1
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Nie LS, Liu XC, Yu L, Liu AK, Sun LJ, Gao SQ, Lin YW. Rational Design of an Artificial Metalloenzyme by Constructing a Metal-Binding Site Close to the Heme Cofactor in Myoglobin. Inorg Chem 2024; 63:18531-18535. [PMID: 39311200 DOI: 10.1021/acs.inorgchem.4c03093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/08/2024]
Abstract
In this study, we constructed a metal-binding site close to the heme cofactor in myoglobin (Mb) by covalently attaching a nonnative metal-binding ligand of bipyridine to Cys46 through the F46C mutation in the heme distal site. The X-ray structure of the designed enzyme, termed F46C-mBpy Mb, was solved in the Cu(II)-bound form, which revealed the formation of a heterodinuclear center of Cu-His-H2O-heme. Cu(II)-F46C-mBpy Mb exhibits not only nitrite reductase reactivity but also cascade reaction activity involving both hydrolysis and oxidation. Furthermore, F46C-mBpy Mb displays Mn-peroxidase activity by the oxidation of Mn2+ to Mn3+ using H2O2 as an oxidant. This study shows that the construction of a nonnative metal-binding site close to the heme cofactor is a convenient approach to creating an artificial metalloenzyme with a heterodinuclear center that confers multiple functions.
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Affiliation(s)
- Lv-Suo Nie
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
| | - Xi-Chun Liu
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
| | - Lu Yu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, Anhui 230031, China
| | - Ao-Kun Liu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, Anhui 230031, China
| | - Li-Juan Sun
- Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Shu-Qin Gao
- Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
- Hengyang Medical School, University of South China, Hengyang 421001, China
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2
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Leone L, De Fenza M, Esposito A, Maglio O, Nastri F, Lombardi A. Peptides and metal ions: A successful marriage for developing artificial metalloproteins. J Pept Sci 2024; 30:e3606. [PMID: 38719781 DOI: 10.1002/psc.3606] [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: 02/19/2024] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 10/12/2024]
Abstract
The mutual relationship between peptides and metal ions enables metalloproteins to have crucial roles in biological systems, including structural, sensing, electron transport, and catalytic functions. The effort to reproduce or/and enhance these roles, or even to create unprecedented functions, is the focus of protein design, the first step toward the comprehension of the complex machinery of nature. Nowadays, protein design allows the building of sophisticated scaffolds, with novel functions and exceptional stability. Recent progress in metalloprotein design has led to the building of peptides/proteins capable of orchestrating the desired functions of different metal cofactors. The structural diversity of peptides allows proper selection of first- and second-shell ligands, as well as long-range electrostatic and hydrophobic interactions, which represent precious tools for tuning metal properties. The scope of this review is to discuss the construction of metal sites in de novo designed and miniaturized scaffolds. Selected examples of mono-, di-, and multi-nuclear binding sites, from the last 20 years will be described in an effort to highlight key artificial models of catalytic or electron-transfer metalloproteins. The authors' goal is to make readers feel like guests at the marriage between peptides and metal ions while offering sources of inspiration for future architects of innovative, artificial metalloproteins.
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Affiliation(s)
- Linda Leone
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Maria De Fenza
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Alessandra Esposito
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Ornella Maglio
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
- Institute of Biostructures and Bioimaging, National Research Council, Naples, Italy
| | - Flavia Nastri
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Angela Lombardi
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
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3
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Pitts WC, Deb A, Penner-Hahn JE, Pecoraro VL. Revving up a Designed Copper Nitrite Reductase Using Non-Coded Active Site Ligands. ACS Catal 2024; 14:4362-4368. [PMID: 39157175 PMCID: PMC11329067 DOI: 10.1021/acscatal.3c06159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/20/2024]
Abstract
Herein, we report a three stranded coiled-coil (3SCC) de novo protein containing a type II copper center (CuT2) composed of 6-membered ring N-heterocycles. This design yields the most active homogenous copper nitrite reductase (CuNiR) mimic in water. We achieved this result by controlling three factors. First, previous studies with Nδ and Nε -Methyl Histidine had indicated that a ligand providing pyridine-like electronic character to the copper site was superior to the more donating Nδ for nitrite reduction. By substitution of the parent histidine with the non-coded amino acids pyridyl alanine (3'-Pyridine [3'Py] vs 4'-Pyridine [4'Py]), an authentic pyridine donor was employed without the complications of the coupling of both electronic and tautomeric effects of histidine or methylated histidine. Second, by changing the position of the nitrogen atom within the active site (4'-Pyridine vs. 3'Pyridine) a doubling of the enzyme's catalytic efficiency resulted. This effect was driven exclusivity by substrate binding to the copper site. Third, we replaced the leucine layer adjacent to the active site with an alanine, and the disparity between the 3'Py and 4'Py became more apparent. The decreased steric bulk minimally impacted the 3'Py derivative; however, the 4'Py K m decreased by an order of magnitude (600 mM to 50 mM), resulting in a 40-fold enhancement in the k cat/K m compared to the analogues histidine site and a 1500-fold improvement compared with the initially reported CuNiR catalyst of this family, TRIW-H. When combined with XANES/EXAFS data, the relaxing of the Cu(I) site to a more 2-coordinate Cu(I) like structure in the resting state increases the overall catalytic efficiency of nitrite reduction via the lowering of K m. This study illustrates how by combining advanced spectroscopic methods, detailed kinetic analysis, and a broad toolbox of amino acid side chain functionality, one can rationally design systems that optimize biomimetic catalysis.
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Affiliation(s)
- Winston C. Pitts
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48108, USA United States
| | - Aniruddha Deb
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48108, United States
| | - James E. Penner-Hahn
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48108, USA United States
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48108, United States
| | - Vincent L. Pecoraro
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48108, USA United States
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48108, United States
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4
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Hoffnagle AM, Tezcan FA. Atomically Accurate Design of Metalloproteins with Predefined Coordination Geometries. J Am Chem Soc 2023; 145:14208-14214. [PMID: 37352018 PMCID: PMC10439731 DOI: 10.1021/jacs.3c04047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2023]
Abstract
We report a new computational protein design method for the construction of oligomeric protein assemblies around metal centers with predefined coordination geometries. We apply this method to design two homotrimeric assemblies, Tet4 and TP1, with tetrahedral and trigonal-pyramidal tris(histidine) metal coordination geometries, respectively, and demonstrate that both assemblies form the targeted metal centers with ≤0.2 Å accuracy. Although Tet4 and TP1 are constructed from the same parent protein building block, they are distinct in terms of their overall architectures, the environment surrounding the metal centers, and their metal-based reactivities, illustrating the versatility of our approach.
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Affiliation(s)
- Alexander M. Hoffnagle
- Department of Chemistry and Biochemistry, University of California, San Diego, CA 92093, USA
| | - F. Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, CA 92093, USA
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5
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Jeong S, Lee K, Yoo SH, Lee HS, Kwon S. Crystalline Metal-Peptide Networks: Structures, Applications, and Future Outlook. Chembiochem 2023; 24:e202200448. [PMID: 36161687 DOI: 10.1002/cbic.202200448] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/23/2022] [Indexed: 01/20/2023]
Abstract
Metal-peptide networks (MPNs), which are assembled from short peptides and metal ions, are considered one of the most fascinating metal-organic coordinated architectures because of their unique and complicated structures. Although MPNs have considerable potential for development into versatile materials, they have not been developed for practical applications because of several underlying limitations, such as designability, stability, and modifiability. In this review, we summarise several important milestones in the development of crystalline MPNs and thoroughly analyse their structural features, such as peptide sequence designs, coordination geometries, cross-linking types, and network topologies. In addition, potential applications such as gas adsorption, guest encapsulation, and chiral recognition are introduced. We believe that this review is a useful survey that can provide insights into the development of new MPNs with more sophisticated structures and novel functions.
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Affiliation(s)
- Seoneun Jeong
- Center for Multiscale Chiral Architectures, Department of Chemistry, KAIST 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Korea
| | - Kwonjung Lee
- Department of Chemistry, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul, 06974, Korea
| | - Sung Hyun Yoo
- Department of Chemistry, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Korea
| | - Hee-Seung Lee
- Center for Multiscale Chiral Architectures, Department of Chemistry, KAIST 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Korea
| | - Sunbum Kwon
- Department of Chemistry, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul, 06974, Korea
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6
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Pirro F, La Gatta S, Arrigoni F, Famulari A, Maglio O, Del Vecchio P, Chiesa M, De Gioia L, Bertini L, Chino M, Nastri F, Lombardi A. A De Novo-Designed Type 3 Copper Protein Tunes Catechol Substrate Recognition and Reactivity. Angew Chem Int Ed Engl 2023; 62:e202211552. [PMID: 36334012 DOI: 10.1002/anie.202211552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Indexed: 11/07/2022]
Abstract
De novo metalloprotein design is a remarkable approach to shape protein scaffolds toward specific functions. Here, we report the design and characterization of Due Rame 1 (DR1), a de novo designed protein housing a di-copper site and mimicking the Type 3 (T3) copper-containing polyphenol oxidases (PPOs). To achieve this goal, we hierarchically designed the first and the second di-metal coordination spheres to engineer the di-copper site into a simple four-helix bundle scaffold. Spectroscopic, thermodynamic, and functional characterization revealed that DR1 recapitulates the T3 copper site, supporting different copper redox states, and being active in the O2 -dependent oxidation of catechols to o-quinones. Careful design of the residues lining the substrate access site endows DR1 with substrate recognition, as revealed by Hammet analysis and computational studies on substituted catechols. This study represents a premier example in the construction of a functional T3 copper site into a designed four-helix bundle protein.
