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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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2
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Kerns S, Biswas A, Minnetian NM, Borovik AS. Artificial Metalloproteins: At the Interface between Biology and Chemistry. JACS AU 2022; 2:1252-1265. [PMID: 35783165 PMCID: PMC9241007 DOI: 10.1021/jacsau.2c00102] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 04/13/2022] [Accepted: 04/15/2022] [Indexed: 05/22/2023]
Abstract
Artificial metalloproteins (ArMs) have recently gained significant interest due to their potential to address issues in a broad scope of applications, including biocatalysis, biotechnology, protein assembly, and model chemistry. ArMs are assembled by the incorporation of a non-native metallocofactor into a protein scaffold. This can be achieved by a number of methods that apply tools of chemical biology, computational de novo design, and synthetic chemistry. In this Perspective, we highlight select systems in the hope of demonstrating the breadth of ArM design strategies and applications and emphasize how these systems address problems that are otherwise difficult to do so with strictly biochemical or synthetic approaches.
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3
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Miller KR, Biswas S, Jasniewski A, Follmer AH, Biswas A, Albert T, Sabuncu S, Bominaar EL, Hendrich MP, Moënne-Loccoz P, Borovik AS. Artificial Metalloproteins with Dinuclear Iron-Hydroxido Centers. J Am Chem Soc 2021; 143:2384-2393. [PMID: 33528256 DOI: 10.1021/jacs.0c12564] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Dinuclear iron centers with a bridging hydroxido or oxido ligand form active sites within a variety of metalloproteins. A key feature of these sites is the ability of the protein to control the structures around the Fe centers, which leads to entatic states that are essential for function. To simulate this controlled environment, artificial proteins have been engineered using biotin-streptavidin (Sav) technology in which Fe complexes from adjacent subunits can assemble to form [FeIII-(μ-OH)-FeIII] cores. The assembly process is promoted by the site-specific localization of the Fe complexes within a subunit through the designed mutation of a tyrosinate side chain to coordinate the Fe centers. An important outcome is that the Sav host can regulate the Fe···Fe separation, which is known to be important for function in natural metalloproteins. Spectroscopic and structural studies from X-ray diffraction methods revealed uncommonly long Fe···Fe separations that change by less than 0.3 Å upon the binding of additional bridging ligands. The structural constraints imposed by the protein host on the di-Fe cores are unique and create examples of active sites having entatic states within engineered artificial metalloproteins.
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Affiliation(s)
- Kelsey R Miller
- Department of Chemistry, 1102 Natural Sciences II, University of California, Irvine, California 92697, United States
| | - Saborni Biswas
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Andrew Jasniewski
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697, United States
| | - Alec H Follmer
- Department of Chemistry, 1102 Natural Sciences II, University of California, Irvine, California 92697, United States
| | - Ankita Biswas
- Department of Chemistry, 1102 Natural Sciences II, University of California, Irvine, California 92697, United States
| | - Therese Albert
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Mail Code HRC3, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, United States
| | - Sinan Sabuncu
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Mail Code HRC3, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, United States
| | - Emile L Bominaar
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Michael P Hendrich
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Pierre Moënne-Loccoz
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Mail Code HRC3, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, United States
| | - A S Borovik
- Department of Chemistry, 1102 Natural Sciences II, University of California, Irvine, California 92697, United States
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4
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Meunier A, Singleton ML, Kauffmann B, Granier T, Lautrette G, Ferrand Y, Huc I. Aromatic foldamers as scaffolds for metal second coordination sphere design. Chem Sci 2020; 11:12178-12186. [PMID: 34094430 PMCID: PMC8162952 DOI: 10.1039/d0sc05143h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 10/11/2020] [Indexed: 11/21/2022] Open
Abstract
As metalloproteins exemplify, the chemical and physical properties of metal centers depend not only on their first but also on their second coordination sphere. Installing arrays of functional groups around the first coordination sphere of synthetic metal complexes is thus highly desirable, but it remains a challenging objective. Here we introduce a novel approach to produce tailored second coordination spheres. We used bioinspired artificial architectures based on aromatic oligoamide foldamers to construct a rigid, modular and well-defined environment around a metal complex. Specifically, aza-aromatic monomers having a tethered [2Fe-2S] cluster have been synthesized and incorporated in conical helical foldamer sequences. Exploiting the modularity and predictability of aromatic oligoamide structures allowed for the straightforward design of a conical architecture able to sequester the metal complex in a confined environment. Even though no direct metal complex-foldamer interactions were purposely designed in this first generation model, crystallography, NMR and IR spectroscopy concurred to show that the aromatic oligoamide backbone alters the structure and fluxional processes of the metal cluster.
