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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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2
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A bound iron porphyrin is redox active in hybrid bacterial reaction centers modified to possess a four-helix bundle domain. Photochem Photobiol Sci 2021; 21:91-99. [PMID: 34850374 DOI: 10.1007/s43630-021-00142-7] [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: 09/29/2021] [Accepted: 11/16/2021] [Indexed: 10/19/2022]
Abstract
In this paper we report the design of hybrid reaction centers with a novel redox-active cofactor. Reaction centers perform the primary photochemistry of photosynthesis, namely the light-induced transfer of an electron from the bacteriochlorophyll dimer to a series of electron acceptors. Hybrid complexes were created by the fusion of an artificial four-helix bundle to the M-subunit of the reaction center. Despite the large modification, optical spectra show that the purified hybrid reaction centers assemble as active complexes that retain the characteristic cofactor absorption peaks and are capable of light-induced charge separation. The four-helix bundle could bind iron-protoporphyrin in either a reduced and oxidized state. After binding iron-protoporphyrin to the hybrid reaction centers, light excitation results in a new derivative signal with a maximum at 402 nm and minimum at 429 nm. This signal increases in amplitude with longer light durations and persists in the dark. No signal is observed when iron-protoporphyrin is added to reaction centers without the four-helix bundle domain or when a redox-inactive zinc-protoporphyrin is bound. The results are consistent with the signal arising from a new redox reaction, electron transfer from the iron-protoporphyrin to the oxidized bacteriochlorophyll dimer. These outcomes demonstrate the feasibility of binding porphyrins to the hybrid reaction centers to gain new light-driven functions.
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3
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Das D, Ainavarapu SRK. Azurin-Derived Peptides: Comparison of Nickel- and Copper-Binding Properties. Inorg Chem 2021; 60:9720-9726. [PMID: 34137603 DOI: 10.1021/acs.inorgchem.1c01007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Metalloproteins are an important class of proteins involved in metal uptake, transport, and electron-transfer reactions. Mimicking the active sites of these proteins through miniaturization is an active area of research with applications in biotechnology and medicine. Azurin is a 128-residue copper-binding cupredoxin protein involved in electron-transfer reactions. Previous studies have reported on the copper-binding-induced spectroscopic and structural properties of peptide loops (11 and 13 residues) from azurin. These azurin peptides exhibited novel stoichiometries. However, the underlying mechanism of fluorescence quenching upon copper binding remains to be understood, whether it is due to electron transfer, energy transfer, or both. Here, we report nickel-binding-associated spectroscopic and structural properties of the azurin peptides. They develop a β-turn upon nickel binding as seen in circular dichroism and exhibit electronic transitions centered at 270 and 450 nm. Unlike copper, which exhibited 1:1 and 1:2 peptide:metal stoichiometries, nickel exhibited only a 1:1 stoichiometry. Tryptophan-containing peptides showed fluorescence quenching upon nickel binding, which is due to electron transfer. These results further suggest that the quenching in copper-bound peptides is also due to electron transfer, which could not be ascertained in previous studies. Overall, azurin peptides provide a platform for studying metal-induced structural and spectroscopic properties using transition-metal ions.
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Affiliation(s)
- Debanjana Das
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Dr. Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Sri Rama Koti Ainavarapu
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Dr. Homi Bhabha Road, Colaba, Mumbai 400005, India
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4
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Ferrando J, Solomon LA. Recent Progress Using De Novo Design to Study Protein Structure, Design and Binding Interactions. Life (Basel) 2021; 11:life11030225. [PMID: 33802210 PMCID: PMC7999464 DOI: 10.3390/life11030225] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/04/2021] [Accepted: 03/05/2021] [Indexed: 12/14/2022] Open
Abstract
De novo protein design is a powerful methodology used to study natural functions in an artificial-protein context. Since its inception, it has been used to reproduce a plethora of reactions and uncover biophysical principles that are often difficult to extract from direct studies of natural proteins. Natural proteins are capable of assuming a variety of different structures and subsequently binding ligands at impressively high levels of both specificity and affinity. Here, we will review recent examples of de novo design studies on binding reactions for small molecules, nucleic acids, and the formation of protein-protein interactions. We will then discuss some new structural advances in the field. Finally, we will discuss some advancements in computational modeling and design approaches and provide an overview of some modern algorithmic tools being used to design these proteins.
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Affiliation(s)
- Juan Ferrando
- Department of Biology, George Mason University, 4400 University Dr, Fairfax, VA 22030, USA;
| | - Lee A. Solomon
- Department of Chemistry and Biochemistry, George Mason University, 10920 George Mason Circle, Manassas, VA 20110, USA
- Correspondence: ; Tel.: +703-993-6418
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5
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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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6
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A de novo binuclear zinc enzyme with DNA cleavage activity. J Biol Inorg Chem 2021; 26:161-167. [PMID: 33469708 DOI: 10.1007/s00775-020-01845-5] [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: 11/19/2020] [Accepted: 12/16/2020] [Indexed: 12/15/2022]
Abstract
Metallohydrolases are broadly used throughout biology, often to catalyze the degradation of macromolecules such as DNA and proteins. Many of these enzymes function with zinc in their active site, and an important subset of these enzymes utilize a binuclear zinc active site. Mimics of these enzymes have been developed, some of which catalyze the digestion of DNA. However, the majority of the mimics that utilize zinc are small molecules, and most are mononuclear. Herein, we report DNA cleavage activity by the de novo designed Due Ferri single-chain (DFsc) protein containing a binuclear zinc active site. This binuclear zinc-protein complex is able to digest plasmid DNA at rates up to 50 ng/h, and these cleavage rates are affected by changes to amino acid residues near the zinc-binding site. These results indicate that the DFsc scaffold is a good model system to carry out careful structure-function relationship studies to understand key structural features that influence reactivity in natural binuclear zinc hydrolases, as it is the first report of a binuclear model system in a protein scaffold.
