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Watanabe Y, Aiba Y, Ariyasu S, Abe S. Molecular Design and Regulation of Metalloenzyme Activities through Two Novel Approaches: Ferritin and P450s. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2020. [DOI: 10.1246/bcsj.20190305] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Yoshihito Watanabe
- Research Center for Materials Science, Nagoya University, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Yuichiro Aiba
- Department of Chemistry, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Shinya Ariyasu
- Department of Chemistry, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Satoshi Abe
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Nagatsuda-cho, Yokohama, Kanagawa, Japan
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Adam SM, Wijeratne GB, Rogler PJ, Diaz DE, Quist DA, Liu JJ, Karlin KD. Synthetic Fe/Cu Complexes: Toward Understanding Heme-Copper Oxidase Structure and Function. Chem Rev 2018; 118:10840-11022. [PMID: 30372042 PMCID: PMC6360144 DOI: 10.1021/acs.chemrev.8b00074] [Citation(s) in RCA: 145] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Heme-copper oxidases (HCOs) are terminal enzymes on the mitochondrial or bacterial respiratory electron transport chain, which utilize a unique heterobinuclear active site to catalyze the 4H+/4e- reduction of dioxygen to water. This process involves a proton-coupled electron transfer (PCET) from a tyrosine (phenolic) residue and additional redox events coupled to transmembrane proton pumping and ATP synthesis. Given that HCOs are large, complex, membrane-bound enzymes, bioinspired synthetic model chemistry is a promising approach to better understand heme-Cu-mediated dioxygen reduction, including the details of proton and electron movements. This review encompasses important aspects of heme-O2 and copper-O2 (bio)chemistries as they relate to the design and interpretation of small molecule model systems and provides perspectives from fundamental coordination chemistry, which can be applied to the understanding of HCO activity. We focus on recent advancements from studies of heme-Cu models, evaluating experimental and computational results, which highlight important fundamental structure-function relationships. Finally, we provide an outlook for future potential contributions from synthetic inorganic chemistry and discuss their implications with relevance to biological O2-reduction.
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Affiliation(s)
- Suzanne M. Adam
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Gayan B. Wijeratne
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Patrick J. Rogler
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Daniel E. Diaz
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - David A. Quist
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Jeffrey J. Liu
- 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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Succinate, an intermediate in metabolism, signal transduction, ROS, hypoxia, and tumorigenesis. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1086-1101. [PMID: 26971832 DOI: 10.1016/j.bbabio.2016.03.012] [Citation(s) in RCA: 318] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 03/06/2016] [Accepted: 03/07/2016] [Indexed: 12/31/2022]
Abstract
Succinate is an important metabolite at the cross-road of several metabolic pathways, also involved in the formation and elimination of reactive oxygen species. However, it is becoming increasingly apparent that its realm extends to epigenetics, tumorigenesis, signal transduction, endo- and paracrine modulation and inflammation. Here we review the pathways encompassing succinate as a metabolite or a signal and how these may interact in normal and pathological conditions.(1).
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Apolar distal pocket mutants of yeast cytochrome c peroxidase: Binding of imidazole, 1-methylimidazole and 4-nitroimidazole to the triAla, triVal, and triLeu variants. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:919-29. [PMID: 25900360 DOI: 10.1016/j.bbapap.2015.04.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Revised: 04/04/2015] [Accepted: 04/14/2015] [Indexed: 11/23/2022]
Abstract
Imidazole binding to three apolar distal heme pocket mutants of yeast cytochrome c peroxidase (CcP) has been investigated between pH4 and 8. The three CcP variants have Arg-48, Trp-51, and His-52 mutated to either all alanine, CcP(triAla), all valine, CcP(triVal), or all leucine residues, CcP(triLeu). The imidazole binding curves for all three mutants are biphasic indicating that each of the mutants exists in at least two conformational states with different affinities for imidazole. At pH7, the high-affinity conformations of the three CcP mutants bind imidazole between 3.8 and 4.7 orders of magnitude stronger than that of wild-type CcP while the low-affinity conformations have binding affinities about 2.5 orders of magnitude larger than wild-type CcP. Imidazole binding to the three CcP mutants is pH dependent with the strongest binding observed at high pH. Apparent pK(a) values for the transition in binding vary between 5.6 and 7.5 for the high-affinity conformations and between 6.2 and 6.8 for the low-affinity conformations of the CcP triple mutants. The kinetics of imidazole binding are also biphasic. The fast phase of imidazole binding to CcP(triAla) and CcP(triLeu) is linearly dependent on the imidazole concentration while the slow phase is independent of imidazole concentration. Both phases of imidazole binding to CcP(triVal) have a hyperbolic dependence on the imidazole concentration. The apparent association rate constants vary between 30 and 170 M(-1)s(-1) while the apparent dissociation rate constants vary between 0.05 and 0.43 s(-1). The CcP triple mutants have higher binding affinities for 1-methylimidazole and 4-nitroimidazole than does wild-type CcP.
