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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 DOI: 10.1021/jacs.4c06243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [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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Yan X, Xiao H, Song J, Li C. Unraveling the Pivotal Roles of Various Metal Ion Centers in the Catalysis of Quercetin 2,4-Dioxygenases. Molecules 2023; 28:6238. [PMID: 37687067 PMCID: PMC10488974 DOI: 10.3390/molecules28176238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 09/10/2023] Open
Abstract
Quercetin 2,4-dioxygenase (QueD) with various transition metal ion co-factors shows great differences, but the internal reasons have not been illustrated in detail. In order to explore the effects of metal ion centers on the catalytic reactivity of QueD, we calculated and compared the minimum energy crossing point (MECP) of dioxygen from the relatively stable triplet state to the active singlet state under different conditions by using the DFT method. It was found that the metal ions play a more important role in the activation of dioxygen compared with the substrate and the protein environment. Simultaneously, the catalytic reactions of the bacterial QueDs containing six different transition metal ions were studied by the QM/MM approach, and we finally obtained the reactivity sequence of metal ions, Ni2+ > Co2+ > Zn2+ > Mn2+ > Fe2+ > Cu2+, which is basically consistent with the previous experimental results. Our calculation results indicate that metal ions act as Lewis acids in the reaction to stabilize the substrate anion and the subsequent superoxo and peroxo species in the reaction, and promote the proton coupled electron transfer (PCET) process. Furthermore, the coordination tendencies of transition metal ion centers also have important effects on the catalytic cycle. These findings have general implications on metalloenzymes, which can expand our understanding on how various metal ions play their key role in modulating catalytic reactivity.
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Affiliation(s)
- Xueyuan Yan
- College of Chemistry & Chemical and Environmental Engineering, Weifang University, Weifang 261061, China
| | - Han Xiao
- State Key Laboratory of Structure of Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
| | - Jinshuai Song
- Institute of Green Catalysis, College of Chemistry, Zhengzhou University, Zhengzhou 450001, China;
| | - Chunsen Li
- State Key Laboratory of Structure of Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
- Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen University, Xiamen 361005, China
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3
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Ajaykamal T, Palaniandavar M. Mononuclear nickel(ii)-flavonolate complexes of tetradentate tripodal 4N ligands as structural and functional models for quercetin 2,4-dioxygenase: structures, spectra, redox and dioxygenase activity. RSC Adv 2023; 13:24674-24690. [PMID: 37601601 PMCID: PMC10436029 DOI: 10.1039/d3ra04834a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 08/01/2023] [Indexed: 08/22/2023] Open
Abstract
Three new nickel(ii)-flavonolate complexes of the type [Ni(L)(fla)](ClO4) 1-3, where L is the tripodal 4N ligand tris(pyrid-2-ylmethyl)amine (tpa, L1) or (pyrid-2-ylmethyl)bis(6-methylpyrid-2-ylmethyl)amine (6-Me2-tpa, L2) or tris(N-Et-benzimidazol-2-ylmethyl)amine (Et-ntb, L3), have been isolated as functional models for Ni(ii)-containing quercetin 2,4-dioxygenase. Single crystal X-ray structures of 1 and 3 reveal that Ni(ii) is involved in π-back bonding with flavonolate (fla-), as evident from enhancement in C[double bond, length as m-dash]O bond length upon coordination [H(fla), 1.232(3); 1, 1.245(7); 3, 1.262(8) Å]. More asymmetric chelation of fla- in 3 than in 1 [Δd = (Ni-Ocarbonyl - Ni-Oenolate): 1, 0.126; 3, 0.182 Å] corresponds to lower π-delocalization in 3 with electron-releasing N-Et substituent. The optimized structures of 1-3 and their geometrical isomers have been computed by DFT methods. The HOMO and LUMO, both localized on Ni(ii)-bound fla-, are highly conjugated bonding π- and antibonding π*-orbitals respectively. They are located higher in energy than the Ni(ii)-based MOs (HOMO-1, dx2-y2; HOMO-2/6, dz2), revealing that the Ni(ii)-bound fla- rather than Ni(ii) would undergo oxidation upon exposure to dioxygen. The results of computational studies, in combination with spectral and electrochemical studies, support the involvement of redox-inactive Ni(ii) in π-back bonding with fla-, tuning the π-delocalization in fla- and hence its activation. Upon exposure to dioxygen, all the flavonolate adducts in DMF solution decompose to produce CO and depside, which then is hydrolyzed to give the corresponding acids at 70 °C. The highest rate of dioxygenase reactivity of 3 (kO2: 3 (29.10 ± 0.16) > 1 (16.67 ± 0.70) > 2 (1.81 ± 0.04 × 10-1 M-1 s-1)), determined by monitoring the disappearance of the LMCT band in the range 440-450 nm, is ascribed to the electron-releasing N-Et substituent on bzim ring, which decreases the π-delocalization in fla- and enhances its activation.
