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Kirsch KE, Little ME, Cundari TR, El-Shaer E, Barone G, Lynch VM, Toledo SA. Direct O 2 mediated oxidation of a Ni(II)N 3O structural model complex for the active site of nickel acireductone dioxygenase (Ni-ARD): characterization, biomimetic reactivity, and enzymatic implications. Dalton Trans 2024; 53:17852-17863. [PMID: 39421893 DOI: 10.1039/d4dt02538e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2024]
Abstract
A new biomimetic model complex of the active site of acireductone dioxygenase (ARD) was synthesized and crystallographically characterized ([Ni(ii)(N-(ethyl-N'Me2)(Py)(2-t-ButPhOH))(OTf)]-1). 1 displays carbon-carbon oxidative cleavage activity in the presence of O2 towards the substrate 2-hydroxyacetophenone. This reactivity was monitored via UV-Visible and NMR spectroscopy. We postulate that the reactivity of 1 with O2 leads to the formation of a putative Ni(III)-superoxo transient species resulting from the direct activation of O2via the nickel center during the oxidative reaction. This proposed intermediate and reaction mechanism were studied in detail using DFT calculations. 1 and its substrate bound derivatives display reactivity toward mild outer sphere oxidants, suggesting ease of access to high valent Ni coordination complexes, consistent with our calculations. If confirmed, the direct activation of O2 at a nickel center could have implications for the mechanism of action of ARD and other nickel-based dioxygenases and their respective non-traditional, enzymatic moonlighting functions, as well as contribute to a general understanding of direct oxidation of nickel(II) coordination complexes by O2.
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Affiliation(s)
- Kelsey E Kirsch
- Department of Chemistry, American University, 4400 Massachusetts Ave NW, Washington, DC, 20016, USA.
| | - Mary E Little
- Department of Chemistry, St Edward's University, 3001 South Congress Ave, Austin, Texas 78704, USA
| | - Thomas R Cundari
- Department of Chemistry, University of North Texas, 1155 Union Cir, Denton, Texas 76203, USA
| | - Emily El-Shaer
- Department of Chemistry, St Edward's University, 3001 South Congress Ave, Austin, Texas 78704, USA
| | - Georgia Barone
- Department of Chemistry, St Edward's University, 3001 South Congress Ave, Austin, Texas 78704, USA
| | - Vincent M Lynch
- Department of Chemistry, The University of Texas at Austin, 120 Inner Campus Dr Stop G2500, Austin, Texas 78712, USA
| | - Santiago A Toledo
- Department of Chemistry, American University, 4400 Massachusetts Ave NW, Washington, DC, 20016, USA.
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2
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Hota PK, Panda S, Phan H, Kim B, Siegler MA, Karlin KD. Dioxygenase Chemistry in Nucleophilic Aldehyde Deformylations Utilizing Dicopper O 2-Derived Peroxide Complexes. J Am Chem Soc 2024; 146:23854-23871. [PMID: 39141923 PMCID: PMC11472664 DOI: 10.1021/jacs.4c06243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2024]
Abstract
The chemistry of copper-dioxygen complexes is relevant to copper enzymes in biology as well as in (ligand)Cu-O2 (or Cu2-O2) species utilized in oxidative transformations. For overall energy considerations, as applicable in chemical synthesis, it is beneficial to have an appropriate atom economy; both O-atoms of O2(g) are transferred to the product(s). However, examples of such dioxygenase-type chemistry are extremely rare or not well documented. Herein, we report on nucleophilic oxidative aldehyde deformylation reactivity by the peroxo-dicopper(II) species [Cu2II(BPMPO-)(O22-)]1+ {BPMPO-H = 2,6-bis{[(bis(2-pyridylmethyl)amino]methyl}-4-methylphenol)} and [Cu2II(XYLO-)(O22-)]1+ (XYLO- = a BPMPO- analogue possessing bis(2-{2-pyridyl}ethyl)amine chelating arms). Their dicopper(I) precursors are dioxygenase catalysts. The O2(g)-derived peroxo-dicopper(II) intermediates react rapidly with aldehydes like 2-phenylpropionaldehyde (2-PPA) and cyclohexanecarboxaldehyde (CCA) in 2-methyltetrahydrofuran at -90 °C. Warming to room temperature (RT) followed by workup results in good yields of formate (HC(O)O-) along with ketones (acetophenone or cyclohexanone). Mechanistic investigation shows that [Cu2II(BPMPO-)(O22-)]1+ species initially reacts reversibly with the aldehydes to form detectable dicopper(II) peroxyhemiacetal intermediates, for which optical titrations provide the Keq (at -90 °C) of 73.6 × 102 M-1 (2-PPA) and 10.4 × 102 M-1 (CCA). In the reaction of [Cu2II(XYLO-)(O22-)]1+ with 2-PPA, product complexes characterized by single-crystal X-ray crystallography are the anticipated dicopper(I) complex, [Cu2I(XYLO-)]1+ plus a mixed-valent Cu(I)Cu(II)-formate species. Formate was further identified and confirmed by 1H NMR spectroscopy and electrospray ionization mass spectrometry (ESI-MS) analysis. Using 18O2(g)-isotope labeling the reaction produced a high yield of 18-O incorporated acetophenone as well as formate. The overall results signify that true dioxygenase reactions have occurred, supported by a thorough mechanistic investigation.
