1
|
Bloomer BJ, Clark DS, Hartwig JF. Progress, Challenges, and Opportunities with Artificial Metalloenzymes in Biosynthesis. Biochemistry 2023; 62:221-228. [PMID: 35195998 DOI: 10.1021/acs.biochem.1c00829] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
In this Perspective, we present progress, outstanding challenges, and opportunities for the incorporation of artificial metalloenzymes (ArMs) into biosynthetic pathways. We first explain discoveries within the field of ArMs that led to the potential inclusion of these enzymes in biosynthesis. We then describe the specific barriers that our laboratory, in collaboration with the laboratories of Keasling and Mukhopadhyay, addressed to establish a biosynthetic pathway containing an ArM. This biosynthesis produced an unnatural cyclopropyl terpenoid by combining heterologous production of the terpene with modification of its terminal alkene by an ArM built from a cytochrome P450. Finally, we describe the remaining challenges and opportunities related to the application of ArMs in synthetic biology.
Collapse
Affiliation(s)
- Brandon J Bloomer
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Douglas S Clark
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States.,Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - John F Hartwig
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| |
Collapse
|
2
|
Acevedo-Rocha CG, Hollmann F, Sanchis J, Sun Z. A Pioneering Career in Catalysis: Manfred T. Reetz. ACS Catal 2020. [DOI: 10.1021/acscatal.0c04108] [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]
Affiliation(s)
| | - Frank Hollmann
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Deft, Netherlands
| | - Joaquin Sanchis
- Monash Institute of Pharmaceutical Sciences, Monash University, 399 Royal Parade, Parkville 3052, Victoria, Australia
| | - Zhoutong Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin, 300308 China
| |
Collapse
|
3
|
Zhao H. What do we learn from enzyme behaviors in organic solvents? - Structural functionalization of ionic liquids for enzyme activation and stabilization. Biotechnol Adv 2020; 45:107638. [PMID: 33002582 DOI: 10.1016/j.biotechadv.2020.107638] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 09/05/2020] [Accepted: 09/25/2020] [Indexed: 12/16/2022]
Abstract
Enzyme activity in nonaqueous media (e.g. conventional organic solvents) is typically lower than in water by several orders of magnitude. There is a rising interest of developing new nonaqueous solvent systems that are more "water-like" and more biocompatible. Therefore, we need to learn from the current state of nonaqueous biocatalysis to overcome its bottleneck and provide guidance for new solvent design. This review firstly focuses on the discussion of how organic solvent properties (such as polarity and hydrophobicity) influence the enzyme activity and stability, and how these properties impact the enzyme's conformation and dynamics. While hydrophobic organic solvents usually lead to the maintenance of enzyme activity, solvents carrying functional groups like hydroxys and ethers (including crown ethers and cyclodextrins) can lead to enzyme activation. Ionic liquids (ILs) are designable solvents that can conveniently incorporate these functional groups. Therefore, we systematically survey these ether- and/or hydroxy-functionalized ILs, and find most of them are highly compatible with enzymes leading to high activity and stability. In particular, ILs carrying both ether and tert-alcohol groups are among the most enzyme-activating solvents. Future direction is to learn from enzyme behaviors in both water and nonaqueous media to design biocompatible "water-like" solvents.
Collapse
Affiliation(s)
- Hua Zhao
- Department of Chemistry and Biochemistry, University of Northern Colorado, Greeley, CO 80639, United States.
| |
Collapse
|
4
|
Qu G, Li A, Acevedo‐Rocha CG, Sun Z, Reetz MT. Die zentrale Rolle der Methodenentwicklung in der gerichteten Evolution selektiver Enzyme. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201901491] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Ge Qu
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 China
| | - Aitao Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-resources Hubei Key Laboratory of Industrial Biotechnology College of Life Sciences Hubei University 368 Youyi Road Wuchang Wuhan 430062 China
| | | | - Zhoutong Sun
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 China
| | - Manfred T. Reetz
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 China
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 45470 Mülheim Deutschland
- Department of Chemistry, Hans-Meerwein-Straße 4 Philipps-Universität 35032 Marburg Deutschland
| |
Collapse
|
5
|
Qu G, Li A, Acevedo‐Rocha CG, Sun Z, Reetz MT. The Crucial Role of Methodology Development in Directed Evolution of Selective Enzymes. Angew Chem Int Ed Engl 2020; 59:13204-13231. [PMID: 31267627 DOI: 10.1002/anie.201901491] [Citation(s) in RCA: 246] [Impact Index Per Article: 61.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Indexed: 12/14/2022]
Affiliation(s)
- Ge Qu
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 China
| | - Aitao Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-resources Hubei Key Laboratory of Industrial Biotechnology College of Life Sciences Hubei University 368 Youyi Road Wuchang Wuhan 430062 China
| | | | - Zhoutong Sun
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 China
| | - Manfred T. Reetz
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 China
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 45470 Mülheim Germany
- Department of Chemistry, Hans-Meerwein-Strasse 4 Philipps-University 35032 Marburg Germany
| |
Collapse
|
6
|
Fischer J, Renn D, Quitterer F, Radhakrishnan A, Liu M, Makki A, Ghorpade S, Rueping M, Arold ST, Groll M, Eppinger J. Robust and Versatile Host Protein for the Design and Evaluation of Artificial Metal Centers. ACS Catal 2019. [DOI: 10.1021/acscatal.9b02896] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Johannes Fischer
- Center for Integrated Protein Science, Department Chemie, Lehrstuhl für Biochemie, Technische Universität München (TUM), D-85747 Garching, Germany
| | - Dominik Renn
- Center for Integrated Protein Science, Department Chemie, Lehrstuhl für Biochemie, Technische Universität München (TUM), D-85747 Garching, Germany
| | - Felix Quitterer
- Center for Integrated Protein Science, Department Chemie, Lehrstuhl für Biochemie, Technische Universität München (TUM), D-85747 Garching, Germany
| | | | | | | | | | | | - Stefan T. Arold
- Centre de Biochimie Structurale, CNRS, INSERM, Université de Montpellier, 34090 Montpellier, France
| | - Michael Groll
- Center for Integrated Protein Science, Department Chemie, Lehrstuhl für Biochemie, Technische Universität München (TUM), D-85747 Garching, Germany
| | | |
Collapse
|
7
|
Crocker L, Fruk L. Flavin Conjugated Polydopamine Nanoparticles Displaying Light-Driven Monooxygenase Activity. Front Chem 2019; 7:278. [PMID: 31080793 PMCID: PMC6497766 DOI: 10.3389/fchem.2019.00278] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 04/04/2019] [Indexed: 11/13/2022] Open
Abstract
A hybrid of flavin and polydopamine (PDA) has been explored as a photocatalyst, drawing inspiration from natural flavoenzymes. Light-driven monoxygenase activity has been demonstrated through the oxidation of indole under blue light irradiation in ambient conditions, to afford indigo and indirubin dyes. Compared to riboflavin, a flavin-polydopamine hybrid is shown to be more resistant to photobleaching and more selective toward dye production. In addition, it has been demonstrated that it can be recycled from the solution and used for up to four cycles without a marked loss of activity, which is a significant improvement compared to other heterogenous flavin catalysts. The mechanism of action has been explored, indicating that the PDA shell plays an important role in the stabilization of the intermediate flavin-peroxy species, an active component of the catalytic system rather than acting only as a passive nanocarrier of active centers.
