1
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Murali R, Pace LA, Sanford RA, Ward LM, Lynes MM, Hatzenpichler R, Lingappa UF, Fischer WW, Gennis RB, Hemp J. Diversity and evolution of nitric oxide reduction in bacteria and archaea. Proc Natl Acad Sci U S A 2024; 121:e2316422121. [PMID: 38900790 PMCID: PMC11214002 DOI: 10.1073/pnas.2316422121] [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: 09/27/2023] [Accepted: 04/24/2024] [Indexed: 06/22/2024] Open
Abstract
Nitrous oxide is a potent greenhouse gas whose production is catalyzed by nitric oxide reductase (NOR) members of the heme-copper oxidoreductase (HCO) enzyme superfamily. We identified several previously uncharacterized HCO families, four of which (eNOR, sNOR, gNOR, and nNOR) appear to perform NO reduction. These families have novel active-site structures and several have conserved proton channels, suggesting that they might be able to couple NO reduction to energy conservation. We isolated and biochemically characterized a member of the eNOR family from the bacterium Rhodothermus marinus and found that it performs NO reduction. These recently identified NORs exhibited broad phylogenetic and environmental distributions, greatly expanding the diversity of microbes in nature capable of NO reduction. Phylogenetic analyses further demonstrated that NORs evolved multiple times independently from oxygen reductases, supporting the view that complete denitrification evolved after aerobic respiration.
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Affiliation(s)
- Ranjani Murali
- Department of Biochemistry, University of Illinois, Urbana-Champaign, Urbana, IL61801
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA91125
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV89154
| | - Laura A. Pace
- Department of Biochemistry, University of Illinois, Urbana-Champaign, Urbana, IL61801
- meliora.bio, Salt Lake City, UT84103
| | - Robert A. Sanford
- Department of Earth Science and Environmental Change, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - L. M. Ward
- Department of Geosciences, Smith College, Northampton, MA01063
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA91125
| | - Mackenzie M. Lynes
- Department of Chemistry and Biochemistry, Thermal Biology Institute, Montana State University, Bozeman, MT59717
- Center for Biofilm Enginering, Montana State University, Bozeman, MT59717
| | - Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Thermal Biology Institute, Montana State University, Bozeman, MT59717
- Center for Biofilm Enginering, Montana State University, Bozeman, MT59717
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT59717
| | - Usha F. Lingappa
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA91125
- Department of Plant and Microbial Biology, University of California, Berkeley, CA94720
| | - Woodward W. Fischer
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA91125
| | - Robert B. Gennis
- Department of Biochemistry, University of Illinois, Urbana-Champaign, Urbana, IL61801
| | - James Hemp
- meliora.bio, Salt Lake City, UT84103
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA91125
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2
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Single atomic Ru in TiO 2 boost efficient electrocatalytic water oxidation to hydrogen peroxide. Sci Bull (Beijing) 2023; 68:613-621. [PMID: 36914544 DOI: 10.1016/j.scib.2023.03.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/05/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023]
Abstract
Electrocatalytic two-electron water oxidation affords a promising approach for distributed production of H2O2 using electricity. However, it suffers from the trade-off between the selectivity and high production rate of H2O2 due to the lack of suitable electrocatalysts. In this study, single atoms of Ru were controllably introduced into titanium dioxide to produce H2O2 through an electrocatalytic two-electron water oxidation reaction. The adsorption energy values of OH intermediates could be tuned by introducing Ru single atoms, offering superior H2O2 production under high current density. Notably, a Faradaic efficiency of 62.8% with an H2O2 production rate of 24.2 μmol min-1 cm-2 (>400 ppm within 10 min) was achieved at a current density of 120 mA cm-2. Consequently, herein, the possibility of high-yield H2O2 production under high current density was demonstrated and the importance of regulating intermediate adsorption during electrocatalysis was evidenced.
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3
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Murali R, Hemp J, Gennis RB. Evolution of quinol oxidation within the heme‑copper oxidoreductase superfamily. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2022; 1863:148907. [PMID: 35944661 DOI: 10.1016/j.bbabio.2022.148907] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 07/09/2022] [Accepted: 08/02/2022] [Indexed: 06/15/2023]
Abstract
The heme‑copper oxidoreductase (HCO) superfamily is a large superfamily of terminal respiratory enzymes that are widely distributed across the three domains of life. The superfamily includes biochemically diverse oxygen reductases and nitric oxide reductases that are pivotal in the pathways of aerobic respiration and denitrification. The adaptation of HCOs to use quinol as the electron donor instead of cytochrome c has significant implication for the respiratory flexibility and energetic efficiency of the respiratory chains that include them. In this work, we explore the adaptation of this scaffold to two different electron donors, cytochromes c and quinols, with extensive sequence analysis of these enzymes from publicly available datasets. Our work shows that quinol oxidation evolved independently within the HCO superfamily at least seven times. Enzymes from only two of these independently evolved clades have been biochemically well-characterized. Combining structural modeling with sequence analysis, we identify putative quinol binding sites in each of the novel quinol oxidases. Our analysis of experimental and modeling data suggests that the quinol binding site appears to have evolved at the same structural position within the scaffold more than once.
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Affiliation(s)
- Ranjani Murali
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91106, USA.
| | - James Hemp
- Metrodora Institute, West Valley City, UT, USA 84119.
| | - Robert B Gennis
- Department of Biochemistry, University of Illinois, Urbana-Champaign, Urbana, IL 61801, USA.