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Affiliation(s)
- Tamilarasan Ajaykamal
- Department of Chemistry, Bharathidasan University Tiruchirapalli 620 024 Tamil Nadu India +91-431-2407043 +91-431-2407125
| | - Mallayan Palaniandavar
- Department of Chemistry, Bharathidasan University Tiruchirapalli 620 024 Tamil Nadu India +91-431-2407043 +91-431-2407125
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Abstract
![]()
Urease
catalyzes the hydrolysis of urea to form ammonia and carbamate,
inducing an overall pH increase that affects both human health and
agriculture. Inhibition, mutagenesis, and kinetic studies have provided
insights into its enzymatic role, but there have been debates on the
substrate binding mode as well as the reaction mechanism. In the present
study, we report quatum mechanics-only (QM-only) and quantum mechanics/molecular
mechanics molecular dynamics (QM/MM MD) calculations on urease that
mainly investigate the binding mode of urea and the mechanism of the
urease-catalyzed hydrolysis reaction. Comparison between the experimental
data and our QM(GFN2-xTB)/MM metadynamics results demonstrates that
urea hydrolysis via a complex with bidentate-bound urea is much more
favorable than via that with monodentate-bound urea for both nucleophilic
attack and the subsequent proton transfer steps. We also indicate
that the bidentate coordination of urea fits the active site with
a closed conformation of the mobile flap and can facilitate the stabilization
of transition states and intermediates by forming multiple hydrogen
bonds with certain active site residues.
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Affiliation(s)
- Toru Saito
- Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozuka-Higashi, Asa-Minami-Ku, Hiroshima 731-3194 Japan
| | - Yu Takano
- Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozuka-Higashi, Asa-Minami-Ku, Hiroshima 731-3194 Japan
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Reilley DJ, Arraf Z, Alexandrova AN. Contrasting Effects of Inhibitors Li + and Be 2+ on Catalytic Cycle of Glycogen Synthase Kinase-3β. J Phys Chem B 2021; 125:9480-9489. [PMID: 34404214 DOI: 10.1021/acs.jpcb.1c05099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ionic lithium shows rare effectiveness for treating bipolar disorder and is a potential drug for neurodegenerative diseases. Unfortunately, lithium suffers from significant drawbacks, mainly a narrow therapeutic window. Among the targets of lithium, glycogen synthase kinase 3β (GSK-3β) may be responsible for its therapeutic effects. The development of alternative, selective inhibitors of this kinase could prevent lithium side effects, but such efforts have met little success so far. An atomistic understanding of Li+ inhibition and the GSK-3β phosphorylation reaction would therefore facilitate the development of new drugs. In this study, we use extensive sampling of catalytic states with our mixed quantum-classical dynamics method QM/DMD and binding affinities from a competitive metal affinity (CMA) approach to expand the atomistic picture of Li+ GSK-3β inhibition. We compare Li+ action with Be2+ and find our results in agreement with in vitro kinetics studies. Ultimately, our simulations show that Li+ inhibition is driven by decreasing the phosphorylation reaction rate, rather than reducing catalytic turnover through tight binding to different GSK-3β states like Be2+ inhibition. The effect of these metals derive from electrostatic differences and especially their smaller atomic radii compared to the native Mg2+ and thus provide insight for the development of GSK-3β inhibitors based on other paradigms.
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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
| | - Zaher Arraf
- Department of Education in Technology and Science, Technion-Israel Institute of Technology, 32000, Haifa, Israel
| | - 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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6
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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: 0.8] [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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7
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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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8
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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: 1.8] [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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9
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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: 1.0] [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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10
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Abstract
The advancements of quantum chemical methods and computer power allow detailed mechanistic investigations of metalloenzymes. In particular, both quantum chemical cluster and combined QM/MM approaches have been used, which have been proven to successfully complement experimental studies. This review starts with a brief introduction of nickel-dependent enzymes and then summarizes theoretical studies on the reaction mechanisms of these enzymes, including NiFe hydrogenase, methyl-coenzyme M reductase, nickel CO dehydrogenase, acetyl CoA synthase, acireductone dioxygenase, quercetin 2,4-dioxygenase, urease, lactate racemase, and superoxide dismutase.