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7
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Kulesha A, Yoon JH, Chester C, D'Souza A, Costeas C, Makhlynets OV. Contributions of primary coordination ligands and importance of outer sphere interactions in UFsc, a de novo designed protein with high affinity for metal ions. J Inorg Biochem 2020; 212:111224. [PMID: 32871348 DOI: 10.1016/j.jinorgbio.2020.111224] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 08/04/2020] [Accepted: 08/05/2020] [Indexed: 12/15/2022]
Abstract
Metalloproteins constitute nearly half of all proteins and catalyze some of the most complex chemical reactions. Recently, we reported a design of 4G-UFsc (Uno Ferro single chain), a single chain four-helical bundle with extraordinarily high (30 pM) affinity for zinc. We evaluated the contribution of different side chains to binding of Co(II), Ni(II), Zn(II) and Mn(II) using systematic mutagenesis of the amino acids that constitute the primary metal coordination and outer spheres. The binding affinity of proteins for metals was then measured using isothermal titration calorimetry. Our results show that both primary metal coordination environment and side chains in the outer sphere of UFsc are highly sensitive to even slight changes and can be adapted to binding different 3d metals, including hard-to-tightly bind metal ions such as Mn(II). The studies on the origins of tight metal binding will guide future metalloprotein design efforts.
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Affiliation(s)
- Alona Kulesha
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, United States
| | - Jennifer H Yoon
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, United States
| | - Cara Chester
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, United States
| | - Areetha D'Souza
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, United States
| | - Christos Costeas
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, United States
| | - Olga V Makhlynets
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, United States.
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8
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Yoon JH, Kulesha AV, Lengyel-Zhand Z, Volkov AN, Rempillo JJ, D'Souza A, Costeas C, Chester C, Caselle ER, Makhlynets OV. Uno Ferro, a de novo Designed Protein, Binds Transition Metals with High Affinity and Stabilizes Semiquinone Radical Anion. Chemistry 2019; 25:15252-15256. [PMID: 31509280 DOI: 10.1002/chem.201904020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Indexed: 11/07/2022]
Abstract
Metalloenzymes often utilize radicals in order to facilitate chemical reactions. Recently, DeGrado and co-workers have discovered that model proteins can efficiently stabilize semiquinone radical anion produced by oxidation of 3,5-di-tert-butylcatechol (DTBC) in the presence of two zinc ions. Here, we show that the number and the nature of metal ions have relatively minor effect on semiquinone stabilization in model proteins, with a single metal ion being sufficient for radical stabilization. The radical is stabilized by both metal ion, hydrophobic sequestration, and interactions with the hydrophilic residues in the protein interior resulting in a remarkable, nearly 500 mV change in the redox potential of the SQ. - /catechol couple compared to bulk aqueous solution. Moreover, we have created 4G-UFsc, a single metal ion-binding protein with pm affinity for zinc that is higher than any other reported model systems and is on par with many natural zinc-containing proteins. We expect that the robust and easy-to-modify DFsc/UFsc family of proteins will become a versatile tool for mechanistic model studies of metalloenzymes.
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Affiliation(s)
- Jennifer H Yoon
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY, 13244, USA
| | - Alona V Kulesha
- 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
| | - Alexander N Volkov
- VIB Centre for Structural Biology, Vlaams Instituut voor Biotechnologie (VIB), Pleinlaan 2, Brussels, 1050, Belgium.,Jean Jeener NMR Centre, Vrije Universiteit Brussel (VUB), Pleinlaan 2, Brussels, 1050, Belgium
| | - Joel J Rempillo
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY, 13244, USA
| | - Areetha D'Souza
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY, 13244, USA
| | - Christos Costeas
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY, 13244, USA
| | - Cara Chester
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY, 13244, USA
| | - Elizabeth R Caselle
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY, 13244, USA
| | - Olga V Makhlynets
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY, 13244, USA
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9
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Chino M, Zhang SQ, Pirro F, Leone L, Maglio O, Lombardi A, DeGrado WF. Spectroscopic and metal binding properties of a de novo metalloprotein binding a tetrazinc cluster. Biopolymers 2018; 109:e23339. [PMID: 30203532 PMCID: PMC6218314 DOI: 10.1002/bip.23229] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 05/18/2018] [Accepted: 05/22/2018] [Indexed: 12/27/2022]
Abstract
De novo design provides an attractive approach, which allows one to test and refine the principles guiding metalloproteins in defining the geometry and reactivity of their metal ion cofactors. Although impressive progress has been made in designing proteins that bind transition metal ions including iron-sulfur clusters, the design of tetranuclear clusters with oxygen-rich environments remains in its infancy. In previous work, we described the design of homotetrameric four-helix bundles that bind tetra-Zn2+ clusters. The crystal structures of the helical proteins were in good agreement with the overall design, and the metal-binding and conformational properties of the helical bundles in solution were consistent with the crystal structures. However, the corresponding apo-proteins were not fully folded in solution. In this work, we design three peptides, based on the crystal structure of the original bundles. One of the peptides forms tetramers in aqueous solution in the absence of metal ions as assessed by CD and NMR. It also binds Zn2+ in the intended stoichiometry. These studies strongly suggest that the desired structure has been achieved in the apo state, providing evidence that the peptide is able to actively impart the designed geometry to the metal cluster.