Collapse
Affiliation(s)
- Leander Crocker
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
| | - Ljiljana Fruk
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
| |
Collapse
|
8
|
Reetz MT. Directed Evolution of Artificial Metalloenzymes: A Universal Means to Tune the Selectivity of Transition Metal Catalysts? Acc Chem Res 2019; 52:336-344. [PMID: 30689339 DOI: 10.1021/acs.accounts.8b00582] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Transition metal catalysts mediate a wide variety of chemo-, stereo-, and regioselective transformations, and therefore play a pivotal role in modern synthetic organic chemistry. Steric and electronic effects of ligands provide organic chemists with an exceedingly useful tool. More than four decades ago, chemists began to think about a different approach, namely, embedding achiral ligand/metal moieties covalently or noncovalently in protein hosts with formation of artificial metalloenzymes. While structurally fascinating, this approach led in each case only to a single (bio)catalyst, with its selectivity and activity being a matter of chance. In order to solve this fundamental problem, my group proposed in 2000-2002 the idea of directed evolution of artificial metalloenzymes. In earlier studies, we had already demonstrated that directed evolution of enzymes constitutes a viable method for enhancing and inverting the stereoselectivity of enzymes as catalysts in organic chemistry. We speculated that it should also be possible to manipulate selectivity and activity of artificial metalloenzymes, which would provide organic chemists with a tool for optimizing essentially any transition metal catalyzed reaction type. In order to put this vision into practice, we first turned to the Whitesides system for artificial metalloenzyme formation, comprising a biotinylated diphosphine/Rh moiety, which is anchored noncovalently to avidin or streptavidin. Following intensive optimization, proof of principle was finally demonstrated in 2006, which opened the door to a new research area. This personal Account critically assesses these early studies as well as subsequent efforts from my group focusing on different protein scaffolds, and includes briefly some of the most important current contributions of other groups. Two primary messages emerge: First, since organic chemists continue to be extremely good at designing and implementing man-made transition metal catalysts, often on a large scale, those scientists that are active in the equally intriguing field of directed evolution of artificial metalloenzymes should be moderate when generalizing claims. All factors required for a truly viable catalytic system need to be considered, especially activity and ease of upscaling. Second, the most exciting and thus far very rare cases of directed evolution of artificial metalloenzymes are those that focus on selective transformations that are not readily possible using state of the art transition metal catalysts.
Collapse
Affiliation(s)
- Manfred T. Reetz
- Chemistry Department, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim Germany
| |
Collapse
|
9
|
Hestericová M, Heinisch T, Alonso-Cotchico L, Maréchal JD, Vidossich P, Ward TR. Directed Evolution of an Artificial Imine Reductase. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201711016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Martina Hestericová
- Department Chemistry; University of Basel; Mattenstrasse 24a, BPR 1096 Basel 4002 Switzerland
| | - Tillman Heinisch
- Department Chemistry; University of Basel; Mattenstrasse 24a, BPR 1096 Basel 4002 Switzerland
| | - Lur Alonso-Cotchico
- Departament de Química; Universitat Autònoma de Barcelona; Edifici C.n. 08193 Cerdonyola del Vallès Barcelona Spain
| | - Jean-Didier Maréchal
- Departament de Química; Universitat Autònoma de Barcelona; Edifici C.n. 08193 Cerdonyola del Vallès Barcelona Spain
| | - Pietro Vidossich
- Departament de Química; Universitat Autònoma de Barcelona; Edifici C.n. 08193 Cerdonyola del Vallès Barcelona Spain
| | - Thomas R. Ward
- Department Chemistry; University of Basel; Mattenstrasse 24a, BPR 1096 Basel 4002 Switzerland
| |
Collapse
|
10
|
Hestericová M, Heinisch T, Alonso-Cotchico L, Maréchal JD, Vidossich P, Ward TR. Directed Evolution of an Artificial Imine Reductase. Angew Chem Int Ed Engl 2018; 57:1863-1868. [PMID: 29265726 DOI: 10.1002/anie.201711016] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 12/14/2017] [Indexed: 11/06/2022]
Abstract
Artificial metalloenzymes, resulting from incorporation of a metal cofactor within a host protein, have received increasing attention in the last decade. The directed evolution is presented of an artificial transfer hydrogenase (ATHase) based on the biotin-streptavidin technology using a straightforward procedure allowing screening in cell-free extracts. Two streptavidin isoforms were yielded with improved catalytic activity and selectivity for the reduction of cyclic imines. The evolved ATHases were stable under biphasic catalytic conditions. The X-ray structure analysis reveals that introducing bulky residues within the active site results in flexibility changes of the cofactor, thus increasing exposure of the metal to the protein surface and leading to a reversal of enantioselectivity. This hypothesis was confirmed by a multiscale approach based mostly on molecular dynamics and protein-ligand dockings.