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Affiliation(s)
- Fabio Pirro
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, 80126, Naples, Italy
| | - Salvatore La Gatta
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, 80126, Naples, Italy
| | - Federica Arrigoni
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Antonino Famulari
- Department of Chemistry, University of Torino, Via Giuria 9, 10125, Torino, Italy.,Department of Condensed Matter Physics, University of of Zaragoza, Calle Pedro Cerbuna 12, 50009, Zaragoza, Spain
| | - Ornella Maglio
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, 80126, Naples, Italy.,Institute of Biostructures and Bioimaging (IBB), National Research Council (CNR), Via Pietro Castellino 111, 80131, Napoli, Italy
| | - Pompea Del Vecchio
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, 80126, Naples, Italy
| | - Mario Chiesa
- Department of Chemistry, University of Torino, Via Giuria 9, 10125, Torino, Italy
| | - Luca De Gioia
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Luca Bertini
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Marco Chino
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, 80126, Naples, Italy
| | - Flavia Nastri
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, 80126, Naples, Italy
| | - Angela Lombardi
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, 80126, Naples, Italy
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7
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Sosa Alfaro V, Waheed SO, Palomino H, Knorrscheidt A, Weissenborn M, Christov CZ, Lehnert N. YfeX - A New Platform for Carbene Transferase Development with High Intrinsic Reactivity. Chemistry 2022; 28:e202201474. [PMID: 35948517 PMCID: PMC9691539 DOI: 10.1002/chem.202201474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Indexed: 01/11/2023]
Abstract
Carbene transfer biocatalysis has evolved from basic science to an area with vast potential for the development of new industrial processes. In this study, we show that YfeX, naturally a peroxidase, has great potential for the development of new carbene transferases, due to its high intrinsic reactivity, especially for the N-H insertion reaction of aromatic and aliphatic primary and secondary amines. YfeX shows high stability against organic solvents (methanol and DMSO), greatly improving turnover of hydrophobic substrates. Interestingly, in styrene cyclopropanation, WT YfeX naturally shows high enantioselectivity, generating the trans product with 87 % selectivity for the (R,R) enantiomer. WT YfeX also catalyzes the Si-H insertion efficiently. Steric effects in the active site were further explored using the R232A variant. Quantum Mechanics/Molecular Mechanics (QM/MM) calculations reveal details on the mechanism of Si-H insertion. YfeX, and potentially other peroxidases, are exciting new targets for the development of improved carbene transferases.
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Affiliation(s)
- Victor Sosa Alfaro
- Department of Chemistry and Department of BiophysicsUniversity of MichiganAnn Arbor, Michigan48109–1055United States
| | - Sodiq O. Waheed
- Department of ChemistryMichigan Technological UniversityHoughton, Michigan49931United States
| | - Hannah Palomino
- Department of Chemistry and Department of BiophysicsUniversity of MichiganAnn Arbor, Michigan48109–1055United States
| | - Anja Knorrscheidt
- Institute of ChemistryMartin-Luther-University Halle-WittenbergKurt-Mothes-Str. 206120HalleGermany
| | - Martin Weissenborn
- Institute of ChemistryMartin-Luther-University Halle-WittenbergKurt-Mothes-Str. 206120HalleGermany
| | - Christo Z. Christov
- Department of ChemistryMichigan Technological UniversityHoughton, Michigan49931United States
| | - Nicolai Lehnert
- Department of Chemistry and Department of BiophysicsUniversity of MichiganAnn Arbor, Michigan48109–1055United States
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8
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Koebke KJ, Pinter TBJ, Pitts WC, Pecoraro VL. Catalysis and Electron Transfer in De Novo Designed Metalloproteins. Chem Rev 2022; 122:12046-12109. [PMID: 35763791 PMCID: PMC10735231 DOI: 10.1021/acs.chemrev.1c01025] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
One of the hallmark advances in our understanding of metalloprotein function is showcased in our ability to design new, non-native, catalytically active protein scaffolds. This review highlights progress and milestone achievements in the field of de novo metalloprotein design focused on reports from the past decade with special emphasis on de novo designs couched within common subfields of bioinorganic study: heme binding proteins, monometal- and dimetal-containing catalytic sites, and metal-containing electron transfer sites. Within each subfield, we highlight several of what we have identified as significant and important contributions to either our understanding of that subfield or de novo metalloprotein design as a discipline. These reports are placed in context both historically and scientifically. General suggestions for future directions that we feel will be important to advance our understanding or accelerate discovery are discussed.
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Affiliation(s)
- Karl J. Koebke
- Department of Chemistry, University of Michigan Ann Arbor, MI 48109 USA
| | | | - Winston C. Pitts
- Department of Chemistry, University of Michigan Ann Arbor, MI 48109 USA
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9
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Van Stappen C, Deng Y, Liu Y, Heidari H, Wang JX, Zhou Y, Ledray AP, Lu Y. Designing Artificial Metalloenzymes by Tuning of the Environment beyond the Primary Coordination Sphere. Chem Rev 2022; 122:11974-12045. [PMID: 35816578 DOI: 10.1021/acs.chemrev.2c00106] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metalloenzymes catalyze a variety of reactions using a limited number of natural amino acids and metallocofactors. Therefore, the environment beyond the primary coordination sphere must play an important role in both conferring and tuning their phenomenal catalytic properties, enabling active sites with otherwise similar primary coordination environments to perform a diverse array of biological functions. However, since the interactions beyond the primary coordination sphere are numerous and weak, it has been difficult to pinpoint structural features responsible for the tuning of activities of native enzymes. Designing artificial metalloenzymes (ArMs) offers an excellent basis to elucidate the roles of these interactions and to further develop practical biological catalysts. In this review, we highlight how the secondary coordination spheres of ArMs influence metal binding and catalysis, with particular focus on the use of native protein scaffolds as templates for the design of ArMs by either rational design aided by computational modeling, directed evolution, or a combination of both approaches. In describing successes in designing heme, nonheme Fe, and Cu metalloenzymes, heteronuclear metalloenzymes containing heme, and those ArMs containing other metal centers (including those with non-native metal ions and metallocofactors), we have summarized insights gained on how careful controls of the interactions in the secondary coordination sphere, including hydrophobic and hydrogen bonding interactions, allow the generation and tuning of these respective systems to approach, rival, and, in a few cases, exceed those of native enzymes. We have also provided an outlook on the remaining challenges in the field and future directions that will allow for a deeper understanding of the secondary coordination sphere a deeper understanding of the secondary coordintion sphere to be gained, and in turn to guide the design of a broader and more efficient variety of ArMs.
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Affiliation(s)
- Casey Van Stappen
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yunling Deng
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yiwei Liu
- Department of Chemistry, University of Illinois, Urbana-Champaign, 505 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Hirbod Heidari
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Jing-Xiang Wang
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yu Zhou
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Aaron P Ledray
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yi Lu
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States.,Department of Chemistry, University of Illinois, Urbana-Champaign, 505 South Mathews Avenue, Urbana, Illinois 61801, United States
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10
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Prakash D, Mitra S, Murphy M, Chakraborty S. Oxidation and Peroxygenation of C–H Bonds by Artificial Cu Peptides (ArCuPs): Improved Catalysis via Selective Outer Sphere Modifications. ACS Catal 2022. [DOI: 10.1021/acscatal.2c01882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Divyansh Prakash
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, United States
| | - Suchitra Mitra
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, United States
| | - Morgan Murphy
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, United States
| | - Saumen Chakraborty
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, United States
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11
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Maity B, Taher M, Mazumdar S, Ueno T. Artificial metalloenzymes based on protein assembly. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2022.214593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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12
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Abstract
Natural metalloproteins perform many functions - ranging from sensing to electron transfer and catalysis - in which the position and property of each ligand and metal, is dictated by protein structure. De novo protein design aims to define an amino acid sequence that encodes a specific structure and function, providing a critical test of the hypothetical inner workings of (metallo)proteins. To date, de novo metalloproteins have used simple, symmetric tertiary structures - uncomplicated by the large size and evolutionary marks of natural proteins - to interrogate structure-function hypotheses. In this Review, we discuss de novo design applications, such as proteins that induce complex, increasingly asymmetric ligand geometries to achieve function, as well as the use of more canonical ligand geometries to achieve stability. De novo design has been used to explore how proteins fine-tune redox potentials and catalyse both oxidative and hydrolytic reactions. With an increased understanding of structure-function relationships, functional proteins including O2-dependent oxidases, fast hydrolases, and multi-proton/multi-electron reductases, have been created. In addition, proteins can now be designed using xeno-biological metals or cofactors and principles from inorganic chemistry to derive new-to-nature functions. These results and the advances in computational protein design suggest a bright future for the de novo design of diverse, functional metalloproteins.
