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Pitts WC, Deb A, Penner-Hahn JE, Pecoraro VL. Revving up a Designed Copper Nitrite Reductase Using Non-Coded Active Site Ligands. ACS Catal 2024; 14:4362-4368. [PMID: 39157175 PMCID: PMC11329067 DOI: 10.1021/acscatal.3c06159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/20/2024]
Abstract
Herein, we report a three stranded coiled-coil (3SCC) de novo protein containing a type II copper center (CuT2) composed of 6-membered ring N-heterocycles. This design yields the most active homogenous copper nitrite reductase (CuNiR) mimic in water. We achieved this result by controlling three factors. First, previous studies with Nδ and Nε -Methyl Histidine had indicated that a ligand providing pyridine-like electronic character to the copper site was superior to the more donating Nδ for nitrite reduction. By substitution of the parent histidine with the non-coded amino acids pyridyl alanine (3'-Pyridine [3'Py] vs 4'-Pyridine [4'Py]), an authentic pyridine donor was employed without the complications of the coupling of both electronic and tautomeric effects of histidine or methylated histidine. Second, by changing the position of the nitrogen atom within the active site (4'-Pyridine vs. 3'Pyridine) a doubling of the enzyme's catalytic efficiency resulted. This effect was driven exclusivity by substrate binding to the copper site. Third, we replaced the leucine layer adjacent to the active site with an alanine, and the disparity between the 3'Py and 4'Py became more apparent. The decreased steric bulk minimally impacted the 3'Py derivative; however, the 4'Py K m decreased by an order of magnitude (600 mM to 50 mM), resulting in a 40-fold enhancement in the k cat/K m compared to the analogues histidine site and a 1500-fold improvement compared with the initially reported CuNiR catalyst of this family, TRIW-H. When combined with XANES/EXAFS data, the relaxing of the Cu(I) site to a more 2-coordinate Cu(I) like structure in the resting state increases the overall catalytic efficiency of nitrite reduction via the lowering of K m. This study illustrates how by combining advanced spectroscopic methods, detailed kinetic analysis, and a broad toolbox of amino acid side chain functionality, one can rationally design systems that optimize biomimetic catalysis.
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Affiliation(s)
- Winston C. Pitts
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48108, USA United States
| | - Aniruddha Deb
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48108, United States
| | - James E. Penner-Hahn
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48108, USA United States
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48108, United States
| | - Vincent L. Pecoraro
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48108, USA United States
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48108, United States
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Stein A, Liang AD, Sahin R, Ward TR. Incorporation of Metal-Chelating Unnatural Amino Acids into HaloTag for Allylic Deamination. J Organomet Chem 2022. [DOI: 10.1016/j.jorganchem.2022.122272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Lenzen K, Planchestainer M, Feller I, Padrosa DR, Paradisi F, Albrecht M. Minimalistic peptidic scaffolds harbouring an artificial carbene-containing amino acid modulate reductase activity. Chem Commun (Camb) 2021; 57:9068-9071. [PMID: 34498652 PMCID: PMC8427656 DOI: 10.1039/d1cc03158a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Inspired by the boom of new artificial metalloenzymes, we developed an Fmoc-protected histidinium salt (Hum) as N-heterocyclic carbene precursor. Hum was placed via solid-phase peptide synthesis into short 7-mer peptides. Upon iridation, the metallo-peptidic construct displayed activity in catalytic hydrogenation that outperforms small molecule analogues and which is dependent on the peptide sequence, a typical feature of metalloenzymes.
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Affiliation(s)
- Karst Lenzen
- Department of Chemistry, Biochemistry & Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland.
| | - Matteo Planchestainer
- Department of Chemistry, Biochemistry & Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland.
| | - Isabelle Feller
- Department of Chemistry, Biochemistry & Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland.
| | - David Roura Padrosa
- Department of Chemistry, Biochemistry & Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland.
| | - Francesca Paradisi
- Department of Chemistry, Biochemistry & Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland.
| | - Martin Albrecht
- Department of Chemistry, Biochemistry & Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland.
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Insights into metalloproteins and metallodrugs from electron paramagnetic resonance spectroscopy. Curr Opin Chem Biol 2021; 61:114-122. [PMID: 33422836 DOI: 10.1016/j.cbpa.2020.11.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/06/2020] [Accepted: 11/25/2020] [Indexed: 11/20/2022]
Abstract
Metal ions play an important role in diverse biological processes, and much of the basic knowledge derived from studying native bioinorganic systems are applied in the synthesis of new molecules with the aim of diagnosing and treating diseases. At first glance, metalloproteins and metallodrugs are very different systems, but metal ion coordination, redox chemistry and substrate binding play essential roles in advancing both of these research fields. In this article, we discuss recent metalloprotein and metallodrug studies where electron paramagnetic resonance spectroscopy served as a major tool to gain a better understanding of metal-based structures and their function.