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Affiliation(s)
- Marco Chino
- Department of Chemical Sciences, University of Napoli “Federico II”, Via Cintia, 46, 80126 Napoli, Italy
| | - Shao-Qing Zhang
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, CA 94158-9001, United States
- Department of Chemistry, University of Pennsylvania, 209 South 33rd Street, Philadelphia, PA 19104-6396, United States
| | - Fabio Pirro
- Department of Chemical Sciences, University of Napoli “Federico II”, Via Cintia, 46, 80126 Napoli, Italy
| | - Linda Leone
- Department of Chemical Sciences, University of Napoli “Federico II”, Via Cintia, 46, 80126 Napoli, Italy
| | - Ornella Maglio
- Department of Chemical Sciences, University of Napoli “Federico II”, Via Cintia, 46, 80126 Napoli, Italy
- Institute of Biostructure and Bioimaging, National Research Council, via Mezzocannone, 16, 80134, Napoli, Italy
| | - Angela Lombardi
- Department of Chemical Sciences, University of Napoli “Federico II”, Via Cintia, 46, 80126 Napoli, Italy
| | - William F. DeGrado
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, CA 94158-9001, United States
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10
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Valdez CE, Morgenstern A, Eberhart ME, Alexandrova AN. Predictive methods for computational metalloenzyme redesign - a test case with carboxypeptidase A. Phys Chem Chem Phys 2018; 18:31744-31756. [PMID: 27841396 DOI: 10.1039/c6cp02247b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Computational metalloenzyme design is a multi-scale problem. It requires treating the metal coordination quantum mechanically, extensive sampling of the protein backbone, and additionally accounting for the polarization of the active site by both the metal cation and the surrounding protein (a phenomenon called electrostatic preorganization). We bring together a combination of theoretical methods that jointly offer these desired qualities: QM/DMD for mixed quantum-classical dynamic sampling, quantum theory of atoms in molecules (QTAIM) for the assessment of electrostatic preorganization, and Density Functional Theory (DFT) for mechanistic studies. Within this suite of principally different methods, there are both complementarity of capabilities and cross-validation. Using these methods, predictions can be made regarding the relative activities of related enzymes, as we show on the native Zn2+-dependent carboxypeptidase A (CPA), and its mutant proteins, which are hypothesized to hydrolyze modified substrates. For the native CPA, we replicated the catalytic mechanism and the rate in close agreement with the experiment, giving validity to the QM/DMD predicted structure, the DFT mechanism, and the QTAIM assessment of catalytic activity. For most sequences of the modified substrate and tried CPA mutants, substantially worsened activity is predicted. However, for the substrate mutant that contains Asp instead of Phe at the C-terminus, one CPA mutant exhibits a reasonable activity, as predicted across the theoretical methods. CPA is a well-studied system, and here it serves as a testing ground for the offered methods.
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Affiliation(s)
- Crystal E Valdez
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Amanda Morgenstern
- Molecular Theory Group, Colorado School of Mines, Golden, Colorado 80401, USA.
| | - Mark E Eberhart
- Molecular Theory Group, Colorado School of Mines, Golden, Colorado 80401, USA.
| | - Anastassia N Alexandrova
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA. and California NanoSystems Institute, Los Angeles, CA 90095, USA
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11
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Zhang SQ, Chino M, Liu L, Tang Y, Hu X, DeGrado WF, Lombardi A. De Novo Design of Tetranuclear Transition Metal Clusters Stabilized by Hydrogen-Bonded Networks in Helical Bundles. J Am Chem Soc 2018; 140:1294-1304. [PMID: 29249157 PMCID: PMC5860638 DOI: 10.1021/jacs.7b08261] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
De novo design provides an attractive approach to test the mechanism by which metalloproteins define the geometry and reactivity of their metal ion cofactors. While there has been considerable progress in designing proteins that bind transition metal ions including iron-sulfur clusters, the design of tetranuclear clusters with oxygen-rich environments has not been accomplished. Here, we describe the design of tetranuclear clusters, consisting of four Zn2+ and four carboxylate oxygens situated at the vertices of a distorted cube-like structure. The tetra-Zn2+ clusters are bound at a buried site within a four-helix bundle, with each helix donating a single carboxylate (Glu or Asp) and imidazole (His) ligand, as well as second- and third-shell ligands. Overall, the designed site consists of four Zn2+ and 16 polar side chains in a fully connected hydrogen-bonded network. The designed proteins have apolar cores at the top and bottom of the bundle, which drive the assembly of the liganding residues near the center of the bundle. The steric bulk of the apolar residues surrounding the binding site was varied to determine how subtle changes in helix-helix packing affect the binding site. The crystal structures of two of four proteins synthesized were in good agreement with the overall design; both formed a distorted cuboidal site stabilized by flanking second- and third-shell interactions that stabilize the primary ligands. A third structure bound a single Zn2+ in an unanticipated geometry, and the fourth bound multiple Zn2+ at multiple sites at partial occupancy. The metal-binding and conformational properties of the helical bundles in solution, probed by circular dichroism spectroscopy, analytical ultracentrifugation, and NMR, were consistent with the crystal structures.
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Affiliation(s)
- Shao-Qing Zhang
- Department of Chemistry, University of Pennsylvania, 209 South 33rd Street, Philadelphia, PA 19104-6396, United States
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, CA 94158-9001, United States
| | - Marco Chino
- Department of Chemical Sciences, University of Napoli “Federico II”, Via Cintia, 46, I-80126 Napoli, Italy
| | - Lijun Liu
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, CA 94158-9001, United States
- DLX Scientific, Lawrence, KS 66049, United States
| | - Youzhi Tang
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, CA 94158-9001, United States
- College of Veterinary Medicine, South China Agricultural University, Guangdong 510642, China
| | - Xiaozhen Hu
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, CA 94158-9001, United States
| | - William F. DeGrado
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, CA 94158-9001, United States
| | - Angela Lombardi
- Department of Chemical Sciences, University of Napoli “Federico II”, Via Cintia, 46, I-80126 Napoli, Italy
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12
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Espiritu E, Olson TL, Williams JC, Allen JP. Binding and Energetics of Electron Transfer between an Artificial Four-Helix Mn-Protein and Reaction Centers from Rhodobacter sphaeroides. Biochemistry 2017; 56:6460-6469. [PMID: 29131579 DOI: 10.1021/acs.biochem.7b00978] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ability of an artificial four-helix bundle Mn-protein, P1, to bind and transfer an electron to photosynthetic reaction centers from the purple bacterium Rhodobacter sphaeroides was characterized using optical spectroscopy. Upon illumination of reaction centers, an electron is transferred from P, the bacteriochlorophyll dimer, to QA, the primary electron acceptor. The P1 Mn-protein can bind to the reaction center and reduce the oxidized bacteriochlorophyll dimer, P+, with a dissociation constant of 1.2 μM at pH 9.4, comparable to the binding constant of c-type cytochromes. Amino acid substitutions of surface residues on the Mn-protein resulted in increases in the dissociation constant to 8.3 μM. The extent of reduction of P+ by the P1 Mn-protein was dependent on the P/P+ midpoint potential and the pH. Analysis of the free energy difference yielded a midpoint potential of approximately 635 mV at pH 9.4 for the Mn cofactor of the P1 Mn-protein, a value similar to those found for other Mn cofactors in proteins. The linear dependence of -56 mV/pH is consistent with one proton being released upon Mn oxidation, allowing the complex to maintain overall charge neutrality. These outcomes demonstrate the feasibility of designing four-helix bundles and other artificial metalloproteins to bind and transfer electrons to bacterial reaction centers and establish the usefulness of this system as a platform for designing sites to bind novel metal cofactors capable of performing complex oxidation-reduction reactions.