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Affiliation(s)
- Matthew J. Chalkley
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, (CA), USA
| | - Samuel I. Mann
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, (CA), USA
| | - William F. DeGrado
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, (CA), USA
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13
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Koebke KJ, Tebo AG, Manickas EC, Deb A, Penner-Hahn JE, Pecoraro VL. Nitrite reductase activity within an antiparallel de novo scaffold. J Biol Inorg Chem 2021; 26:855-862. [PMID: 34487215 PMCID: PMC11232943 DOI: 10.1007/s00775-021-01889-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 07/26/2021] [Indexed: 12/28/2022]
Abstract
Copper nitrite reductase (CuNiR) is a copper enzyme that converts nitrite to nitric oxide and is an important part of the global nitrogen cycle in bacteria. The relatively simple CuHis3 binding site of the CuNiR active site has made it an enticing target for small molecule modeling and de novo protein design studies. We have previously reported symmetric CuNiR models within parallel three stranded coiled coil systems, with activities that span a range of three orders of magnitude. In this report, we investigate the same CuHis3 binding site within an antiparallel three helical bundle scaffold, which allows the design of asymmetric constructs. We determine that a simple CuHis3 binding site can be designed within this scaffold with enhanced activity relative to the comparable construct in parallel coiled coils. Incorporating more complex designs or repositioning this binding site can decrease this activity as much as 15 times. Comparing these constructs, we reaffirm a previous result in which a blue shift in the 1s to 4p transition energy determined by Cu(I) X-ray absorption spectroscopy is correlated with an enhanced activity within imidazole-based constructs. With this step and recent successful electron transfer site designs within this scaffold, we are one step closer to a fully functional de novo designed nitrite reductase.
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Affiliation(s)
- Karl J Koebke
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Alison G Tebo
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, USA
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | | | - Aniruddha Deb
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - James E Penner-Hahn
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
- Department of Biophysics, University of Michigan, Ann Arbor, MI, USA
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14
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Lella M, Mahalakshmi R. De novo
design of metal‐binding cleft in a
Trp‐Trp
stapled thermostable β‐hairpin peptide. Pept Sci (Hoboken) 2021. [DOI: 10.1002/pep2.24240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Muralikrishna Lella
- Molecular Biophysics Laboratory, Department of Biological Sciences Indian Institute of Science Education and Research Bhopal India
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory, Department of Biological Sciences Indian Institute of Science Education and Research Bhopal India
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15
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Mitra S, Prakash D, Rajabimoghadam K, Wawrzak Z, Prasad P, Wu T, Misra SK, Sharp JS, Garcia-Bosch I, Chakraborty S. De Novo Design of a Self-Assembled Artificial Copper Peptide that Activates and Reduces Peroxide. ACS Catal 2021; 11:10267-10278. [DOI: 10.1021/acscatal.1c02132] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Suchitra Mitra
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, United States
| | - Divyansh Prakash
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, United States
| | | | - Zdzislaw Wawrzak
- Argonne National Laboratory, 9700 S. Cass Avenue, Argonne, Illinois 60439, United States
| | - Pallavi Prasad
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, United States
| | - Tong Wu
- Department of Chemistry, Southern Methodist University, Dallas, Texas 75275, United States
| | - Sandeep K. Misra
- Department of Biomolecular Sciences, University of Mississippi, University, Mississippi 38677, United States
| | - Joshua S. Sharp
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, United States
- Department of Biomolecular Sciences, University of Mississippi, University, Mississippi 38677, United States
| | - Isaac Garcia-Bosch
- Department of Chemistry, Southern Methodist University, Dallas, Texas 75275, United States
| | - Saumen Chakraborty
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, United States
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16
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Abou Zeid L, Pell A, Tytus T, Delangle P, Bresson C. Separation of multiphosphorylated cyclopeptides and their positional isomers by hydrophilic interaction liquid chromatography (HILIC) coupled to electrospray ionization mass spectrometry (ESI-MS). J Chromatogr B Analyt Technol Biomed Life Sci 2021; 1177:122792. [PMID: 34102536 DOI: 10.1016/j.jchromb.2021.122792] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/17/2021] [Accepted: 05/19/2021] [Indexed: 10/21/2022]
Abstract
Peptides are efficient models used in different fields such as toxicology to study the interactions of several contaminants at the molecular scale, requiring the development of bio-analytical strategies. In this context, Hydrophilic interaction liquid chromatography (HILIC) coupled to electrospray ionization mass spectrometry (ESI-MS) was used to separate synthetic multiphosphorylated cyclopeptides and their positional isomers at physiological pH. We assessed (i) the selectivity of eleven HILIC columns, from different manufacturers and packed with diverse polar sorbents, and (ii) the effect of mobile phase composition on the separation selectivity. The best selectivity and baseline resolution were achieved with the columns grafted by neutral sorbents amide and diol. Furthermore, we investigated the HILIC retention mechanism of these peptides by examining the effect of the number of phosphorylated residues in the peptide scaffold on their retention. The peptide behavior followed the classical hydrophilic partitioning mechanism exclusively on amide and diol columns. This trend was not fully respected on bare and hybrid silica due to the attractive/repulsive interactions of the deprotonated surface silanol groups with the Arginine or Glutamate residues in the peptide scaffold according to the peptide sequence. The position of the phosphorylated amino acid in the peptide backbone also showed to have an impact on the retention, making possible the separation of positional isomers of these multiphosphorylated cyclic peptides using HILIC.
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Affiliation(s)
- Lana Abou Zeid
- Université Paris-Saclay, CEA, Service d'Etudes Analytiques et de Réactivité des Surfaces, F-91191 Gif-sur-Yvette, France; Sorbonne Université, F-75005 Paris, France.
| | - Albert Pell
- Université Paris-Saclay, CEA, Service d'Etudes Analytiques et de Réactivité des Surfaces, F-91191 Gif-sur-Yvette, France
| | - Théo Tytus
- Université Paris-Saclay, CEA, Service d'Etudes Analytiques et de Réactivité des Surfaces, F-91191 Gif-sur-Yvette, France
| | - Pascale Delangle
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, 38 000 Grenoble, France
| | - Carole Bresson
- Université Paris-Saclay, CEA, Service d'Etudes Analytiques et de Réactivité des Surfaces, F-91191 Gif-sur-Yvette, France
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17
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Hamley IW. Biocatalysts Based on Peptide and Peptide Conjugate Nanostructures. Biomacromolecules 2021; 22:1835-1855. [PMID: 33843196 PMCID: PMC8154259 DOI: 10.1021/acs.biomac.1c00240] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/31/2021] [Indexed: 12/15/2022]
Abstract
Peptides and their conjugates (to lipids, bulky N-terminals, or other groups) can self-assemble into nanostructures such as fibrils, nanotubes, coiled coil bundles, and micelles, and these can be used as platforms to present functional residues in order to catalyze a diversity of reactions. Peptide structures can be used to template catalytic sites inspired by those present in natural enzymes as well as simpler constructs using individual catalytic amino acids, especially proline and histidine. The literature on the use of peptide (and peptide conjugate) α-helical and β-sheet structures as well as turn or disordered peptides in the biocatalysis of a range of organic reactions including hydrolysis and a variety of coupling reactions (e.g., aldol reactions) is reviewed. The simpler design rules for peptide structures compared to those of folded proteins permit ready ab initio design (minimalist approach) of effective catalytic structures that mimic the binding pockets of natural enzymes or which simply present catalytic motifs at high density on nanostructure scaffolds. Research on these topics is summarized, along with a discussion of metal nanoparticle catalysts templated by peptide nanostructures, especially fibrils. Research showing the high activities of different classes of peptides in catalyzing many reactions is highlighted. Advances in peptide design and synthesis methods mean they hold great potential for future developments of effective bioinspired and biocompatible catalysts.