Collapse
Affiliation(s)
- Martina Hestericová
- Department Chemistry, University of Basel, Mattenstrasse 24a, BPR 1096, Basel, 4002, Switzerland
| | - Tillman Heinisch
- Department Chemistry, University of Basel, Mattenstrasse 24a, BPR 1096, Basel, 4002, Switzerland
| | - Lur Alonso-Cotchico
- Departament de Química, Universitat Autònoma de Barcelona, Edifici C.n., 08193, Cerdonyola del Vallès, Barcelona, Spain
| | - Jean-Didier Maréchal
- Departament de Química, Universitat Autònoma de Barcelona, Edifici C.n., 08193, Cerdonyola del Vallès, Barcelona, Spain
| | - Pietro Vidossich
- Departament de Química, Universitat Autònoma de Barcelona, Edifici C.n., 08193, Cerdonyola del Vallès, Barcelona, Spain
| | - Thomas R Ward
- Department Chemistry, University of Basel, Mattenstrasse 24a, BPR 1096, Basel, 4002, Switzerland
| |
Collapse
|
11
|
Deshpande AR, Pochapsky TC, Ringe D. The Metal Drives the Chemistry: Dual Functions of Acireductone Dioxygenase. Chem Rev 2017; 117:10474-10501. [PMID: 28731690 DOI: 10.1021/acs.chemrev.7b00117] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Acireductone dioxygenase (ARD) from the methionine salvage pathway (MSP) is a unique enzyme that exhibits dual chemistry determined solely by the identity of the divalent transition-metal ion (Fe2+ or Ni2+) in the active site. The Fe2+-containing isozyme catalyzes the on-pathway reaction using substrates 1,2-dihydroxy-3-keto-5-methylthiopent-1-ene (acireductone) and dioxygen to generate formate and the ketoacid precursor of methionine, 2-keto-4-methylthiobutyrate, whereas the Ni2+-containing isozyme catalyzes an off-pathway shunt with the same substrates, generating methylthiopropionate, carbon monoxide, and formate. The dual chemistry of ARD was originally discovered in the bacterium Klebsiella oxytoca, but it has recently been shown that mammalian ARD enzymes (mouse and human) are also capable of catalyzing metal-dependent dual chemistry in vitro. This is particularly interesting, since carbon monoxide, one of the products of off-pathway reaction, has been identified as an antiapoptotic molecule in mammals. In addition, several biochemical and genetic studies have indicated an inhibitory role of human ARD in cancer. This comprehensive review describes the biochemical and structural characterization of the ARD family, the proposed experimental and theoretical approaches to establishing mechanisms for the dual chemistry, insights into the mechanism based on comparison with structurally and functionally similar enzymes, and the applications of this research to the field of artificial metalloenzymes and synthetic biology.
Collapse
Affiliation(s)
- Aditi R Deshpande
- Departments of Biochemistry and ‡Chemistry and §the Rosenstiel Institute for Basic Biomedical Research, Brandeis University , Waltham, Massachusetts 02454, United States
| | - Thomas C Pochapsky
- Departments of Biochemistry and ‡Chemistry and §the Rosenstiel Institute for Basic Biomedical Research, Brandeis University , Waltham, Massachusetts 02454, United States
| | - Dagmar Ringe
- Departments of Biochemistry and ‡Chemistry and §the Rosenstiel Institute for Basic Biomedical Research, Brandeis University , Waltham, Massachusetts 02454, United States
| |
Collapse
|
12
|
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: 500] [Impact Index Per Article: 71.4] [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.
Collapse
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
| |
Collapse
|
13
|
Sansiaume-Dagousset E, Urvoas A, Chelly K, Ghattas W, Maréchal JD, Mahy JP, Ricoux R. Neocarzinostatin-based hybrid biocatalysts for oxidation reactions. Dalton Trans 2015; 43:8344-54. [PMID: 24728274 DOI: 10.1039/c4dt00151f] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
An anionic iron(III)-porphyrin-testosterone conjugate 1-Fe has been synthesized and fully characterized. It has been further associated with a neocarzinostatin variant, NCS-3.24, to generate a new artificial metalloenzyme following the so-called 'Trojan Horse' strategy. This new 1-Fe-NCS-3.24 biocatalyst showed an interesting catalytic activity as it was found able to catalyze the chemoselective and slightly enantioselective (ee = 13%) sulfoxidation of thioanisole by H2O2. Molecular modelling studies show that a synergy between the binding of the steroid moiety and that of the porphyrin macrocycle into the protein binding site can explain the experimental results, indicating a better affinity of 1-Fe for the NCS-3.24 variant than testosterone and testosterone-hemisuccinate themselves. They also show that the Fe-porphyrin complex is sandwiched between the two subdomains of the protein providing with good complementarities. However, the artificial cofactor entirely fills the cavity and its metal ion remains widely exposed to the solvent which explains the moderate enantioselectivity observed. Some possible improvements in the "Trojan Horse" strategy for obtaining better catalysts of selective oxidations are presented.
Collapse
Affiliation(s)
- Elodie Sansiaume-Dagousset
- Institut de Chimie Moléculaire et des Matériaux d'Orsay, UMR 8182 CNRS, Laboratoire de Chimie Bioorganique et Bioinorganique, Bât. 420, Université Paris-sud, 91405 Orsay Cedex, France.