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Bhagi-Damodaran A, Petrik ID, Marshall NM, Robinson H, Lu Y. Systematic tuning of heme redox potentials and its effects on O2 reduction rates in a designed oxidase in myoglobin. J Am Chem Soc 2014; 136:11882-5. [PMID: 25076049 PMCID: PMC4151708 DOI: 10.1021/ja5054863] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Indexed: 11/28/2022]
Abstract
Cytochrome c Oxidase (CcO) is known to catalyze the reduction of O2 to H2O efficiently with a much lower overpotential than most other O2 reduction catalysts. However, methods by which the enzyme fine-tunes the reduction potential (E°) of its active site and the corresponding influence on the O2 reduction activity are not well understood. In this work, we report systematic tuning of the heme E° in a functional model of CcO in myoglobin containing three histidines and one tyrosine in the distal pocket of heme. By removing hydrogen-bonding interactions between Ser92 and the proximal His ligand and a heme propionate, and increasing hydrophobicity of the heme pocket through Ser92Ala mutation, we have increased the heme E° from 95 ± 2 to 123 ± 3 mV. Additionally, replacing the native heme b in the CcO mimic with heme a analogs, diacetyl, monoformyl, and diformyl hemes, that posses electron-withdrawing groups, resulted in higher E° values of 175 ± 5, 210 ± 6, and 320 ± 10 mV, respectively. Furthermore, O2 consumption studies on these CcO mimics revealed a strong enhancement in O2 reduction rates with increasing heme E°. Such methods of tuning the heme E° through a combination of secondary sphere mutations and heme substitutions can be applied to tune E° of other heme proteins, allowing for comprehensive investigations of the relationship between E° and enzymatic activity.
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Affiliation(s)
- Ambika Bhagi-Damodaran
- Department
of Chemistry, University of Illinois, Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Igor D. Petrik
- Department
of Chemistry, University of Illinois, Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Nicholas M. Marshall
- Department
of Chemistry, University of Illinois, Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Howard Robinson
- Department
of Biology, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Yi Lu
- Department
of Chemistry, University of Illinois, Urbana−Champaign, Urbana, Illinois 61801, United States
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Vidossich P, Magistrato A. QM/MM molecular dynamics studies of metal binding proteins. Biomolecules 2014; 4:616-45. [PMID: 25006697 PMCID: PMC4192665 DOI: 10.3390/biom4030616] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 06/05/2014] [Accepted: 06/06/2014] [Indexed: 11/16/2022] Open
Abstract
Mixed quantum-classical (quantum mechanical/molecular mechanical (QM/MM)) simulations have strongly contributed to providing insights into the understanding of several structural and mechanistic aspects of biological molecules. They played a particularly important role in metal binding proteins, where the electronic effects of transition metals have to be explicitly taken into account for the correct representation of the underlying biochemical process. In this review, after a brief description of the basic concepts of the QM/MM method, we provide an overview of its capabilities using selected examples taken from our work. Specifically, we will focus on heme peroxidases, metallo-β-lactamases, α-synuclein and ligase ribozymes to show how this approach is capable of describing the catalytic and/or structural role played by transition (Fe, Zn or Cu) and main group (Mg) metals. Applications will reveal how metal ions influence the formation and reduction of high redox intermediates in catalytic cycles and enhance drug metabolism, amyloidogenic aggregate formation and nucleic acid synthesis. In turn, it will become manifest that the protein frame directs and modulates the properties and reactivity of the metal ions.
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Affiliation(s)
- Pietro Vidossich
- Department of Chemistry, Autonomous University of Barcelona, 08193 Cerdanyola del Vallés, Spain.
| | - Alessandra Magistrato
- CNR-IOM-Democritos National Simulation Center c/o, International School for Advanced Studies (SISSA/ISAS), via Bonomea 265, 34165 Trieste, Italy.