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Affiliation(s)
- Ian W. Hamley
- Department of Chemistry, University of Reading, RG6 6AD Reading, United Kingdom
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18
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Kakkis A, Gagnon D, Esselborn J, Britt RD, Tezcan FA. Metal‐Templated Design of Chemically Switchable Protein Assemblies with High‐Affinity Coordination Sites. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202009226] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Albert Kakkis
- Department of Chemistry and Biochemistry University of California, San Diego 9500 Gilman Drive La Jolla CA 92093 USA
| | - Derek Gagnon
- Department of Chemistry and Biochemistry University of California, San Diego 9500 Gilman Drive La Jolla CA 92093 USA
| | - Julian Esselborn
- Department of Chemistry and Biochemistry University of California, San Diego 9500 Gilman Drive La Jolla CA 92093 USA
| | - R. David Britt
- Department of Chemistry University of California, Davis 1 Shields Avenue Davis CA 95616 USA
| | - F. Akif Tezcan
- Department of Chemistry and Biochemistry University of California, San Diego 9500 Gilman Drive La Jolla CA 92093 USA
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19
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Pinter TBJ, Manickas EC, Tolbert AE, Koebke KJ, Deb A, Penner-Hahn JE, Pecoraro VL. Making or Breaking Metal-Dependent Catalytic Activity: The Role of Stammers in Designed Three-Stranded Coiled Coils. Angew Chem Int Ed Engl 2020; 59:20445-20449. [PMID: 32748510 PMCID: PMC7722090 DOI: 10.1002/anie.202008356] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/21/2020] [Indexed: 12/31/2022]
Abstract
While many life-critical reactions would be infeasibly slow without metal cofactors, a detailed understanding of how protein structure can influence catalytic activity remains elusive. Using de novo designed three-stranded coiled coils (TRI and Grand peptides formed using a heptad repeat approach), we examine how the insertion of a three residue discontinuity, known as a stammer insert, directly adjacent to a (His)3 metal binding site alters catalytic activity. The stammer, which locally alters the twist of the helix, significantly increases copper-catalyzed nitrite reductase activity (CuNiR). In contrast, the well-established zinc-catalyzed carbonic anhydrase activity (p-nitrophenyl acetate, pNPA) is effectively ablated. This study illustrates how the perturbation of the protein sequence using non-coordinating and non-acid base residues in the helical core can perturb metalloenzyme activity through the simple expedient of modifying the helical pitch adjacent to the catalytic center.
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Affiliation(s)
- Tyler B. J. Pinter
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA, 48109
| | | | - Audrey E. Tolbert
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA, 48109
| | - Karl J. Koebke
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA, 48109
| | - Aniruddha Deb
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA, 48109
| | - James E. Penner-Hahn
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA, 48109
| | - Vincent L. Pecoraro
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA, 48109
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20
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Pinter TBJ, Manickas EC, Tolbert AE, Koebke KJ, Deb A, Penner‐Hahn JE, Pecoraro VL. Making or Breaking Metal‐Dependent Catalytic Activity: The Role of Stammers in Designed Three‐Stranded Coiled Coils. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202008356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | | | - Audrey E. Tolbert
- Department of Chemistry University of Michigan Ann Arbor MI 48109 USA
| | - Karl J. Koebke
- Department of Chemistry University of Michigan Ann Arbor MI 48109 USA
| | - Aniruddha Deb
- Department of Chemistry University of Michigan Ann Arbor MI 48109 USA
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21
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Kakkis A, Gagnon D, Esselborn J, Britt RD, Tezcan FA. Metal-Templated Design of Chemically Switchable Protein Assemblies with High-Affinity Coordination Sites. Angew Chem Int Ed Engl 2020; 59:21940-21944. [PMID: 32830423 DOI: 10.1002/anie.202009226] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/13/2020] [Indexed: 11/09/2022]
Abstract
To mimic a hypothetical pathway for protein evolution, we previously tailored a monomeric protein (cyt cb562 ) for metal-mediated self-assembly, followed by re-design of the resulting oligomers for enhanced stability and metal-based functions. We show that a single hydrophobic mutation on the cyt cb562 surface drastically alters the outcome of metal-directed oligomerization to yield a new trimeric architecture, (TriCyt1)3. This nascent trimer was redesigned into second and third-generation variants (TriCyt2)3 and (TriCyt3)3 with increased structural stability and preorganization for metal coordination. The three TriCyt variants combined furnish a unique platform to 1) provide tunable coupling between protein quaternary structure and metal coordination, 2) enable the construction of metal/pH-switchable protein oligomerization motifs, and 3) generate a robust metal coordination site that can coordinate all mid-to-late first-row transition-metal ions with high affinity.
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Affiliation(s)
- Albert Kakkis
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Derek Gagnon
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Julian Esselborn
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - R David Britt
- Department of Chemistry, University of California, Davis, 1 Shields Avenue, Davis, CA, 95616, USA
| | - F Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
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22
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Koebke KJ, Alfaro VS, Pinter TBJ, Deb A, Lehnert N, Tard C, Penner-Hahn JE, Pecoraro VL. Traversing the Red-Green-Blue Color Spectrum in Rationally Designed Cupredoxins. J Am Chem Soc 2020; 142:15282-15294. [PMID: 32786767 DOI: 10.1021/jacs.0c04757] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Blue copper proteins have a constrained Cu(II) geometry that has proven difficult to recapitulate outside native cupredoxin folds. Previous work has successfully designed green copper proteins which could be tuned blue using exogenous ligands, but the question of how one can create a self-contained blue copper site within a de novo scaffold, especially one removed from a cupredoxin fold, remained. We have recently reported a red copper protein site within a three helical bundle scaffold which we later revisited and determined to be a nitrosocyanin mimic, with a CuHis2CysGlu binding site. We now report efforts to rationally design this construct toward either green or blue copper chromophores using mutation strategies that have proven successful in native cupredoxins. By rotating the metal binding site, we created a de novo green copper protein. This in turn was converted to a blue copper protein by removing an axial methionine. Following this rational sequence, we have successfully created red, green, and blue copper proteins within an alpha helical fold, enabling comparisons for the first time of their structure and function disconnected from the overall cupredoxin fold.
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Affiliation(s)
- Karl J Koebke
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Victor Sosa Alfaro
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Tyler B J Pinter
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Aniruddha Deb
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Nicolai Lehnert
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Cédric Tard
- LCM, CNRS, Ecole Polytechnique, IP Paris, F-91128 Palaiseau, France
| | - James E Penner-Hahn
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Vincent L Pecoraro
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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23
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Pinter TBJ, Koebke KJ, Pecoraro VL. Catalysis and Electron Transfer in De Novo Designed Helical Scaffolds. Angew Chem Int Ed Engl 2020; 59:7678-7699. [PMID: 31441170 PMCID: PMC7035182 DOI: 10.1002/anie.201907502] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Indexed: 12/31/2022]
Abstract
The relationship between protein structure and function is one of the greatest puzzles within biochemistry. De novo metalloprotein design is a way to wipe the board clean and determine what is required to build in function from the ground up in an unrelated structure. This Review focuses on protein design efforts to create de novo metalloproteins within alpha-helical scaffolds. Examples of successful designs include those with carbonic anhydrase or nitrite reductase activity by incorporating a ZnHis3 or CuHis3 site, or that recapitulate the spectroscopic properties of unique electron-transfer sites in cupredoxins (CuHis2 Cys) or rubredoxins (FeCys4 ). This work showcases the versatility of alpha helices as scaffolds for metalloprotein design and the progress that is possible through careful rational design. Our studies cover the invariance of carbonic anhydrase activity with different site positions and scaffolds, refinement of our cupredoxin models, and enhancement of nitrite reductase activity up to 1000-fold.
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Affiliation(s)
- Tyler B. J. Pinter
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, United States, 48109-1055
| | - Karl J. Koebke
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, United States, 48109-1055
| | - Vincent L. Pecoraro
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, United States, 48109-1055
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24
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Pinter TBJ, Koebke KJ, Pecoraro VL. Katalyse und Elektronentransfer in helikalen De‐novo‐Gerüststrukturen. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201907502] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Tyler B. J. Pinter
- Department of Chemistry University of Michigan Ann Arbor Michigan 48109-1055 USA
| | - Karl J. Koebke
- Department of Chemistry University of Michigan Ann Arbor Michigan 48109-1055 USA
| | - Vincent L. Pecoraro
- Department of Chemistry University of Michigan Ann Arbor Michigan 48109-1055 USA
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25
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Roy B, Pal S, Govindaraju T. Intrinsic Role of Molecular Architectonics in Enhancing the Catalytic Activity of Lead in Glucose Hydrolysis. ACS APPLIED MATERIALS & INTERFACES 2020; 12:14057-14063. [PMID: 32134618 DOI: 10.1021/acsami.0c01803] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Lewis acidity plays a key role in the catalytic activity of lead ion (PbII) in the hydrolysis of glucose in solution under harsh synthetic conditions. We report a number of structurally similar d-gluconamide amphiphiles as functional organic ligands with active an -NH center capable of coordinating PbII (viz., PbII-N-C) in basic condition to enhance the catalytic efficiency through the scheme of molecular architectonics. Amphiphiles with different hydrophobic unit form assembly-architectures with a varying second coordination sphere around the active metal ion center. As a result, the active PbII center in each architecture exhibits substantially different efficiency toward catalyzing the glucose hydrolysis under ambient temperature. The catalytic performance of the dynamic and reversible gluconamide-PbII assembly-architectures are highly dependent on their chemical environments in solution. Further, the active PbII center of gluconamide-PbII complex in the assembly architecture and dispersed states exhibits distinct outcomes with the former being a superior catalyst than the latter as well as PbII alone. The current study demonstrates the potential of molecular architectonics that relies on the hydrophobic units of designer functional amphiphiles to enrich surface electron density with enhanced σ-donation ability through space which substantially improves the catalytic efficiency of PbII toward glucose hydrolysis at ambient temperature.