| | | | | | | | | | | | | |
Collapse
|
14
|
Currin A, Swainston N, Day PJ, Kell DB. Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently. Chem Soc Rev 2015; 44:1172-239. [PMID: 25503938 PMCID: PMC4349129 DOI: 10.1039/c4cs00351a] [Citation(s) in RCA: 256] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Indexed: 12/21/2022]
Abstract
The amino acid sequence of a protein affects both its structure and its function. Thus, the ability to modify the sequence, and hence the structure and activity, of individual proteins in a systematic way, opens up many opportunities, both scientifically and (as we focus on here) for exploitation in biocatalysis. Modern methods of synthetic biology, whereby increasingly large sequences of DNA can be synthesised de novo, allow an unprecedented ability to engineer proteins with novel functions. However, the number of possible proteins is far too large to test individually, so we need means for navigating the 'search space' of possible protein sequences efficiently and reliably in order to find desirable activities and other properties. Enzymologists distinguish binding (Kd) and catalytic (kcat) steps. In a similar way, judicious strategies have blended design (for binding, specificity and active site modelling) with the more empirical methods of classical directed evolution (DE) for improving kcat (where natural evolution rarely seeks the highest values), especially with regard to residues distant from the active site and where the functional linkages underpinning enzyme dynamics are both unknown and hard to predict. Epistasis (where the 'best' amino acid at one site depends on that or those at others) is a notable feature of directed evolution. The aim of this review is to highlight some of the approaches that are being developed to allow us to use directed evolution to improve enzyme properties, often dramatically. We note that directed evolution differs in a number of ways from natural evolution, including in particular the available mechanisms and the likely selection pressures. Thus, we stress the opportunities afforded by techniques that enable one to map sequence to (structure and) activity in silico, as an effective means of modelling and exploring protein landscapes. Because known landscapes may be assessed and reasoned about as a whole, simultaneously, this offers opportunities for protein improvement not readily available to natural evolution on rapid timescales. Intelligent landscape navigation, informed by sequence-activity relationships and coupled to the emerging methods of synthetic biology, offers scope for the development of novel biocatalysts that are both highly active and robust.
Collapse
Affiliation(s)
- Andrew Currin
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
| | - Neil Swainston
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- School of Computer Science , The University of Manchester , Manchester M13 9PL , UK
| | - Philip J. Day
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- Faculty of Medical and Human Sciences , The University of Manchester , Manchester M13 9PT , UK
| | - Douglas B. Kell
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
| |
Collapse
|
15
|
Mahy JP, Maréchal JD, Ricoux R. Various strategies for obtaining oxidative artificial hemoproteins with a catalytic oxidative activity: from "Hemoabzymes" to "Hemozymes"? J PORPHYR PHTHALOCYA 2015. [DOI: 10.1142/s1088424614500813] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The design of artificial hemoproteins that could lead to new biocatalysts for selective oxidation reactions using clean oxidants such as O 2 or H 2 O 2 under ecocompatible conditions constitutes a really promising challenge for a wide range of industrial applications. In vivo, such reactions are performed by heme-thiolate proteins, cytochromes P450, that catalyze the oxidation of drugs by dioxygen in the presence of electrons delivered from NADPH by cytochrome P450 reductase. Several strategies were used to design new artificial hemoproteins to mimic these enzymes, that associate synthetic metalloporphyrin derivatives to a protein that is supposed to induce a selectivity in the catalyzed reaction. A first generation of artificial hemoproteins or "hemoabzymes" was obtained by the non-covalent association of synthetic hemes such as N-methyl-mesoporphyrin IX, Fe(III) -α3β-tetra-o-carboxyphenylporphyrin or microperoxidase 8 with monoclonal antibodies raised against these cofactors. The obtained antibody-metalloporphyrin complexes displayed a peroxidase activity and some of them catalyzed the regio-selective nitration of phenols by H 2 O 2/ NO 2 and the stereo-selective oxidation of sulphides by H 2 O 2. A second generation of artificial hemoproteins or "hemozymes", was obtained by the non-covalent association of non-relevant proteins with metalloporphyrin derivatives. Several strategies were used, the most successful of which, named "host-guest" strategy involved the non-covalent incorporation of metalloporphyrin derivatives into easily affordable proteins. The artificial hemoproteins obtained were found to be able to perform efficiently the stereoselective oxidation of organic compounds such as sulphides and alkenes by H 2 O 2 and KHSO 5.
Collapse
Affiliation(s)
- Jean-Pierre Mahy
- Institut de Chimie Moléculaire et des Matériaux d'Orsay, UMR 8182 CNRS, Laboratoire de Chimie, Bioorganique et Bioinorganique, Bât. 420, Université Paris-sud, 91405 Orsay Cedex, France
| | - Jean-Didier Maréchal
- Departament de Química, Universitat Autònoma de Barcelona, Edifici C.n., 08193 Cerdonyola del Vallès, Barcelona, Spain
| | - Rémy Ricoux
- Institut de Chimie Moléculaire et des Matériaux d'Orsay, UMR 8182 CNRS, Laboratoire de Chimie, Bioorganique et Bioinorganique, Bât. 420, Université Paris-sud, 91405 Orsay Cedex, France
| |
Collapse
|
16
|
Mahy JP, Maréchal JD, Ricoux R. From “hemoabzymes” to “hemozymes”: towards new biocatalysts for selective oxidations. Chem Commun (Camb) 2015; 51:2476-94. [DOI: 10.1039/c4cc08169b] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Two generations of artificial hemoproteins have been obtained: “hemoabzymes”, by non-covalent association of synthetic hemes with monoclonal antibodies raised against these cofactors and “hemozymes”, by non-covalent association of non-relevant proteins with metalloporphyrin derivatives. A review of the different strategies employed as well as their structural and catalytic properties is presented here.
Collapse
Affiliation(s)
- J.-P. Mahy
- Institut de Chimie Moléculaire et des Matériaux d'Orsay
- UMR 8182 CNRS
- Laboratoire de Chimie Bioorganique et Bioinorganique
- 91435 Orsay Cedex
- France
| | - J.-D. Maréchal
- Departament de Química
- Universitat Autònoma de Barcelona
- Barcelona
- Spain
| | - R. Ricoux
- Institut de Chimie Moléculaire et des Matériaux d'Orsay
- UMR 8182 CNRS
- Laboratoire de Chimie Bioorganique et Bioinorganique
- 91435 Orsay Cedex
- France
| |
Collapse
|
17
|
Basauri-Molina M, Riemersma CF, Würdemann MA, Kleijn H, Klein Gebbink RJM. Lipase active site covalent anchoring of Rh(NHC) catalysts: towards chemoselective artificial metalloenzymes. Chem Commun (Camb) 2015; 51:6792-5. [DOI: 10.1039/c4cc09700a] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Artificial metallo-enzymes derived from active site-inhibited lipases show chemoselective reactivity in catalytic hydrogenations. Embedding of a non-natural metallic center leads to full and competitive selectivity.