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Ercan S, Arslan N, Kocakaya SO, Pirinccioglu N, Williams A. Experimental and theoretical study of the mechanism of hydrolysis of substituted phenyl hexanoates catalysed by globin in the presence of surfactant. J Mol Model 2014; 20:2096. [PMID: 24562853 DOI: 10.1007/s00894-014-2096-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2013] [Accepted: 11/28/2013] [Indexed: 10/25/2022]
Abstract
The bimolecular rate constants for the globin- and alkali-catalysed hydrolysis of substituted phenyl hexanoates in the absence and presence of cetyltrimethylammonium bromide (CTAB) obey Brønsted equations with β(lg) = -0.53 (globin-catalysed), -0.68 (globin-catalysed in CTAB), -0.34 (in water) and -0.74 (in CTAB), respectively. The slopes indicate that the microsolvation environments associated with the transition states of the catalysed reactions are different from those that occur in aqueous medium. The slope (-0.74) for the reaction in CTAB implies that it proceeds in a less polar medium. The larger β(lg) value (-0.53) obtained for the globin-catalysed reaction compared to that for the uncatalysed one may be attributed to either the less polar microenvironments of the transition states or the involvement of one of the imidazole groups as a nucleophile. The results from a study of the effect of pH on the reactivity provide evidence for the latter assumption. All of the ligands were docked into the hydrophobic pocket of the protein, and the resulting docking scores ranged from -30.76 to -23.61 kcal mol⁻¹. Molecular dynamic simulations and MM-PBSA/GBSA calculations performed for the complexes gave insight into the binding modes of globin to the esters, which are consistent with experimental results. The calculations yielded comparable free energies of binding to the experimental ones for 4-nitrophenyl and 4-chloro-2-nitrophenyl hexanoates. In conclusion, information obtained from the linear free-energy relationship is still very useful for elucidating the mechanisms of organic reactions, including enzyme-catalysed reactions. This approach is further supported by the utilization of computational tools.
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Affiliation(s)
- Selami Ercan
- Faculty of Science and Literature, Department of Chemistry, University of Batman, Batman, Turkey
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Erman JE, Kilheeney H, Bidwai AK, Ayala CE, Vitello LB. Peroxygenase activity of cytochrome c peroxidase and three apolar distal heme pocket mutants: hydroxylation of 1-methoxynaphthalene. BMC BIOCHEMISTRY 2013; 14:19. [PMID: 23895311 PMCID: PMC3733812 DOI: 10.1186/1471-2091-14-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 07/25/2013] [Indexed: 11/10/2022]
Abstract
BACKGROUND The cytochrome P450s are monooxygenases that insert oxygen functionalities into a wide variety of organic substrates with high selectivity. There is interest in developing efficient catalysts based on the "peroxide shunt" pathway in the cytochrome P450s, which uses H2O2 in place of O2/NADPH as the oxygenation agent. We report on our initial studies using cytochrome c peroxidase (CcP) as a platform to develop specific "peroxygenation" catalysts. RESULTS The peroxygenase activity of CcP was investigated using 1-methoxynaphthalene as substrate. 1-Methoxynaphthalene hydroxylation was monitored using Russig's blue formation at standard reaction conditions of 0.50 mM 1-methoxynaphthalene, 1.00 mM H2O2, pH 7.0, 25°C. Wild-type CcP catalyzes the hydroxylation of 1-methoxynaphthalene with a turnover number of 0.0044 ± 0.0001 min-1. Three apolar distal heme pocket mutants of CcP were designed to enhance binding of 1-methoxynaphthalene near the heme, constructed, and tested for hydroxylation activity. The highest activity was observed for CcP(triAla), a triple mutant with Arg48, Trp51, and His52 simultaneously mutated to alanine residues. The turnover number of CcP(triAla) is 0.150 ± 0.008 min-1, 34-fold greater than wild-type CcP and comparable to the naphthalene hydroxylation activity of rat liver microsomal cytochrome P450. While wild-type CcP is very stable to oxidative degradation by excess hydrogen peroxide, CcP(triAla) is inactivated within four cycles of the peroxygenase reaction. CONCLUSIONS Protein engineering of CcP can increase the rate of peroxygenation of apolar substrates but the initial constructs are more susceptible to oxidative degradation than wild-type enzyme. Further developments will require constructs with increased rates and selectivity while maintaining the stability of wild-type CcP toward oxidative degradation by hydrogen peroxide.