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4
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Rational Design of an Artificial Nuclease by Engineering a Hetero-Dinuclear Center of Mg-Heme in Myoglobin. ACS Catal 2020. [DOI: 10.1021/acscatal.0c04572] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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5
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Lin YW. Rational Design of Artificial Metalloproteins and Metalloenzymes with Metal Clusters. Molecules 2019; 24:E2743. [PMID: 31362341 PMCID: PMC6696605 DOI: 10.3390/molecules24152743] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 07/24/2019] [Accepted: 07/26/2019] [Indexed: 01/22/2023] Open
Abstract
Metalloproteins and metalloenzymes play important roles in biological systems by using the limited metal ions, complexes, and clusters that are associated with the protein matrix. The design of artificial metalloproteins and metalloenzymes not only reveals the structure and function relationship of natural proteins, but also enables the synthesis of artificial proteins and enzymes with improved properties and functions. Acknowledging the progress in rational design from single to multiple active sites, this review focuses on recent achievements in the design of artificial metalloproteins and metalloenzymes with metal clusters, including zinc clusters, cadmium clusters, iron-sulfur clusters, and copper-sulfur clusters, as well as noble metal clusters and others. These metal clusters were designed in both native and de novo protein scaffolds for structural roles, electron transfer, or catalysis. Some synthetic metal clusters as functional models of native enzymes are also discussed. These achievements provide valuable insights for deep understanding of the natural proteins and enzymes, and practical clues for the further design of artificial enzymes with functions comparable or even beyond those of natural counterparts.
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Affiliation(s)
- Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China.
- Laboratory of Protein Structure and Function, University of South China, Hengyang 421001, China.
- Hunan Key Laboratory for the Design and Application of Actinide Complexes, University of South China, Hengyang 421001, China.
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6
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Heme redox potentials hold the key to reactivity differences between nitric oxide reductase and heme-copper oxidase. Proc Natl Acad Sci U S A 2018; 115:6195-6200. [PMID: 29802230 DOI: 10.1073/pnas.1720298115] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Despite high structural homology between NO reductases (NORs) and heme-copper oxidases (HCOs), factors governing their reaction specificity remain to be understood. Using a myoglobin-based model of NOR (FeBMb) and tuning its heme redox potentials (E°') to cover the native NOR range, through manipulating hydrogen bonding to the proximal histidine ligand and replacing heme b with monoformyl (MF-) or diformyl (DF-) hemes, we herein demonstrate that the E°' holds the key to reactivity differences between NOR and HCO. Detailed electrochemical, kinetic, and vibrational spectroscopic studies, in tandem with density functional theory calculations, demonstrate a strong influence of heme E°' on NO reduction. Decreasing E°' from +148 to -130 mV significantly impacts electronic properties of the NOR mimics, resulting in 180- and 633-fold enhancements in NO association and heme-nitrosyl decay rates, respectively. Our results indicate that NORs exhibit finely tuned E°' that maximizes their enzymatic efficiency and helps achieve a balance between opposite factors: fast NO binding and decay of dinitrosyl species facilitated by low E°' and fast electron transfer facilitated by high E°'. Only when E°' is optimally tuned in FeBMb(MF-heme) for NO binding, heme-nitrosyl decay, and electron transfer does the protein achieve multiple (>35) turnovers, previously not achieved by synthetic or enzyme-based NOR models. This also explains a long-standing question in bioenergetics of selective cross-reactivity in HCOs. Only HCOs with heme E°' in a similar range as NORs (between -59 and 200 mV) exhibit NOR reactivity. Thus, our work demonstrates efficient tuning of E°' in various metalloproteins for their optimal functionality.
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7
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Reed JH, Shi Y, Zhu Q, Chakraborty S, Mirts EN, Petrik ID, Bhagi-Damodaran A, Ross M, Moënne-Loccoz P, Zhang Y, Lu Y. Manganese and Cobalt in the Nonheme-Metal-Binding Site of a Biosynthetic Model of Heme-Copper Oxidase Superfamily Confer Oxidase Activity through Redox-Inactive Mechanism. J Am Chem Soc 2017; 139:12209-12218. [PMID: 28768416 PMCID: PMC5673108 DOI: 10.1021/jacs.7b05800] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The presence of a nonheme metal, such as copper and iron, in the heme-copper oxidase (HCO) superfamily is critical to the enzymatic activity of reducing O2 to H2O, but the exact mechanism the nonheme metal ion uses to confer and fine-tune the activity remains to be understood. We herein report that manganese and cobalt can bind to the same nonheme site and confer HCO activity in a heme-nonheme biosynthetic model in myoglobin. While the initial rates of O2 reduction by the Mn, Fe, and Co derivatives are similar, the percentages of reactive oxygen species (ROS) formation are 7%, 4%, and 1% and the total turnovers are 5.1 ± 1.1, 13.4 ± 0.7, and 82.5 ± 2.5, respectively. These results correlate with the trends of nonheme-metal-binding dissociation constants (35, 22, and 9 μM) closely, suggesting that tighter metal binding can prevent ROS release from the active site, lessen damage to the protein, and produce higher total turnover numbers. Detailed spectroscopic, electrochemical, and computational studies found no evidence of redox cycling of manganese or cobalt in the enzymatic reactions and suggest that structural and electronic effects related to the presence of different nonheme metals lead to the observed differences in reactivity. This study of the roles of nonheme metal ions beyond the Cu and Fe found in native enzymes has provided deeper insights into nature's choice of metal ion and reaction mechanism and allows for finer control of the enzymatic activity, which is a basis for the design of efficient catalysts for the oxygen reduction reaction in fuel cells.