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Affiliation(s)
- Eduardo Espiritu
- School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287-1604, United States
| | - Tien L Olson
- School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287-1604, United States
| | - JoAnn C Williams
- School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287-1604, United States
| | - James P Allen
- School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287-1604, United States
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13
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Olson TL, Espiritu E, Edwardraja S, Canarie E, Flores M, Williams JC, Ghirlanda G, Allen JP. Biochemical and spectroscopic characterization of dinuclear Mn-sites in artificial four-helix bundle proteins. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2017; 1858:945-954. [PMID: 28882760 DOI: 10.1016/j.bbabio.2017.08.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 08/28/2017] [Accepted: 08/31/2017] [Indexed: 01/18/2023]
Abstract
To better understand metalloproteins with Mn-clusters, we have designed artificial four-helix bundles to have one, two, or three dinuclear metal centers able to bind Mn(II). Circular dichroism measurements showed that the Mn-proteins have substantial α-helix content, and analysis of electron paramagnetic resonance spectra is consistent with the designed number of bound Mn-clusters. The Mn-proteins were shown to catalyze the conversion of hydrogen peroxide into molecular oxygen. The loss of hydrogen peroxide was dependent upon the concentration of protein with bound Mn, with the proteins containing multiple Mn-clusters showing greater activity. Using an oxygen sensor, the oxygen concentration was found to increase with a rate up to 0.4μM/min, which was dependent upon the concentrations of hydrogen peroxide and the Mn-protein. In addition, the Mn-proteins were shown to serve as electron donors to bacterial reaction centers using optical spectroscopy. Similar binding of the Mn-proteins to reaction centers was observed with an average dissociation constant of 2.3μM. The Mn-proteins with three metal centers were more effective at this electron transfer reaction than the Mn-proteins with one or two metal centers. Thus, multiple Mn-clusters can be incorporated into four-helix bundles with the capability of performing catalysis and electron transfer to a natural protein.
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Affiliation(s)
- Tien L Olson
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Eduardo Espiritu
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | | | - Elizabeth Canarie
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Marco Flores
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - JoAnn C Williams
- 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
| | - James P Allen
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA.
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Schwizer F, Okamoto Y, Heinisch T, Gu Y, Pellizzoni MM, Lebrun V, Reuter R, Köhler V, Lewis JC, Ward TR. Artificial Metalloenzymes: Reaction Scope and Optimization Strategies. Chem Rev 2017; 118:142-231. [PMID: 28714313 DOI: 10.1021/acs.chemrev.7b00014] [Citation(s) in RCA: 490] [Impact Index Per Article: 70.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The incorporation of a synthetic, catalytically competent metallocofactor into a protein scaffold to generate an artificial metalloenzyme (ArM) has been explored since the late 1970's. Progress in the ensuing years was limited by the tools available for both organometallic synthesis and protein engineering. Advances in both of these areas, combined with increased appreciation of the potential benefits of combining attractive features of both homogeneous catalysis and enzymatic catalysis, led to a resurgence of interest in ArMs starting in the early 2000's. Perhaps the most intriguing of potential ArM properties is their ability to endow homogeneous catalysts with a genetic memory. Indeed, incorporating a homogeneous catalyst into a genetically encoded scaffold offers the opportunity to improve ArM performance by directed evolution. This capability could, in turn, lead to improvements in ArM efficiency similar to those obtained for natural enzymes, providing systems suitable for practical applications and greater insight into the role of second coordination sphere interactions in organometallic catalysis. Since its renaissance in the early 2000's, different aspects of artificial metalloenzymes have been extensively reviewed and highlighted. Our intent is to provide a comprehensive overview of all work in the field up to December 2016, organized according to reaction class. Because of the wide range of non-natural reactions catalyzed by ArMs, this was done using a functional-group transformation classification. The review begins with a summary of the proteins and the anchoring strategies used to date for the creation of ArMs, followed by a historical perspective. Then follows a summary of the reactions catalyzed by ArMs and a concluding critical outlook. This analysis allows for comparison of similar reactions catalyzed by ArMs constructed using different metallocofactor anchoring strategies, cofactors, protein scaffolds, and mutagenesis strategies. These data will be used to construct a searchable Web site on ArMs that will be updated regularly by the authors.