Collapse
Affiliation(s)
- M. Basauri-Molina
- Organic Chemistry and Catalysis
- Debye Institute for Nanomaterials Science
- Utrecht University
- 3584CG Utrecht
- The Netherlands
| | - C. F. Riemersma
- Organic Chemistry and Catalysis
- Debye Institute for Nanomaterials Science
- Utrecht University
- 3584CG Utrecht
- The Netherlands
| | - M. A. Würdemann
- Organic Chemistry and Catalysis
- Debye Institute for Nanomaterials Science
- Utrecht University
- 3584CG Utrecht
- The Netherlands
| | - H. Kleijn
- Organic Chemistry and Catalysis
- Debye Institute for Nanomaterials Science
- Utrecht University
- 3584CG Utrecht
- The Netherlands
| | - R. J. M. Klein Gebbink
- Organic Chemistry and Catalysis
- Debye Institute for Nanomaterials Science
- Utrecht University
- 3584CG Utrecht
- The Netherlands
| |
Collapse
|
18
|
|
19
|
Zhao J, Kardashliev T, Joëlle Ruff A, Bocola M, Schwaneberg U. Lessons from diversity of directed evolution experiments by an analysis of 3,000 mutations. Biotechnol Bioeng 2014; 111:2380-9. [DOI: 10.1002/bit.25302] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 05/14/2014] [Accepted: 05/27/2014] [Indexed: 12/20/2022]
Affiliation(s)
- Jing Zhao
- Lehrstuhl für Biotechnologie; RWTH Aachen University; Worringerweg 3 52074 Aachen Germany
| | - Tsvetan Kardashliev
- Lehrstuhl für Biotechnologie; RWTH Aachen University; Worringerweg 3 52074 Aachen Germany
| | - Anna Joëlle Ruff
- Lehrstuhl für Biotechnologie; RWTH Aachen University; Worringerweg 3 52074 Aachen Germany
| | - Marco Bocola
- Lehrstuhl für Biotechnologie; RWTH Aachen University; Worringerweg 3 52074 Aachen Germany
| | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie; RWTH Aachen University; Worringerweg 3 52074 Aachen Germany
| |
Collapse
|
20
|
Urvoas A, Ghattas W, Maréchal JD, Avenier F, Bellande F, Mao W, Ricoux R, Mahy JP. Neocarzinostatin-based hybrid biocatalysts with a RNase like activity. Bioorg Med Chem 2014; 22:5678-86. [PMID: 24984934 DOI: 10.1016/j.bmc.2014.05.063] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 05/24/2014] [Accepted: 05/28/2014] [Indexed: 11/16/2022]
Abstract
A new zinc(II)-cofactor coupled to a testosterone anchor, zinc(II)-N,N-bis(2-pyridylmethyl)-1,3-diamino-propa-2-ol-N'(17'-succinimidyltestosterone) (Zn-Testo-BisPyPol) 1-Zn has been synthesized and fully characterized. It has been further associated with a neocarzinostatin variant, NCS-3.24, to generate a new artificial metalloenzyme following the so-called 'Trojan horse' strategy. This new 1-Zn-NCS-3.24 biocatalyst showed an interesting catalytic activity as it was found able to catalyze the hydrolysis of the RNA model HPNP with a good catalytic efficiency (kcat/KM=13.6M(-1)s(-1) at pH 7) that places it among the best artificial catalysts for this reaction. Molecular modeling studies showed that a synergy between the binding of the steroid moiety and that of the BisPyPol into the protein binding site can explain the experimental results, indicating a better affinity of 1-Zn for the NCS-3.24 variant than testosterone and testosterone-hemisuccinate themselves. They also show that the artificial cofactor entirely fills the cavity, the testosterone part of 1-Zn being bound to one the two subdomains of the protein providing with good complementarities whereas its metal ion remains widely exposed to the solvent which made it a valuable tool for the catalysis of hydrolysis reactions, such as that of HPNP. Some possible improvements in the 'Trojan horse' strategy for obtaining better catalysts of selective reactions will be further studied.
Collapse
Affiliation(s)
- Agathe Urvoas
- Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, UMR 8619 CNRS, Laboratoire de Modélisation et d'Ingénierie des Protéines, Bât. 430, Université Paris XI, 91405 Orsay Cedex, France
| | - Wadih Ghattas
- Institut de Chimie Moléculaire et des Matériaux d'Orsay, UMR 8182 CNRS, Laboratoire de Chimie Bioorganique et Bioinorganique, Bât. 420, Université Paris-sud, 91405 Orsay Cedex, France
| | - Jean-Didier Maréchal
- Departament de Química, Universitat Autònoma de Barcelona, Edifici C.n., Cerdonyola del Vallès, 08193 Barcelona, Spain
| | - Frédéric Avenier
- Institut de Chimie Moléculaire et des Matériaux d'Orsay, UMR 8182 CNRS, Laboratoire de Chimie Bioorganique et Bioinorganique, Bât. 420, Université Paris-sud, 91405 Orsay Cedex, France
| | - Felix Bellande
- Institut de Chimie Moléculaire et des Matériaux d'Orsay, UMR 8182 CNRS, Laboratoire de Chimie Bioorganique et Bioinorganique, Bât. 420, Université Paris-sud, 91405 Orsay Cedex, France
| | - Wei Mao
- Institut de Chimie Moléculaire et des Matériaux d'Orsay, UMR 8182 CNRS, Laboratoire de Chimie Bioorganique et Bioinorganique, Bât. 420, Université Paris-sud, 91405 Orsay Cedex, France
| | - Rémy Ricoux
- Institut de Chimie Moléculaire et des Matériaux d'Orsay, UMR 8182 CNRS, Laboratoire de Chimie Bioorganique et Bioinorganique, Bât. 420, Université Paris-sud, 91405 Orsay Cedex, France.