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Abstract
Lactic acid bacteria (LAB) are of profound importance in food production and infection medicine. LAB do not rely on heme (protoheme IX) for growth and are unable to synthesize this cofactor but are generally able to assemble a small repertoire of heme-containing proteins if heme is provided from an exogenous source. These features are in contrast to other bacteria, which synthesize their heme or depend on heme for growth. We here present the cellular function of heme proteins so far identified in LAB and discuss their biogenesis as well as applications of the extraordinary heme physiology of LAB.
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Demarche P, Junghanns C, Nair RR, Agathos SN. Harnessing the power of enzymes for environmental stewardship. Biotechnol Adv 2012; 30:933-53. [DOI: 10.1016/j.biotechadv.2011.05.013] [Citation(s) in RCA: 132] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Accepted: 05/13/2011] [Indexed: 11/17/2022]
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Nakajima H, Osami S, Watanabe Y. Molecular Design of Heme Proteins for Future Application. CATALYSIS SURVEYS FROM ASIA 2011. [DOI: 10.1007/s10563-011-9117-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Behera RK, Goyal S, Mazumdar S. Modification of the heme active site to increase the peroxidase activity of thermophilic cytochrome P450: A rational approach. J Inorg Biochem 2010; 104:1185-94. [DOI: 10.1016/j.jinorgbio.2010.07.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2010] [Revised: 07/13/2010] [Accepted: 07/15/2010] [Indexed: 11/28/2022]
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14
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Kruithof CA, Berger A, Dijkstra HP, Soulimani F, Visser T, Lutz M, Spek AL, Gebbink RJMK, van Koten G. Sulfato-bridged ECE-pincer palladium(ii) complexes: structures in the solid-state and in solution, and catalytic properties. Dalton Trans 2009:3306-14. [DOI: 10.1039/b816936e] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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15
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Battistuzzi G, Bellei M, Casella L, Bortolotti CA, Roncone R, Monzani E, Sola M. Redox reactivity of the heme Fe3+/Fe2+ couple in native myoglobins and mutants with peroxidase-like activity. J Biol Inorg Chem 2007; 12:951-8. [PMID: 17576605 DOI: 10.1007/s00775-007-0267-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2007] [Accepted: 05/21/2007] [Indexed: 10/23/2022]
Abstract
The reaction enthalpy and entropy for the one-electron reduction of the ferric heme in horse heart and sperm whale aquometmyoglobins (Mb) have been determined exploiting a spectroelectrochemical approach. Also investigated were the T67R, T67K, T67R/S92D and T67R/S92D Mb-H variants (the latter containing a protoheme-L: -histidine methyl ester) of sperm whale Mb, which feature peroxidase-like activity. The reduction potential (E degrees ') in all species consists of an enthalpic term which disfavors Fe(3+) reduction and a larger entropic contribution which instead selectively stabilizes the reduced form. This behavior differs from that of the heme redox enzymes and electron transport proteins investigated so far. The reduction thermodynamics in the series of sperm whale Mb variants show an almost perfect enthalpy-entropy compensation, indicating that the mutation-induced changes in DeltaH(o')(rc) and DeltaS(o')(rc) are dominated by reduction-induced solvent reorganization effects. The modest changes in E degrees ' originate from the enthalpic effects of the electrostatic interactions of the heme with the engineered charged residues. The small influence that the mutations exert on the reduction potential of myoglobin suggests that the increased peroxidase activity of the variants is not related to changes in the redox reactivity of the heme iron, but are likely related to a more favored substrate orientation within the distal heme cavity.
