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Ben Aoun S, Ibrahim SM. An engineered thermally tolerant apo-cytochrome scaffold for metal-less incorporation of heme derivative. PLoS One 2023; 18:e0293972. [PMID: 37943746 PMCID: PMC10635480 DOI: 10.1371/journal.pone.0293972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 10/20/2023] [Indexed: 11/12/2023] Open
Abstract
Cytochrome c552 from Thermus thermophilus is one of the hot topics for creating smart biomaterials as it possesses remarkable stability, is tolerant to multiple mutations and has therefore been recently reported for a number of functionalizations upon substitution of the original prosthetic group with an artificial prosthetic group. However, all of the substitutions were driven by the coordination through the axial ligands followed by complete reconstitution with a metal-porphyrin complex. This limits the scope of the cytochrome c for incorporating a metal-less non-natural heme species that could improve the versatility of cytochrome c for a new generation of engineered cytochrome proteins for further enhancement in their functionalities such as biocatalysts. In this connection, a new variant of Cytochrome c (rC552 C14A) from Thermus thermophilus was reported, where an easy approach to remove the original prosthetic group was achieved, followed by the incorporation of a number of metal-PPIX derivatives that ultimately led to the formation of artificial c-type cytochromes through covalent bonding. The apo-cytochrome was found to be thermally tolerant and to possess a distinctive overall structure as that of the wild type, as was evident from the corresponding CD spectra, which ultimately encouraged reconstitution with a metal-less protoporphyrin derivative for better understanding the role of axial ligands in the reconstitution process. Successful reconstitution was achieved, resulting in a new type of Cytochrome b-type artificial protein without the metal in its active site, indicating the non-involvement of the axial ligand. In order to prove the non-involvement of the axial ligand, a subsequent double mutant (C14A/M69A) was constructed, replacing the methionine at 69 position with non-coordinating alanine residue. Accordingly, the apo-C14A/M69A was prepared and found to be extremely stable as the earlier mutants and the WT showed no signs of denaturation, even at the elevated temperature of 98°C. Subsequently, heme b was successfully incorporated into the apo-C14A/M69A, which demonstrated itself as a highly thermally tolerant protein scaffold for incorporating a metal-less artificial prosthetic group in the absence of the axial ligand. Further improvement in the reconstitution process is achieved by replacing the methionine at 69 position with phenyl alanine (C14A/M69F mutant), resulting in further stabilization of heme species, possibly through non-covalent π-interactions, as corroborated by molecular docking.
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Affiliation(s)
- Sami Ben Aoun
- Faculty of Science, Department of Chemistry, Taibah University, Al-Madinah Al-Munawarah, Saudi Arabia
| | - Sheikh Muhammad Ibrahim
- Faculty of Science, Chemistry Department, Islamic University of Madinah, Al-Madinah Al-Munawarah, Saudi Arabia
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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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Mondal A, Das M, Mazumdar S. Substitution of iron with cobalt in the prosthetic group of bacterial cytochrome P450: Effects on the stability and structure of the protein. Inorganica Chim Acta 2019. [DOI: 10.1016/j.ica.2018.12.043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Abstract
An artificial peroxidase with thermal tolerance and high catalytic activity has been successfully prepared by mutagenesis of an electron transfer protein, cytochrome c552 from Thermus thermophilus. The mutant enzymes were rationally designed based on the general peroxidase mechanism and spectroscopic analyses of an active intermediate formed in the catalytic reaction. Stopped flow UV-vis spectroscopy and EPR spectroscopy with a rapid freezing sample technique revealed that the initial double mutant, V49D/M69A, which was designed to reproduce the peroxidase mechanism, formed an active oxo-ferryl heme intermediate with a protein radical predominantly localized on Tyr45 during the catalytic reaction. The magnetic power saturation measurement obtained from EPR studies showed little interaction between the oxo-ferryl heme and the tyrosyl radical. Kinetics studies indicated that the isolated oxo-ferryl heme component in the active intermediate was a possible cause of heme degradation during the reaction with H2O2. Strong interaction between the oxo-ferryl heme and the radical was achieved by replacing Tyr45 with tryptophan (resulting in the Y45W/V49D/M69A mutant), which was similar to a tryptophanyl radical found in active intermediates of some catalase-peroxidases. Compared to the protein radical intermediates of V49D/M69A mutant, those of the Y45W/V49D/M69A mutant showed higher reactivity to an organic substrate than to H2O2. The Y45W/V49D/M69A mutant exhibited improved peroxidase activity and thermal tolerance.
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Affiliation(s)
- Y Watanabe
- Research Center of Materials Science, Nagoya University, Nagoya, Japan
| | - H Nakajima
- Graduate School of Science, Osaka City University, Osaka, Japan.
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Husband J, Aaron MS, Bains RK, Lewis AR, Warren JJ. Catalytic reduction of dioxygen with modified Thermus thermophilus cytochrome c552. J Inorg Biochem 2016; 157:8-14. [PMID: 26816109 DOI: 10.1016/j.jinorgbio.2016.01.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 12/23/2015] [Accepted: 01/18/2016] [Indexed: 10/22/2022]
Abstract
Efficient catalysis of the oxygen reduction reaction (ORR) is of central importance to function in fuel cells. Metalloproteins, such as laccase (Cu) or cytochrome c oxidase (Cu/Fe-heme) carry out the 4H(+)/4e(-) reduction quite efficiently, but using large, complex protein frameworks. Smaller heme proteins also can carry out ORR, but less efficiently. To gain greater insight into features that promote efficient ORR, we expressed, characterized, and investigated the electrochemical behavior of six new mutants of cytochrome c552 from Thermus thermophilus: V49S/M69A, V49T/M69A, L29D/V49S/M69A, P27A/P28A/L29D/V49S/M69A, and P27A/P28A/L29D/V49T/M69A. Mutation to V49 causes only minor shifts to Fe(III/II) reduction potentials (E°'), but introduction of Ser provides a hydrogen bond donor that slightly enhances oxygen reduction activity. Mutation of L29 to D induces small shifts in heme optical spectra, but not to E°' (within experimental error). Replacement of P27 and P28 with A in both positions induces a -50 mV shift in E°', again with small changes to the optical spectra. Both the optical spectra and reduction potentials have signatures consistent with peroxidase enzymes. The V49S and V49T mutations have the largest impact of ORR catalysis, suggesting that increased electron density at the Fe site does not improve O2 reduction chemistry.