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11
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Emergence of metal selectivity and promiscuity in metalloenzymes. J Biol Inorg Chem 2019; 24:517-531. [DOI: 10.1007/s00775-019-01667-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 05/13/2019] [Indexed: 01/27/2023]
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12
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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: 1.2] [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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13
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Sekowska A, Ashida H, Danchin A. Revisiting the methionine salvage pathway and its paralogues. Microb Biotechnol 2019; 12:77-97. [PMID: 30306718 PMCID: PMC6302742 DOI: 10.1111/1751-7915.13324] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 08/24/2018] [Accepted: 09/14/2018] [Indexed: 12/17/2022] Open
Abstract
Methionine is essential for life. Its chemistry makes it fragile in the presence of oxygen. Aerobic living organisms have selected a salvage pathway (the MSP) that uses dioxygen to regenerate methionine, associated to a ratchet-like step that prevents methionine back degradation. Here, we describe the variation on this theme, developed across the tree of life. Oxygen appeared long after life had developed on Earth. The canonical MSP evolved from ancestors that used both predecessors of ribulose bisphosphate carboxylase oxygenase (RuBisCO) and methanethiol in intermediate steps. We document how these likely promiscuous pathways were also used to metabolize the omnipresent by-products of S-adenosylmethionine radical enzymes as well as the aromatic and isoprene skeleton of quinone electron acceptors.
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Affiliation(s)
- Agnieszka Sekowska
- Institute of Cardiometabolism and NutritionHôpital de la Pitié‐SalpêtrièreParisFrance
| | - Hiroki Ashida
- Graduate School of Human Development and EnvironmentKobe UniversityKobeJapan
| | - Antoine Danchin
- Institute of Cardiometabolism and NutritionHôpital de la Pitié‐SalpêtrièreParisFrance
- Institute of Synthetic BiologyShenzhen Institutes of Advanced StudiesShenzhenChina
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14
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Ivan DA, Gremillion AJ, Sanchez A, Sanchez S, Lynch VM, Toledo SA. The first structural model for the resting state of the active site of nickel acireductone dioxygenase (Ni-ARD). INORG CHEM COMMUN 2018. [DOI: 10.1016/j.inoche.2018.01.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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15
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Valdez CE, Morgenstern A, Eberhart ME, Alexandrova AN. Predictive methods for computational metalloenzyme redesign - a test case with carboxypeptidase A. Phys Chem Chem Phys 2018; 18:31744-31756. [PMID: 27841396 DOI: 10.1039/c6cp02247b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Computational metalloenzyme design is a multi-scale problem. It requires treating the metal coordination quantum mechanically, extensive sampling of the protein backbone, and additionally accounting for the polarization of the active site by both the metal cation and the surrounding protein (a phenomenon called electrostatic preorganization). We bring together a combination of theoretical methods that jointly offer these desired qualities: QM/DMD for mixed quantum-classical dynamic sampling, quantum theory of atoms in molecules (QTAIM) for the assessment of electrostatic preorganization, and Density Functional Theory (DFT) for mechanistic studies. Within this suite of principally different methods, there are both complementarity of capabilities and cross-validation. Using these methods, predictions can be made regarding the relative activities of related enzymes, as we show on the native Zn2+-dependent carboxypeptidase A (CPA), and its mutant proteins, which are hypothesized to hydrolyze modified substrates. For the native CPA, we replicated the catalytic mechanism and the rate in close agreement with the experiment, giving validity to the QM/DMD predicted structure, the DFT mechanism, and the QTAIM assessment of catalytic activity. For most sequences of the modified substrate and tried CPA mutants, substantially worsened activity is predicted. However, for the substrate mutant that contains Asp instead of Phe at the C-terminus, one CPA mutant exhibits a reasonable activity, as predicted across the theoretical methods. CPA is a well-studied system, and here it serves as a testing ground for the offered methods.