| | - Jean-Pierre Mahy
- Institut de Chimie Moléculaire et des Matériaux d'Orsay, UMR 8182 CNRS, Laboratoire de Chimie Bioorganique et Bioinorganique, Bât. 420, Université Paris-sud, 91405 Orsay Cedex, France.
| |
Collapse
|
21
|
Raynal M, Ballester P, Vidal-Ferran A, van Leeuwen PWNM. Supramolecular catalysis. Part 2: artificial enzyme mimics. Chem Soc Rev 2013; 43:1734-87. [PMID: 24365792 DOI: 10.1039/c3cs60037h] [Citation(s) in RCA: 673] [Impact Index Per Article: 61.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The design of artificial catalysts able to compete with the catalytic proficiency of enzymes is an intense subject of research. Non-covalent interactions are thought to be involved in several properties of enzymatic catalysis, notably (i) the confinement of the substrates and the active site within a catalytic pocket, (ii) the creation of a hydrophobic pocket in water, (iii) self-replication properties and (iv) allosteric properties. The origins of the enhanced rates and high catalytic selectivities associated with these properties are still a matter of debate. Stabilisation of the transition state and favourable conformations of the active site and the product(s) are probably part of the answer. We present here artificial catalysts and biomacromolecule hybrid catalysts which constitute good models towards the development of truly competitive artificial enzymes.
Collapse
Affiliation(s)
- Matthieu Raynal
- Institute of Chemical Research of Catalonia (ICIQ), Av. Països Catalans 16, 43007 Tarragona, Spain.
| | | | | | | |
Collapse
|
22
|
Yang H, Srivastava P, Zhang C, Lewis JC. A general method for artificial metalloenzyme formation through strain-promoted azide-alkyne cycloaddition. Chembiochem 2013; 15:223-7. [PMID: 24376040 DOI: 10.1002/cbic.201300661] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Indexed: 12/29/2022]
Abstract
Strain-promoted azide-alkyne cycloaddition (SPAAC) can be used to generate artificial metalloenzymes (ArMs) from scaffold proteins containing a p-azido-L-phenylalanine (Az) residue and catalytically active bicyclononyne-substituted metal complexes. The high efficiency of this reaction allows rapid ArM formation when using Az residues within the scaffold protein in the presence of cysteine residues or various reactive components of cellular lysate. In general, cofactor-based ArM formation allows the use of any desired metal complex to build unique inorganic protein materials. SPAAC covalent linkage further decouples the native function of the scaffold from the installation process because it is not affected by native amino acid residues; as long as an Az residue can be incorporated, an ArM can be generated. We have demonstrated the scope of this method with respect to both the scaffold and cofactor components and established that the dirhodium ArMs generated can catalyze the decomposition of diazo compounds and both Si-H and olefin insertion reactions involving these carbene precursors.
Collapse
Affiliation(s)
- Hao Yang
- Department of Chemistry, University of Chicago, 5735 S. Ellis Ave., Chicago, IL 60637 (USA)
| | | | | | | |
Collapse
|
23
|
Reiner T, Jantke D, Marziale AN, Raba A, Eppinger J. Metal-conjugated affinity labels: a new concept to create enantioselective artificial metalloenzymes. ChemistryOpen 2013; 2:50-4. [PMID: 24551533 PMCID: PMC3646430 DOI: 10.1002/open.201200044] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Indexed: 01/18/2023] Open
Affiliation(s)
- Thomas Reiner
- Chemistry Department, Technische Universität München Lichtenbergstr. 4, 85748 Garching (Germany)
| | - Dominik Jantke
- KAUST Catalysis Center, KCC, King Abdullah University of Science and Technology KAUST, Thuwal 23955-6900 (Saudi Arabia)
| | - Alexander N Marziale
- KAUST Catalysis Center, KCC, King Abdullah University of Science and Technology KAUST, Thuwal 23955-6900 (Saudi Arabia)
| | - Andreas Raba
- Chemistry Department, Technische Universität München Lichtenbergstr. 4, 85748 Garching (Germany)
| | - Jörg Eppinger
- KAUST Catalysis Center, KCC, King Abdullah University of Science and Technology KAUST, Thuwal 23955-6900 (Saudi Arabia)
| |
Collapse
|
24
|
Reetz MT. Artificial Metalloenzymes as Catalysts in Stereoselective Diels-Alder Reactions. CHEM REC 2012; 12:391-406. [DOI: 10.1002/tcr.201100043] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Indexed: 11/05/2022]
|
25
|
Fujieda N, Hasegawa A, Ishihama KI, Itoh S. Artificial Dicopper Oxidase: Rational Reprogramming of Bacterial Metallo-β-lactamase into a Catechol Oxidase. Chem Asian J 2012; 7:1203-7. [DOI: 10.1002/asia.201101014] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Indexed: 11/09/2022]
|
26
|
|
27
|
Creus M, Ward TR. Design and Evolution of Artificial Metalloenzymes: Biomimetic Aspects. PROGRESS IN INORGANIC CHEMISTRY 2011. [DOI: 10.1002/9781118148235.ch4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
|
28
|
Garner DK, Liang L, Barrios DA, Zhang JL, Lu Y. Covalent Anchor Positions Play an Important Role in Tuning Catalytic Properties of a Rationally Designed MnSalen-containing Metalloenzyme. ACS Catal 2011; 1:1083-1089. [PMID: 22013554 PMCID: PMC3194002 DOI: 10.1021/cs200258e] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Two questions important to the success in metalloenzyme design are how to attach or anchor metal cofactors inside protein scaffolds, and in what way such positioning affects enzymatic properties. We have previously reported a dual anchoring method to position a nonnative cofactor, MnSalen (1), inside the heme cavity of apo sperm whale myoglobin (Mb) and showed that the dual anchoring can increase both the activity and enantioselectivity over the single anchoring methods, making this artificial enzyme an ideal system to address the above questions. Here we report systematic investigations of the effect of different covalent attachment or anchoring positions on reactivity and selectivity of sulfoxidation by the MnSalen-containing Mb enzymes. We have found that changing the left anchor from Y103C to T39C has an almost identical effect of increasing rate by 1.8-fold and increasing selectivity by +14% for S, whether the right anchor is L72C or S108C. At the same time, regardless of the identity of the left anchor, changing the right anchor from S108C to L72C increases rate by 4-fold and selectivity by +66%. The right anchor site was observed to have a greater influence than the left anchor site on the reactivity and selectivity in sulfoxidation of a wide scope of other ortho-, meta- and para- substituted substrates. The 1•Mb(T39C/L72C) showed the highest reactivity (TON up to 2.31 min(-1)) and selectivity (ee% up to 83%) among the different anchoring positions examined. Molecular dynamic simulations indicate that these changes in reactivity and selectivity may be due to the steric effects of the linker arms inside the protein cavity. These results indicate that small differences in the anchor positions can result in significant changes in reactivity and enantioselectivity, probably through steric interactions with substrates when they enter the substrate-binding pocket, and that the effects of right and left anchor positions are independent and additive in nature. The finding that the anchoring arms can influence both the positioning of the cofactor and steric control of substrate entrance will help design better functional metalloenzymes with predicted catalytic activity and selectivity.