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Affiliation(s)
- Julian H. Reed
- Department of Biochemistry, University of Illinois at
Urbana-Champaign, Urbana, IL, 61801, USA
| | - Yelu Shi
- Department of Biomedical Engineering, Chemistry, and Biological
Sciences, Stevens Institute of Technology, Hoboken, NJ, 07030, USA
| | - Qianhong Zhu
- Division of Environmental & Biomolecular Systems, Institute
of Environmental Health, Oregon Health & Science University, Portland, OR,
97239, USA
| | - Saumen Chakraborty
- Department of Chemistry & Biochemistry, University of
Mississippi, Oxford, Mississippi, 38677, USA
| | - Evan N. Mirts
- Center for Biophysics and Quantitative Biology, University of
Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Igor D. Petrik
- Department of Chemistry, University of Illinois at Urbana-Champaign,
Urbana, IL, 61801, USA
| | - Ambika Bhagi-Damodaran
- Department of Pharmaceutical Chemistry, University of California,
San Francisco, San Francisco, CA, 94143, USA
| | - Matthew Ross
- Department of Chemistry, Northwestern University, Evanston, IL,
60208, USA
| | - Pierre Moënne-Loccoz
- Division of Environmental & Biomolecular Systems, Institute
of Environmental Health, Oregon Health & Science University, Portland, OR,
97239, USA
| | - Yong Zhang
- Department of Biomedical Engineering, Chemistry, and Biological
Sciences, Stevens Institute of Technology, Hoboken, NJ, 07030, USA
| | - Yi Lu
- Department of Biochemistry, University of Illinois at
Urbana-Champaign, Urbana, IL, 61801, USA
- Center for Biophysics and Quantitative Biology, University of
Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign,
Urbana, IL, 61801, USA
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8
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Schwizer F, Okamoto Y, Heinisch T, Gu Y, Pellizzoni MM, Lebrun V, Reuter R, Köhler V, Lewis JC, Ward TR. Artificial Metalloenzymes: Reaction Scope and Optimization Strategies. Chem Rev 2017; 118:142-231. [PMID: 28714313 DOI: 10.1021/acs.chemrev.7b00014] [Citation(s) in RCA: 490] [Impact Index Per Article: 70.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The incorporation of a synthetic, catalytically competent metallocofactor into a protein scaffold to generate an artificial metalloenzyme (ArM) has been explored since the late 1970's. Progress in the ensuing years was limited by the tools available for both organometallic synthesis and protein engineering. Advances in both of these areas, combined with increased appreciation of the potential benefits of combining attractive features of both homogeneous catalysis and enzymatic catalysis, led to a resurgence of interest in ArMs starting in the early 2000's. Perhaps the most intriguing of potential ArM properties is their ability to endow homogeneous catalysts with a genetic memory. Indeed, incorporating a homogeneous catalyst into a genetically encoded scaffold offers the opportunity to improve ArM performance by directed evolution. This capability could, in turn, lead to improvements in ArM efficiency similar to those obtained for natural enzymes, providing systems suitable for practical applications and greater insight into the role of second coordination sphere interactions in organometallic catalysis. Since its renaissance in the early 2000's, different aspects of artificial metalloenzymes have been extensively reviewed and highlighted. Our intent is to provide a comprehensive overview of all work in the field up to December 2016, organized according to reaction class. Because of the wide range of non-natural reactions catalyzed by ArMs, this was done using a functional-group transformation classification. The review begins with a summary of the proteins and the anchoring strategies used to date for the creation of ArMs, followed by a historical perspective. Then follows a summary of the reactions catalyzed by ArMs and a concluding critical outlook. This analysis allows for comparison of similar reactions catalyzed by ArMs constructed using different metallocofactor anchoring strategies, cofactors, protein scaffolds, and mutagenesis strategies. These data will be used to construct a searchable Web site on ArMs that will be updated regularly by the authors.
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Affiliation(s)
- Fabian Schwizer
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Yasunori Okamoto
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Tillmann Heinisch
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Yifan Gu
- Searle Chemistry Laboratory, University of Chicago , 5735 S. Ellis Ave., Chicago, Illinois 60637, United States
| | - Michela M Pellizzoni
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Vincent Lebrun
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Raphael Reuter
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Valentin Köhler
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Jared C Lewis
- Searle Chemistry Laboratory, University of Chicago , 5735 S. Ellis Ave., Chicago, Illinois 60637, United States
| | - Thomas R Ward
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
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9
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Hu S, He B, Du KJ, Wang XJ, Gao SQ, Lin YW. Peroxidase Activity of a c-Type Cytochrome b5 in the Non-Native State is Comparable to that of Native Peroxidases. ChemistryOpen 2017. [PMID: 28638761 PMCID: PMC5474653 DOI: 10.1002/open.201700055] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The design of artificial metalloenzymes has achieved tremendous progress, although few designs can achieve catalytic performances comparable to that of native enzymes. Moreover, the structure and function of artificial metalloenzymes in non‐native states has rarely been explored. Herein, we found that a c‐type cytochrome b5 (Cyt b5), N57C/S71C Cyt b5, with heme covalently attached to the protein matrix through two Cys–heme linkages, adopts a non‐native state with an open heme site after guanidine hydrochloride (Gdn⋅HCl)‐induced unfolding, which facilitates H2O2 activation and substrate binding. Stopped‐flow kinetic studies further revealed that c‐type Cyt b5 in the non‐native state exhibited impressive peroxidase activity comparable to that of native peroxidases, such as the most efficient horseradish peroxidase. This study presents an alternative approach to the design of functional artificial metalloenzymes by exploring enzymatic functions in non‐native states.