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Affiliation(s)
- Crystal E Valdez
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Amanda Morgenstern
- Molecular Theory Group, Colorado School of Mines, Golden, Colorado 80401, USA.
| | - Mark E Eberhart
- Molecular Theory Group, Colorado School of Mines, Golden, Colorado 80401, USA.
| | - Anastassia N Alexandrova
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA. and California NanoSystems Institute, Los Angeles, CA 90095, USA
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16
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Valasatava Y, Rosato A, Furnham N, Thornton JM, Andreini C. To what extent do structural changes in catalytic metal sites affect enzyme function? J Inorg Biochem 2018; 179:40-53. [PMID: 29161638 PMCID: PMC5760197 DOI: 10.1016/j.jinorgbio.2017.11.002] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 11/02/2017] [Accepted: 11/04/2017] [Indexed: 01/09/2023]
Abstract
About half of known enzymatic reactions involve metals. Enzymes belonging to the same superfamily often evolve to catalyze different reactions on the same structural scaffold. The work presented here investigates how functional differentiation, within superfamilies that contain metalloenzymes, relates to structural changes at the catalytic metal site. In general, when the catalytic metal site is unchanged across the enzymes of a superfamily, the functional differentiation within the superfamily tends to be low and the mechanism conserved. Conversely, all types of structural changes in the metal binding site are observed for superfamilies with high functional differentiation. Overall, the catalytic role of the metal ions appears to be one of the most conserved features of the enzyme mechanism within metalloenzyme superfamilies. In particular, when the catalytic role of the metal ion does not involve a redox reaction (i.e. there is no exchange of electrons with the substrate), this role is almost always maintained even when the site undergoes significant structural changes. In these enzymes, functional diversification is most often associated with modifications in the surrounding protein matrix, which has changed so much that the enzyme chemistry is significantly altered. On the other hand, in more than 50% of the examples where the metal has a redox role in catalysis, changes at the metal site modify its catalytic role. Further, we find that there are no examples in our dataset where metal sites with a redox role are lost during evolution. SYNOPSIS In this paper we investigate how functional diversity within superfamilies of metalloenzymes relates to structural changes at the catalytic metal site. Evolution tends to strictly conserve the metal site. When changes occur, they do not modify the catalytic role of non-redox metals whereas they affect the role of redox-active metals.
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Affiliation(s)
- Yana Valasatava
- Magnetic Resonance Center, University of Florence, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Antonio Rosato
- Magnetic Resonance Center, University of Florence, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Nicholas Furnham
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
| | - Janet M Thornton
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Claudia Andreini
- Magnetic Resonance Center, University of Florence, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, 50019 Sesto Fiorentino, Italy.
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17
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Miłaczewska A, Kot E, Amaya JA, Makris TM, Zając M, Korecki J, Chumakov A, Trzewik B, Kędracka-Krok S, Minor W, Chruszcz M, Borowski T. On the Structure and Reaction Mechanism of Human Acireductone Dioxygenase. Chemistry 2018; 24:5225-5237. [PMID: 29193386 DOI: 10.1002/chem.201704617] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Indexed: 12/24/2022]
Abstract
Acireductone dioxygenase (ARD) is an intriguing enzyme from the methionine salvage pathway that is capable of catalysing two different oxidation reactions with the same substrate depending on the type of the metal ion in the active site. To date, the structural information regarding the ARD-acireductone complex is limited and possible reaction mechanisms are still under debate. The results of joint experimental and computational studies undertaken to advance knowledge about ARD are reported. The crystal structure of an ARD from Homo sapiens was determined with selenomethionine. EPR spectroscopy suggested that binding acireductone triggers one protein residue to dissociate from Fe2+ , which allows NO (and presumably O2 ) to bind directly to the metal. Mössbauer spectroscopic data (interpreted with the aid of DFT calculations) was consistent with bidentate binding of acireductone to Fe2+ and concomitant dissociation of His88 from the metal. Major features of Fe vibrational spectra obtained for the native enzyme and upon addition of acireductone were reproduced by QM/MM calculations for the proposed models. A computational (QM/MM) study of the reaction mechanisms suggests that Fe2+ promotes O-O bond homolysis, which elicits cleavage of the C1-C2 bond of the substrate. Higher M3+ /M2+ redox potentials of other divalent metals do not support this pathway, and instead the reaction proceeds similarly to the key reaction step in the quercetin 2,3-dioxygenase mechanism.