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Affiliation(s)
- Pradip Kumar Hota
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Sanjib Panda
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Hai Phan
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Bohee Kim
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Maxime A Siegler
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Kenneth D Karlin
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
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3
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Kaur R, Aboelnga MM, Nikkel DJ, Wetmore SD. The metal dependence of single-metal mediated phosphodiester bond cleavage: a QM/MM study of a multifaceted human enzyme. Phys Chem Chem Phys 2022; 24:29130-29140. [PMID: 36444615 DOI: 10.1039/d2cp04338f] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Nucleases catalyze the cleavage of phosphodiester bonds in nucleic acids using a range of metal cofactors. Although it is well accepted that many nucleases rely on two metal ions, the one-metal mediated pathway is debated. Furthermore, one-metal mediated nucleases maintain activity in the presence of many different metals, but the underlying reasons for this broad metal specificity are unknown. The human apurinic/apyrimidinic endonuclease (APE1), which plays a key role in DNA repair, transcription regulation, and gene expression, is a prototypical example of a one-metal dependent nuclease. Although Mg2+ is the native metal cofactor, APE1 remains catalytically active in the presence of several metals, with the rate decreasing as Mg2+ > Mn2+ > Ni2+ > Zn2+, while Ca2+ completely abolished the activity. The present work uses quantum mechanics-molecular mechanics techniques to map APE1-facilitated phosphodiester bond hydrolysis in the presence of these metals. The structural differences in stationary points along the reaction pathway shed light on the interplay between several factors that allow APE1 to remain catalytically active for various metals, with the trend in the barrier heights correlating with the experimentally reported APE1 catalytic activity. In contrast, Ca2+ significantly changes the metal coordination and active site geometry, and thus completely inhibits catalysis. Our work thereby provides support for the controversial single-metal mediated phosphodiester bond cleavage and clarifies uncertainties regarding the role of the metal and metal identity in this important reaction. This information is key for future medicinal and biotechnological applications including disease diagnosis and treatment, and protein engineering.
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Affiliation(s)
- Rajwinder Kaur
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, T1K 3M4, Canada.
| | - Mohamed M Aboelnga
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, T1K 3M4, Canada.
| | - Dylan J Nikkel
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, T1K 3M4, Canada.
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, T1K 3M4, Canada.
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4
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Liu X, Garber A, Ryan J, Deshpande A, Ringe D, Pochapsky TC. A Model for the Solution Structure of Human Fe(II)-Bound Acireductone Dioxygenase and Interactions with the Regulatory Domain of Matrix Metalloproteinase I (MMP-I). Biochemistry 2020; 59:4238-4249. [PMID: 33135413 PMCID: PMC7768908 DOI: 10.1021/acs.biochem.0c00724] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The metalloenzyme acireductone dioxygenase (ARD) shows metal-dependent physical and enzymatic activities depending upon the metal bound in the active site. The Fe(II)-bound enzyme catalyzes the penultimate step of the methionine salvage pathway, converting 1,2-dihydroxy-5-(methylthio)pent-1-en-3-one (acireductone) into formate and the ketoacid precursor of methionine, 2-keto-4-thiomethyl-2-oxobutanoate, using O2 as the oxidant. If Ni(II) is bound, an off-pathway shunt occurs, producing 3-methylthiopropionate, formate, and carbon monoxide from the same acireductone substrate. The solution structure of the Fe(II)-bound human enzyme, HsARD, is described and compared with the structures of Ni-bound forms of the closely related mouse enzyme, MmARD. Potential rationales for the different reactivities of the two isoforms are discussed. The human enzyme has been found to regulate the activity of matrix metalloproteinase I (MMP-I), which is involved in tumor metastasis, by binding the cytoplasmic transmembrane tail peptide of MMP-I. Nuclear magnetic resonance titration of HsARD with the MMP-I tail peptide permits identification of the peptide binding site on HsARD, a cleft anterior to the metal binding site adjacent to a dynamic proline-rich loop.