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Affiliation(s)
- Shan Hu
- School of Chemistry and Chemical Engineering University of South China Hengyang 421001 P.R. China
| | - Bo He
- School of Chemistry and Chemical Engineering University of South China Hengyang 421001 P.R. China
| | - Ke-Jie Du
- School of Chemistry and Chemical Engineering University of South China Hengyang 421001 P.R. China
| | - Xiao-Juan Wang
- School of Chemistry and Chemical Engineering University of South China Hengyang 421001 P.R. China
| | - Shu-Qin Gao
- Laboratory of Protein Structure and Function University of South China Hengyang 421001 P.R. China
| | - Ying-Wu Lin
- School of Chemistry and Chemical Engineering University of South China Hengyang 421001 P.R. China.,Laboratory of Protein Structure and Function University of South China Hengyang 421001 P.R. China
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10
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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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11
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Nastri F, Chino M, Maglio O, Bhagi-Damodaran A, Lu Y, Lombardi A. Design and engineering of artificial oxygen-activating metalloenzymes. Chem Soc Rev 2016; 45:5020-54. [PMID: 27341693 PMCID: PMC5021598 DOI: 10.1039/c5cs00923e] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Many efforts are being made in the design and engineering of metalloenzymes with catalytic properties fulfilling the needs of practical applications. Progress in this field has recently been accelerated by advances in computational, molecular and structural biology. This review article focuses on the recent examples of oxygen-activating metalloenzymes, developed through the strategies of de novo design, miniaturization processes and protein redesign. Considerable progress in these diverse design approaches has produced many metal-containing biocatalysts able to adopt the functions of native enzymes or even novel functions beyond those found in Nature.
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Affiliation(s)
- Flavia Nastri
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia, 80126 Naples, Italy
| | - Marco Chino
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia, 80126 Naples, Italy
| | - Ornella Maglio
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia, 80126 Naples, Italy
- IBB, CNR, Via Mezzocannone 16, 80134 Naples, Italy
| | - Ambika Bhagi-Damodaran
- Department of Chemistry, University of Illinois at Urbana-Champaign, A322 CLSL, 600 South Mathews Avenue, Urbana, IL 61801
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, A322 CLSL, 600 South Mathews Avenue, Urbana, IL 61801
| | - Angela Lombardi
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia, 80126 Naples, Italy
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12
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Bhagi-Damodaran A, Hosseinzadeh P, Mirts E, Reed J, Petrik ID, Lu Y. Design of Heteronuclear Metalloenzymes. Methods Enzymol 2016; 580:501-37. [PMID: 27586347 PMCID: PMC5156654 DOI: 10.1016/bs.mie.2016.05.050] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Heteronuclear metalloenzymes catalyze some of the most fundamentally interesting and practically useful reactions in nature. However, the presence of two or more metal ions in close proximity in these enzymes makes them more difficult to prepare and study than homonuclear metalloenzymes. To meet these challenges, heteronuclear metal centers have been designed into small and stable proteins with rigid scaffolds to understand how these heteronuclear centers are constructed and the mechanism of their function. This chapter describes methods for designing heterobinuclear metal centers in a protein scaffold by giving specific examples of a few heme-nonheme bimetallic centers engineered in myoglobin and cytochrome c peroxidase. We provide step-by-step procedures on how to choose the protein scaffold, design a heterobinuclear metal center in the protein scaffold computationally, incorporate metal ions into the protein, and characterize the resulting metalloproteins, both structurally and functionally. Finally, we discuss how an initial design can be further improved by rationally tuning its secondary coordination sphere, electron/proton transfer rates, and the substrate affinity.
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Affiliation(s)
- A Bhagi-Damodaran
- University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - P Hosseinzadeh
- University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - E Mirts
- University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - J Reed
- University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - I D Petrik
- University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Y Lu
- University of Illinois at Urbana-Champaign, Urbana, IL, United States.
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13
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Lo FC, Hsieh CC, Maestre-Reyna M, Chen CY, Ko TP, Horng YC, Lai YC, Chiang YW, Chou CM, Chiang CH, Huang WN, Lin YH, Bohle DS, Liaw WF. Crystal Structure Analysis of the Repair of Iron Centers Protein YtfE and Its Interaction with NO. Chemistry 2016; 22:9768-76. [DOI: 10.1002/chem.201600990] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Indexed: 11/07/2022]
Affiliation(s)
- Feng-Chun Lo
- Department of Chemistry; National Tsing Hua University; Hsinchu 30013 Taiwan
| | - Chang-Chih Hsieh
- Department of Chemistry; National Tsing Hua University; Hsinchu 30013 Taiwan
| | | | - Chin-Yu Chen
- Department of Life Sciences; National Central University; Taoyuan Taiwan
| | - Tzu-Ping Ko
- Institute of Biological Chemistry; Academia Sinica; Taipei Taiwan
| | - Yih-Chern Horng
- Department of Chemistry; National Changhua University of Education; Changhua Taiwan
| | - Yei-Chen Lai
- Department of Chemistry; National Tsing Hua University; Hsinchu 30013 Taiwan
| | - Yun-Wei Chiang
- Department of Chemistry; National Tsing Hua University; Hsinchu 30013 Taiwan
| | - Chih-Mao Chou
- Department of Life Sciences; National Central University; Taoyuan Taiwan
| | | | - Wei-Ning Huang