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Affiliation(s)
- Antoine Meunier
- Université de Bordeaux, CNRS, Bordeaux Institut National Polytechnique, CBMN (UMR 5248), IECB 2 Rue Robert Escarpit 33600 Pessac France
| | - Michael L Singleton
- Université de Bordeaux, CNRS, Bordeaux Institut National Polytechnique, CBMN (UMR 5248), IECB 2 Rue Robert Escarpit 33600 Pessac France
| | - Brice Kauffmann
- Université de Bordeaux, CNRS, INSERM, Institut Européen de Chimie et Biologie (UMS 3033) 2 Rue Robert Escarpit 33600 Pessac France
| | - Thierry Granier
- Université de Bordeaux, CNRS, Bordeaux Institut National Polytechnique, CBMN (UMR 5248), IECB 2 Rue Robert Escarpit 33600 Pessac France
| | - Guillaume Lautrette
- Université de Bordeaux, CNRS, Bordeaux Institut National Polytechnique, CBMN (UMR 5248), IECB 2 Rue Robert Escarpit 33600 Pessac France
| | - Yann Ferrand
- Université de Bordeaux, CNRS, Bordeaux Institut National Polytechnique, CBMN (UMR 5248), IECB 2 Rue Robert Escarpit 33600 Pessac France
| | - Ivan Huc
- Université de Bordeaux, CNRS, Bordeaux Institut National Polytechnique, CBMN (UMR 5248), IECB 2 Rue Robert Escarpit 33600 Pessac France
- Department of Pharmacy, Centre for Integrated Protein Science, Ludwig-Maximilians-Universität Butenandtstraße 5-13 D-81377 Munich Germany
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5
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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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6
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Miller KR, Paretsky JD, Follmer AH, Heinisch T, Mittra K, Gul S, Kim IS, Fuller FD, Batyuk A, Sutherlin KD, Brewster AS, Bhowmick A, Sauter NK, Kern J, Yano J, Green MT, Ward TR, Borovik AS. Artificial Iron Proteins: Modeling the Active Sites in Non-Heme Dioxygenases. Inorg Chem 2020; 59:6000-6009. [PMID: 32309932 PMCID: PMC7219546 DOI: 10.1021/acs.inorgchem.9b03791] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An important class of non-heme dioxygenases contains a conserved Fe binding site that consists of a 2-His-1-carboxylate facial triad. Results from structural biology show that, in the resting state, these proteins are six-coordinate with aqua ligands occupying the remaining three coordination sites. We have utilized biotin-streptavidin (Sav) technology to design new artificial Fe proteins (ArMs) that have many of the same structural features found within active sites of these non-heme dioxygenases. An Sav variant was isolated that contains the S112E mutation, which installed a carboxylate side chain in the appropriate position to bind to a synthetic FeII complex confined within Sav. Structural studies using X-ray diffraction (XRD) methods revealed a facial triad binding site that is composed of two N donors from the biotinylated ligand and the monodentate coordination of the carboxylate from S112E. Two aqua ligands complete the primary coordination sphere of the FeII center with both involved in hydrogen bond networks within Sav. The corresponding FeIII protein was also prepared and structurally characterized to show a six-coordinate complex with two exogenous acetato ligands. The FeIII protein was further shown to bind an exogenous azido ligand through replacement of one acetato ligand. Spectroscopic studies of the ArMs in solution support the results found by XRD.