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Affiliation(s)
- Xinyue Liu
- Department of Chemistry, Brandeis University, 415 South St., Waltham MA 02454-9110, USA
| | - Abigail Garber
- Department of Biochemistry, Brandeis University, 415 South St., Waltham MA 02454-9110, USA
| | - Julia Ryan
- Department of Biochemistry, Brandeis University, 415 South St., Waltham MA 02454-9110, USA
| | - Aditi Deshpande
- Department of Biochemistry, Brandeis University, 415 South St., Waltham MA 02454-9110, USA
| | - Dagmar Ringe
- Department of Chemistry, Brandeis University, 415 South St., Waltham MA 02454-9110, USA
- Department of Biochemistry, Brandeis University, 415 South St., Waltham MA 02454-9110, USA
- Rosenstiel Institute for Basic Biomedical Research, Brandeis University, 415 South St., Waltham MA 02454-9110 USA
| | - Thomas C. Pochapsky
- Department of Chemistry, Brandeis University, 415 South St., Waltham MA 02454-9110, USA
- Department of Biochemistry, Brandeis University, 415 South St., Waltham MA 02454-9110, USA
- Rosenstiel Institute for Basic Biomedical Research, Brandeis University, 415 South St., Waltham MA 02454-9110 USA
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5
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A family of structural and functional models for the active site of a unique dioxygenase: Acireductone dioxygenase (ARD). J Inorg Biochem 2020; 212:111253. [PMID: 32949987 DOI: 10.1016/j.jinorgbio.2020.111253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 08/15/2020] [Accepted: 09/06/2020] [Indexed: 11/20/2022]
Abstract
We report the synthesis and biomimetic activity of a family of model complexes with relevance to acireductone dioxygenase (ARD), an enzyme that displays dual function based on metal identity found in the methionine salvage pathway (MSP). Three complexes with related structural motifs were synthesized and characterized derived from phenolate, and pyridine N4O Schiff-base ligands. They display pseudo-octahedral Ni(II)-N4O ligand coordination with water at the sixth site, in close alignment to the structure in the resting state of ARD. The three featured complexes exhibit carbon‑carbon bond cleavage activation of lithium acetylacetonate, which was used as a model enzyme substrate. Computationally derived mechanistic routes for the observed reactivity consistent with experimental conditions are herein proposed. The mechanism suggests the possibility of Ni(II)-substrate interactions, followed by oxygen insertion. These results constitute only the third functional model system of ARD, in an attempt to further advance biomimetic contributions to the ongoing debate of ARD's unique metal mediated, regioselective oxidative cleavage.
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6
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Reilley DJ, Fuller JT, Nechay MR, Victor M, Li W, Ruberry JD, Mujika JI, Lopez X, Alexandrova AN. Toxic and Physiological Metal Uptake and Release by Human Serum Transferrin. Biophys J 2020; 118:2979-2988. [PMID: 32497515 PMCID: PMC7300305 DOI: 10.1016/j.bpj.2020.05.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 04/03/2020] [Accepted: 04/29/2020] [Indexed: 10/24/2022] Open
Abstract
An atomistic understanding of metal transport in the human body is critical to anticipate the side effects of metal-based therapeutics and holds promise for new drugs and drug delivery designs. Human serum transferrin (hTF) is a central part of the transport processes because of its ubiquitous ferrying of physiological Fe(III) and other transition metals to tightly controlled parts of the body. There is an atomistic mechanism for the uptake process with Fe(III), but not for the release process, or for other metals. This study provides initial insight into these processes for a range of transition metals-Ti(IV), Co(III), Fe(III), Ga(III), Cr(III), Fe(II), Zn(II)-through fully atomistic, extensive quantum mechanical/discrete molecular dynamics sampling and provides, to our knowledge, a new technique we developed to calculate relative binding affinities between metal cations and the protein. It identifies protonation of Tyr188 as a trigger for metal release rather than protonation of Lys206 or Lys296. The study identifies the difficulty of metal release from hTF as potentially related to cytotoxicity. Simulations identify a few critical interactions that stabilize the metal binding site in a flexible, nuanced manner.