- Department of Biotechnology; Yuanpei University; Hsinchu Taiwan
| | - Yi-Hung Lin
- National Synchrotron Radiation Research Center Hsinchu; Taiwan
| | - D. Scott Bohle
- Department of Chemistry; McGill University; 801 Sherbrooke Street West Montreal QC H3A2K6 Canada
| | - Wen-Feng Liaw
- Department of Chemistry; National Tsing Hua University; Hsinchu 30013 Taiwan
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14
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Wu LB, Yuan H, Zhou H, Gao SQ, Nie CM, Tan X, Wen GB, Lin YW. An intramolecular disulfide bond designed in myoglobin fine-tunes both protein structure and peroxidase activity. Arch Biochem Biophys 2016; 600:47-55. [DOI: 10.1016/j.abb.2016.04.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 04/12/2016] [Accepted: 04/23/2016] [Indexed: 01/08/2023]
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15
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Wu LB, Yuan H, Gao SQ, You Y, Nie CM, Wen GB, Lin YW, Tan X. Regulating the nitrite reductase activity of myoglobin by redesigning the heme active center. Nitric Oxide 2016; 57:21-29. [PMID: 27108710 DOI: 10.1016/j.niox.2016.04.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 04/13/2016] [Accepted: 04/20/2016] [Indexed: 10/21/2022]
Abstract
Heme proteins perform diverse functions in living systems, of which nitrite reductase (NIR) activity receives much attention recently. In this study, to better understand the structural elements responsible for the NIR activity, we used myoglobin (Mb) as a model heme protein and redesigned the heme active center, by introducing one or two distal histidines, and by creating a channel to the heme center with removal of the native distal His64 gate (His to Ala mutation). UV-Vis kinetic studies, combined with EPR studies, showed that a single distal histidine with a suitable position to the heme iron, i.e., His43, is crucial for nitrite (NO2(-)) to nitric oxide (NO) reduction. Moreover, creation of a water channel to the heme center significantly enhanced the NIR activity compared to the corresponding mutant without the channel. In addition, X-ray crystallographic studies of F43H/H64A Mb and its complexes with NO2(-) or NO revealed a unique hydrogen-bonding network in the heme active center, as well as unique substrate and product binding models, providing valuable structural information for the enhanced NIR activity. These findings enriched our understanding of the structure and NIR activity relationship of heme proteins. The approach of creating a channel in this study is also useful for rational design of other functional heme proteins.
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Affiliation(s)
- Lei-Bin Wu
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
| | - Hong Yuan
- Department of Chemistry & Institute of Biomedical Science, Fudan University, Shanghai 200433, China
| | - Shu-Qin Gao
- Laboratory of Protein Structure and Function, University of South China, Hengyang 421001, China
| | - Yong You
- Laboratory of Protein Structure and Function, University of South China, Hengyang 421001, China
| | - Chang-Ming Nie
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
| | - Ge-Bo Wen
- Laboratory of Protein Structure and Function, University of South China, Hengyang 421001, China
| | - Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China; Laboratory of Protein Structure and Function, University of South China, Hengyang 421001, China.
| | - Xiangshi Tan
- Department of Chemistry & Institute of Biomedical Science, Fudan University, Shanghai 200433, China.
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16
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Chuang CH, Liaw WF, Hung CH. Conversion of Nitric Oxide into Nitrous Oxide as Triggered by the Polarization of Coordinated NO by Hydrogen Bonding. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201512063] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Chuan-Hung Chuang
- Institute of Chemistry; Academia Sinica; Nankang 11529 Taipei Taiwan
- Department of Chemistry; National Tsing Hua University; Hsinchu 30013 Taiwan
| | - Wen-Feng Liaw
- Department of Chemistry; National Tsing Hua University; Hsinchu 30013 Taiwan
| | - Chen-Hsiung Hung
- Institute of Chemistry; Academia Sinica; Nankang 11529 Taipei Taiwan
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17
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Chuang CH, Liaw WF, Hung CH. Conversion of Nitric Oxide into Nitrous Oxide as Triggered by the Polarization of Coordinated NO by Hydrogen Bonding. Angew Chem Int Ed Engl 2016; 55:5190-4. [DOI: 10.1002/anie.201512063] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 02/08/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Chuan-Hung Chuang
- Institute of Chemistry; Academia Sinica; Nankang 11529 Taipei Taiwan
- Department of Chemistry; National Tsing Hua University; Hsinchu 30013 Taiwan
| | - Wen-Feng Liaw
- Department of Chemistry; National Tsing Hua University; Hsinchu 30013 Taiwan
| | - Chen-Hsiung Hung
- Institute of Chemistry; Academia Sinica; Nankang 11529 Taipei Taiwan
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18
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Świderek K, Tuñón I, Moliner V, Bertran J. Computational strategies for the design of new enzymatic functions. Arch Biochem Biophys 2015; 582:68-79. [PMID: 25797438 PMCID: PMC4554825 DOI: 10.1016/j.abb.2015.03.013] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 03/09/2015] [Accepted: 03/13/2015] [Indexed: 11/28/2022]
Abstract
In this contribution, recent developments in the design of biocatalysts are reviewed with particular emphasis in the de novo strategy. Studies based on three different reactions, Kemp elimination, Diels-Alder and Retro-Aldolase, are used to illustrate different success achieved during the last years. Finally, a section is devoted to the particular case of designed metalloenzymes. As a general conclusion, the interplay between new and more sophisticated engineering protocols and computational methods, based on molecular dynamics simulations with Quantum Mechanics/Molecular Mechanics potentials and fully flexible models, seems to constitute the bed rock for present and future successful design strategies.