Collapse
Affiliation(s)
- Dewain K. Garner
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Lei Liang
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Rare Earth Materials Chemistry and Applications, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - David A. Barrios
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Jun-Long Zhang
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Rare Earth Materials Chemistry and Applications, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Yi Lu
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
| |
Collapse
|
29
|
Effect of the immobilization protocol on the properties of lipase B from Candida antarctica in organic media: Enantiospecifc production of atenolol acetate. ACTA ACUST UNITED AC 2011. [DOI: 10.1016/j.molcatb.2011.04.008] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
30
|
Abstract
The development of new catalytic methods to functionalize carbon-hydrogen (C-H) bonds continues to progress at a rapid pace due to the significant economic and environmental benefits of these transformations over traditional synthetic methods. In nature, enzymes catalyze regio- and stereoselective C-H bond functionalization using transformations ranging from hydroxylation to hydroalkylation under ambient reaction conditions. The efficiency of these enzymes relative to analogous chemical processes has led to their increased use as biocatalysts in preparative and industrial applications. Furthermore, unlike small molecule catalysts, enzymes can be systematically optimized via directed evolution for a particular application and can be expressed in vivo to augment the biosynthetic capability of living organisms. While a variety of technical challenges must still be overcome for practical application of many enzymes for C-H bond functionalization, continued research on natural enzymes and on novel artificial metalloenzymes will lead to improved synthetic processes for efficient synthesis of complex molecules. In this critical review, we discuss the most prevalent mechanistic strategies used by enzymes to functionalize non-acidic C-H bonds, the application and evolution of these enzymes for chemical synthesis, and a number of potential biosynthetic capabilities uniquely enabled by these powerful catalysts (110 references).
Collapse
Affiliation(s)
| | - Pedro S. Coelho
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., MC210-41, Pasadena, CA 91125-4100, USA
| | - Frances H. Arnold
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., MC210-41, Pasadena, CA 91125-4100, USA
| |
Collapse
|
31
|
Chen Y, Tang W, Mou J, Li Z. High-Throughput Method for Determining the Enantioselectivity of Enzyme-Catalyzed Hydroxylations Based on Mass Spectrometry. Angew Chem Int Ed Engl 2010; 49:5278-83. [DOI: 10.1002/anie.201001772] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
32
|
Podtetenieff J, Taglieber A, Bill E, Reijerse EJ, Reetz MT. An Artificial Metalloenzyme: Creation of a Designed Copper Binding Site in a Thermostable Protein. Angew Chem Int Ed Engl 2010; 49:5151-5. [PMID: 20572232 DOI: 10.1002/anie.201002106] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- John Podtetenieff
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | | | | | | | | |
Collapse
|
33
|
Chen Y, Tang W, Mou J, Li Z. High-Throughput Method for Determining the Enantioselectivity of Enzyme-Catalyzed Hydroxylations Based on Mass Spectrometry. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201001772] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
34
|
Podtetenieff J, Taglieber A, Bill E, Reijerse E, Reetz M. An Artificial Metalloenzyme: Creation of a Designed Copper Binding Site in a Thermostable Protein. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201002106] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
35
|
Pordea A, Creus M, Letondor C, Ivanova A, Ward T. Improving the enantioselectivity of artificial transfer hydrogenases based on the biotin–streptavidin technology by combinations of point mutations. Inorganica Chim Acta 2010. [DOI: 10.1016/j.ica.2009.02.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
36
|
Galarneau A, Sartori F, Cangiotti M, Mineva T, Renzo FD, Ottaviani MF. Sponge Mesoporous Silica Formation Using Disordered Phospholipid Bilayers as Template. J Phys Chem B 2010; 114:2140-52. [DOI: 10.1021/jp908828q] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anne Galarneau
- Institut Charles Gerhardt Montpellier, UMR 5253 CNRS/UM2/ENSCM /UM1, ENSCM, 8 rue de l’Ecole Normale, 34296 Montpellier Cedex 5, France, and Department of Geological Sciences, Chemical and Environmental Technologies, University of Urbino, Loc. Crocicchia, 61029 Urbino, Italy
| | - Federica Sartori
- Institut Charles Gerhardt Montpellier, UMR 5253 CNRS/UM2/ENSCM /UM1, ENSCM, 8 rue de l’Ecole Normale, 34296 Montpellier Cedex 5, France, and Department of Geological Sciences, Chemical and Environmental Technologies, University of Urbino, Loc. Crocicchia, 61029 Urbino, Italy
| | - Michela Cangiotti
- Institut Charles Gerhardt Montpellier, UMR 5253 CNRS/UM2/ENSCM /UM1, ENSCM, 8 rue de l’Ecole Normale, 34296 Montpellier Cedex 5, France, and Department of Geological Sciences, Chemical and Environmental Technologies, University of Urbino, Loc. Crocicchia, 61029 Urbino, Italy
| | - Tzonka Mineva
- Institut Charles Gerhardt Montpellier, UMR 5253 CNRS/UM2/ENSCM /UM1, ENSCM, 8 rue de l’Ecole Normale, 34296 Montpellier Cedex 5, France, and Department of Geological Sciences, Chemical and Environmental Technologies, University of Urbino, Loc. Crocicchia, 61029 Urbino, Italy
| | - Francesco Di Renzo