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Affiliation(s)
- Bappaditya Roy
- Bioorganic Chemistry Laboratory, New Chemistry Unit and School of Advanced Materials (SAMat), Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru 560064, Karnataka, India
| | - Satyajit Pal
- Bioorganic Chemistry Laboratory, New Chemistry Unit and School of Advanced Materials (SAMat), Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru 560064, Karnataka, India
| | - Thimmaiah Govindaraju
- Bioorganic Chemistry Laboratory, New Chemistry Unit and School of Advanced Materials (SAMat), Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru 560064, Karnataka, India
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26
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Tolbert AE, Ervin CS, Ruckthong L, Paul TJ, Jayasinghe-Arachchige VM, Neupane KP, Stuckey JA, Prabhakar R, Pecoraro VL. Heteromeric three-stranded coiled coils designed using a Pb(II)(Cys) 3 template mediated strategy. Nat Chem 2020; 12:405-411. [PMID: 32123337 DOI: 10.1038/s41557-020-0423-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 01/19/2020] [Indexed: 11/09/2022]
Abstract
Three-stranded coiled coils are peptide structures constructed from amphipathic heptad repeats. Here we show that it is possible to form pure heterotrimeric three-stranded coiled coils by combining three distinct characteristics: (1) a cysteine sulfur layer for metal coordination, (2) a thiophilic, trigonal pyramidal metalloid (Pb(II)) that binds to these sulfurs and (3) an adjacent layer of reduced steric bulk generating a cavity where water can hydrogen bond to the cysteine sulfur atoms. Cysteine substitution in an a site yields Pb(II)A2B heterotrimers, while d sites provide pure Pb(II)C2D or Pb(II)CD2 scaffolds. Altering the metal from Pb(II) to Hg(II) or shifting the relative position of the sterically less demanding layer removes heterotrimer specificity. Because only two of the eight or ten hydrophobic layers are perturbed, catalytic sites can be introduced at other regions of the scaffold. A Zn(II)(histidine)3(H2O) centre can be incorporated at a remote location without perturbing the heterotrimer selectivity, suggesting a unique strategy to prepare dissymmetric catalytic sites within self-assembling de novo-designed proteins.
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Affiliation(s)
- Audrey E Tolbert
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | | | - Leela Ruckthong
- Department of Chemistry, Faculty of Science, King Mongkut's University of Technology, Thonburi (KMUTT), Bangkok, Thailand
| | - Thomas J Paul
- Department of Chemistry, University of Miami, Coral Gables, FL, USA
| | | | - Kosh P Neupane
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Jeanne A Stuckey
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, Coral Gables, FL, USA
| | - Vincent L Pecoraro
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA. .,Department of Biophysics, University of Michigan, Ann Arbor, MI, USA.
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27
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Abstract
Proteins are molecular machines whose function depends on their ability to achieve complex folds with precisely defined structural and dynamic properties. The rational design of proteins from first-principles, or de novo, was once considered to be impossible, but today proteins with a variety of folds and functions have been realized. We review the evolution of the field from its earliest days, placing particular emphasis on how this endeavor has illuminated our understanding of the principles underlying the folding and function of natural proteins, and is informing the design of macromolecules with unprecedented structures and properties. An initial set of milestones in de novo protein design focused on the construction of sequences that folded in water and membranes to adopt folded conformations. The first proteins were designed from first-principles using very simple physical models. As computers became more powerful, the use of the rotamer approximation allowed one to discover amino acid sequences that stabilize the desired fold. As the crystallographic database of protein structures expanded in subsequent years, it became possible to construct proteins by assembling short backbone fragments that frequently recur in Nature. The second set of milestones in de novo design involves the discovery of complex functions. Proteins have been designed to bind a variety of metals, porphyrins, and other cofactors. The design of proteins that catalyze hydrolysis and oxygen-dependent reactions has progressed significantly. However, de novo design of catalysts for energetically demanding reactions, or even proteins that bind with high affinity and specificity to highly functionalized complex polar molecules remains an importnant challenge that is now being achieved. Finally, the protein design contributed significantly to our understanding of membrane protein folding and transport of ions across membranes. The area of membrane protein design, or more generally of biomimetic polymers that function in mixed or non-aqueous environments, is now becoming increasingly possible.
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28
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Mathieu E, Tolbert AE, Koebke KJ, Tard C, Iranzo O, Penner-Hahn JE, Policar C, Pecoraro V. Rational De Novo Design of a Cu Metalloenzyme for Superoxide Dismutation. Chemistry 2020; 26:249-258. [PMID: 31710732 PMCID: PMC6944188 DOI: 10.1002/chem.201903808] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/04/2019] [Indexed: 01/16/2023]
Abstract
Superoxide dismutases (SODs) are highly efficient enzymes for superoxide dismutation and the first line of defense against oxidative stress. These metalloproteins contain a redox-active metal ion in their active site (Mn, Cu, Fe, Ni) with a tightly controlled reduction potential found in a close range around the optimal value of 0.36 V versus the normal hydrogen electrode (NHE). Rationally designed proteins with well-defined three-dimensional structures offer new opportunities for obtaining functional SOD mimics. Here, we explore four different copper-binding scaffolds: H3 (His3 ), H4 (His4 ), H2 DH (His3 Asp with two His and one Asp in the same plane) and H3 D (His3 Asp with three His in the same plane) by using the scaffold of the de novo protein GRα3 D. EPR and XAS analysis of the resulting copper complexes demonstrates that they are good CuII -bound structural mimics of Cu-only SODs. Furthermore, all the complexes exhibit SOD activity, though three orders of magnitude slower than the native enzyme, making them the first de novo copper SOD mimics.
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Affiliation(s)
- Emilie Mathieu
- Laboratoire des biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
- These authors contributed equally to this work
| | - Audrey E. Tolbert
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48103
- These authors contributed equally to this work
| | - Karl J. Koebke
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48103
| | - Cédric Tard
- LCM, CNRS, Ecole Polytechnique, IP Paris, F-91128 Palaiseau, France
| | - Olga Iranzo
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille, France
| | | | - Clotilde Policar
- Laboratoire des biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Vincent Pecoraro
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48103
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29
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Jeong WJ, Yu J, Song WJ. Proteins as diverse, efficient, and evolvable scaffolds for artificial metalloenzymes. Chem Commun (Camb) 2020; 56:9586-9599. [DOI: 10.1039/d0cc03137b] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
We have extracted and categorized the desirable properties of proteins that are adapted as the scaffolds for artificial metalloenzymes.
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Affiliation(s)
- Woo Jae Jeong
- Department of Chemistry
- Seoul National University
- Seoul 08826
- Republic of Korea
| | - Jaeseung Yu
- Department of Chemistry
- Seoul National University
- Seoul 08826
- Republic of Korea
| | - Woon Ju Song
- Department of Chemistry
- Seoul National University
- Seoul 08826
- Republic of Korea
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30
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Plegaria JS, Yates MD, Glaven SM, Kerfeld CA. Redox Characterization of Electrode-Immobilized Bacterial Microcompartment Shell Proteins Engineered To Bind Metal Centers. ACS APPLIED BIO MATERIALS 2019; 3:685-692. [DOI: 10.1021/acsabm.9b01023] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
| | - Matthew D. Yates
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Sarah M. Glaven
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Cheryl A. Kerfeld
- Environmental Genomics and Systems Biology and Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
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31
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Garai A, Delangle P. Recent advances in uranyl binding in proteins thanks to biomimetic peptides. J Inorg Biochem 2019; 203:110936. [PMID: 31864150 DOI: 10.1016/j.jinorgbio.2019.110936] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 11/05/2019] [Accepted: 11/17/2019] [Indexed: 12/29/2022]
Abstract
Uranium is an element belonging to the actinide series. It is ubiquitous in rock, soil, and water. Uranium is found in the ecosystem due to mining and milling industrial activities and processing to nuclear fuel, but also to the extensive use of phosphate fertilizers. Understanding uranium binding in vivo is critical, first to deepen our knowledge of molecular events leading to chemical toxicity, but also to provide new mechanistic information useful for the development of efficient decorporation treatments to be applied in case of intoxication. The most stable form in physiological conditions is the uranyl cation (UO22+), in which uranium oxidation state is +VI. This short review presents uranyl coordination properties and chelation, and what is currently known about uranium binding to proteins. Although several target proteins have been identified, the UO22+ binding sites have barely been identified. Biomimetic approaches using model peptides are good options to shed light on high affinity uranyl binding sites in proteins. A strategy based on constrained cyclodecapeptides allowed recently to propose a tetraphosphate binding site for uranyl that provides an affinity similar to the one measured with the phosphoprotein osteopontin.
