1
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Shin HE, Pan C, Curran DM, Bateman TJ, Chong DHY, Ng D, Shah M, Moraes TF. Prevalence of Slam-dependent hemophilins in Gram-negative bacteria. J Bacteriol 2024; 206:e0002724. [PMID: 38814789 DOI: 10.1128/jb.00027-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 05/08/2024] [Indexed: 06/01/2024] Open
Abstract
Iron acquisition systems are crucial for pathogen growth and survival in iron-limiting host environments. To overcome nutritional immunity, bacterial pathogens evolved to use diverse mechanisms to acquire iron. Here, we examine a heme acquisition system that utilizes hemophores called hemophilins which are also referred to as HphAs in several Gram-negative bacteria. In this study, we report three new HphA structures from Stenotrophomonas maltophilia, Vibrio harveyi, and Haemophilus parainfluenzae. Structural determination of HphAs revealed an N-terminal clamp-like domain that binds heme and a C-terminal eight-stranded β-barrel domain that shares the same architecture as the Slam-dependent Neisserial surface lipoproteins. The genetic organization of HphAs consists of genes encoding a Slam homolog and a TonB-dependent receptor (TBDR). We investigated the Slam-HphA system in the native organism or the reconstituted system in Escherichia coli cells and found that the efficient secretion of HphA depends on Slam. The TBDR also played an important role in heme uptake and conferred specificity for its cognate HphA. Furthermore, bioinformatic analysis of HphA homologs revealed that HphAs are conserved in the alpha, beta, and gammaproteobacteria. Together, these results show that the Slam-dependent HphA-type hemophores are prevalent in Gram-negative bacteria and further expand the role of Slams in transporting soluble proteins. IMPORTANCE This paper describes the structure and function of a family of Slam (Type IX secretion System) secreted hemophores that bacteria use to uptake heme (iron) while establishing an infection. Using structure-based bioinformatics analysis to define the diversity and prevalence of this heme acquisition pathway, we discovered that a large portion of gammaproteobacterial harbors this system. As organisms, including Acinetobacter baumannii, utilize this system to facilitate survival during host invasion, the identification of this heme acquisition system in bacteria species is valuable information and may represent a target for antimicrobials.
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Affiliation(s)
- Hyejin Esther Shin
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Chuxi Pan
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - David M Curran
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Thomas J Bateman
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Derrick H Y Chong
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Dixon Ng
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Megha Shah
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Trevor F Moraes
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
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2
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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: 132] [Impact Index Per Article: 22.0] [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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3
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Biosynthetic approach to modeling and understanding metalloproteins using unnatural amino acids. Sci China Chem 2016. [DOI: 10.1007/s11426-016-0343-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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4
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Bhagi-Damodaran A, Petrik I, Lu Y. Using Biosynthetic Models of Heme-Copper Oxidase and Nitric Oxide Reductase in Myoglobin to Elucidate Structural Features Responsible for Enzymatic Activities. Isr J Chem 2016; 56:773-790. [PMID: 27994254 PMCID: PMC5161413 DOI: 10.1002/ijch.201600033] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
In biology, a heme-Cu center in heme-copper oxidases (HCOs) is used to catalyze the four-electron reduction of oxygen to water, while a heme-nonheme diiron center in nitric oxide reductases (NORs) is employed to catalyze the two-electron reduction of nitric oxide to nitrous oxide. Although much progress has been made in biochemical and biophysical studies of HCOs and NORs, structural features responsible for similarities and differences within the two enzymatic systems remain to be understood. Here, we discuss the progress made in the design and characterization of myoglobin-based enzyme models of HCOs and NORs. In particular, we focus on use of these models to understand the structure-function relations between HCOs and NORs, including the role of nonheme metals, conserved amino acids in the active site, heme types and hydrogen-bonding network in tuning enzymatic activities and total turnovers. Insights gained from these studies are summarized and future directions are proposed.