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Affiliation(s)
- Kelsey R. Miller
- Department of Chemistry, 1102 Natural Science II, University of California, Irvine, CA 9269
| | - Jonathan D. Paretsky
- Department of Chemistry, 1102 Natural Science II, University of California, Irvine, CA 9269
| | - Alec H. Follmer
- Department of Chemistry, 1102 Natural Science II, University of California, Irvine, CA 9269
| | - Tillmann Heinisch
- Department of Chemistry, University of Basel, PO Box 3350, Mattenstrasse 24a, BPR 1096, CH-4002 Basel, Switzerland
| | - Kaustuv Mittra
- Department of Molecular Biosciences and Biochemistry, University of California, Irvine, CA 92697
| | - Sheraz Gul
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - In-Sik Kim
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Franklin D. Fuller
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025 USA
| | - Alexander Batyuk
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025 USA
| | - Kyle D. Sutherlin
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Aaron S. Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Asmit Bhowmick
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Nicholas K. Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Michael T. Green
- Department of Chemistry, 1102 Natural Science II, University of California, Irvine, CA 9269
- Department of Molecular Biosciences and Biochemistry, University of California, Irvine, CA 92697
| | - Thomas R. Ward
- Department of Chemistry, University of Basel, PO Box 3350, Mattenstrasse 24a, BPR 1096, CH-4002 Basel, Switzerland
| | - A. S. Borovik
- Department of Chemistry, 1102 Natural Science II, University of California, Irvine, CA 9269
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7
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Roy A, Vaughn MD, Tomlin J, Booher GJ, Kodis G, Simmons CR, Allen JP, Ghirlanda G. Enhanced Photocatalytic Hydrogen Production by Hybrid Streptavidin-Diiron Catalysts. Chemistry 2020; 26:6240-6246. [PMID: 32201996 DOI: 10.1002/chem.202000204] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/24/2020] [Indexed: 01/22/2023]
Abstract
Hybrid protein-organometallic catalysts are being explored for selective catalysis of a number of reactions, because they utilize the complementary strengths of proteins and of organometallic complex. Herein, we present an artificial hydrogenase, StrepH2, built by incorporating a biotinylated [Fe-Fe] hydrogenase organometallic mimic within streptavidin. This strategy takes advantage of the remarkable strength and specificity of biotin-streptavidin recognition, which drives quantitative incorporation of the biotinylated diironhexacarbonyl center into streptavidin, as confirmed by UV/Vis spectroscopy and X-ray crystallography. FTIR spectra of StrepH2 show characteristic peaks at shift values indicative of interactions between the catalyst and the protein scaffold. StrepH2 catalyzes proton reduction to hydrogen in aqueous media during photo- and electrocatalysis. Under photocatalytic conditions, the protein-embedded catalyst shows enhanced efficiency and prolonged activity compared to the isolated catalyst. Transient absorption spectroscopy data suggest a mechanism for the observed increase in activity underpinned by an observed longer lifetime for the catalytic species FeI Fe0 when incorporated within streptavidin compared to the biotinylated catalyst in solution.
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Affiliation(s)
- Anindya Roy
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA.,Present Address: Molecular Engineering and Sciences, Institute for Protein Design, University of Washington, Seattle, WA, 98195-1655, USA
| | - Michael D Vaughn
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - John Tomlin
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Garrett J Booher
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Gerdenis Kodis
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Chad R Simmons
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - James P Allen
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Giovanna Ghirlanda
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
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8
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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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9
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Alwan KB, Welch EF, Arias RJ, Gambill BF, Blackburn NJ. Rational Design of a Histidine-Methionine Site Modeling the M-Center of Copper Monooxygenases in a Small Metallochaperone Scaffold. Biochemistry 2019; 58:3097-3108. [PMID: 31243953 DOI: 10.1021/acs.biochem.9b00312] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mononuclear copper monooxygenases peptidylglycine monooxygenase (PHM) and dopamine β-monooxygenase (DBM) catalyze the hydroxylation of high energy C-H bonds utilizing a pair of chemically distinct copper sites (CuH and CuM) separated by 11 Å. In earlier work, we constructed single-site PHM variants that were designed to allow the study of the M- and H-centers independently in order to place their reactivity sequentially along the catalytic pathway. More recent crystallographic studies suggest that these single-site variants may not be truly representative of the individual active sites. In this work, we describe an alternative approach that uses a rational design to construct an artificial PHM model in a small metallochaperone scaffold. Using site-directed mutagenesis, we constructed variants that provide a His2Met copper-binding ligand set that mimics the M-center of PHM. The results show that the model accurately reproduces the chemical and spectroscopic properties of the M-center, including details of the methionine coordination, and the properties of Cu(I) and Cu(II) states in the presence of endogenous ligands such as CO and azide. The rate of reduction of the Cu(II) form of the model by the chromophoric reductant N,N'-dimethyl phenylenediamine (DMPD) has been compared with that of the PHM M-center, and the reaction chemistry of the Cu(I) forms with molecular oxygen has also been explored, revealing an unusually low reactivity toward molecular oxygen. This latter finding emphasizes the importance of substrate triggering of oxygen reactivity and implies that the His2Met ligand set, while necessary, is insufficient on its own to activate oxygen in these enzyme systems.