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Affiliation(s)
- Anna Miłaczewska
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239, Krakow, Poland.,University of Virginia, Department of Molecular Physiology and Biological Physics, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA
| | - Ewa Kot
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239, Krakow, Poland
| | - José A Amaya
- University of South Carolina, Department of Chemistry and Biochemistry, 631 Sumter Street, Columbia, SC, 29208, USA
| | - Thomas M Makris
- University of South Carolina, Department of Chemistry and Biochemistry, 631 Sumter Street, Columbia, SC, 29208, USA
| | - Marcin Zając
- National Synchrotron Radiation Centre Solaris, Jagiellonian University, ul. Czerwone Maki 98, 30-392, Kraków, Poland
| | - Józef Korecki
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239, Krakow, Poland.,AGH University of Science and Technology, Faculty of Physics and Applied Computer Science, al. Mickiewicza 30, 30-059, Kraków, Poland
| | - Aleksandr Chumakov
- European Synchrotron Radiation Facility (ESRF), P.O. Box 220, F-, 38043, Grenoble, France
| | - Bartosz Trzewik
- Jagiellonian University, Faculty of Chemistry, ul. Romana Ingardena 3, 30-060, Kraków, Poland
| | - Sylwia Kędracka-Krok
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Krakow, Poland.,Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387, Krakow, Poland
| | - Władek Minor
- University of Virginia, Department of Molecular Physiology and Biological Physics, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA
| | - Maksymilian Chruszcz
- University of South Carolina, Department of Chemistry and Biochemistry, 631 Sumter Street, Columbia, SC, 29208, USA
| | - Tomasz Borowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239, Krakow, Poland
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18
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Li H, Wang X, Tian G, Liu Y. Insights into the dioxygen activation and catalytic mechanism of the nickel-containing quercetinase. Catal Sci Technol 2018. [DOI: 10.1039/c8cy00187a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The catalytic mechanism of Ni-QueDFLA was elucidated by QM/MM calculations, and the different reactivities of nickel and iron were illuminated.
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Affiliation(s)
- Hong Li
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan
- China
| | - Xiya Wang
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan
- China
| | - Ge Tian
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan
- China
| | - Yongjun Liu
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan
- China
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19
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Deshpande AR, Pochapsky TC, Ringe D. The Metal Drives the Chemistry: Dual Functions of Acireductone Dioxygenase. Chem Rev 2017; 117:10474-10501. [PMID: 28731690 DOI: 10.1021/acs.chemrev.7b00117] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Acireductone dioxygenase (ARD) from the methionine salvage pathway (MSP) is a unique enzyme that exhibits dual chemistry determined solely by the identity of the divalent transition-metal ion (Fe2+ or Ni2+) in the active site. The Fe2+-containing isozyme catalyzes the on-pathway reaction using substrates 1,2-dihydroxy-3-keto-5-methylthiopent-1-ene (acireductone) and dioxygen to generate formate and the ketoacid precursor of methionine, 2-keto-4-methylthiobutyrate, whereas the Ni2+-containing isozyme catalyzes an off-pathway shunt with the same substrates, generating methylthiopropionate, carbon monoxide, and formate. The dual chemistry of ARD was originally discovered in the bacterium Klebsiella oxytoca, but it has recently been shown that mammalian ARD enzymes (mouse and human) are also capable of catalyzing metal-dependent dual chemistry in vitro. This is particularly interesting, since carbon monoxide, one of the products of off-pathway reaction, has been identified as an antiapoptotic molecule in mammals. In addition, several biochemical and genetic studies have indicated an inhibitory role of human ARD in cancer. This comprehensive review describes the biochemical and structural characterization of the ARD family, the proposed experimental and theoretical approaches to establishing mechanisms for the dual chemistry, insights into the mechanism based on comparison with structurally and functionally similar enzymes, and the applications of this research to the field of artificial metalloenzymes and synthetic biology.