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Affiliation(s)
- Aditya Garai
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, F-38000 Grenoble, France
| | - Pascale Delangle
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, F-38000 Grenoble, France.
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32
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Marshall LR, Zozulia O, Lengyel-Zhand Z, Korendovych IV. Minimalist de novo Design of Protein Catalysts. ACS Catal 2019; 9:9265-9275. [PMID: 34094654 PMCID: PMC8174531 DOI: 10.1021/acscatal.9b02509] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The field of protein design has grown enormously in the past few decades. In this review we discuss the minimalist approach to design of artificial enzymes, in which protein sequences are created with the minimum number of elements for folding and function. This method relies on identifying starting points in catalytically inert scaffolds for active site installation. The progress of the field from the original helical assemblies of the 1980s to the more complex structures of the present day is discussed, highlighting the variety of catalytic reactions which have been achieved using these methods. We outline the strengths and weaknesses of the minimalist approaches, describe representative design cases and put it in the general context of the de novo design of proteins.
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Affiliation(s)
- Liam R. Marshall
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
| | - Oleksii Zozulia
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
| | - Zsofia Lengyel-Zhand
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
| | - Ivan V. Korendovych
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
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33
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Boyle AL, Rabe M, Crone NSA, Rhys GG, Soler N, Voskamp P, Pannu NS, Kros A. Selective coordination of three transition metal ions within a coiled-coil peptide scaffold. Chem Sci 2019; 10:7456-7465. [PMID: 31489168 PMCID: PMC6713864 DOI: 10.1039/c9sc01165j] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 06/19/2019] [Indexed: 12/13/2022] Open
Abstract
Designing peptides that fold and assemble in response to metal ions tests our understanding of how peptide folding and metal binding influence one another. Here, histidine residues are introduced into the hydrophobic core of a coiled-coil trimer, generating a peptide that self-assembles upon the addition of metal ions. HisAD, the resulting peptide, is unstructured in the absence of metal and folds selectively to form an α-helical construct upon complexation with Cu(ii) and Ni(ii) but not Co(ii) or Zn(ii). The structure, and metal-binding ability, of HisAD is probed using a combination of circular dichroism (CD) spectroscopy, analytical ultracentrifugation (AUC), nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography. These show the peptide is trimeric and binds to both Cu(ii) and Ni(ii) in a 1 : 1 ratio with the histidine residues involved in the metal coordination, as designed. The X-ray crystal structure of the HisAD-Cu(ii) complex reveals the trimeric HisAD peptide coordinates three Cu(ii) ions; this is the first example of such a structure. Additionally, HisAD demonstrates an unprecedented discrimination between transition metal ions, the basis of which is likely to be related to the stability of the peptide-metal complexes formed.
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Affiliation(s)
- Aimee L Boyle
- Leiden Institute of Chemistry , Leiden University , Einsteinweg 55 , 2333 CC Leiden , The Netherlands .
| | - Martin Rabe
- Max-Planck-Institut für Eisenforschung GmbH , Max-Planck-Straße 1 , 40237 Düsseldorf , Germany
| | - Niek S A Crone
- Leiden Institute of Chemistry , Leiden University , Einsteinweg 55 , 2333 CC Leiden , The Netherlands .
| | - Guto G Rhys
- School of Chemistry , University of Bristol , Cantock's Close , Bristol , BS8 1TS , UK
| | - Nicolas Soler
- Structural Biology Unit , Institute of Molecular Biology of Barcelona (IBMB-CSIC) , Baldiri Reixac 15 , 08028 Barcelona , Spain
| | - Patrick Voskamp
- Leiden Institute of Chemistry , Leiden University , Einsteinweg 55 , 2333 CC Leiden , The Netherlands .
| | - Navraj S Pannu
- Leiden Institute of Chemistry , Leiden University , Einsteinweg 55 , 2333 CC Leiden , The Netherlands .
| | - Alexander Kros
- Leiden Institute of Chemistry , Leiden University , Einsteinweg 55 , 2333 CC Leiden , The Netherlands .
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34
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Selvan D, Prasad P, Farquhar ER, Shi Y, Crane S, Zhang Y, Chakraborty S. Redesign of a Copper Storage Protein into an Artificial Hydrogenase. ACS Catal 2019; 9:5847-5859. [PMID: 31341700 DOI: 10.1021/acscatal.9b00360] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We report the construction of an artificial hydrogenase (ArH) by reengineering a Cu storage protein (Cspl) into a Ni-binding protein (NBP) employing rational metalloprotein design. The hypothesis driven design approach involved deleting existing Cu sites of Csp1 and identification of a target tetrathiolate Ni binding site within the protein scaffold followed by repacking the hydrophobic core. Guided by modeling, the NBP was expressed and purified in high purity. NBP is a well-folded and stable construct displaying native-like unfolding behavior. Spectroscopic and computational studies indicated that the NBP bound nickel in a distorted square planar geometry that validated the design. Ni(II)-NBP is active for photo-induced H2 evolution following a reductive quenching mechanism. Ni(II)-NBP catalyzed H+ reduction to H2 gas electrochemically as well. Analysis of the catalytic voltammograms established a proton-coupled electron transfer (PCET) mechanism. Electrolysis studies confirmed H2 evolution with quantitative Faradaic yields. Our studies demonstrate an important scope of rational metalloprotein design that allows imparting functions into protein scaffolds that have natively not evolved to possess the same function of the target metalloprotein constructs.
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Affiliation(s)
- Dhanashree Selvan
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, United States
| | - Pallavi Prasad
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, United States
| | - Erik R. Farquhar
- Case Western Reserve University Center for Synchrotron Biosciences, NSLS-II, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Yelu Shi
- Department of Chemistry and Chemical Biology, Stevens Institute of Technology, 1 Castle Point on Hudson, Hoboken, New Jersey 07030, United States
| | - Skyler Crane
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, United States
| | - Yong Zhang
- Department of Chemistry and Chemical Biology, Stevens Institute of Technology, 1 Castle Point on Hudson, Hoboken, New Jersey 07030, United States
| | - Saumen Chakraborty
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, United States
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35
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Lin Y. Rational design of heme enzymes for biodegradation of pollutants toward a green future. Biotechnol Appl Biochem 2019; 67:484-494. [DOI: 10.1002/bab.1788] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 06/06/2019] [Indexed: 12/28/2022]
Affiliation(s)
- Ying‐Wu Lin
- School of Chemistry and Chemical Engineering University of South China Hengyang People's Republic of China
- Laboratory of Protein Structure and Function University of South China Hengyang People's Republic of China
- Hunan Key Laboratory for the Design and Application of Actinide Complexes University of South China Hengyang People's Republic of China
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36
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Laporte FA, Lebrun C, Vidaud C, Delangle P. Phosphate-Rich Biomimetic Peptides Shed Light on High-Affinity Hyperphosphorylated Uranyl Binding Sites in Phosphoproteins. Chemistry 2019; 25:8570-8578. [PMID: 30908736 DOI: 10.1002/chem.201900646] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Indexed: 12/31/2022]
Abstract
Some phosphoproteins such as osteopontin (OPN) have been identified as high-affinity uranyl targets. However, the binding sites required for interaction with uranyl and therefore involved in its toxicity have not been identified in the whole protein. The biomimetic approach proposed here aimed to decipher the nature of these sites and should help to understand the role of the multiple phosphorylations in UO2 2+ binding. Two hyperphosphorylated cyclic peptides, pS168 and pS1368 containing up to four phosphoserine (pSer) residues over the ten amino acids present in the sequences, were synthesized with all reactions performed in the solid phase, including post-phosphorylation. These β-sheet-structured peptides present four coordinating residues from four amino acid side chains pointing to the metal ion, either three pSer and one glutamate in pS168 or four pSer in pS1368 . Significantly, increasing the number of pSer residues up to four in the cyclodecapeptide scaffolds produced molecules with an affinity constant for UO2 2+ that is as large as that reported for osteopontin at physiological pH. The phosphate-rich pS1368 can thus be considered a relevant model of UO2 2+ coordination in this intrinsically disordered protein, which wraps around the metal ion to gather four phosphate groups in the UO2 2+ coordination sphere. These model hyperphosphorylated peptides are highly selective for UO2 2+ with respect to endogenous Ca2+ , which makes them good starting structures for selective UO2 2+ complexation.