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Affiliation(s)
- Fabian Schwizer
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Yasunori Okamoto
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Tillmann Heinisch
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Yifan Gu
- Searle Chemistry Laboratory, University of Chicago , 5735 S. Ellis Ave., Chicago, Illinois 60637, United States
| | - Michela M Pellizzoni
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Vincent Lebrun
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Raphael Reuter
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Valentin Köhler
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Jared C Lewis
- Searle Chemistry Laboratory, University of Chicago , 5735 S. Ellis Ave., Chicago, Illinois 60637, United States
| | - Thomas R Ward
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
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15
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Nastri F, Chino M, Maglio O, Bhagi-Damodaran A, Lu Y, Lombardi A. Design and engineering of artificial oxygen-activating metalloenzymes. Chem Soc Rev 2016; 45:5020-54. [PMID: 27341693 PMCID: PMC5021598 DOI: 10.1039/c5cs00923e] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Many efforts are being made in the design and engineering of metalloenzymes with catalytic properties fulfilling the needs of practical applications. Progress in this field has recently been accelerated by advances in computational, molecular and structural biology. This review article focuses on the recent examples of oxygen-activating metalloenzymes, developed through the strategies of de novo design, miniaturization processes and protein redesign. Considerable progress in these diverse design approaches has produced many metal-containing biocatalysts able to adopt the functions of native enzymes or even novel functions beyond those found in Nature.
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Affiliation(s)
- Flavia Nastri
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia, 80126 Naples, Italy
| | - Marco Chino
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia, 80126 Naples, Italy
| | - Ornella Maglio
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia, 80126 Naples, Italy
- IBB, CNR, Via Mezzocannone 16, 80134 Naples, Italy
| | - Ambika Bhagi-Damodaran
- Department of Chemistry, University of Illinois at Urbana-Champaign, A322 CLSL, 600 South Mathews Avenue, Urbana, IL 61801
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, A322 CLSL, 600 South Mathews Avenue, Urbana, IL 61801
| | - Angela Lombardi
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia, 80126 Naples, Italy
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16
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REBACK MATTHEWL, GINOVSKA BOJANA, BUCHKO GARRYW, DUTTA ARNAB, PRIYADARSHANI NILUSHA, KIER BRANDONL, HELM MONTEL, RAUGEI SIMONE, SHAW WENDYJ. Investigating the role of chain and linker length on the catalytic activity of an H 2 production catalyst containing a β-hairpin peptide. J COORD CHEM 2016; 69:1730-1747. [PMID: 33093711 PMCID: PMC7577397 DOI: 10.1080/00958972.2016.1188924] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 03/23/2016] [Indexed: 12/20/2022]
Abstract
Building on our recent report of an active H2 production catalyst [Ni(PPh 2NProp-peptide)2]2+ (Prop = para-phenylpropionic acid, peptide (R10) = WIpPRWTGPR-NH2, p = D-proline and P2N = 1-aza-3,6-diphosphacycloheptane) that contains structured β-hairpin peptides, here we investigate how H2 production is effected by: (1) the length of the hairpin (eight or ten residues) and (2) limiting the flexibility between the peptide and the core complex by altering the length of the linker: para-phenylpropionic acid (three carbons) or para-benzoic acid (one carbon). Reduction of the peptide chain length from ten to eight residues increases or maintains the catalytic current for H2 production for all complexes, suggesting a non-productive steric interaction at longer peptide lengths. While the structure of the hairpin appears largely intact for the complexes, NMR data are consistent with differences in dynamic behavior which may contribute to the observed differences in catalytic activity. Molecular dynamics simulations demonstrate that complexes with a one-carbon linker have the desired effect of restricting the motion of the hairpin relative to the complex; however, the catalytic currents are significantly reduced compared to complexes containing a three-carbon linker as a result of the electron withdrawing nature of the -COOH group. These results demonstrate the complexity and interrelated nature of the outer coordination sphere on catalysis.
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Affiliation(s)
| | - BOJANA GINOVSKA
- Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - GARRY W. BUCHKO
- Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - ARNAB DUTTA
- Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | | | | | - MONTE L. HELM
- Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - SIMONE RAUGEI
- Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - WENDY J. SHAW
- Pacific Northwest National Laboratory, Richland, WA 99352, USA
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17
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Chino M, Maglio O, Nastri F, Pavone V, DeGrado WF, Lombardi A. Artificial Diiron Enzymes with a De Novo Designed Four-Helix Bundle Structure. Eur J Inorg Chem 2015; 2015:3371-3390. [PMID: 27630532 PMCID: PMC5019575 DOI: 10.1002/ejic.201500470] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Indexed: 12/26/2022]
Abstract
A single polypeptide chain may provide an astronomical number of conformers. Nature selected only a trivial number of them through evolution, composing an alphabet of scaffolds, that can afford the complete set of chemical reactions needed to support life. These structural templates are so stable that they allow several mutations without disruption of the global folding, even having the ability to bind several exogenous cofactors. With this perspective, metal cofactors play a crucial role in the regulation and catalysis of several processes. Nature is able to modulate the chemistry of metals, adopting only a few ligands and slightly different geometries. Several scaffolds and metal-binding motifs are representing the focus of intense interest in the literature. This review discusses the widespread four-helix bundle fold, adopted as a scaffold for metal binding sites in the context of de novo protein design to obtain basic biochemical components for biosensing or catalysis. In particular, we describe the rational refinement of structure/function in diiron-oxo protein models from the due ferri (DF) family. The DF proteins were developed by us through an iterative process of design and rigorous characterization, which has allowed a shift from structural to functional models. The examples reported herein demonstrate the importance of the synergic application of de novo design methods as well as spectroscopic and structural characterization to optimize the catalytic performance of artificial enzymes.