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Affiliation(s)
- Aditi R Deshpande
- Departments of Biochemistry and ‡Chemistry and §the Rosenstiel Institute for Basic Biomedical Research, Brandeis University , Waltham, Massachusetts 02454, United States
| | - Thomas C Pochapsky
- Departments of Biochemistry and ‡Chemistry and §the Rosenstiel Institute for Basic Biomedical Research, Brandeis University , Waltham, Massachusetts 02454, United States
| | - Dagmar Ringe
- Departments of Biochemistry and ‡Chemistry and §the Rosenstiel Institute for Basic Biomedical Research, Brandeis University , Waltham, Massachusetts 02454, United States
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20
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Yu MJ, Chen SL. From NAD + to Nickel Pincer Complex: A Significant Cofactor Evolution Presented by Lactate Racemase. Chemistry 2017; 23:7545-7557. [PMID: 28374531 DOI: 10.1002/chem.201700405] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Indexed: 02/02/2023]
Abstract
Lactate racemase (LarA), a new nickel enzyme discovered recently, catalyzes the racemization between d- and l-lactates with a novel nickel pincer cofactor (Ni-PTTMN) derived from nicotinic acid. In this study, by using DFT and a 200-atom active-site model, LarA is revealed to employ a modified proton-coupled hydride-transfer mechanism in which a hydride is transferred to a cofactor pyridine carbon from the substrate α-carbon along with proton transfer from the substrate hydroxy group to a histidine, and then moved back from the opposite side. Tyr294 and Lys298 provide significant acceleration effects by orientating substrates and stabilizing the negative charge developing at the substrate hydroxy oxygen. The barrier was determined to be 12.0 kcal mol-1 , which reveals enhanced racemase activity relative to the LarA reaction using NAD+ -like cofactors. Compared with NAD+ , Ni-PTTMN has a stronger hydride-addition reactivity in moderate and high environmental polarity and may fit perfectly the moderately polar active site of LarA.
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Affiliation(s)
- Ming-Jia Yu
- Key Laboratory of Cluster Science of the Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, P.R. China
| | - Shi-Lu Chen
- Key Laboratory of Cluster Science of the Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, P.R. China
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21
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Oxygen activation by mononuclear Mn, Co, and Ni centers in biology and synthetic complexes. J Biol Inorg Chem 2016; 22:407-424. [PMID: 27853875 DOI: 10.1007/s00775-016-1402-7] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 10/21/2016] [Indexed: 10/20/2022]
Abstract
The active sites of metalloenzymes that catalyze O2-dependent reactions generally contain iron or copper ions. However, several enzymes are capable of activating O2 at manganese or nickel centers instead, and a handful of dioxygenases exhibit activity when substituted with cobalt. This minireview summarizes the catalytic properties of oxygenases and oxidases with mononuclear Mn, Co, or Ni active sites, including oxalate-degrading oxidases, catechol dioxygenases, and quercetin dioxygenase. In addition, recent developments in the O2 reactivity of synthetic Mn, Co, or Ni complexes are described, with an emphasis on the nature of reactive intermediates featuring superoxo-, peroxo-, or oxo-ligands. Collectively, the biochemical and synthetic studies discussed herein reveal the possibilities and limitations of O2 activation at these three "overlooked" metals.
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22
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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: 2.0] [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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23
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Deshpande AR, Wagenpfeil K, Pochapsky TC, Petsko GA, Ringe D. Metal-Dependent Function of a Mammalian Acireductone Dioxygenase. Biochemistry 2016; 55:1398-407. [PMID: 26858196 PMCID: PMC5319410 DOI: 10.1021/acs.biochem.5b01319] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The two acireductone dioxygenase (ARD) isozymes from the methionine salvage pathway of Klebsiella oxytoca are the only known pair of naturally occurring metalloenzymes with distinct chemical and physical properties determined solely by the identity of the divalent transition metal ion (Fe(2+) or Ni(2+)) in the active site. We now show that this dual chemistry can also occur in mammals. ARD from Mus musculus (MmARD) was studied to relate the metal ion identity and three-dimensional structure to enzyme function. The iron-containing isozyme catalyzes the cleavage of 1,2-dihydroxy-3-keto-5-(thiomethyl)pent-1-ene (acireductone) by O2 to formate and the ketoacid precursor of methionine, which is the penultimate step in methionine salvage. The nickel-bound form of ARD catalyzes an off-pathway reaction resulting in formate, carbon monoxide (CO), and 3-(thiomethyl) propionate. Recombinant MmARD was expressed and purified to obtain a homogeneous enzyme with a single transition metal ion bound. The Fe(2+)-bound protein, which shows about 10-fold higher activity than that of others, catalyzes on-pathway chemistry, whereas the Ni(2+), Co(2+), or Mn(2+) forms exhibit off-pathway chemistry, as has been seen with ARD from Klebsiella. Thermal stability of the isozymes is strongly affected by the metal ion identity, with Ni(2+)-bound MmARD being the most stable, followed by Co(2+) and Fe(2+), and Mn(2+)-bound ARD being the least stable. Ni(2+)- and Co(2+)-bound MmARD were crystallized, and the structures of the two proteins found to be similar. Enzyme-ligand complexes provide insight into substrate binding, metal coordination, and the catalytic mechanism.