- Institut Charles Gerhardt Montpellier, UMR 5253 CNRS/UM2/ENSCM /UM1, ENSCM, 8 rue de l’Ecole Normale, 34296 Montpellier Cedex 5, France, and Department of Geological Sciences, Chemical and Environmental Technologies, University of Urbino, Loc. Crocicchia, 61029 Urbino, Italy
| | - M. Francesca Ottaviani
- Institut Charles Gerhardt Montpellier, UMR 5253 CNRS/UM2/ENSCM /UM1, ENSCM, 8 rue de l’Ecole Normale, 34296 Montpellier Cedex 5, France, and Department of Geological Sciences, Chemical and Environmental Technologies, University of Urbino, Loc. Crocicchia, 61029 Urbino, Italy
| |
Collapse
|
37
|
Cedrone F, Niel S, Roca S, Bhatnagar T, Ait-abdelkader N, Torre C, Krumm H, Maichele A, T. Reetz M, C. Baratti J. Directed Evolution of the Epoxide Hydrolase fromAspergillus niger. BIOCATAL BIOTRANSFOR 2009. [DOI: 10.1080/102420310001630137] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
38
|
Vriamont N, Govaerts B, Grenouillet P, de Bellefon C, Riant O. Design of a Genetic Algorithm for the Simulated Evolution of a Library of Asymmetric Transfer Hydrogenation Catalysts. Chemistry 2009; 15:6267-78. [DOI: 10.1002/chem.200802192] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
39
|
Paramesvaran J, Hibbert EG, Russell AJ, Dalby PA. Distributions of enzyme residues yielding mutants with improved substrate specificities from two different directed evolution strategies. Protein Eng Des Sel 2009; 22:401-11. [DOI: 10.1093/protein/gzp020] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
40
|
|
41
|
Hackenberger C, Schwarzer D. Chemoselektive Ligations- und Modifikationsstrategien für Peptide und Proteine. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200801313] [Citation(s) in RCA: 204] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
42
|
Hackenberger C, Schwarzer D. Chemoselective Ligation and Modification Strategies for Peptides and Proteins. Angew Chem Int Ed Engl 2008; 47:10030-74. [DOI: 10.1002/anie.200801313] [Citation(s) in RCA: 651] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
|
43
|
Reetz M. Kombinatorische Übergangsmetallkatalyse: Mischungen einzähniger Liganden zur Kontrolle der Enantio-, Diastereo- und Regioselektivität. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200704327] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
44
|
Reetz M. Combinatorial Transition-Metal Catalysis: Mixing Monodentate Ligands to Control Enantio-, Diastereo-, and Regioselectivity. Angew Chem Int Ed Engl 2008; 47:2556-88. [DOI: 10.1002/anie.200704327] [Citation(s) in RCA: 223] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
45
|
Reetz MT, Rentzsch M, Pletsch A, Taglieber A, Hollmann F, Mondière RJG, Dickmann N, Höcker B, Cerrone S, Haeger MC, Sterner R. A Robust Protein Host for Anchoring Chelating Ligands and Organocatalysts. Chembiochem 2008; 9:552-64. [DOI: 10.1002/cbic.200700413] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
46
|
|
47
|
Zhang JL, Garner DK, Liang L, Chen Q, Lu Y. Protein scaffold of a designed metalloenzyme enhances the chemoselectivity in sulfoxidation of thioanisole. Chem Commun (Camb) 2008:1665-7. [PMID: 18368158 DOI: 10.1039/b718915j] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We demonstrate that incorporation of MnSalen into a protein scaffold enhances the chemoselectivity in sulfoxidation of thioanisole and find that both the polarity and hydrogen bonding of the protein scaffold play an important role in tuning the chemoselectivity.
Collapse
Affiliation(s)
- Jun-Long Zhang
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | | | | | | | | |
Collapse
|
48
|
Rasmussen BS, Pedersen JM, Sørensen J, Egebjerg J, Schiøtt B, Mortensen KK, Skrydstrup T. Enantioselective proteins: selection, binding studies and molecular modeling of antibodies with affinity towards hydrophobic BINOL derivatives. Chembiochem 2008; 8:1974-80. [PMID: 17924375 DOI: 10.1002/cbic.200700295] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
In this paper, the initial steps towards the design of novel artificial metalloenzymes that exploit proteins as a second coordination sphere for traditional metal-ligand catalysis are described. Phage display was employed to select and study antibody fragments capable of recognizing hydrophobic BINOL derivatives designed to mimic BINAP, a widely used ligand in asymmetric metal-catalyzed reactions. The binding affinities of the selected antibodies towards a series of haptens were evaluated by using ELISA assays. A homology model of one of the most selective antibodies was constructed, and a computer-assisted ligand-docking study was carried out to elucidate the binding of the hapten. It was shown that, due to the hydrophobic nature of the haptens, a higher level of theoretical treatment was required to identify the correct binding modes. A small selection of the antibodies was found to discriminate between enantiomers and small structural modifications of the BINOL derivatives. The selectivities arise from hydrophobic interactions, and we propose that the identified set of antibodies provides a foundation for a novel route to artificial metalloenzymes.
Collapse
Affiliation(s)
- Brian Schou Rasmussen
- Department of Chemistry and Interdisciplinary Nanoscience Center, University of Aarhus, Langelandsgade 140, 8000 Aarhus C, Denmark.
| | | | | | | | | | | | | |
Collapse
|
49
|
Directed Evolution of Stereoselective Hybrid Catalysts. TOP ORGANOMETAL CHEM 2008. [DOI: 10.1007/3418_2008_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
50
|
Four-, six- and eight-coordinated lead(II) complexes with amine- or amide-type tripodal ligands. INORG CHEM COMMUN 2007. [DOI: 10.1016/j.inoche.2007.06.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|