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Affiliation(s)
- Gianantonio Battistuzzi
- Department of Chemistry, University of Modena and Reggio Emilia, Via Campi 183, 41100 Modena, Italy
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Nicolis S, Casella L, Roncone R, Dallacosta C, Monzani E. Heme-peptide complexes as peroxidase models. CR CHIM 2007. [DOI: 10.1016/j.crci.2006.09.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Lu Y. Metalloprotein and metallo-DNA/RNAzyme design: current approaches, success measures, and future challenges. Inorg Chem 2007; 45:9930-40. [PMID: 17140190 PMCID: PMC2533576 DOI: 10.1021/ic052007t] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Specific metal-binding sites have been found in not only proteins but also DNA and RNA molecules. Together these metalloenzymes consist of a major portion of the enzyme family and can catalyze some of the most difficult biological reactions. Designing these metalloenzymes can be both challenging and rewarding because it can provide deeper insights into the structure and function of proteins and cheaper and more stable alternatives for biochemical and biotechnological applications. Toward this goal, both rational and combinatorial approaches have been used. The rational approach is good for designing metalloenzymes that are well characterized, such as heme proteins, while the combinatorial approach is better at designing those whose structures are poorly understood, such as metallo-DNA/RNAzymes. Among the rational approaches, de novo design is at its best when metal-binding sites reside in a scaffold whose structure has been designed de novo (e.g., alpha-helical bundles). Otherwise, design using native scaffolds can be equally effective, allowing more choices of scaffolds whose structural stability is often more resistant to multiple mutations. In addition, computational and empirical designs have both enjoyed successes. Because of the limitation in defining structural parameters for metal-binding sites, a computational approach is restricted to mostly metal-binding sites that are well defined, such as mono- or homonuclear centers. An empirical approach, even though it is less restrictive in the metal-binding sites to be designed, depends heavily on one's knowledge and choice of templates and targets. An emerging approach is a combination of both computational and empirical approaches. The success of these approaches can be measured not only by three-dimensional structural comparison between the designed and target enzymes but also by the total amount of insight obtained from the design process and studies of the designed enzymes. One of the biggest advantages of designed metalloenzymes is the potential of placing two different metal-binding sites in the same protein framework for comparison. A final measure of success is how one can utilize the insight gained from the intellectual exercise to design new metalloenzymes, including those with unprecedented structures and functions. Future challenges include designing more complex metalloenzymes such as heteronuclear metal centers with strong nanomolar or better affinities. A key to meeting this challenge is to focus on the design of not only primary but also secondary coordination spheres using a combination of improved computer programs, experimental design, and high-resolution crystallography.
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Affiliation(s)
- Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
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Pfister TD, Mirarefi AY, Gengenbach AJ, Zhao X, Danstrom C, Conatser N, Gao YG, Robinson H, Zukoski CF, Wang AHJ, Lu Y. Kinetic and crystallographic studies of a redesigned manganese-binding site in cytochrome c peroxidase. J Biol Inorg Chem 2006; 12:126-37. [PMID: 17021923 DOI: 10.1007/s00775-006-0171-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2006] [Accepted: 08/25/2006] [Indexed: 10/24/2022]
Abstract
Manganese peroxidase (MnP) from the white rot fungus Phanerochaete chrysosporium contains a manganese-binding site that plays a critical role in its function. Previously, a Mn(II)-binding site was designed into cytochrome c peroxidase (CcP) based on sequence homology (Yeung et al. in Chem. Biol. 4:215-222, 1997; Gengenbach et al. in Biochemistry 38:11425-11432, 1999). Here, we report a redesign of this site based on X-ray structural comparison of MnP and CcP. The variant, CcP(D37E, V45E, H181E), displays 2.5-fold higher catalytic efficiency (k (cat)/K (M)) than the variant in the original design, mostly due to a stronger K (M) of 1.9 mM (vs. 4.1 mM). High-resolution X-ray crystal structures of a metal-free form and a form with Co(II) at the designed Mn(II) site were also obtained. The metal ion in the engineered metal-binding site overlays well with Mn(II) bound in MnP, suggesting that this variant is the closest structural model of the Mn(II)-binding site in MnP for which a crystal structure exists. A major difference arises in the distances of the ligands to the metal; the metal-ligand interactions in the CcP variant are much weaker than the corresponding interactions in MnP, probably owing to partial occupancy of metal ion at the designed site, difference in the identity of metal ions (Co(II) rather than Mn(II)) and other interactions in the second coordination sphere. These results indicate that the metal ion, the ligands, and the environment around the metal-binding site play important roles in tuning the structure and function of metalloenzymes.
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Affiliation(s)
- Thomas D Pfister
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, IL 61801, USA
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Kruithof CA, Casado MA, Guillena G, Egmond MR, van der Kerk-van Hoof A, Heck AJR, Klein Gebbink RJM, van Koten G. Lipase Active-Site-Directed Anchoring of Organometallics: Metallopincer/Protein Hybrids. Chemistry 2005; 11:6869-77. [PMID: 16224766 DOI: 10.1002/chem.200500671] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The work described herein presents a strategy for the regioselective introduction of organometallic complexes into the active site of the lipase cutinase. Nitrophenol phosphonate esters, well known for their lipase inhibitory activity, are used as anchor functionalities and were found to be ideal tools to develop a single-site-directed immobilization method. A small series of phosphonate esters, covalently attached to ECE "pincer"-type d8-metal complexes through a propyl tether (ECE=[C6H3(CH2E)(2)-2,6]-; E=NR2 or SR), were designed and synthesized. Cutinase was treated with these organometallic phosphonate esters and the new metal-complex/protein hybrids were identified as containing exactly one organometallic unit per protein. The organometallic proteins were purified by membrane dialysis and analyzed by ESI-mass spectrometry. The major advantages of this strategy are: 1) one transition metal can be introduced regioselectively and, hence, the metal environment can potentially be fine-tuned; 2) purification procedures are facile due to the use of pre-synthesized metal complexes; and, most importantly, 3) the covalent attachment of robust organometallic pincer complexes to an enzyme is achieved, which will prevent metal leaching from these hybrids. The approach presented herein can be regarded as a tool in the development of regio- and enantioselective catalyst as well as analytical probes for studying enzyme properties (e.g., structure) and, hence, is a "proof-of-principle design" study in enzyme chemistry.