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Affiliation(s)
- K Świderek
- Departament de Química Física, Universitat de València, 46100 Burjasot, Spain; Institute of Applied Radiation Chemistry, Lodz University of Technology, 90-924 Lodz, Poland
| | - I Tuñón
- Departament de Química Física, Universitat de València, 46100 Burjasot, Spain
| | - V Moliner
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castellón, Spain
| | - J Bertran
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
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19
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Manganese-Substituted Myoglobin: Characterization and Reactivity of an Oxidizing Intermediate towards a Weak C-H Bond. INORGANICS 2015. [DOI: 10.3390/inorganics3020219] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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20
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Muñoz Robles V, Ortega-Carrasco E, Alonso-Cotchico L, Rodriguez-Guerra J, Lledós A, Maréchal JD. Toward the Computational Design of Artificial Metalloenzymes: From Protein–Ligand Docking to Multiscale Approaches. ACS Catal 2015. [DOI: 10.1021/acscatal.5b00010] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Victor Muñoz Robles
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola
del Vallès, Barcelona, Spain
| | - Elisabeth Ortega-Carrasco
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola
del Vallès, Barcelona, Spain
| | - Lur Alonso-Cotchico
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola
del Vallès, Barcelona, Spain
| | - Jaime Rodriguez-Guerra
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola
del Vallès, Barcelona, Spain
| | - Agustí Lledós
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola
del Vallès, Barcelona, Spain
| | - Jean-Didier Maréchal
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola
del Vallès, Barcelona, Spain
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21
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Hydrogen-bonding network in heme active site regulates the hydrolysis activity of myoglobin. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.molcatb.2014.11.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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22
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Du JF, Li W, Li L, Wen GB, Lin YW, Tan X. Regulating the coordination state of a heme protein by a designed distal hydrogen-bonding network. ChemistryOpen 2014; 4:97-101. [PMID: 25969804 PMCID: PMC4420578 DOI: 10.1002/open.201402108] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Indexed: 01/03/2023] Open
Abstract
Heme coordination state determines the functional diversity of heme proteins. Using myoglobin as a model protein, we designed a distal hydrogen-bonding network by introducing both distal glutamic acid (Glu29) and histidine (His43) residues and regulated the heme into a bis-His coordination state with native ligands His64 and His93. This resembles the heme site in natural bis-His coordinated heme proteins such as cytoglobin and neuroglobin. A single mutation of L29E or F43H was found to form a distinct hydrogen-bonding network involving distal water molecules, instead of the bis-His heme coordination, which highlights the importance of the combination of multiple hydrogen-bonding interactions to regulate the heme coordination state. Kinetic studies further revealed that direct coordination of distal His64 to the heme iron negatively regulates fluoride binding and hydrogen peroxide activation by competing with the exogenous ligands. The new approach developed in this study can be generally applicable for fine-tuning the structure and function of heme proteins.
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Affiliation(s)
- Jun-Fang Du
- School of Chemistry and Chemical Engineering, University of South China Hengyang, 421001, (P. R. China))
| | - Wei Li
- Department of Chemistry and Institute of Biomedical Science, Fudan University Shanghai, 200433, (P. R. China)
| | - Lianzhi Li
- School of Chemistry and Chemical Engineering, Liaocheng University Liaocheng, 252059, (P. R. China)
| | - Ge-Bo Wen
- Laboratory of Protein Structure and Function, University of South China Hengyang, 421001, (P. R. China)
| | - Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China Hengyang, 421001, (P. R. China)) ; Laboratory of Protein Structure and Function, University of South China Hengyang, 421001, (P. R. China)
| | - Xiangshi Tan
- Department of Chemistry and Institute of Biomedical Science, Fudan University Shanghai, 200433, (P. R. China)
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23
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Lin YW, Nagao S, Zhang M, Shomura Y, Higuchi Y, Hirota S. Rational design of heterodimeric protein using domain swapping for myoglobin. Angew Chem Int Ed Engl 2014; 54:511-5. [PMID: 25370865 DOI: 10.1002/anie.201409267] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Indexed: 11/12/2022]
Abstract
Protein design is a useful method to create novel artificial proteins. A rational approach to design a heterodimeric protein using domain swapping for horse myoglobin (Mb) was developed. As confirmed by X-ray crystallographic analysis, a heterodimeric Mb with two different active sites was produced efficiently from two surface mutants of Mb, in which the charges of two amino acids involved in the dimer salt bridges were reversed in each mutant individually, with the active site of one mutant modified. This study shows that the method of constructing heterodimeric Mb with domain swapping is useful for designing artificial multiheme proteins.
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Affiliation(s)
- Ying-Wu Lin
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192 (Japan); School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001 (China)
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24
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Lin YW, Nagao S, Zhang M, Shomura Y, Higuchi Y, Hirota S. Rational Design of Heterodimeric Protein using Domain Swapping for Myoglobin. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201409267] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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25
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You Y, Liu F, Du KJ, Wen GB, Lin YW. Structural and functional alterations of myoglobin by glucose-protein interactions. J Mol Model 2014; 20:2358. [DOI: 10.1007/s00894-014-2358-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2014] [Accepted: 06/15/2014] [Indexed: 11/29/2022]
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26
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Duarte AG, Cordas CM, Moura JJ, Moura I. Steady-state kinetics with nitric oxide reductase (NOR): New considerations on substrate inhibition profile and catalytic mechanism. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:375-84. [DOI: 10.1016/j.bbabio.2014.01.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Revised: 12/28/2013] [Accepted: 01/02/2014] [Indexed: 10/25/2022]
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27
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Metalloenzyme design and engineering through strategic modifications of native protein scaffolds. Curr Opin Chem Biol 2014; 19:67-75. [PMID: 24513641 DOI: 10.1016/j.cbpa.2014.01.006] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 01/03/2014] [Accepted: 01/03/2014] [Indexed: 10/25/2022]
Abstract
Metalloenzymes are among the major targets of protein design and engineering efforts aimed at attaining novel and efficient catalysis for biochemical transformation and biomedical applications, due to the diversity of functions imparted by the metallo-cofactors along with the versatility of the protein environment. Naturally evolved protein scaffolds can often serve as robust foundations for sustaining artificial active sites constructed by rational design, directed evolution, or a combination of the two strategies. Accumulated knowledge of structure-function relationship and advancement of tools such as computational algorithms and unnatural amino acids incorporation all contribute to the design of better metalloenzymes with catalytic properties approaching the needs of practical applications.