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Affiliation(s)
- Marco Chino
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia, 80126 Naples, Italy
| | - Ornella Maglio
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia, 80126 Naples, Italy
- IBB, CNR, Via Mezzocannone 16, 80134 Naples, Italy
| | - Flavia Nastri
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia, 80126 Naples, Italy
| | - Vincenzo Pavone
- Department of Structural and Functional Biology, University of Naples “Federico II”, Via Cintia, 80126 Naples, Italy
| | - William F. DeGrado
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco San Francisco, CA 94158, USA
| | - Angela Lombardi
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia, 80126 Naples, Italy
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18
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Yu F, Cangelosi VM, Zastrow ML, Tegoni M, Plegaria JS, Tebo AG, Mocny CS, Ruckthong L, Qayyum H, Pecoraro VL. Protein design: toward functional metalloenzymes. Chem Rev 2014; 114:3495-578. [PMID: 24661096 PMCID: PMC4300145 DOI: 10.1021/cr400458x] [Citation(s) in RCA: 340] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Fangting Yu
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | | | | | | | - Alison G. Tebo
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | - Leela Ruckthong
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Hira Qayyum
- University of Michigan, Ann Arbor, Michigan 48109, United States
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19
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20
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Reback ML, Buchko GW, Kier BL, Ginovska-Pangovska B, Xiong Y, Lense S, Hou J, Roberts JAS, Sorensen CM, Raugei S, Squier TC, Shaw WJ. Enzyme design from the bottom up: an active nickel electrocatalyst with a structured peptide outer coordination sphere. Chemistry 2014; 20:1510-4. [PMID: 24443316 DOI: 10.1002/chem.201303976] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Indexed: 11/07/2022]
Abstract
Catalytic, peptide-containing metal complexes with a well-defined peptide structure have the potential to enhance molecular catalysts through an enzyme-like outer coordination sphere. Here, we report the synthesis and characterization of an active, peptide-based metal complex built upon the well-characterized hydrogen production catalyst [Ni(P(Ph)2N(Ph))2](2+) (P(Ph)2N(Ph)=1,3,6-triphenyl-1-aza-3,6-diphosphacycloheptane). The incorporated peptide maintains its β-hairpin structure when appended to the metal core, and the electrocatalytic activity of the peptide-based metal complex (≈100,000 s(-1)) is enhanced compared to the parent complex ([Ni(P(Ph)2N(APPA))2](2+); ≈50,500 s(-1)). The combination of an active molecular catalyst with a structured peptide provides a scaffold that permits the incorporation of features of an enzyme-like outer-coordination sphere necessary to create molecular electrocatalysts with enhanced functionality.
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21
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Dutta A, Lense S, Hou J, Engelhard MH, Roberts JAS, Shaw WJ. Minimal proton channel enables H2 oxidation and production with a water-soluble nickel-based catalyst. J Am Chem Soc 2013; 135:18490-6. [PMID: 24206187 DOI: 10.1021/ja407826d] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Hydrogenase enzymes use first-row transition metals to interconvert H2 with protons and electrons, reactions that are important for the storage and recovery of energy from intermittent sources such as solar, hydroelectric, and wind. Here we present Ni(P(Cy)2N(Gly)2)2, a water-soluble molecular electrocatalyst with the amino acid glycine built into the diphosphine ligand framework. Proton transfer between the outer coordination sphere carboxylates and the second coordination sphere pendant amines is rapid, as observed by cyclic voltammetry and FTIR spectroscopy, indicating that the carboxylate groups may participate in proton transfer during catalysis. This complex oxidizes H2 (1-33 s(-1)) at low overpotentials (150-365 mV) over a range of pH values (0.1-9.0) and produces H2 under identical solution conditions (>2400 s(-1) at pH 0.5). Enzymes employ proton channels for the controlled movement of protons over long distances-the results presented here demonstrate the effects of a simple two-component proton channel in a synthetic molecular electrocatalyst.
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Affiliation(s)
- Arnab Dutta
- Pacific Northwest National Laboratory , Richland, Washington 99352, United States
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22
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Zastrow ML, Pecoraro VL. Designing functional metalloproteins: from structural to catalytic metal sites. Coord Chem Rev 2013; 257:2565-2588. [PMID: 23997273 PMCID: PMC3756834 DOI: 10.1016/j.ccr.2013.02.007] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Metalloenzymes efficiently catalyze some of the most important and difficult reactions in nature. For many years, coordination chemists have effectively used small molecule models to understand these systems. More recently, protein design has been shown to be an effective approach for mimicking metal coordination environments. Since the first designed proteins were reported, much success has been seen for incorporating metal sites into proteins and attaining the desired coordination environment but until recently, this has been with a lack of significant catalytic activity. Now there are examples of designed metalloproteins that, although not yet reaching the activity of native enzymes, are considerably closer. In this review, we highlight work leading up to the design of a small metalloprotein containing two metal sites, one for structural stability (HgS3) and the other a separate catalytic zinc site to mimic carbonic anhydrase activity (ZnN3O). The first section will describe previous studies that allowed for a high affinity thiolate site that binds heavy metals in a way that stabilizes three-stranded coiled coils. The second section will examine ways of preparing histidine rich environments that lead to metal based hydrolytic catalysts. We will also discuss other recent examples of the design of structural metal sites and functional metalloenzymes. Our work demonstrates that attaining the proper first coordination geometry of a metal site can lead to a significant fraction of catalytic activity, apparently independent of the type of secondary structure of the surrounding protein environment. We are now in a position to begin to meet the challenge of building a metalloenzyme systematically from the bottom-up by engineering and analyzing interactions directly around the metal site and beyond.
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Affiliation(s)
- Melissa L. Zastrow
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
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23
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Ball ZT. Designing enzyme-like catalysts: a rhodium(II) metallopeptide case study. Acc Chem Res 2013; 46:560-70. [PMID: 23210518 DOI: 10.1021/ar300261h] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Chemists have long been fascinated by metalloenzymes and their chemistry. Because enzymes are essential for biological processes and to life itself, they present a key to understanding the world around us. At the same time, if chemists could harness the reactivity and selectivity of enzymes in designed transition-metal catalysts, we would have access to a powerful practical advance in chemistry. But the design of enzyme-like catalysts from scratch presents enormous challenges. Simplified, designed systems often don't provide the opportunity to mimic the complex features of enzymes such as selectivity in polyfunctional environments and access to reactive intermediates incompatible with bulk aqueous solution. Extensive efforts by numerous groups have led to remarkable designed metalloproteins that contain complex folds, including well-defined secondary and tertiary structure surrounding complex polymetallic centers. These structural achievements, however, have not yet led to general approaches to useful catalysts; continued efforts and new insights are needed. Our efforts have combined the attributes of enzymatic and traditional catalysis, bringing the benefits of polypeptide ligands to bear on completely nonbiological transition-metal centers. With a focus on designing useful catalytic activity, we have examined rhodium(II) carboxylates, bound to peptide chains through carboxylate side chains. Among other advantages, these complexes are stable and catalytically active in water. Our efforts have centered on two main interests: (1) understanding how Nature's ligand of choice, polypeptides, can be used to control the chemistry of nonbiological metal centers, and (2) mimicking metalloenzyme characteristics in designed, nonbiological catalysts. This Account conveys our motivation and goals for these studies, outlines progress to date, and discusses the future of enzyme-like catalyst design. In particular, these studies have resulted in on-bead, high-throughput screens for asymmetric metallopeptide catalysts. In addition, peptide-based molecular recognition strategies have facilitated the site-specific modification of protein substrates. Molecular recognition enables site-specific, proximity-driven modification of a broad range of amino acids, and the concepts outlined here are compatible with natural protein substrates and with complex, cell-like environments. We have also explored rhodium metallopeptides as hybrid organic-inorganic inhibitor molecules that block protein-protein interactions.