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Affiliation(s)
- Cornelis A Kruithof
- Debye Institute, Organic Synthesis and Catalysis, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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20
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Lu Y. Design and engineering of metalloproteins containing unnatural amino acids or non-native metal-containing cofactors. Curr Opin Chem Biol 2005; 9:118-26. [PMID: 15811795 DOI: 10.1016/j.cbpa.2005.02.017] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An emerging branch of metalloprotein design and engineering is on the horizon, where unnatural amino acids or non-native metal-containing cofactors are employed in the design and engineering process. These endeavors have been shown to be quite effective in elucidating the precise roles of key residues in protein structures and functions, in providing guiding principles on protein design, in fine-tuning the protein properties to an unprecedented level, and in expanding the repertoire of protein functionalities, and thus its range of applications.
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Affiliation(s)
- Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
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21
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Denisov IG, Makris TM, Sligar SG, Schlichting I. Structure and Chemistry of Cytochrome P450. Chem Rev 2005; 105:2253-77. [PMID: 15941214 DOI: 10.1021/cr0307143] [Citation(s) in RCA: 1512] [Impact Index Per Article: 79.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ilia G Denisov
- Department of Biochemistry, Center for Biophysics and Computational Biology, University of Illinois, Urbana-Champaign, 61801, USA
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22
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Braun M, Rubio IG, Thöny-Meyer L. A heme tag for in vivo synthesis of artificial cytochromes. Appl Microbiol Biotechnol 2004; 67:234-9. [PMID: 15834717 DOI: 10.1007/s00253-004-1804-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2004] [Revised: 09/27/2004] [Accepted: 10/19/2004] [Indexed: 11/27/2022]
Abstract
A genetic approach is described here that enables the specific covalent attachment of heme via a short C-terminal peptide tag to an otherwise non-heme-binding protein. Covalent attachment of heme to the apo-protein is catalysed by the cytochrome c maturation system of Escherichia coli. While its original enzymatic activity is retained, the resulting heme-tagged protein is red, has peroxidase activity and is redox active. The presence or absence of a C-terminal histidine tag results in low-spin heme iron with six- or high-spin heme iron with five coordinate ligands, respectively. The heme tag can be used as a tool for the rational design of artificial c-type cytochromes and metalloenzymes, thereby overcoming previous limitations set by chemical approaches. Moreover, the tag allows direct visualisation of the red fusion protein during purification.
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Affiliation(s)
- Martin Braun
- Institut für Mikrobiologie, ETH Hönggerberg, Wolfgang-Pauli-Str. 10, 8093, Zürich, Switzerland.
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23
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Yamaguchi H, Tsubouchi K, Kawaguchi K, Horita E, Harada A. Peroxidase Activity of Cationic Metalloporphyrin-Antibody Complexes. Chemistry 2004; 10:6179-86. [PMID: 15515084 DOI: 10.1002/chem.200305692] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Peroxidase activity of a complex of water-soluble cationic metalloporphyrin with anti-cationic porphyrin antibody is reported. Antibody 12E11G, which was prepared by immunization with a conjugate of 5-(4-carboxyphenyl)-10,15,20-tris(4-methylpyridyl)porphine iodide (3MPy1C), bound to tetramethylpyridylporphyrin iron complex (FeIII-TMPyP) with the dissociation constant of 2.6 x 10(-7) M. The complex of antibody 12E11G with FeIII-TMPyP catalyzed oxidation of pyrogallol, catechol, and guaiacol. A Lineweaver-Burk plot for the oxidation of pyrogallol catalyzed by the FeIII-TMPyP-antibody complex showed Km=8.6 mM and kcat=680 min(-1). Under the same conditions, Km and kcat for horseradish peroxidase (HRP) were 0.8 mM and 1750 min(-1), respectively. Although the binding interaction of the antibody to the substrates was one order lower than that of native HRP, the peroxidase activity of this system was in the same order of magnitude as that of HRP.