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28
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Chakraborty S, Reed J, Ross M, Nilges MJ, Petrik ID, Ghosh S, Hammes-Schiffer S, Sage JT, Zhang Y, Schulz CE, Lu Y. Spectroscopic and Computational Study of a Nonheme Iron Nitrosyl Center in a Biosynthetic Model of Nitric Oxide Reductase. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201308431] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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29
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Chakraborty S, Reed J, Ross M, Nilges MJ, Petrik ID, Ghosh S, Hammes-Schiffer S, Sage JT, Zhang Y, Schulz CE, Lu Y. Spectroscopic and computational study of a nonheme iron nitrosyl center in a biosynthetic model of nitric oxide reductase. Angew Chem Int Ed Engl 2014; 53:2417-21. [PMID: 24481708 DOI: 10.1002/anie.201308431] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 11/27/2013] [Indexed: 11/07/2022]
Abstract
A major barrier to understanding the mechanism of nitric oxide reductases (NORs) is the lack of a selective probe of NO binding to the nonheme FeB center. By replacing the heme in a biosynthetic model of NORs, which structurally and functionally mimics NORs, with isostructural ZnPP, the electronic structure and functional properties of the FeB nitrosyl complex was probed. This approach allowed observation of the first S=3/2 nonheme {FeNO}(7) complex in a protein-based model system of NOR. Detailed spectroscopic and computational studies show that the electronic state of the {FeNO}(7) complex is best described as a high spin ferrous iron (S=2) antiferromagnetically coupled to an NO radical (S=1/2) [Fe(2+)-NO(.)]. The radical nature of the FeB -bound NO would facilitate N-N bond formation by radical coupling with the heme-bound NO. This finding, therefore, supports the proposed trans mechanism of NO reduction by NORs.
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Affiliation(s)
- Saumen Chakraborty
- Department of Chemistry and Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL (USA)
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30
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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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31
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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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32
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Lin YW, Wang J. Structure and function of heme proteins in non-native states: a mini-review. J Inorg Biochem 2013; 129:162-71. [PMID: 23916118 DOI: 10.1016/j.jinorgbio.2013.07.023] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 07/11/2013] [Accepted: 07/13/2013] [Indexed: 12/12/2022]
Abstract
Heme proteins perform various biological functions ranging from electron transfer, oxygen binding and transport, catalysis, to signaling. Although adopting proper native states is very important for these functions, progresses in representative heme proteins, including cytochrome c (cyt c), cytochrome b5 (cyt b5), myoglobin (Mb), neuroglobin (Ngb), cytochrome P450 (CYP) and heme-based sensor proteins such as CO sensor CooA, showed that various native functions, or new functions evolved, are also closely associated with non-native states. The structure and function relationship of heme proteins in non-native states is thus as important as that in native states for elucidating the precise roles of heme proteins in biological systems.
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Affiliation(s)
- Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China.
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33
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Peroxidase activity of a myoglobin mutant with three distal histidines forming a metal-binding site: Implications for the cross-reactivity of cytochrome c oxidase. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.molcatb.2013.02.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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34
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Lin YW, Sawyer EB, Wang J. Rational heme protein design: all roads lead to Rome. Chem Asian J 2013; 8:2534-44. [PMID: 23704071 DOI: 10.1002/asia.201300291] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Indexed: 01/03/2023]
Abstract
Heme proteins are among the most abundant and important metalloproteins, exerting diverse biological functions including oxygen transport, small molecule sensing, selective C-H bond activation, nitrite reduction, and electron transfer. Rational heme protein designs focus on the modification of the heme-binding active site and the heme group, protein hybridization and domain swapping, and de novo design. These strategies not only provide us with unique advantages for illustrating the structure-property-reactivity-function (SPRF) relationship of heme proteins in nature but also endow us with the ability to create novel biocatalysts and biosensors.
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Affiliation(s)
- Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001 (China)
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35
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Sun MH, Li W, Liu JH, Wen GB, Tan X, Lin YW. Structural and nitrite reductase activity comparisons of myoglobins with one to three distal histidines. RSC Adv 2013. [DOI: 10.1039/c3ra40839f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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36
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McLaughlin MP, Retegan M, Bill E, Payne TM, Shafaat HS, Peña S, Sudhamsu J, Ensign AA, Crane BR, Neese F, Holland PL. Azurin as a protein scaffold for a low-coordinate nonheme iron site with a small-molecule binding pocket. J Am Chem Soc 2012; 134:19746-57. [PMID: 23167247 PMCID: PMC3515693 DOI: 10.1021/ja308346b] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The apoprotein of Pseudomonas aeruginosa azurin binds iron(II) to give a 1:1 complex, which has been characterized by electronic absorption, Mössbauer, and NMR spectroscopies, as well as X-ray crystallography and quantum-chemical computations. Despite potential competition by water and other coordinating residues, iron(II) binds tightly to the low-coordinate site. The iron(II) complex does not react with chemical redox agents to undergo oxidation or reduction. Spectroscopically calibrated quantum-chemical computations show that the complex has high-spin iron(II) in a pseudotetrahedral coordination environment, which features interactions with side chains of two histidines and a cysteine as well as the C═O of Gly45. In the (5)A(1) ground state, the d(z(2)) orbital is doubly occupied. Mutation of Met121 to Ala leaves the metal site in a similar environment but creates a pocket for reversible binding of small anions to the iron(II) center. Specifically, azide forms a high-spin iron(II) complex and cyanide forms a low-spin iron(II) complex.