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Affiliation(s)
- Zachary T. Ball
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
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24
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Wilson TD, Yu Y, Lu Y. Understanding copper-thiolate containing electron transfer centers by incorporation of unnatural amino acids and the CuA center into the type 1 copper protein azurin. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2012.06.015] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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25
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Faiella M, Maglio O, Nastri F, Lombardi A, Lista L, Hagen WR, Pavone V. De novo design, synthesis and characterisation of MP3, a new catalytic four-helix bundle hemeprotein. Chemistry 2012; 18:15960-71. [PMID: 23150230 DOI: 10.1002/chem.201201404] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Revised: 09/12/2012] [Indexed: 12/31/2022]
Abstract
A new artificial metalloenzyme, MP3 (MiniPeroxidase 3), designed by combining the excellent structural properties of four-helix bundle protein scaffolds with the activity of natural peroxidases, was synthesised and characterised. This new hemeprotein model was developed by covalently linking the deuteroporphyrin to two peptide chains of different compositions to obtain an asymmetric helix-loop-helix/heme/helix-loop-helix sandwich arrangement, characterised by 1) a His residue on one chain that acts as an axial ligand to the iron ion; 2) a vacant distal site that is able to accommodate exogenous ligands or substrates; and 3) an Arg residue in the distal site that should assist in hydrogen peroxide activation to give an HRP-like catalytic process. MP3 was synthesised and characterised as its iron complex. CD measurements revealed the high helix-forming propensity of the peptide, confirming the appropriateness of the model procedure; UV/Vis, MCD and EPR experiments gave insights into the coordination geometry and the spin state of the metal. Kinetic experiments showed that Fe(III)-MP3 possesses peroxidase-like activity comparable to R38A-hHRP, highlighting the possibility of mimicking the functional features of natural enzymes. The synergistic application of de novo design methods, synthetic procedures, and spectroscopic characterisation, described herein, demonstrates a method by which to implement and optimise catalytic activity for an enzyme mimetic.
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Affiliation(s)
- Marina Faiella
- Department of Chemical Sciences, Complesso Universitario Monte S. Angelo, University of Naples Federico II, Via Cintia, 80126 Naples, Italy.
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Shaw WJ. The Outer-Coordination Sphere: Incorporating Amino Acids and Peptides as Ligands for Homogeneous Catalysts to Mimic Enzyme Function. CATALYSIS REVIEWS-SCIENCE AND ENGINEERING 2012. [DOI: 10.1080/01614940.2012.679453] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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27
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Reig AJ, Pires MM, Snyder RA, Wu Y, Jo H, Kulp DW, Butch SE, Calhoun JR, Szyperski T, Szyperski TG, Solomon EI, DeGrado WF. Alteration of the oxygen-dependent reactivity of de novo Due Ferri proteins. Nat Chem 2012; 4:900-6. [PMID: 23089864 PMCID: PMC3568993 DOI: 10.1038/nchem.1454] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Accepted: 08/09/2012] [Indexed: 12/18/2022]
Abstract
De novo proteins provide a unique opportunity for investigating the structure-function relationships of metalloproteins in a minimal, well-defined, and controlled scaffold. Herein, we describe the rational programming of function in a de novo designed di-iron carboxylate protein from the due ferri family. Originally created to catalyze O2-dependent, two-electron oxidation of hydroquinones, the protein was reprogrammed to catalyze the selective N-hydroxylation of arylamines by remodeling the substrate access cavity and introducing a critical third His ligand to the metal binding cavity. Additional second-and third-shell modifications were required to stabilize the His ligand in the core of the protein. These changes resulted in at least a 106 –fold increase in the relative rates of the two reactions. This result highlights the potential for using de novo proteins as scaffolds for future investigations of geometric and electronic factors that influence the catalytic tuning of di-iron active sites.