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Affiliation(s)
- David J Reilley
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California
| | - Jack T Fuller
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California
| | - Michael R Nechay
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California
| | - Marie Victor
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California; Institut Lumire Matire, Villeurbanne, France
| | - Wei Li
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts
| | - Josiah D Ruberry
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California
| | - Jon I Mujika
- Kimika Fakultatea, Euskal Herriko Unibertsitatea (UPV/EHU) and Donostia, International Physics Center, Donostia, Euskadi, Spain
| | - Xabier Lopez
- Kimika Fakultatea, Euskal Herriko Unibertsitatea (UPV/EHU) and Donostia, International Physics Center, Donostia, Euskadi, Spain
| | - Anastassia N Alexandrova
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California; California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California.
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7
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Reilley DJ, Hennefarth MR, Alexandrova AN. The Case for Enzymatic Competitive Metal Affinity Methods. ACS Catal 2020; 10:2298-2307. [PMID: 34012720 PMCID: PMC8130888 DOI: 10.1021/acscatal.9b04831] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- David J Reilley
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, CA 90095-1569, USA
| | - Matthew R Hennefarth
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, CA 90095-1569, USA
| | - Anastassia N Alexandrova
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, CA 90095-1569, USA
- California NanoSystems Institute, University of California, Los Angeles, 570 Westwood Plaza, Los Angeles, California 90095-1569, USA
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8
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Reilley DJ, Popov KI, Dokholyan NV, Alexandrova AN. Uncovered Dynamic Coupling Resolves the Ambiguous Mechanism of Phenylalanine Hydroxylase Oxygen Binding. J Phys Chem B 2019; 123:4534-4539. [PMID: 31038957 DOI: 10.1021/acs.jpcb.9b02893] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Phenylalanine hydroxylase (PAH) is an iron enzyme catalyzing the oxidation of l-Phe to l-Tyr during phenylalanine catabolism. Dysfunction of PAH leads to the debilitating condition phenylketonuria (PKU), which prompted research into the structure and function of PAH over the last 50 years. Despite intensive study, there is no consensus on the atomistic details of the mechanism of O2 binding and splitting by wild-type (WT) PAH and how it varies with PKU-inducing mutations, Arg158Gln and Glu280Lys. We studied structures involved in a proposed mechanism for the WT and mutants using extensive mixed quantum-classical molecular dynamics simulations. Simulations reveal a previously unobserved dynamic coupling between the active site and the mutation sites, suggesting how they can affect the catalytic performance of PAH. Furthermore, the effect of the coupling on the PAH structure agrees with and expands our understanding of the experimentally observed differences in activity between the WT and mutants.
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Affiliation(s)
- David J Reilley
- Department of Chemistry and Biochemistry , University of California, Los Angeles , Los Angeles , California 90095-1569 , United States
| | - Konstantin I Popov
- Department of Biochemistry and Biophysics , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Nikolay V Dokholyan
- Department of Biochemistry and Biophysics , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States.,Department of Pharmacology, Department of Biochemistry & Molecular Biology , Penn State University College of Medicine , Hershey , Pennsylvania 17033 , United States
| | - Anastassia N Alexandrova
- Department of Chemistry and Biochemistry , University of California, Los Angeles , Los Angeles , California 90095-1569 , United States.,California NanoSystems Institute, Los Angeles , California 90095-1569 , United States
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9
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Nechay MR, Gallup NM, Morgenstern A, Smith QA, Eberhart ME, Alexandrova AN. Histone Deacetylase 8: Characterization of Physiological Divalent Metal Catalysis. J Phys Chem B 2016; 120:5884-95. [DOI: 10.1021/acs.jpcb.6b00997] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Michael R. Nechay
- Department
of Chemistry and Biochemistry, University of California, Los Angeles, Los
Angeles, California 90095, United States
| | - Nathan M. Gallup
- Department
of Chemistry and Biochemistry, University of California, Los Angeles, Los
Angeles, California 90095, United States
| | - Amanda Morgenstern
- Molecular
Theory Group, Colorado School of Mines, Golden, Colorado 80401, United States
| | - Quentin A. Smith
- Department
of Chemistry and Biochemistry, University of California, Los Angeles, Los
Angeles, California 90095, United States
| | - Mark E. Eberhart
- Molecular
Theory Group, Colorado School of Mines, Golden, Colorado 80401, United States
| | - Anastassia N. Alexandrova
- Department
of Chemistry and Biochemistry, University of California, Los Angeles, Los
Angeles, California 90095, United States
- California NanoSystems Institute, Los Angeles, California 90095, United States
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10
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11
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Pordea A. Metal-binding promiscuity in artificial metalloenzyme design. Curr Opin Chem Biol 2015; 25:124-32. [PMID: 25603469 DOI: 10.1016/j.cbpa.2014.12.035] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 12/16/2014] [Accepted: 12/18/2014] [Indexed: 01/16/2023]
Abstract
This review presents recent examples of metal-binding promiscuity in protein scaffolds and highlights the effect of metal variation on catalytic functionality. Naturally evolved binding sites, as well as unnatural amino acids and cofactors can bind a diverse range of metals, including non-biological transition elements. Computational screening and rational design have been successfully used to create promiscuous binding-sites. Incorporation of non-native metals into proteins expands the catalytic range of transformations catalysed by enzymes and enhances their potential for application in chemicals synthesis.