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Affiliation(s)
- Fanny A Laporte
- INAC SyMMES, Université Grenoble Alpes, CEA, CNRS, 38000, Grenoble, France
| | - Colette Lebrun
- INAC SyMMES, Université Grenoble Alpes, CEA, CNRS, 38000, Grenoble, France
| | - Claude Vidaud
- CEA, Fundamental Research Division, Biosciences and Biotechnologies Institute of Aix-Marseille, 30207, Bagnols sur Céze, France
| | - Pascale Delangle
- INAC SyMMES, Université Grenoble Alpes, CEA, CNRS, 38000, Grenoble, France
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37
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Koebke KJ, Pecoraro VL. Noncoded Amino Acids in de Novo Metalloprotein Design: Controlling Coordination Number and Catalysis. Acc Chem Res 2019; 52:1160-1167. [PMID: 30933479 DOI: 10.1021/acs.accounts.9b00032] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The relationship between structure and function has long been one of the major points of investigation in Biophysics. Understanding how much, or how little, of a protein's often complicated structure is necessary for its function can lead to directed therapeutic strategies and would allow one to design proteins for specific desired functions. Studying protein function by de novo design builds the functionality from the ground up in a completely unrelated and noncoded protein scaffold. Our lab has used this strategy to study heavy and transition metal binding within the TRI family of three stranded coiled coil (3SCC) constructs to understand coordination geometry and metalloenzyme catalytic control within a protein environment. These peptides contain hydrophobic layers within the interior of the 3SCC, which one can mutate to metal binding residues to create a minimal metal binding site, while solid phase synthesis allows our lab to easily incorporate a number of noncoded amino acids including d enantiomers of binding or secondary coordination sphere amino acids, penicillamine, or methylated versions of histidine. Our studies of Cd(II) binding to Cys3 environments have determined, largely through the use of 113Cd NMR and 111mCd PAC, that the coordination environment around a heavy metal can be controlled by incorporating noncoded amino acids in either the primary or secondary coordination spheres. We found mutating the metal binding amino acids to l-Pen can enforce trigonal Cd(II)S3 geometry exclusively compared to the mixed coordination determined for l-Cys coordination. The same result can be achieved with secondary sphere mutations as well by incorporating d-Leu above a Cys3. We hypothesize this latter effect is due to the increased steric packing above the metal binding site that occurs when the l-Leu oriented toward the N-terminus of the scaffold is mutated to d-Leu and oriented toward the C-terminus. Mutating the layer below Cys3 to d-Leu instead formed a mixed 4- and 5-coordinate Cd(II)S3(H2O) and Cd(II)S3(H2O)2 construct as steric bulk was decreased below the metal binding site. We have also applied noncoded amino acids to metalloenzyme systems by incorporating His residues that are methylated at the δ- or ε-nitrogen to enforce Cu(I) ligation to the opposite open nitrogen of His and found a 2 orders of magnitude increased catalytic efficiency for nitrite reductase activity with ε-nitrogen coordination compared to δ-nitrogen. These results exemplify the ability to tune coordination environment and catalytic efficiency within a de novo scaffold as well as the utility of noncoded amino acids to increase the chemist's toolbox. By furthering our understanding of metalloprotein design one could envision, through our use of amino acids not normally available to nature, that protein design laboratories will soon be capable of outperforming the native systems previously used as their benchmark of successful design. The ability to design proteins at this level would have far reaching and exciting benefits within various fields including medical and industrial applications.
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Affiliation(s)
- Karl J. Koebke
- Department of Chemistry, University of Michigan Ann Arbor, Michigan 48109, United States
| | - Vincent L. Pecoraro
- Department of Chemistry, University of Michigan Ann Arbor, Michigan 48109, United States
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38
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Koebke KJ, Yu F, Van Stappen C, Pinter TBJ, Deb A, Penner-Hahn JE, Pecoraro VL. Methylated Histidines Alter Tautomeric Preferences that Influence the Rates of Cu Nitrite Reductase Catalysis in Designed Peptides. J Am Chem Soc 2019; 141:7765-7775. [PMID: 30983335 PMCID: PMC6824201 DOI: 10.1021/jacs.9b00196] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Copper proteins have the capacity to serve as both redox active catalysts and purely electron transfer centers. A longstanding question in this field is how the function of histidine ligated Cu centers are modulated by δ vs ε-nitrogen ligation of the imidazole. Evaluating the impact of these coordination modes on structure and function by comparative analysis of deposited crystal structures is confounded by factors such as differing protein folds and disparate secondary coordination spheres that make direct comparison of these isomers difficult. Here, we present a series of de novo designed proteins using the noncanonical amino acids 1-methyl-histidine and 3-methyl-histidine to create Cu nitrite reductases where δ- or ε-nitrogen ligation is enforced by the opposite nitrogen's methylation as a means of directly comparing these two ligation states in the same protein fold. We find that ε-nitrogen ligation allows for a better nitrite reduction catalyst, displaying 2 orders of magnitude higher activity than the δ-nitrogen ligated construct. Methylation of the δ nitrogen, combined with a secondary sphere mutation we have previously published, has produced a new record for efficiency within a homogeneous aqueous system, improving by 1 order of magnitude the previously published most efficient construct. Furthermore, we have measured Michaelis-Menten kinetics on these highly active constructs, revealing that the remaining barriers to matching the catalytic efficiency ( kcat/ KM) of native Cu nitrite reductase involve both substrate binding ( KM) and catalysis ( kcat).
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Affiliation(s)
- Karl J. Koebke
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Fangting Yu
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Casey Van Stappen
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Tyler B. J. Pinter
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Aniruddha Deb
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - James E. Penner-Hahn
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Vincent L. Pecoraro
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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39
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Studer S, Hansen DA, Pianowski ZL, Mittl PRE, Debon A, Guffy SL, Der BS, Kuhlman B, Hilvert D. Evolution of a highly active and enantiospecific metalloenzyme from short peptides. Science 2018; 362:1285-1288. [DOI: 10.1126/science.aau3744] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 10/31/2018] [Indexed: 12/22/2022]
Abstract
Primordial sequence signatures in modern proteins imply ancestral origins tracing back to simple peptides. Although short peptides seldom adopt unique folds, metal ions might have templated their assembly into higher-order structures in early evolution and imparted useful chemical reactivity. Recapitulating such a biogenetic scenario, we have combined design and laboratory evolution to transform a zinc-binding peptide into a globular enzyme capable of accelerating ester cleavage with exacting enantiospecificity and high catalytic efficiency (kcat/KM~ 106M−1s−1). The simultaneous optimization of structure and function in a naïve peptide scaffold not only illustrates a plausible enzyme evolutionary pathway from the distant past to the present but also proffers exciting future opportunities for enzyme design and engineering.