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Affiliation(s)
| | - Igor Petrik
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL. 61801
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL. 61801
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5
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Yu Y, Cui C, Liu X, Petrik ID, Wang J, Lu Y. A Designed Metalloenzyme Achieving the Catalytic Rate of a Native Enzyme. J Am Chem Soc 2015; 137:11570-3. [PMID: 26318313 PMCID: PMC4676421 DOI: 10.1021/jacs.5b07119] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Terminal
oxidases catalyze four-electron reduction of oxygen to
water, and the energy harvested is utilized to drive the synthesis
of adenosine triphosphate. While much effort has been made to design
a catalyst mimicking the function of terminal oxidases, most biomimetic
catalysts have much lower activity than native oxidases. Herein we
report a designed oxidase in myoglobin with an O2 reduction
rate (52 s–1) comparable to that of a native cytochrome
(cyt) cbb3 oxidase (50 s–1) under identical conditions. We achieved this goal by engineering
more favorable electrostatic interactions between a functional oxidase
model designed in sperm whale myoglobin and its native redox partner,
cyt b5, resulting in a 400-fold electron
transfer (ET) rate enhancement. Achieving high activity equivalent
to that of native enzymes in a designed metalloenzyme offers deeper
insight into the roles of tunable processes such as ET in oxidase
activity and enzymatic function and may extend into applications such
as more efficient oxygen reduction reaction catalysts for biofuel
cells.
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Affiliation(s)
| | | | - Xiaohong Liu
- Laboratory of Non-coding RNA, Institute of Biophysics, Chinese Academy of Sciences , 15 Datun Road, Chaoyang District, Beijing 100101, P. R. China
| | | | - Jiangyun Wang
- Laboratory of Non-coding RNA, Institute of Biophysics, Chinese Academy of Sciences , 15 Datun Road, Chaoyang District, Beijing 100101, P. R. China
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6
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Yu Y, Lv X, Li J, Zhou Q, Cui C, Hosseinzadeh P, Mukherjee A, Nilges MJ, Wang J, Lu Y. Defining the role of tyrosine and rational tuning of oxidase activity by genetic incorporation of unnatural tyrosine analogs. J Am Chem Soc 2015; 137:4594-7. [PMID: 25672571 PMCID: PMC4676419 DOI: 10.1021/ja5109936] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Indexed: 12/31/2022]
Abstract
While a conserved tyrosine (Tyr) is found in oxidases, the roles of phenol ring pKa and reduction potential in O2 reduction have not been defined despite many years of research on numerous oxidases and their models. These issues represent major challenges in our understanding of O2 reduction mechanism in bioenergetics. Through genetic incorporation of unnatural amino acid analogs of Tyr, with progressively decreasing pKa of the phenol ring and increasing reduction potential, in the active site of a functional model of oxidase in myoglobin, a linear dependence of both the O2 reduction activity and the fraction of H2O formation with the pKa of the phenol ring has been established. By using these unnatural amino acids as spectroscopic probe, we have provided conclusive evidence for the location of a Tyr radical generated during reaction with H2O2, by the distinctive hyperfine splitting patterns of the halogenated tyrosines and one of its deuterated derivatives incorporated at the 33 position of the protein. These results demonstrate for the first time that enhancing the proton donation ability of the Tyr enhances the oxidase activity, allowing the Tyr analogs to augment enzymatic activity beyond that of natural Tyr.
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Affiliation(s)
- Yang Yu
- Center of Biophysics and Computational Biology, Department of Chemistry, Department of Biochemistry, Illinois EPR Research
Center, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Xiaoxuan Lv
- Laboratory
of Non-Coding RNA, Institute of Biophysics, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, P. R. China
- University of Chinese
Academy of Sciences, Beijing 100049, P. R. China
| | - Jiasong Li
- Laboratory
of Non-Coding RNA, Institute of Biophysics, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, P. R. China
- University of Chinese
Academy of Sciences, Beijing 100049, P. R. China
| | - Qing Zhou
- Laboratory
of Non-Coding RNA, Institute of Biophysics, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, P. R. China
- University of Chinese
Academy of Sciences, Beijing 100049, P. R. China
| | - Chang Cui
- Center of Biophysics and Computational Biology, Department of Chemistry, Department of Biochemistry, Illinois EPR Research
Center, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Parisa Hosseinzadeh
- Center of Biophysics and Computational Biology, Department of Chemistry, Department of Biochemistry, Illinois EPR Research
Center, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Arnab Mukherjee
- Center of Biophysics and Computational Biology, Department of Chemistry, Department of Biochemistry, Illinois EPR Research
Center, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Mark J. Nilges
- Center of Biophysics and Computational Biology, Department of Chemistry, Department of Biochemistry, Illinois EPR Research
Center, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Jiangyun Wang
- Laboratory
of Non-Coding RNA, Institute of Biophysics, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, P. R. China
- University of Chinese
Academy of Sciences, Beijing 100049, P. R. China
| | - Yi Lu
- Center of Biophysics and Computational Biology, Department of Chemistry, Department of Biochemistry, Illinois EPR Research
Center, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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7
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Bill NL, Trukhina O, Sessler JL, Torres T. Supramolecular electron transfer-based switching involving pyrrolic macrocycles. A new approach to sensor development? Chem Commun (Camb) 2015; 51:7781-94. [DOI: 10.1039/c4cc10193f] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The potential utility of energy transfer in the design of pyrrolic macrocycle-based molecular switches and ability to serve as the readout motif for molecular sensors development is discussed.