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Planchestainer M, McMaster J, Schulz C, Paradisi F, Albrecht M. Carbene-Induced Rescue of Catalytic Activity in Deactivated Nitrite Reductase Mutant. Chemistry 2020; 26:15206-15211. [PMID: 32543723 DOI: 10.1002/chem.202002444] [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: 05/18/2020] [Indexed: 11/10/2022]
Abstract
The role of His145 in the T1 copper center of nitrite reductase (NiR) is pivotal for the activity of the enzyme. Mutation to a glycine at this position enables the reconstitution of the T1 center by the addition of imidazole as exogenous ligands, however the catalytic activity is only marginally rescued. Here, we demonstrate that the uptake of 1,3-dimethylimidazolylidene as N-heterocyclic carbene (NHC) by the H145G NiR mutant instead of imidazole yields a significantly more active catalyst, suggesting a beneficial role of such C-bonding. Spectroscopic analyses of the formed H145G≈NHC variant as well as an analogue without the catalytic T2 copper center reveal no significant alteration of the T1 site compared to the wild type or the variant containing imidazole as exogenous N-bound surrogate of H145. However, the presence of the carbene doubles the catalytic activity of the mutant compared to the imidazole variant. This enhanced activity has been attributed to a faster electron transfer to the T1 center in the NHC variant and a concomitant change of the rate-limiting step.
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Affiliation(s)
- Matteo Planchestainer
- University of Bern, Department of Chemistry & Biochemistry, Freiestr. 3, 3012, Bern, Switzerland.,University of Nottingham, School of Chemistry, University Park, Nottingham, NG7 2RD, UK
| | - Jonathan McMaster
- University of Nottingham, School of Chemistry, University Park, Nottingham, NG7 2RD, UK
| | - Christine Schulz
- Max-Planck Institut für Kohlenforschung, Department of Molecular Theory and Spectroscopy, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
| | - Francesca Paradisi
- University of Bern, Department of Chemistry & Biochemistry, Freiestr. 3, 3012, Bern, Switzerland.,University of Nottingham, School of Chemistry, University Park, Nottingham, NG7 2RD, UK
| | - Martin Albrecht
- University of Bern, Department of Chemistry & Biochemistry, Freiestr. 3, 3012, Bern, Switzerland
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Delaude L. The Chemistry of Azolium‐Carboxylate Zwitterions and Related Compounds: a Survey of the Years 2009–2020. Adv Synth Catal 2020. [DOI: 10.1002/adsc.202000639] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Lionel Delaude
- Laboratory of CatalysisMolSys Research UnitInstitut de Chimie Organique (B6a)Université de Liège Allée du six Août 13 4000 Liège Belgium
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Ségaud N, McMaster J, van Koten G, Albrecht M. Imidazolylidene Cu(II) Complexes: Synthesis Using Imidazolium Carboxylate Precursors and Structure Rearrangement Pathways. Inorg Chem 2019; 58:16047-16058. [PMID: 31714752 DOI: 10.1021/acs.inorgchem.9b02568] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Copper(II) complexes of type (NHC)CuX2 (X = OAc, Cl, Br, BF4, and NO3) bearing monodentate N-heterocyclic carbenes (NHCs) were prepared by in situ decarboxylation of imidazolium carboxylates as a new synthetic methodology for Cu(II)-NHC complexes. In contrast to the classical deprotonation method, the decarboxylation protocol does not require anaerobic conditions and provides access to complexes with NHCs that are unstable as free carbenes such as N,N'-diisopropyl-imidazolylidene and N,N'-dimethyl-imidazolylidene. Spectroscopic evidence of the formation of the Cu-CNHC bond is provided by UV-vis and EPR, in particular by the 44 MHz carbene hyperfine coupling constant using a 13C-labeled imidazolylidene ligand. A variation of the nature of the carbene N-substituents and the anions bound to the Cu(II) center is possible with this methodology. These variations strongly influence the stability of the complexes. Structural rearrangement and ligand reorganization was observed during recrystallization, which are comprised of heterolytic Cu-CNHC bond dissociation for unstable NHC ligands as well as homolytic Cu-X bond cleavage and disproportionation reactions depending on the nature of the anion X in the copper complex.
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Affiliation(s)
- Nathalie Ségaud
- Department of Chemistry & Biochemistry , University of Bern , Freiestrasse 3 , 3012 Bern , Switzerland
| | - Jonathan McMaster
- School of Chemistry , University of Nottingham, University Park , Nottingham NG7 2RD , United Kingdom
| | - Gerard van Koten
- Organic Chemistry and Catalysis, Debye Institute for Materials Science, Faculty of Science , Utrecht University , 3584CG Utrecht , The Netherlands
| | - Martin Albrecht
- Department of Chemistry & Biochemistry , University of Bern , Freiestrasse 3 , 3012 Bern , Switzerland
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