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Affiliation(s)
| | - Marius Retegan
- Max Planck Institute for Chemical Energy Conversion, Mülheim an der Ruhr, Germany
| | - Eckhard Bill
- Max Planck Institute for Chemical Energy Conversion, Mülheim an der Ruhr, Germany
| | - Thomas M. Payne
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853
| | - Hannah S. Shafaat
- Max Planck Institute for Chemical Energy Conversion, Mülheim an der Ruhr, Germany
| | - Salvador Peña
- Department of Chemistry, University of Rochester, Rochester, New York 14618
| | - Jawahar Sudhamsu
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853
| | - Amy A. Ensign
- Department of Chemistry, University of Rochester, Rochester, New York 14618
| | - Brian R. Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853
| | - Frank Neese
- Max Planck Institute for Chemical Energy Conversion, Mülheim an der Ruhr, Germany
| | - Patrick L. Holland
- Department of Chemistry, University of Rochester, Rochester, New York 14618
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37
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Hyster TK, Knörr L, Ward TR, Rovis T. Biotinylated Rh(III) complexes in engineered streptavidin for accelerated asymmetric C-H activation. Science 2012; 338:500-3. [PMID: 23112327 DOI: 10.1126/science.1226132] [Citation(s) in RCA: 645] [Impact Index Per Article: 53.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Enzymes provide an exquisitely tailored chiral environment to foster high catalytic activities and selectivities, but their native structures are optimized for very specific biochemical transformations. Designing a protein to accommodate a non-native transition metal complex can broaden the scope of enzymatic transformations while raising the activity and selectivity of small-molecule catalysis. Here, we report the creation of a bifunctional artificial metalloenzyme in which a glutamic acid or aspartic acid residue engineered into streptavidin acts in concert with a docked biotinylated rhodium(III) complex to enable catalytic asymmetric carbon-hydrogen (C-H) activation. The coupling of benzamides and alkenes to access dihydroisoquinolones proceeds with up to nearly a 100-fold rate acceleration compared with the activity of the isolated rhodium complex and enantiomeric ratios as high as 93:7.
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Affiliation(s)
- Todd K Hyster
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA
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38
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Steiner K, Schwab H. Recent advances in rational approaches for enzyme engineering. Comput Struct Biotechnol J 2012; 2:e201209010. [PMID: 24688651 PMCID: PMC3962183 DOI: 10.5936/csbj.201209010] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 10/16/2012] [Accepted: 10/18/2012] [Indexed: 11/29/2022] Open
Abstract
Enzymes are an attractive alternative in the asymmetric syntheses of chiral building blocks. To meet the requirements of industrial biotechnology and to introduce new functionalities, the enzymes need to be optimized by protein engineering. This article specifically reviews rational approaches for enzyme engineering and de novo enzyme design involving structure-based approaches developed in recent years for improvement of the enzymes’ performance, broadened substrate range, and creation of novel functionalities to obtain products with high added value for industrial applications.
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Affiliation(s)
- Kerstin Steiner
- ACIB GmbH, (Austrian Centre of Industrial Biotechnology), c/o TU Graz, 8010 Graz, Austria
| | - Helmut Schwab
- ACIB GmbH, (Austrian Centre of Industrial Biotechnology), c/o TU Graz, 8010 Graz, Austria ; Institute of Molecular Biotechnology, TU Graz, 8010 Graz, Austria
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39
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Simon J, Klotz MG. Diversity and evolution of bioenergetic systems involved in microbial nitrogen compound transformations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1827:114-35. [PMID: 22842521 DOI: 10.1016/j.bbabio.2012.07.005] [Citation(s) in RCA: 214] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Revised: 07/10/2012] [Accepted: 07/19/2012] [Indexed: 11/18/2022]
Abstract
Nitrogen is an essential element of life that needs to be assimilated in its most reduced form, ammonium. On the other hand, nitrogen exists in a multitude of oxidation states and, consequently, nitrogen compounds (NCs) serve as electron donor and/or acceptors in many catabolic pathways including various forms of microbial respiration that contribute to the global biogeochemical nitrogen cycle. Some of these NCs are also known as reactive nitrogen species able to cause nitrosative stress because of their high redox reactivity. The best understood processes of the nitrogen cycle are denitrification and ammonification (both beginning with nitrate reduction to nitrite), nitrification (aerobic oxidation of ammonium and nitrite) and anaerobic ammonium oxidation (anammox). This review presents examples of the diverse architecture, either elucidated or anticipated, and the high degree of modularity of the corresponding respiratory electron transport processes found in Bacteria and Archaea, and relates these to their respective bioenergetic mechanisms of proton motive force generation. In contrast to the multiplicity of enzymes that catalyze NC transformations, the number of proteins or protein modules involved in connecting electron transport to and from these enzymes with the quinone/quinol pool is comparatively small. These quinone/quinol-reactive protein modules consist of cytochromes b and c and iron-sulfur proteins. Conclusions are drawn towards the evolutionary relationships of bioenergetic systems involved in NC transformation and deduced aspects of the evolution of the biogeochemical nitrogen cycle are presented. This article is part of a Special Issue entitled: The evolutionary aspects of bioenergetic systems.
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Affiliation(s)
- Jörg Simon
- Microbial Energy Conversion and Biotechnology, Department of Biology, Technische Universität Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany.
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