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40
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Taylor LLK, Riddell IA, Smulders MMJ. Selbstorganisation von funktionellen diskreten dreidimensionalen Architekturen in Wasser. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201806297] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Lauren L. K. Taylor
- School of Chemistry; University of Manchester; Oxford Road M13 9PL Großbritannien
| | - Imogen A. Riddell
- School of Chemistry; University of Manchester; Oxford Road M13 9PL Großbritannien
| | - Maarten M. J. Smulders
- Laboratory of Organic Chemistry; Wageningen University, P.O. Box 8026; 6700EG Wageningen Niederlande
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41
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Taylor LLK, Riddell IA, Smulders MMJ. Self-Assembly of Functional Discrete Three-Dimensional Architectures in Water. Angew Chem Int Ed Engl 2018; 58:1280-1307. [DOI: 10.1002/anie.201806297] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Indexed: 01/01/2023]
Affiliation(s)
| | - Imogen A. Riddell
- School of Chemistry; University of Manchester; Oxford Road M13 9PL UK
| | - Maarten M. J. Smulders
- Laboratory of Organic Chemistry; Wageningen University, P.O. Box 8026; 6700EG Wageningen The Netherlands
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42
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Rink WM, Thomas F. De Novo Designed α-Helical Coiled-Coil Peptides as Scaffolds for Chemical Reactions. Chemistry 2018; 25:1665-1677. [DOI: 10.1002/chem.201802849] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Indexed: 01/31/2023]
Affiliation(s)
- W. Mathis Rink
- Institute of Organic and Biomolecular Chemistry; Georg-August-Universität Göttingen; Tammannstraße 2 37077 Göttingen Germany
| | - Franziska Thomas
- Institute of Organic and Biomolecular Chemistry; Georg-August-Universität Göttingen; Tammannstraße 2 37077 Göttingen Germany
- Center for Biostructural Imaging of Neurodegeneration; Von-Siebold-Straße 3a 37075 Göttingen Germany
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43
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Chuang WJ, Narwane M, Chen HY, Kao CL, Huang B, Hsu KM, Wang YM, Hsu SCN. Nitric oxide-release study of a bio-inspired copper(i)-nitrito complex under chemical and biological conditions. Dalton Trans 2018; 47:13151-13157. [PMID: 30175363 DOI: 10.1039/c8dt02281j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The selective and efficient nitrite reduction process is ubiquitous in biological systems. To understand copper-mediated nitrite reduction, we developed a bio-inspired model system to investigate the mechanism of copper-containing nitrite reductase. A well-characterized copper(i)-nitrate complex with amino functionalized 2-(diphenylphosphino)aniline ligands, [(Ph2PC6H4(o-NH2))2Cu(ONO)], demonstrated the aniline protonation will cause NO release in an acidic environment. To further understand NO releasing ability, we also performed pH-dependency experiments and confocal imaging to release NO under physiological buffer conditions. According to titration and spectroscopic studies on the protonation reaction of complex [(Ph2PC6H4(o-NH2))2Cu(ONO)], we proposed a mechanistic pathway for proton transfer and NO release. Furthermore, DFT calculations predicted that the release of NO takes place via aniline in both organic and aqueous media. These results highlight the importance of the proton-rich microenvironment around the copper(i)-nitrite core to induce nitrate reduction in a chemical and biological environment.
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Affiliation(s)
- Wan-Jung Chuang
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
| | - Manmath Narwane
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
| | - Hsing-Yin Chen
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
| | - Chai-Lin Kao
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung 807, Taiwan. and Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
| | - Bin Huang
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Kuang-Mei Hsu
- Department of Biological Science and Technology, Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu 300, Taiwan.
| | - Yun-Ming Wang
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung 807, Taiwan and Department of Biological Science and Technology, Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu 300, Taiwan.
| | - Sodio C N Hsu
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung 807, Taiwan. and Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
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44
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Koebke KJ, Pecoraro VL. Development of de Novo Copper Nitrite Reductases: Where We Are and Where We Need To Go. ACS Catal 2018; 8:8046-8057. [PMID: 30294504 DOI: 10.1021/acscatal.8b02153] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The development of redox-active metalloprotein catalysts is a challenging objective of de novo protein design. Within this Perspective we detail our efforts to create a redox-active Cu nitrite reductase (NiR) by incorporating Cu into the hydrophobic interior of well-defined three-stranded coiled coils (3SCCs). The scaffold contains three histidine residues that provide a layer of three nitrogen donors that mimic the type 2 catalytic site of NiR. We have found that this strategy successfully produces an active and stable CuNiR model that functions for over 1000 turnovers. Spectroscopic evidence indicates that the Cu(I) site has a lower coordination number in comparison to the enzyme, whereas the Cu(II) geometry may more faithfully reproduce the NiR type 2 center. Mutations at the helical interface successfully produce a hydrogen bond between an interfacial Glu residue and the Culigating His residue, which allows for the tuning of the redox potential over a 100 mV range. We successfully created constructs with as much as a 120-fold improvement from the original design by modifying the steric bulk above or below the Cu binding site. These systems are now the most active water-soluble and stable artificial NiR catalysts yet produced. Several avenues for improving the catalytic efficiency of later designs are detailed within this Perspective, including adjustment of their resting oxidation state, the use of asymmetric scaffolds to allow for single amino acid mutation within the second coordination sphere, and the design of hydrogen-bonding networks to tune residue orientation and electronics. Through these studies the TRI-H system has given insight into the difficulties that arise in creating a de novo redox active enzyme. Work to improve upon this model will provide strategies by which redox-active de novo enzymes may be tuned and detail how native enzymes accomplish catalytic efficiencies through proton gated redox catalysis.
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Affiliation(s)
- Karl J. Koebke
- Department of Chemistry, University of Michigan Ann Arbor, Michigan 48109, United States
| | - Vincent L. Pecoraro
- Department of Chemistry, University of Michigan Ann Arbor, Michigan 48109, United States
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45
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Abstract
Self-assembly of molecules often results in new emerging properties. Even very short peptides can self-assemble into structures with a variety of physical and structural characteristics. Remarkably, many peptide assemblies show high catalytic activity in model reactions reaching efficiencies comparable to those found in natural enzymes by weight. In this review, we discuss different strategies used to rationally develop self-assembled peptide catalysts with natural and unnatural backbones as well as with metal-containing cofactors.
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Affiliation(s)
- O Zozulia
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA.
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46
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Cioncoloni G, Roger I, Wheatley PS, Wilson C, Morris RE, Sproules S, Symes MD. Proton-Coupled Electron Transfer Enhances the Electrocatalytic Reduction of Nitrite to NO in a Bioinspired Copper Complex. ACS Catal 2018. [DOI: 10.1021/acscatal.8b00361] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Giacomo Cioncoloni
- WestCHEM, School of Chemistry, University of Glasgow, University Avenue, Glasgow G12 8QQ, United Kingdom
| | - Isolda Roger
- WestCHEM, School of Chemistry, University of Glasgow, University Avenue, Glasgow G12 8QQ, United Kingdom
| | - Paul S. Wheatley
- EaStCHEM School of Chemistry, University of St Andrews, Purdie Building, St Andrews KY16 9ST, United Kingdom
| | - Claire Wilson
- WestCHEM, School of Chemistry, University of Glasgow, University Avenue, Glasgow G12 8QQ, United Kingdom
| | - Russell E. Morris
- EaStCHEM School of Chemistry, University of St Andrews, Purdie Building, St Andrews KY16 9ST, United Kingdom
| | - Stephen Sproules
- WestCHEM, School of Chemistry, University of Glasgow, University Avenue, Glasgow G12 8QQ, United Kingdom
| | - Mark D. Symes
- WestCHEM, School of Chemistry, University of Glasgow, University Avenue, Glasgow G12 8QQ, United Kingdom
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47
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Koebke KJ, Yu F, Salerno E, Van Stappen C, Tebo AG, Penner-Hahn JE, Pecoraro VL. Modifying the Steric Properties in the Second Coordination Sphere of Designed Peptides Leads to Enhancement of Nitrite Reductase Activity. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201712757] [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)
- Karl J. Koebke
- Department of Chemistry; University of Michigan; Ann Arbor MI 48109 USA
| | - Fangting Yu
- Department of Chemistry; University of Michigan; Ann Arbor MI 48109 USA
| | - Elvin Salerno
- Department of Chemistry; University of Michigan; Ann Arbor MI 48109 USA
| | - Casey Van Stappen
- Department of Chemistry; University of Michigan; Ann Arbor MI 48109 USA
| | - Alison G. Tebo
- Department of Chemistry; University of Michigan; Ann Arbor MI 48109 USA
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48
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Koebke KJ, Yu F, Salerno E, Van Stappen C, Tebo AG, Penner-Hahn JE, Pecoraro VL. Modifying the Steric Properties in the Second Coordination Sphere of Designed Peptides Leads to Enhancement of Nitrite Reductase Activity. Angew Chem Int Ed Engl 2018; 57:3954-3957. [PMID: 29316146 DOI: 10.1002/anie.201712757] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Indexed: 11/10/2022]
Abstract
Protein design is a useful strategy to interrogate the protein structure-function relationship. We demonstrate using a highly modular 3-stranded coiled coil (TRI-peptide system) that a functional type 2 copper center exhibiting copper nitrite reductase (NiR) activity exhibits the highest homogeneous catalytic efficiency under aqueous conditions for the reduction of nitrite to NO and H2 O. Modification of the amino acids in the second coordination sphere of the copper center increases the nitrite reductase activity up to 75-fold compared to previously reported systems. We find also that steric bulk can be used to enforce a three-coordinate CuI in a site, which tends toward two-coordination with decreased steric bulk. This study demonstrates the importance of the second coordination sphere environment both for controlling metal-center ligation and enhancing the catalytic efficiency of metalloenzymes and their analogues.
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Affiliation(s)
- Karl J Koebke
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Fangting Yu
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Elvin Salerno
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Casey Van Stappen
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Alison G Tebo
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Vincent L Pecoraro
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
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Design of artificial metalloproteins/metalloenzymes by tuning noncovalent interactions. J Biol Inorg Chem 2017; 23:7-25. [DOI: 10.1007/s00775-017-1506-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Accepted: 09/20/2017] [Indexed: 12/12/2022]
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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: 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.
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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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