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Affiliation(s)
- Katherine B Alwan
- Department of Chemical Physiology and Biochemistry , Oregon Health & Sciences University , Portland , Oregon 97239 , United States
| | - Evan F Welch
- Department of Chemical Physiology and Biochemistry , Oregon Health & Sciences University , Portland , Oregon 97239 , United States
| | - Renee J Arias
- Department of Chemical Physiology and Biochemistry , Oregon Health & Sciences University , Portland , Oregon 97239 , United States
| | - Ben F Gambill
- Department of Chemical Physiology and Biochemistry , Oregon Health & Sciences University , Portland , Oregon 97239 , United States
| | - Ninian J Blackburn
- Department of Chemical Physiology and Biochemistry , Oregon Health & Sciences University , Portland , Oregon 97239 , United States
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10
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Koebke KJ, Ruckthong L, Meagher JL, Mathieu E, Harland J, Deb A, Lehnert N, Policar C, Tard C, Penner-Hahn JE, Stuckey JA, Pecoraro VL. Clarifying the Copper Coordination Environment in a de Novo Designed Red Copper Protein. Inorg Chem 2018; 57:12291-12302. [PMID: 30226758 DOI: 10.1021/acs.inorgchem.8b01989] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cupredoxins are copper-dependent electron-transfer proteins that can be categorized as blue, purple, green, and red depending on the spectroscopic properties of the Cu(II) bound forms. Interestingly, despite significantly different first coordination spheres and nuclearity, all cupredoxins share a common Greek Key β-sheet fold. We have previously reported the design of a red copper protein within a completely distinct three-helical bundle protein, α3DChC2. (1) While this design demonstrated that a β-barrel fold was not requisite to recapitulate the properties of a native cupredoxin center, the parent peptide α3D was not sufficiently stable to allow further study through additional mutations. Here we present the design of an elongated protein GRANDα3D (GRα3D) with Δ Gu = -11.4 kcal/mol compared to the original design's -5.1 kcal/mol. Diffraction quality crystals were grown of GRα3D (a first for an α3D peptide) and solved to a resolution of 1.34 Å. Examination of this structure suggested that Glu41 might interact with the Cu in our previously reported red copper protein. The previous bis(histidine)(cysteine) site (GRα3DChC2) was designed into this new scaffold and a series of variant constructs were made to explore this hypothesis. Mutation studies around Glu41 not only prove the proposed interaction, but also enabled tuning of the constructs' hyperfine coupling constant from 160 to 127 × 10-4 cm-1. X-ray absorption spectroscopy analysis is consistent with these hyperfine coupling differences being the result of variant 4p mixing related to coordination geometry changes. These studies not only prove that an Glu41-Cu interaction leads to the α3DChC2 construct's red copper protein like spectral properties, but also exemplify the exact control one can have in a de novo construct to tune the properties of an electron-transfer Cu site.