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Affiliation(s)
| | | | - Thomas C. Pochapsky
- Department of Biochemistry, Brandeis University, Waltham, MA 02454,Department of Chemistry, Brandeis University, Waltham, MA 02454,Rosenstiel Institute for Basic Biomedical Research, Brandeis University, Waltham, MA 02454
| | - Gregory A. Petsko
- Department of Biochemistry, Brandeis University, Waltham, MA 02454,Department of Chemistry, Brandeis University, Waltham, MA 02454,Helen and Robert Appel Alzheimer’s Disease Research Institute, Weill Cornell Medical College, New York, NY 10065
| | - Dagmar Ringe
- Department of Biochemistry, Brandeis University, Waltham, MA 02454,Department of Chemistry, Brandeis University, Waltham, MA 02454,Rosenstiel Institute for Basic Biomedical Research, Brandeis University, Waltham, MA 02454,Corresponding Author. To whom correspondence should be addressed. . Phone: 781-736-4902
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25
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26
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27
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Nechay MR, Valdez CE, Alexandrova AN. Computational Treatment of Metalloproteins. J Phys Chem B 2015; 119:5945-56. [DOI: 10.1021/acs.jpcb.5b00028] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Michael R. Nechay
- Department
of Chemistry and Biochemistry and ‡California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Crystal E. Valdez
- Department
of Chemistry and Biochemistry and ‡California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Anastassia N. Alexandrova
- Department
of Chemistry and Biochemistry and ‡California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
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28
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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: 26] [Impact Index Per Article: 2.9] [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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29
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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: 101] [Impact Index Per Article: 10.1] [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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30
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Allpress CJ, Berreau LM. A Nickel‐Containing Model System of Acireductone Dioxygenases that Utilizes a C(1)‐H Acireductone Substrate. Eur J Inorg Chem 2014. [DOI: 10.1002/ejic.201402254] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Caleb J. Allpress
- Department of Chemistry and Biochemistry, Utah State University, 0300 Old Main Hill, Logan, UT 84322‐0300, USA, http://lisaberreau.org/
| | - Lisa M. Berreau
- Department of Chemistry and Biochemistry, Utah State University, 0300 Old Main Hill, Logan, UT 84322‐0300, USA, http://lisaberreau.org/
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31
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Cu,Zn-superoxide dismutase without Zn is folded but catalytically inactive. J Mol Biol 2014; 426:4112-4124. [PMID: 25083917 DOI: 10.1016/j.jmb.2014.07.016] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 07/05/2014] [Accepted: 07/20/2014] [Indexed: 02/04/2023]
Abstract
Amyotrophic lateral sclerosis has been linked to the gain of aberrant function of superoxide dismutase, Cu,Zn-SOD1 upon protein misfolding. The mechanism of SOD1 misfolding is thought to involve mutations leading to the loss of Zn, followed by protein unfolding and aggregation. We show that the removal of Zn from SOD1 may not lead to an immediate unfolding but immediately deactivates the enzyme through a combination of subtle structural and electronic effects. Using quantum mechanics/discrete molecular dynamics, we showed that both Zn-less wild-type (WT)-SOD1 and its D124N mutant that does not bind Zn have at least metastable folded states. In those states, the reduction potential of Cu increases, leading to the presence of detectable amounts of Cu(I) instead of Cu(II) in the active site, as confirmed experimentally. The Cu(I) protein cannot participate in the catalytic Cu(I)-Cu(II) cycle. However, even without the full reduction to Cu(I), the Cu site in the Zn-less variants of SOD1 is shown to be catalytically incompetent: unable to bind superoxide in a way comparable to the WT-SOD1. The changes are more radical and different in the D124N Zn-less mutant than in the Zn-less WT-SOD1, suggesting D124N being perhaps not the most adequate model for Zn-less SOD1. Overall, Zn in SOD1 appears to be influencing the Cu site directly by adjusting its reduction potential and geometry. Thus, the role of Zn in SOD1 is not just structural, as was previously thought; it is a vital part of the catalytic machinery.
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32
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Valdez CE, Gallup NM, Alexandrova AN. Co2+ acireductone dioxygenase: Fe2+ mechanism, Ni2+ mechanism, or something else? Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.04.055] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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33
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Affiliation(s)
- Michael J Maroney
- Department of Chemistry, University of Massachusetts , Amherst, Massachusetts 01003, United States
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