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Affiliation(s)
- Nathan L. Bill
- Departamento de Química Orgánica
- Facultad de Ciencias
- Universidad Autónoma de Madrid
- 28049-Madrid
- Spain
| | - Olga Trukhina
- Departamento de Química Orgánica
- Facultad de Ciencias
- Universidad Autónoma de Madrid
- 28049-Madrid
- Spain
| | | | - Tomás Torres
- Departamento de Química Orgánica
- Facultad de Ciencias
- Universidad Autónoma de Madrid
- 28049-Madrid
- Spain
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8
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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: 68] [Impact Index Per Article: 6.8] [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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9
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Yu Y, Mukherjee A, Nilges MJ, Hosseinzadeh P, Miner KD, Lu Y. Direct EPR observation of a tyrosyl radical in a functional oxidase model in myoglobin during both H2O2 and O2 reactions. J Am Chem Soc 2014; 136:1174-1177. [PMID: 24383850 PMCID: PMC3955430 DOI: 10.1021/ja4091885] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Tyrosine is a conserved redox-active amino acid that plays important roles in heme-copper oxidases (HCO). Despite the widely proposed mechanism that involves a tyrosyl radical, its direct observation under O2 reduction conditions remains elusive. Using a functional oxidase model in myoglobin called F33Y-Cu(B)Mb that contains an engineered tyrosine, we report herein direct observation of a tyrosyl radical during both reactions of H2O2 with oxidized protein and O2 with reduced protein by electron paramagnetic resonance spectroscopy, providing a firm support for the tyrosyl radical in the HCO enzymatic mechanism.
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Affiliation(s)
- Yang Yu
- Center for Biophysics and Computational Biology, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
| | - Arnab Mukherjee
- Department of Chemistry, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
| | - Mark J. Nilges
- The Illinois EPR Research Center, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
| | - Parisa Hosseinzadeh
- Department of Biochemistry, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
| | - Kyle D. Miner
- Department of Biochemistry, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
| | - Yi Lu
- Center for Biophysics and Computational Biology, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
- Department of Biochemistry, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
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10
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Lin Y, Wang J, Lu Y. Functional tuning and expanding of myoglobin by rational protein design. Sci China Chem 2014. [DOI: 10.1007/s11426-014-5063-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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11
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Dong SS, Du KJ, You Y, Liu F, Wen GB, Lin YW. Peroxidase-like activity of L29H myoglobin with two cooperative distal histidines on electrode using O2 as an oxidant. J Electroanal Chem (Lausanne) 2013. [DOI: 10.1016/j.jelechem.2013.09.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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12
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Hunter CL, Mauk AG. Engineered metalloregulation of azide binding affinity and reduction potential of horse heart myoglobin. Dalton Trans 2013; 42:3151-5. [PMID: 23250011 DOI: 10.1039/c2dt32558f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Metal ion binding to a previously reported variant of horse heart myoglobin (Lys45Glu/Lys63Glu) with a metal ion binding site on the surface of the protein that is adjacent to the haem binding site has been shown to influence ligand binding and electrochemical properties of the protein. For example, the K(d) (μM) for binding of azide to this variant decreases from 277 ± 9 to 32 ± 3 following addition of a saturating concentration of Mn(2+) (the value for the wild-type protein under the same conditions is 26 ± 1). Similarly, the midpoint reduction potential E(m) (mV vs. standard hydrogen electrode) increases from 9 to 40 in the presence of a saturating concentration of Mn(2+) (the value for the wild-type protein under the same conditions is 45 ± 2). These results demonstrate the potential value of engineered metal ion binding sites as a means of regulating the functional properties of even simple haem proteins.