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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
| | | | | | | | - Clotilde Policar
- Laboratoire des biomolécules, LBM, Département de chimie , École normale supérieure, PSL University, Sorbonne Université, CNRS , 75005 Paris , France
| | - Cédric Tard
- LCM, CNRS, Ecole Polytechnique , Université Paris-Saclay , 91128 Palaiseau Cedex , France
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11
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Mann SI, Heinisch T, Ward TR, Borovik AS. Coordination chemistry within a protein host: regulation of the secondary coordination sphere. Chem Commun (Camb) 2018; 54:4413-4416. [PMID: 29645031 DOI: 10.1039/c8cc01931b] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Secondary coordination spheres of metal complexes are instrumental in controlling properties that are linked to function. To study these effects in aqueous solutions artificial Cu proteins have been developed using biotin-streptavidin (Sav) technology and their binding of external azide ions investigated. Parallel binding studies were done in crystallo on single crystals of the artificial Cu proteins. Spectroscopic changes in solution are consistent with azide binding to the Cu centers. Structural studies corroborate that a Cu-N3 unit is present in each Sav subunit and reveal the composition of hydrogen bonding (H-bonding) networks that include the coordinated azido ligand. The networks involve amino acid residues and water molecules within the secondary coordination sphere. Mutation of these residues to ones that cannot form H-bonds caused a measurble change in the equilibrium binding constants that were measured in solution. These findings further demonstrate the utility of biotin-Sav technology to prepare water-stable inorganic complexes whose structures can be controlled within both primary and secondary coordination spheres.
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Affiliation(s)
- Samuel I Mann
- Department of Chemistry, 1102 Natural Science II, University of California, Irvine, CA 92697, USA.
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Keller SG, Probst B, Heinisch T, Alberto R, Ward TR. Photo-Driven Hydrogen Evolution by an Artificial Hydrogenase Utilizing the Biotin-Streptavidin Technology. Helv Chim Acta 2018. [DOI: 10.1002/hlca.201800036] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Sascha G. Keller
- Department of Chemistry; University of Basel; Mattenstrasse 24a 4002 Basel Switzerland
| | - Benjamin Probst
- Department of Chemistry; University of Zürich; Winterthurerstrasse 190 8057 Zürich Switzerland
| | - Tillmann Heinisch
- Department of Chemistry; University of Basel; Mattenstrasse 24a 4002 Basel Switzerland
| | - Roger Alberto
- Department of Chemistry; University of Zürich; Winterthurerstrasse 190 8057 Zürich Switzerland
| | - Thomas R. Ward
- Department of Chemistry; University of Basel; Mattenstrasse 24a 4002 Basel Switzerland
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Olshansky L, Huerta-Lavorie R, Nguyen AI, Vallapurackal J, Furst A, Tilley TD, Borovik AS. Artificial Metalloproteins Containing Co 4O 4 Cubane Active Sites. J Am Chem Soc 2018; 140:2739-2742. [PMID: 29401385 PMCID: PMC5866047 DOI: 10.1021/jacs.7b13052] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Artificial metalloproteins (ArMs) containing Co4O4 cubane active sites were constructed via biotin-streptavidin technology. Stabilized by hydrogen bonds (H-bonds), terminal and cofacial CoIII-OH2 moieties are observed crystallographically in a series of immobilized cubane sites. Solution electrochemistry provided correlations of oxidation potential and pH. For variants containing Ser and Phe adjacent to the metallocofactor, 1e-/1H+ chemistry predominates until pH 8, above which the oxidation becomes pH-independent. Installation of Tyr proximal to the Co4O4 active site provided a single H-bond to one of a set of cofacial CoIII-OH2 groups. With this variant, multi-e-/multi-H+ chemistry is observed, along with a change in mechanism at pH 9.5 that is consistent with Tyr deprotonation. With structural similarities to both the oxygen-evolving complex of photosystem II (H-bonded Tyr) and to thin film water oxidation catalysts (Co4O4 core), these findings bridge synthetic and biological systems for water oxidation, highlighting the importance of secondary sphere interactions in mediating multi-e-/multi-H+ reactivity.