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Affiliation(s)
- Hiroyasu Yamaguchi
- Department of Macromolecular Science, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
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24
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Roncone R, Monzani E, Labò S, Sanangelantoni AM, Casella L. Catalytic activity, stability, unfolding, and degradation pathways of engineered and reconstituted myoglobins. J Biol Inorg Chem 2004; 10:11-24. [PMID: 15565498 DOI: 10.1007/s00775-004-0606-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2004] [Accepted: 10/13/2004] [Indexed: 10/26/2022]
Abstract
The structural and functional consequences of engineering a positively charged Lys residue and replacing the natural heme with a heme-L-His derivative in the active site of sperm whale myoglobin (Mb) have been investigated. The main structural change caused by the distal T67K mutation appears to be mobilization of the propionate-7 group. Reconstitution of wild-type and T67K Mb with heme-L-His relaxes the protein fragment around the heme because it involves the loss of the interaction of one of the propionate groups which stabilize heme binding to the protein. This modification increases the accessibility of exogenous ligands or substrates to the active site. The catalytic activity of the reconstituted proteins in peroxidase-type reactions is thus significantly increased, particularly with T67K Mb. The T67K mutation slightly reduces the thermodynamic stability and the chemical stability of Mb during catalysis, but somewhat more marked effects are observed by cofactor reconstitution. Hydrogen peroxide, in fact, induces pseudo-peroxidase activity but also promotes oxidative damage of the protein. The mechanism of protein degradation involves two pathways, which depend on the evolution of radical species generated on protein residues by the Mb active species and on the reactivity of phenoxy radicals produced during turnover. Both protein oligomers and heme-protein cross-links have been detected upon inactivation.
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Affiliation(s)
- Raffaella Roncone
- Dipartimento di Chimica Generale, Università di Pavia, Via Taramelli 12, 27100 Pavia, Italy
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25
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Carey JR, Ma SK, Pfister TD, Garner DK, Kim HK, Abramite JA, Wang Z, Guo Z, Lu Y. A site-selective dual anchoring strategy for artificial metalloprotein design. J Am Chem Soc 2004; 126:10812-3. [PMID: 15339144 DOI: 10.1021/ja046908x] [Citation(s) in RCA: 191] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Introducing nonnative metal ions or metal-containing prosthetic groups into a protein can dramatically expand the repertoire of its functionalities and thus its range of applications. Particularly challenging is the control of substrate-binding and thus reaction selectivity such as enantioselectivity. To meet this challenge, both non-covalent and single-point attachments of metal complexes have been demonstrated previously. Since the protein template did not evolve to bind artificial metal complexes tightly in a single conformation, efforts to restrict conformational freedom by modifying the metal complexes and/or the protein are required to achieve high enantioselectivity using the above two strategies. Here we report a novel site-selective dual anchoring (two-point covalent attachment) strategy to introduce an achiral manganese salen complex (Mn(salen)), into apo sperm whale myoglobin (Mb) with bioconjugation yield close to 100%. The enantioselective excess increases from 0.3% for non-covalent, to 12.3% for single point, and to 51.3% for dual anchoring attachments. The dual anchoring method has the advantage of restricting the conformational freedom of the metal complex in the protein and can be generally applied to protein incorporation of other metal complexes with minimal structural modification to either the metal complex or the protein.
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Affiliation(s)
- James R Carey
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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26
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Abstract
The first full assignment of (1)H NMR chemical shifts for iron corroles and the first synthesis of a series of (halogeno)iron corroles reveal very large effects of the axial ligands on the corresponding spectra, which apparently reflect differences in the relative importance of metal-to-corrole and corrole-to-metal pi-donation. These findings pave the way for a thorough analysis of the electronic structures of such complexes.
