metal-metal competition in the toxicity mechanisms of diverse essential metals.
Topics: Animals; Bacteria; Drug Resistance, Bacterial; Gene Expression Regulation, Bacterial; Homeostasis; Humans; Membrane Transport Proteins; Metalloproteins; Metals; Models, Biological; Oxidative Stress
PubMed: 28528650
DOI: 10.1016/bs.ampbs.2017.01.003 -
Chemical Communications (Cambridge,... Nov 2021Supramolecules, which are formed by assembling multiple molecules by noncovalent intermolecular interactions instead of covalent bonds, often show additional properties... (Review)
Review
Supramolecules, which are formed by assembling multiple molecules by noncovalent intermolecular interactions instead of covalent bonds, often show additional properties that cannot be exhibited by a single molecule. Supramolecules have evolved into molecular machines in the field of chemistry, and various supramolecular proteins are responsible for life activities in the field of biology. The design and creation of supramolecular proteins will lead to development of new enzymes, functional biomaterials, drug delivery systems, etc.; thus, the number of studies on the regulation of supramolecular proteins is increasing year by year. Several methods, including disulfide bond, metal coordination, and surface-surface interaction, have been utilized to construct supramolecular proteins. In nature, proteins have been shown to form oligomers by 3D domain swapping (3D-DS), a phenomenon in which a structural region is exchanged between molecules of the same protein. We have been studying the mechanism of 3D-DS and utilizing 3D-DS to construct supramolecular metalloproteins. Cytochrome forms cyclic oligomers and polymers by 3D-DS, whereas other metalloproteins, such as various -type cytochromes and azurin form small oligomers and myoglobin forms a compact dimer. We have also utilized 3D-DS to construct heterodimers with different active sites, a protein nanocage encapsulating a Zn-SO cluster in the internal cavity, and a tetrahedron with a designed building block protein. Protein oligomer formation was controlled for the 3D-DS dimer of a dimer-monomer transition protein. This article reviews our research on supramolecular metalloproteins.
Topics: Macromolecular Substances; Metalloproteins; Models, Molecular
PubMed: 34714300
DOI: 10.1039/d1cc04608j -
Metallomics : Integrated Biometal... Dec 2020Understanding the biological process involving metals and biomolecules in the brain is essential for establishing the origin of neurological disorders, such as... (Review)
Review
Understanding the biological process involving metals and biomolecules in the brain is essential for establishing the origin of neurological disorders, such as neurodegenerative and psychiatric diseases. From this perspective, this critical review presents recent advances in this topic, showing possible mechanisms involving the disruption of metal homeostasis and the pathogenesis of neurological disorders. We also discuss the main challenges observed in metallomics studies associated with neurological disorders, including those related to sample preparation and analyte quantification.
Topics: Animals; Brain; Homeostasis; Humans; Mental Disorders; Metalloproteins; Metals; Nervous System Diseases
PubMed: 33237082
DOI: 10.1039/d0mt00234h -
Accounts of Chemical Research May 2021Rigorous substrate selectivity is a hallmark of enzyme catalysis. This selectivity is generally ascribed to a thermodynamically favorable process of substrate binding to... (Review)
Review
Rigorous substrate selectivity is a hallmark of enzyme catalysis. This selectivity is generally ascribed to a thermodynamically favorable process of substrate binding to the enzyme active site based upon complementary physiochemical characteristics, which allows both acquisition and orientation. However, this chemical selectivity is more difficult to rationalize for diminutive molecules that possess too narrow a range of physical characteristics to allow either precise positioning or discrimination between a substrate and an inhibitor. Foremost among these small molecules are dissolved gases such as H, N, O, CO, CO, NO, NO, NH, and CH so often encountered in metalloenzyme catalysis. Nevertheless, metalloenzymes have evolved to metabolize these small-molecule substrates with high selectivity and efficiency.The soluble methane monooxygenase enzyme (sMMO) acts upon two of these small molecules, O and CH, to generate methanol as part of the C1 metabolic pathway of methanotrophic organisms. sMMO is capable of oxidizing many alternative hydrocarbon substrates. Remarkably, however, it will preferentially oxidize methane, the substrate with the fewest discriminating physical characteristics and the strongest C-H bond. Early studies led us to broadly attribute this specificity to the formation of a "molecular sieve" in which a methane- and oxygen-sized tunnel provides a size-selective route from bulk solvent to the completely buried sMMO active site. Indeed, recent cryogenic and serial femtosecond ambient temperature crystallographic studies have revealed such a route in sMMO. A detailed study of the sMMO tunnel considered here in the context of small-molecule tunnels identified in other metalloenzymes reveals three discrete characteristics that contribute to substrate selectivity and positioning beyond that which can be provided by the active site itself. Moreover, the dynamic nature of many tunnels allows an exquisite coordination of substrate binding and reaction phases of the catalytic cycle. Here we differentiate between the highly selective molecular tunnel, which allows only the one-dimensional transit of small molecules, and the larger, less-selective channels found in typical enzymes. Methods are described to identify and characterize tunnels as well as to differentiate them from channels. In metalloenzymes which metabolize dissolved gases, we posit that the contribution of tunnels is so great that they should be considered to be extensions of the active site itself. A full understanding of catalysis by these enzymes requires an appreciation of the roles played by tunnels. Such an understanding will also facilitate the use of the enzymes or their synthetic mimics in industrial or pharmaceutical applications.
Topics: Biocatalysis; Catalytic Domain; Metalloproteins; Models, Molecular; Oxygenases; Small Molecule Libraries
PubMed: 33886257
DOI: 10.1021/acs.accounts.1c00058 -
Current Opinion in Structural Biology Dec 2021An estimated half of all proteins contain a metal, with these being essential for a tremendous variety of biological functions. X-ray crystallography is the major method... (Review)
Review
An estimated half of all proteins contain a metal, with these being essential for a tremendous variety of biological functions. X-ray crystallography is the major method for obtaining structures at high resolution of these metalloproteins, but there are considerable challenges to obtain intact structures due to the effects of radiation damage. Serial crystallography offers the prospect of determining low-dose synchrotron or effectively damage free XFEL structures at room temperature and enables time-resolved or dose-resolved approaches. Complementary spectroscopic data can validate redox and or ligand states within metalloprotein crystals. In this opinion, we discuss developments in the application of serial crystallographic approaches to metalloproteins and comment on future directions.
Topics: Catalysis; Crystallography, X-Ray; Metalloproteins; Spectrum Analysis; Synchrotrons
PubMed: 34455163
DOI: 10.1016/j.sbi.2021.07.007