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Affiliation(s)
- Lisa Olshansky
- Department of Chemistry, University of California, Irvine , Irvine, California 92697, United States
| | - Raúl Huerta-Lavorie
- Department of Chemistry, University of California, Berkeley , Berkeley, California 94720, United States
| | - Andy I Nguyen
- Department of Chemistry, University of California, Berkeley , Berkeley, California 94720, United States
| | - Jaicy Vallapurackal
- Department of Chemistry, University of California, Irvine , Irvine, California 92697, United States
| | - Ariel Furst
- Department of Chemistry, University of California, Berkeley , Berkeley, California 94720, United States
| | - T Don Tilley
- Department of Chemistry, University of California, Berkeley , Berkeley, California 94720, United States
- Chemical Science Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - A S Borovik
- Department of Chemistry, University of California, Irvine , Irvine, California 92697, United States
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Colomban C, Martin-Diaconescu V, Parella T, Goeb S, García-Simón C, Lloret-Fillol J, Costas M, Ribas X. Design of Zn-, Cu-, and Fe-Coordination Complexes Confined in a Self-Assembled Nanocage. Inorg Chem 2018; 57:3529-3539. [PMID: 29293325 DOI: 10.1021/acs.inorgchem.7b02852] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The encapsulation of coordination complexes in a tetragonal prismatic nanocage (1·(BArF)8) built from Zn-porphyrin and macrocyclic Pd-clip-based synthons is described. The functional duality of the guest ligand L1 allows for its encapsulation inside the cage 1·(BArF)8, along with the simultaneous coordination of ZnII, CuII, or FeIII metal ions. Remarkably, the coordination chemistry inside the host-guest adduct L1⊂1·(BArF)8 occurs in both solution solution and solid state. The resulting confined metallocomplexes have been characterized by means of UV-vis, ESI-HRMS, NMR, and EPR techniques. Furthermore, the emission of the Zn-porphyrin fluorophores of 1·(BArF)8 is strongly quenched by the encapsulation of paramagnetic complexes, representing a remarkable example of guest-dependent tuning of the host fluorescence.
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Affiliation(s)
- Cédric Colomban
- Institut de Química Computacional i Catàlisi , Universitat de Girona, Campus Montilivi , 17003 Girona , Catalonia , Spain
| | - Vlad Martin-Diaconescu
- Institute of Chemical Research of Catalonia (ICIQ) , The Barcelona Institute of Science and Technology , Avinguda Paisos Catalans 16 , 43007 Tarragona , Catalonia , Spain
| | - Teodor Parella
- Servei de RMN, Facultat de Ciències , Universitat Autònoma de Barcelona, Campus UAB , E-08193 Bellaterra , Catalonia , Spain
| | - Sébastien Goeb
- Université d'Angers, CNRS UMR 6200 , Laboratoire MOLTECH-Anjou , 2 bd Lavoisier , 49045 Angers Cedex , France
| | - Cristina García-Simón
- Institut de Química Computacional i Catàlisi , Universitat de Girona, Campus Montilivi , 17003 Girona , Catalonia , Spain
| | - Julio Lloret-Fillol
- Institute of Chemical Research of Catalonia (ICIQ) , The Barcelona Institute of Science and Technology , Avinguda Paisos Catalans 16 , 43007 Tarragona , Catalonia , Spain
| | - Miquel Costas
- Institut de Química Computacional i Catàlisi , Universitat de Girona, Campus Montilivi , 17003 Girona , Catalonia , Spain
| | - Xavi Ribas
- Institut de Química Computacional i Catàlisi , Universitat de Girona, Campus Montilivi , 17003 Girona , Catalonia , Spain
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Keller SG, Pannwitz A, Mallin H, Wenger OS, Ward TR. Streptavidin as a Scaffold for Light-Induced Long-Lived Charge Separation. Chemistry 2017; 23:18019-18024. [PMID: 29024136 DOI: 10.1002/chem.201703885] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Indexed: 01/03/2023]
Abstract
Long-lived photo-driven charge separation is demonstrated by assembling a triad on a protein scaffold. For this purpose, a biotinylated triarylamine was added to a RuII -streptavidin conjugate bearing a methyl viologen electron acceptor covalently linked to the N-terminus of streptavidin. To improve the rate and lifetime of the electron transfer, a negative patch consisting of up to three additional negatively charged amino acids was engineered through mutagenesis close to the biotin-binding pocket of streptavidin. Time-resolved laser spectroscopy revealed that the covalent attachment and the negative patch were beneficial for charge separation within the streptavidin hosted triad; the charge separated state was generated within the duration of the excitation laser pulse, and lifetimes up to 3120 ns could be achieved with the optimized supramolecular triad.