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13
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Nienhaus K, Olson JS, Nienhaus GU. An engineered heme-copper center in myoglobin: CO migration and binding. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1824-31. [PMID: 23459127 DOI: 10.1016/j.bbapap.2013.02.031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 02/19/2013] [Accepted: 02/20/2013] [Indexed: 11/19/2022]
Abstract
We have investigated CO migration and binding in CuBMb, a copper-binding myoglobin double mutant (L29H-F43H), by using Fourier transform infrared spectroscopy and flash photolysis over a wide temperature range. This mutant was originally engineered with the aim to mimic the catalytic site of heme-copper oxidases. Comparison of the wild-type protein Mb and CuBMb shows that the copper ion in the distal pocket gives rise to significant effects on ligand binding to the heme iron. In Mb and copper-free CuBMb, primary and secondary ligand docking sites are accessible upon photodissociation. In copper-bound CuBMb, ligands do not migrate to secondary docking sites but rather coordinate to the copper ion. Ligands entering the heme pocket from the outside normally would not be captured efficiently by the tight distal pocket housing the two additional large imidazole rings. Binding at the Cu ion, however, ensures efficient trapping in CuBMb. The Cu ion also restricts the motions of the His64 side chain, which is the entry/exit door for ligand movement into the active site, and this restriction results in enhanced geminate and slow bimolecular CO rebinding. These results support current mechanistic views of ligand binding in hemoglobins and the role of the CuB in the active of heme-copper oxidases. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins.
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Affiliation(s)
- Karin Nienhaus
- Institute of Applied Physics and Center for Functional Nanostructures, Karlsruhe Institute of Technology, Karlsruhe, Germany
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14
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Miner KD, Mukherjee A, Gao YG, Null EL, Petrik ID, Zhao X, Yeung N, Robinson H, Lu Y. A Designed Functional Metalloenzyme that Reduces O2to H2O with Over One Thousand Turnovers. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201201981] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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15
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Miner KD, Mukherjee A, Gao YG, Null EL, Petrik ID, Zhao X, Yeung N, Robinson H, Lu Y. A designed functional metalloenzyme that reduces O2 to H2O with over one thousand turnovers. Angew Chem Int Ed Engl 2012; 51:5589-92. [PMID: 22539151 DOI: 10.1002/anie.201201981] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Indexed: 11/09/2022]
Affiliation(s)
- Kyle D Miner
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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16
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Park JS, Karnas E, Ohkubo K, Chen P, Kadish KM, Fukuzumi S, Bielawski CW, Hudnall TW, Lynch VM, Sessler JL. Ion-Mediated Electron Transfer in a Supramolecular Donor-Acceptor Ensemble. Science 2010; 329:1324-7. [DOI: 10.1126/science.1192044] [Citation(s) in RCA: 146] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Jung Su Park
- Department of Chemistry and Biochemistry, University Station-A5300, University of Texas, Austin, TX 78712–0165, USA
| | - Elizabeth Karnas
- Department of Chemistry and Biochemistry, University Station-A5300, University of Texas, Austin, TX 78712–0165, USA
| | - Kei Ohkubo
- Department of Material and Life Science, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| | - Ping Chen
- Department of Chemistry, University of Houston, Houston, TX 77204–5003, USA
| | - Karl M. Kadish
- Department of Chemistry, University of Houston, Houston, TX 77204–5003, USA
| | - Shunichi Fukuzumi
- Department of Material and Life Science, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
- Department of Bioinspired Science, Ewha Womans University, Seoul 120-750, Korea
| | - Christopher W. Bielawski
- Department of Chemistry and Biochemistry, University Station-A5300, University of Texas, Austin, TX 78712–0165, USA
| | - Todd W. Hudnall
- Department of Chemistry and Biochemistry, University Station-A5300, University of Texas, Austin, TX 78712–0165, USA
| | - Vincent M. Lynch
- Department of Chemistry and Biochemistry, University Station-A5300, University of Texas, Austin, TX 78712–0165, USA
| | - Jonathan L. Sessler