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Affiliation(s)
- Jonathan Husband
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
| | - Michael S Aaron
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
| | - Rajneesh K Bains
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
| | - Andrew R Lewis
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
| | - Jeffrey J Warren
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada.
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Preface. Methods Enzymol 2016; 580:xvii-xxii. [DOI: 10.1016/s0076-6879(16)30242-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Matsuo T, Hirota S. Artificial enzymes with protein scaffolds: Structural design and modification. Bioorg Med Chem 2014; 22:5638-56. [DOI: 10.1016/j.bmc.2014.06.021] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 06/09/2014] [Accepted: 06/11/2014] [Indexed: 01/04/2023]
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Behera RK, Nakajima H, Rajbongshi J, Watanabe Y, Mazumdar S. Thermodynamic Effects of the Alteration of the Axial Ligand on the Unfolding of Thermostable Cytochrome c. Biochemistry 2013; 52:1373-84. [DOI: 10.1021/bi300982v] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rabindra Kumar Behera
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha
Road, Colaba, Mumbai 400005, India
| | - Hiroshi Nakajima
- Department of Chemistry, Graduate
School of Science, Nagoya University, Nagoya
464-8602, Japan
| | - Jitumani Rajbongshi
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha
Road, Colaba, Mumbai 400005, India
- Department
of Chemistry, Gauhati University, Guwahati
781014, India
| | - Yoshihito Watanabe
- Department of Chemistry, Graduate
School of Science, Nagoya University, Nagoya
464-8602, Japan
| | - Shyamalava Mazumdar
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha
Road, Colaba, Mumbai 400005, India
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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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Ghosh MK, Rajbongshi J, Basumatary D, Mazumdar S. Role of the Surface-Exposed Leucine 155 in the Metal Ion Binding Loop of the CuA Domain of Cytochrome c Oxidase from Thermus thermophilus on the Function and Stability of the Protein. Biochemistry 2012; 51:2443-52. [DOI: 10.1021/bi2017574] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Manas Kumar Ghosh
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Colaba, Mumbai
400005, India
| | - Jitumani Rajbongshi
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Colaba, Mumbai
400005, India
- Department
of Chemistry, Gauhati University, Guwahati
781014, India
| | - Debajani Basumatary
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Colaba, Mumbai
400005, India
| | - Shyamalava Mazumdar
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Colaba, Mumbai
400005, India
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Jain A, Lense S, Linehan JC, Raugei S, Cho H, DuBois DL, Shaw WJ. Incorporating peptides in the outer-coordination sphere of bioinspired electrocatalysts for hydrogen production. Inorg Chem 2011; 50:4073-85. [PMID: 21456543 DOI: 10.1021/ic1025872] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Four new cyclic 1,5-diaza-3,7-diphosphacyclooctane ligands have been prepared and used to synthesize [Ni(P(Ph)(2)N(R)(2))(2)](2+) complexes in which R is a mono- or dipeptide. These complexes represent a first step in the development of an outer-coordination sphere for this class of complexes that can mimic the outer-coordination sphere of the active sites of hydrogenase enzymes. Importantly, these complexes retain the electrocatalytic activity of the parent [Ni(P(Ph)(2)N(Ph)(2))(2)](2+) complex in an acetonitrile solution with turnover frequencies for hydrogen production ranging from 14 to 25 s(-1) in the presence of p-cyanoanilinium trifluoromethanesulfonate and from 135 to 1000 s(-1) in the presence of protonated dimethylformamide, with moderately low overpotentials, ∼0.3 V. The addition of small amounts of water results in rate increases of 2-7 times. Unlike the parent complex, these complexes demonstrate dynamic structural transformations in solution. These results establish a building block from which larger peptide scaffolding can be added to allow the [Ni(P(R)(2)N(R')(2))(2)](2+) molecular catalytic core to begin to mimic the multifunctional outer-coordination sphere of enzymes.
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Affiliation(s)
- Avijita Jain
- Chemical and Materials Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
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Nakajima H, Osami S, Watanabe Y. Molecular Design of Heme Proteins for Future Application. CATALYSIS SURVEYS FROM ASIA 2011. [DOI: 10.1007/s10563-011-9117-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Shoji O, Watanabe Y. Design of H2O2-dependent oxidation catalyzed by hemoproteins. Metallomics 2011; 3:379-88. [DOI: 10.1039/c0mt00090f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Behera RK, Goyal S, Mazumdar S. Modification of the heme active site to increase the peroxidase activity of thermophilic cytochrome P450: A rational approach. J Inorg Biochem 2010; 104:1185-94. [DOI: 10.1016/j.jinorgbio.2010.07.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2010] [Revised: 07/13/2010] [Accepted: 07/15/2010] [Indexed: 11/28/2022]
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Nakajima H, Ramanathan K, Kawaba N, Watanabe Y. Rational engineering of Thermus thermophilus cytochrome c552 to a thermally tolerant artificial peroxidase. Dalton Trans 2010; 39:3105-14. [DOI: 10.1039/b924365h] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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