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Affiliation(s)
- Anca Pordea
- Department of Chemical and Environmental Engineering, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom.
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12
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Valdez CE, Smith QA, Nechay MR, Alexandrova AN. Mysteries of metals in metalloenzymes. Acc Chem Res 2014; 47:3110-7. [PMID: 25207938 DOI: 10.1021/ar500227u] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Natural metalloenzymes are often the most proficient catalysts in terms of their activity, selectivity, and ability to operate at mild conditions. However, metalloenzymes are occasionally surprising in their selection of catalytic metals, and in their responses to metal substitution. Indeed, from the isolated standpoint of producing the best catalyst, a chemist designing from first-principles would likely choose a different metal. For example, some enzymes employ a redox active metal where a simple Lewis acid is needed. Such are several hydrolases. In other cases, substitution of a non-native metal leads to radical improvements in reactivity. For example, histone deacetylase 8 naturally operates with Zn(2+) in the active site but becomes much more active with Fe(2+). For β-lactamases, the replacement of the native Zn(2+) with Ni(2+) was suggested to lead to higher activity as predicted computationally. There are also intriguing cases, such as Fe(2+)- and Mn(2+)-dependent ribonucleotide reductases and W(4+)- and Mo(4+)-dependent DMSO reductases, where organisms manage to circumvent the scarcity of one metal (e.g., Fe(2+)) by creating protein structures that utilize another metal (e.g., Mn(2+)) for the catalysis of the same reaction. Naturally, even though both metal forms are active, one of the metals is preferred in every-day life, and the other metal variant remains dormant until an emergency strikes in the cell. These examples lead to certain questions. When are catalytic metals selected purely for electronic or structural reasons, implying that enzymatic catalysis is optimized to its maximum? When are metal selections a manifestation of competing evolutionary pressures, where choices are dictated not just by catalytic efficiency but also by other factors in the cell? In other words, how can enzymes be improved as catalysts merely through the use of common biological building blocks available to cells? Addressing these questions is highly relevant to the enzyme design community, where the goal is to prepare maximally efficient quasi-natural enzymes for the catalysis of reactions that interest humankind. Due to competing evolutionary pressures, many natural enzymes may not have evolved to be ideal catalysts and can be improved for the isolated purpose of catalysis in vitro when the competing factors are removed. The goal of this Account is not to cover all the possible stories but rather to highlight how variable enzymatic catalysis can be. We want to bring up possible factors affecting the evolution of enzyme structure, and the large- and intermediate-scale structural and electronic effects that metals can induce in the protein, and most importantly, the opportunities for optimization of these enzymes for catalysis in vitro.
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Affiliation(s)
- Crystal E. Valdez
- Department
of Chemistry and Biochemistry, and ‡California NanoSystems Institute, University of California, Los Angeles, California 90095, United States
| | - Quentin A. Smith
- Department
of Chemistry and Biochemistry, and ‡California NanoSystems Institute, University of California, Los Angeles, California 90095, United States
| | - Michael R. Nechay
- Department
of Chemistry and Biochemistry, and ‡California NanoSystems Institute, University of California, Los Angeles, California 90095, United States
| | - Anastassia N. Alexandrova
- Department
of Chemistry and Biochemistry, and ‡California NanoSystems Institute, University of California, Los Angeles, California 90095, United States
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