- Department of Chemistry and Biochemistry, University Station-A5300, University of Texas, Austin, TX 78712–0165, USA
- Department of Chemistry, Yonsei University, Seoul 120-749, Korea
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17
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Yeung N, Lu Y. One heme, diverse functions: using biosynthetic myoglobin models to gain insights into heme-copper oxidases and nitric oxide reductases. Chem Biodivers 2008; 5:1437-1454. [PMID: 18729107 PMCID: PMC2770894 DOI: 10.1002/cbdv.200890134] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Natasha Yeung
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801, USA
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801, USA
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18
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Cañon-Mancisidor W, Spodine E, Venegas-Yazigi D, Rojas D, Manzur J, Alvarez S. Electrochemical Behavior of Copper Complexes with Substituted Polypyridinic Ligands: An Experimental and Theoretical Study. Inorg Chem 2008; 47:3687-92. [PMID: 18366154 DOI: 10.1021/ic702104u] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | | | | | | | - Santiago Alvarez
- Departamento de Química Inorgànica i Centre de Recerca en Química Teòrica, Universitat de Barcelona, Barcelona, Spain
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19
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Zhao X, Yeung N, Russell BS, Garner DK, Lu Y. Catalytic reduction of NO to N2O by a designed heme copper center in myoglobin: implications for the role of metal ions. J Am Chem Soc 2007; 128:6766-7. [PMID: 16719438 PMCID: PMC2531162 DOI: 10.1021/ja058822p] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The effects of metal ions on the reduction of nitric oxide (NO) with a designed heme copper center in myoglobin (F43H/L29H sperm whale Mb, CuBMb) were investigated under reducing anaerobic conditions using UV-vis and EPR spectroscopic techniques as well as GC/MS. In the presence of Cu(I), catalytic reduction of NO to N2O by CuBMb was observed with turnover number of 2 mol NO.mol CuBMb-1.min-1, close to 3 mol NO.mol enzyme-1.min-1 reported for the ba3 oxidases from T. thermophilus. Formation of a His-heme-NO species was detected by UV-vis and EPR spectroscopy. In comparison to the EPR spectra of ferrous-CuBMb-NO in the absence of metal ions, the EPR spectra of ferrous-CuBMb-NO in the presence of Cu(I) showed less-resolved hyperfine splitting from the proximal histidine, probably due to weakening of the proximal His-heme bond. In the presence of Zn(II), formation of a five-coordinate ferrous-CuBMb-NO species, resulting from cleavage of the proximal heme Fe-His bond, was shown by UV-vis and EPR spectroscopic studies. The reduction of NO to N2O was not observed in the presence of Zn(II). Control experiments using wild-type myoglobin indicated no reduction of NO in the presence of either Cu(I) or Zn(II). These results suggest that both the identity and the oxidation state of the metal ion in the CuB center are important for NO reduction. A redox-active metal ion is required to deliver electrons, and a higher oxidation state is preferred to weaken the heme iron-proximal histidine toward a five-coordinate key intermediate in NO reduction.
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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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Abstract
Inorganic chemistry and biology can benefit greatly from each other. Although synthetic and physical inorganic chemistry have been greatly successful in clarifying the role of metal ions in biological systems, the time may now be right to utilize biological systems to advance coordination chemistry. One such example is the use of small, stable, easy-to-make, and well-characterized proteins as ligands to synthesize novel inorganic compounds. This biosynthetic inorganic chemistry is possible thanks to a number of developments in biology. This review summarizes the progress in the synthesis of close models of complex metalloproteins, followed by a description of recent advances in using the approach for making novel compounds that are unprecedented in either inorganic chemistry or biology. The focus is mainly on synthetic "tricks" learned from biology, as well as novel structures and insights obtained. The advantages and disadvantages of this biosynthetic approach are discussed.
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Affiliation(s)
- Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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