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Affiliation(s)
- Sascha G Keller
- Department of Chemistry, University of Basel, Mattenstrasse 24a, CH-4002, Basel, Switzerland
| | - Andrea Pannwitz
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, CH-4056, Basel, Switzerland
| | - Hendrik Mallin
- Department of Chemistry, University of Basel, Mattenstrasse 24a, CH-4002, Basel, Switzerland
| | - Oliver S Wenger
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, CH-4056, Basel, Switzerland
| | - Thomas R Ward
- Department of Chemistry, University of Basel, Mattenstrasse 24a, CH-4002, Basel, Switzerland
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Mann SI, Heinisch T, Ward TR, Borovik AS. Peroxide Activation Regulated by Hydrogen Bonds within Artificial Cu Proteins. J Am Chem Soc 2017; 139:17289-17292. [PMID: 29117678 DOI: 10.1021/jacs.7b10452] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Copper-hydroperoxido species (CuII-OOH) have been proposed to be key intermediates in biological and synthetic oxidations. Using biotin-streptavidin (Sav) technology, artificial copper proteins have been developed to stabilize a CuII-OOH complex in solution and in crystallo. Stability is achieved because the Sav host provides a local environment around the Cu-OOH that includes a network of hydrogen bonds to the hydroperoxido ligand. Systematic deletions of individual hydrogen bonds to the Cu-OOH complex were accomplished using different Sav variants and demonstrated that stability is achieved with a single hydrogen bond to the proximal O-atom of the hydroperoxido ligand: changing this interaction to only include the distal O-atom produced a reactive variant that oxidized an external substrate.
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Affiliation(s)
- Samuel I Mann
- Department of Chemistry, University of California , 1102 Natural Science II, Irvine, California 92697, United States
| | - Tillmann Heinisch
- Department of Chemistry, University of Basel , P.O. Box 3350, Mattenstrasse 24a, BPR 1096, CH-4002 Basel, Switzerland
| | - Thomas R Ward
- Department of Chemistry, University of Basel , P.O. Box 3350, Mattenstrasse 24a, BPR 1096, CH-4002 Basel, Switzerland
| | - A S Borovik
- Department of Chemistry, University of California , 1102 Natural Science II, Irvine, California 92697, United States
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Computational approaches for de novo design and redesign of metal-binding sites on proteins. Biosci Rep 2017; 37:BSR20160179. [PMID: 28167677 PMCID: PMC5482196 DOI: 10.1042/bsr20160179] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 02/06/2017] [Accepted: 02/06/2017] [Indexed: 12/25/2022] Open
Abstract
Metal ions play pivotal roles in protein structure, function and stability. The functional and structural diversity of proteins in nature expanded with the incorporation of metal ions or clusters in proteins. Approximately one-third of these proteins in the databases contain metal ions. Many biological and chemical processes in nature involve metal ion-binding proteins, aka metalloproteins. Many cellular reactions that underpin life require metalloproteins. Most of the remarkable, complex chemical transformations are catalysed by metalloenzymes. Realization of the importance of metal-binding sites in a variety of cellular events led to the advancement of various computational methods for their prediction and characterization. Furthermore, as structural and functional knowledgebase about metalloproteins is expanding with advances in computational and experimental fields, the focus of the research is now shifting towards de novo design and redesign of metalloproteins to extend nature’s own diversity beyond its limits. In this review, we will focus on the computational toolbox for prediction of metal ion-binding sites, de novo metalloprotein design and redesign. We will also give examples of tailor-made artificial metalloproteins designed with the computational toolbox.
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Bauer CA, Hansen A, Grimme S. The Fractional Occupation Number Weighted Density as a Versatile Analysis Tool for Molecules with a Complicated Electronic Structure. Chemistry 2017; 23:6150-6164. [DOI: 10.1002/chem.201604682] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Indexed: 02/05/2023]
Affiliation(s)
- Christoph Alexander Bauer
- Mulliken Center for Theoretical Chemistry; Institut für Physikalische und Theoretische Chemie der Rheinischen Friedrich-Wilhelms-Universität Bonn; Beringstr. 4 53115 Bonn Germany
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry; Institut für Physikalische und Theoretische Chemie der Rheinischen Friedrich-Wilhelms-Universität Bonn; Beringstr. 4 53115 Bonn Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry; Institut für Physikalische und Theoretische Chemie der Rheinischen Friedrich-Wilhelms-Universität Bonn; Beringstr. 4 53115 Bonn Germany
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