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Affiliation(s)
- Liliya Simkhovich
- Department of Chemistry and Institute of Catalysis Science and Technology, Technion - Israel Institute of Technology, Haifa 32000, Israel
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27
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Affiliation(s)
- Charles J Reedy
- Department of Chemistry, Columbia University, 3000 Broadway, MC 3121, New York, New York 10027, USA
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28
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Roncone R, Monzani E, Nicolis S, Casella L. Engineering and Prosthetic‐Group Modification of Myoglobin: Peroxidase Activity, Chemical Stability and Unfolding Properties. Eur J Inorg Chem 2004. [DOI: 10.1002/ejic.200400126] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Raffaella Roncone
- Dipartimento di Chimica Generale, Via Taramelli 12, 27100 Pavia, Italy, Fax: (internat.) +39‐0382‐528544
| | - Enrico Monzani
- Dipartimento di Chimica Generale, Via Taramelli 12, 27100 Pavia, Italy, Fax: (internat.) +39‐0382‐528544
| | - Stefania Nicolis
- Dipartimento di Chimica Generale, Via Taramelli 12, 27100 Pavia, Italy, Fax: (internat.) +39‐0382‐528544
| | - Luigi Casella
- Dipartimento di Chimica Generale, Via Taramelli 12, 27100 Pavia, Italy, Fax: (internat.) +39‐0382‐528544
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29
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Matsunaga I, Shiro Y. Peroxide-utilizing biocatalysts: structural and functional diversity of heme-containing enzymes. Curr Opin Chem Biol 2004; 8:127-32. [PMID: 15062772 DOI: 10.1016/j.cbpa.2004.01.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Heme-containing enzymes, such as peroxidases, catalase and peroxygenase P450 all utilize peroxides for their specific reactions. A variety of reactions catalyzed by such heme-containing enzymes involve a common, highly reactive intermediate, the so-called compound I (oxo-ferryl porphyrin pi-cation radical), which is generated via the reaction of peroxide with a ferric heme iron. However, the main reaction catalyzed by the heme-containing enzyme is determined by the accessibility of substrates to their active sites. Using the accumulated knowledge, we delineate a view, in which machineries of the heme-containing enzymes, especially the heme distal side structures, precisely regulate their functions in terms of sharing a common reactive intermediate. We also show the possibility that a hemoprotein of one functionality can be engineered to that with another functionality by modifying the heme distal side elements, on the basis of molecular-based mechanistic and structural data on these peroxide-utilizing enzymes.
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Affiliation(s)
- Isamu Matsunaga
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
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30
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Watanabe Y, Ueno T. Introduction of P450, Peroxidase, and Catalase Activities into Myoglobin by Site-Directed Mutagenesis: Diverse Reactivities of Compound I. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2003. [DOI: 10.1246/bcsj.76.1309] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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31
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Sigman JA, Kim HK, Zhao X, Carey JR, Lu Y. The role of copper and protons in heme-copper oxidases: kinetic study of an engineered heme-copper center in myoglobin. Proc Natl Acad Sci U S A 2003; 100:3629-34. [PMID: 12655052 PMCID: PMC152973 DOI: 10.1073/pnas.0737308100] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To probe the role of copper and protons in heme-copper oxidase (HCO), we have performed kinetic studies on an engineered heme-copper center in sperm whale myoglobin (Leu-29 --> HisPhe-43 --> His, called Cu(B)Mb) that closely mimics the heme-copper center in HCO. In the absence of metal ions, the engineered Cu(B) center in Cu(B)Mb decreases the O(2) binding affinity of the heme. However, addition of Ag(I), a redox-inactive mimic of Cu(I), increases the O(2)-binding affinity. More importantly, copper ion in the Cu(B) center is essential for O(2) reduction, as no O(2) reduction can be observed in copper-free, Zn(II), or Ag(I) derivatives of Cu(B)Mb. Instead of producing a ferryl-heme as in HCO, the Cu(B)Mb generates verdoheme because the engineered Cu(B)Mb may lack a hydrogen bonding network that delivers protons to promote the heterolytic OO cleavage necessary for the formation of ferryl-heme. Reaction of oxidized Cu(B)Mb with H(2)O(2), a species equivalent in oxidation state to 2e(-), reduced O(2) but, possessing the extra protons, resulted in ferryl-heme formation, as in HCO. The results showed that the Cu(B) center plays a critical role in O(2) binding and reduction, and that proton delivery during the O(2) reduction is important to avoid heme degradation and to promote the HCO reaction.
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Affiliation(s)
- Jeffrey A Sigman
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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32
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Abstract
Advances in bioinorganic chemistry since the 1970s have been driven by three factors: rapid determination of high-resolution structures of proteins and other biomolecules, utilization of powerful spectroscopic tools for studies of both structures and dynamics, and the widespread use of macromolecular engineering to create new biologically relevant structures. Today, very large molecules can be manipulated at will, with the result that certain proteins and nucleic acids themselves have become versatile model systems for elucidating biological function.
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Affiliation(s)
- Harry B Gray
- Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA.
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