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Affiliation(s)
- Amanda J Reig
- Department of Biochemistry & Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
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28
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Ferrer S, Ruiz-Pernía J, Martí S, Moliner V, Tuñón I, Bertrán J, Andrés J. Hybrid schemes based on quantum mechanics/molecular mechanics simulations goals to success, problems, and perspectives. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2012; 85:81-142. [PMID: 21920322 DOI: 10.1016/b978-0-12-386485-7.00003-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The development of characterization techniques, advanced synthesis methods, as well as molecular modeling has transformed the study of systems in a well-established research field. The current research challenges in biocatalysis and biotransformation evolve around enzyme discovery, design, and optimization. How can we find or create enzymes that catalyze important synthetic reactions, even reactions that may not exist in nature? What is the source of enzyme catalytic power? To answer these and other related questions, the standard strategies have evolved from trial-and-error methodologies based on chemical knowledge, accumulated experience, and common sense into a clearly multidisciplinary science that allows one to reach the molecular design of tailor-made enzyme catalysts. This is even more so when one refers to enzyme catalysts, for which the detailed structure and composition are known and can be manipulated to introduce well-defined residues which can be implicated in the chemical rearrangements taking place in the active site. The methods and techniques of theoretical and computational chemistry are becoming more and more important in both understanding the fundamental biological roles of enzymes and facilitating their utilization in biotechnology. Improvement of the catalytic function of enzymes is important from scientific and industrial viewpoints, and to put this fact in the actual perspective as well as the potentialities, we recommend the very recent report of Sanderson [Sanderson, K. (2011). Chemistry: enzyme expertise. Nature 471, 397.]. Great fundamental advances have been made toward the ab initio design of enzyme catalysts based on molecular modeling. This has been based on the molecular mechanistic knowledge of the reactions to be catalyzed, together with the development of advanced synthesis and characterization techniques. The corresponding molecular mechanism can be studied by means of powerful quantum chemical calculations. The catalytic active site can be optimized to improve the transition state analogues (TSA) and to enhance the catalytic activity, even improve the active site to favor a desired direction of some promiscuous enzymes. In this chapter, we give a brief introduction, the state of the art, and future prospects and implications of enzyme design. Current computational tools to assist experimentalists for the design and engineering of proteins with desired catalytic properties are described. The interplay between enzyme design, molecular simulations, and experiments will be presented to emphasize the interdisciplinary nature of this research field. This text highlights the recent advances and examples selected from our laboratory are shown, of how the applications of these tools are a first attempt to de novo design of protein active sites. Identification of neutral/advantageous/deleterious mutation platforms can be exploited to penetrate some of Nature's closely guarded secrets of chemical reactivity. In this chapter, we give a brief introduction, the state of the art, and future prospects and implications of enzyme design. The first part describes briefly how the molecular modeling is carried out. Then, we discuss the requirements of hybrid quantum mechanical/molecular mechanics molecular dynamics (QM/MM MD) simulations, analyzing what are the basis of these theoretical methodologies, how we can use them with a view to its application in the study of enzyme catalysis, and what are the best methodologies for assessing its catalytic potential. In the second part, we focus on some selected examples, taking as a common guide the chorismate to prephenate rearrangement, studying the corresponding molecular mechanism in vacuo, in solution and in an enzyme environment. In addition, examples involving catalytic antibodies (CAs) and promiscuous enzymes will be presented. Finally, a special emphasis is made to provide some hints about the logical evolution that can be anticipated in this research field. Moreover, it helps in understanding the open directions in this area of knowledge and highlights the importance of computational approaches in discovering specific drugs and the impact on the rational design of tailor-made enzymes.
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Affiliation(s)
- Silvia Ferrer
- Departamento de Química Física y Analítica, Universitat Jaume I, Castellón, Spain
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29
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Robles VM, Ortega-Carrasco E, Fuentes EG, Lledós A, Maréchal JD. What can molecular modelling bring to the design of artificial inorganic cofactors? Faraday Discuss 2011; 148:137-59; discussion 207-28. [DOI: 10.1039/c004578k] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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30
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Torres Martin de Rosales R, Faiella M, Farquhar E, Que L, Andreozzi C, Pavone V, Maglio O, Nastri F, Lombardi A. Spectroscopic and metal-binding properties of DF3: an artificial protein able to accommodate different metal ions. J Biol Inorg Chem 2010; 15:717-28. [PMID: 20225070 DOI: 10.1007/s00775-010-0639-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2009] [Accepted: 02/14/2010] [Indexed: 10/19/2022]
Abstract
The design, synthesis, and metal-binding properties of DF3, a new de novo designed di-iron protein model are described ("DF" represents due ferri, Italian for "two iron," "di-iron"). DF3 is the latest member of the DF family of synthetic proteins. They consist of helix-loop-helix hairpins, designed to dimerize and form an antiparallel four-helix bundle that encompasses a metal-binding site similar to those of non-heme carboxylate-bridged di-iron proteins. Unlike previous DF proteins, DF3 is highly soluble in water (up to 3 mM) and forms stable complexes with several metal ions (Zn, Co, and Mn), with the desired secondary structure and the expected stoichiometry of two ions per protein. UV-vis studies of Co(II) and Fe(III) complexes confirm a metal-binding environment similar to previous di-Co(II)- and di-Fe(III)-DF proteins, including the presence of a mu-oxo-di-Fe(III) unit. Interestingly, UV-vis, EPR, and resonance Raman studies suggest the interaction of a tyrosine adjacent to the di-Fe(III) center. The design of DF3 was aimed at increasing the accessibility of small molecules to the active site of the four-helix bundle. Indeed, binding of azide to the di-Fe(III) site demonstrates a more accessible metal site compared with previous DFs. In fact, fitting of the binding curve to the Hill equation allows us to quantify a 150% accessibility enhancement, with respect to DF2. All these results represent a significant step towards the development of a functional synthetic DF metalloprotein.
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Faiella M, Andreozzi C, de Rosales RTM, Pavone V, Maglio O, Nastri F, DeGrado WF, Lombardi A. An artificial di-iron oxo-protein with phenol oxidase activity. Nat Chem Biol 2009; 5:882-4. [PMID: 19915535 PMCID: PMC3808167 DOI: 10.1038/nchembio.257] [Citation(s) in RCA: 157] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2009] [Accepted: 09/15/2009] [Indexed: 12/11/2022]
Abstract
Here we report the de novo design and NMR structure of a four-helical bundle di-iron protein with phenol oxidase activity. The introduction of the cofactor-binding and phenol-binding sites required the incorporation of residues that were detrimental to the free energy of folding of the protein. Sufficient stability was, however, obtained by optimizing the sequence of a loop distant from the active site.
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Affiliation(s)
- Marina Faiella
- Department of Chemistry, University Federico II of Napoli, Complesso Universitario Monte S. Angelo, Italy
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Koay M, Antonkine M, Gärtner W, Lubitz W. Modelling Low-Potential [Fe4S4] Clusters in Proteins. Chem Biodivers 2008; 5:1571-1587. [DOI: 10.1002/cbdv.200890145] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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