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Xu S, Wu H, Liu S, Du P, Wang H, Yang H, Xu W, Chen S, Song L, Li J, Shi X, Wang ZG. A supramolecular metalloenzyme possessing robust oxidase-mimetic catalytic function. Nat Commun 2023; 14:4040. [PMID: 37419896 PMCID: PMC10328989 DOI: 10.1038/s41467-023-39779-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 06/23/2023] [Indexed: 07/09/2023] Open
Abstract
Enzymes fold into unique three-dimensional structures to distribute their reactive amino acid residues, but environmental changes can disrupt their essential folding and lead to irreversible activity loss. The de novo synthesis of enzyme-like active sites is challenging due to the difficulty of replicating the spatial arrangement of functional groups. Here, we present a supramolecular mimetic enzyme formed by self-assembling nucleotides with fluorenylmethyloxycarbonyl (Fmoc)-modified amino acids and copper. This catalyst exhibits catalytic functions akin those of copper cluster-dependent oxidases, and catalytic performance surpasses to date-reported artificial complexes. Our experimental and theoretical results reveal the crucial role of periodic arrangement of amino acid components, enabled by fluorenyl stacking, in forming oxidase-mimetic copper clusters. Nucleotides provide coordination atoms that enhance copper activity by facilitating the formation of a copper-peroxide intermediate. The catalyst shows thermophilic behavior, remaining active up to 95 °C in an aqueous environment. These findings may aid the design of advanced biomimetic catalysts and offer insights into primordial redox enzymes.
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Affiliation(s)
- Shichao Xu
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Haifeng Wu
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Siyuan Liu
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Peidong Du
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Hui Wang
- Laboratory of Theoretical and Computational Nanoscience, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China.
| | - Haijun Yang
- Department of Chemistry, Tsinghua University, Beijing, 10084, China
| | - Wenjie Xu
- National Synchrotron Radiation Laboratory, CAS Center for Excellence in Nanoscience, University of Science and Technology of China, Hefei, 230029, China
| | - Shuangming Chen
- National Synchrotron Radiation Laboratory, CAS Center for Excellence in Nanoscience, University of Science and Technology of China, Hefei, 230029, China
| | - Li Song
- National Synchrotron Radiation Laboratory, CAS Center for Excellence in Nanoscience, University of Science and Technology of China, Hefei, 230029, China
| | - Jikun Li
- Institute of Chemistry, Chinese Academy of Sciences (ICCAS), Beijing, 100190, China
| | - Xinghua Shi
- Laboratory of Theoretical and Computational Nanoscience, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Zhen-Gang Wang
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, China.
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Nye DB, Johnson EA, Mai MH, Lecomte JTJ. Replacement of the heme axial lysine as a test of conformational adaptability in the truncated hemoglobin THB1. J Inorg Biochem 2019; 201:110824. [PMID: 31514090 DOI: 10.1016/j.jinorgbio.2019.110824] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 09/03/2019] [Accepted: 09/03/2019] [Indexed: 10/26/2022]
Abstract
Amino acid replacement is a useful strategy to assess the roles of axial heme ligands in the function of native heme proteins. THB1, the protein product of the Chlamydomonas reinhardtii THB1 gene, is a group 1 truncated hemoglobin that uses a lysine residue in the E helix (Lys53, at position E10 by reference to myoglobin) as an iron ligand at neutral pH. Phylogenetic evidence shows that many homologous proteins have a histidine, methionine or arginine at the same position. In THB1, these amino acids would each be expected to convey distinct reactive properties if replacing the native lysine as an axial ligand. To explore the ability of the group 1 truncated Hb fold to support alternative ligation schemes and distal pocket conformations, the properties of the THB1 variants K53A as a control, K53H, K53M, and K53R were investigated by electronic absorption, EPR, and NMR spectroscopies. We found that His53 is capable of heme ligation in both the Fe(III) and Fe(II) states, that Met53 can coordinate only in the Fe(II) state, and that Arg53 stabilizes a hydroxide ligand in the Fe(III) state. The data illustrate that the group 1 truncated Hb fold can tolerate diverse rearrangement of the heme environment and has a strong tendency to use two protein side chains as iron ligands despite accompanying structural perturbations. Access to various redox pairs and different responses to pH make this protein an excellent test case for energetic and dynamic studies of heme ligation.
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Affiliation(s)
- Dillon B Nye
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | - Eric A Johnson
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | - Melissa H Mai
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | - Juliette T J Lecomte
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA.
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He C, Ogata H, Lubitz W. Elucidation of the heme active site electronic structure affecting the unprecedented nitrite dismutase activity of the ferriheme b proteins, the nitrophorins. Chem Sci 2016; 7:5332-5340. [PMID: 30155185 PMCID: PMC6020753 DOI: 10.1039/c6sc01019a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 04/23/2016] [Indexed: 12/14/2022] Open
Abstract
Nitrophorins (NPs) catalyze the nitrite dismutation reaction that is unprecedented in ferriheme proteins. Despite progress in studying the reaction mechanism, fundamental issues regarding the correlation of the structural features with the nitrite dismutase activity of NPs remain elusive. On the other hand, it has been shown that the nitrite complexes of NPs are unique among those of the ferriheme proteins since some of their electron paramagnetic resonance (EPR) spectra show significant highly anisotropic low spin (HALS) signals with large gmax values over 3.2. The origin of HALS signals in ferriheme proteins or models is not well understood, especially in cases where axial ligands other than histidine are present. In this study several mutations were introduced in NP4. The related nitrite coordination and dismutation reaction were investigated. As a result, the EPR spectra of the NP-nitrite complexes were found to be tightly correlated with the extent of heme ruffling and protonation state of the proximal His ligand-dictated by an extended H-bonding network at the heme active site. Furthermore, it is established that the two factors are essential in determining the nitrite dismutase activity of NPs. These results may provide a valuable guide for identifying or designing novel heme proteins with similar activity.
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Affiliation(s)
- Chunmao He
- Max Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36 , D-45470 , Mülheim an der Ruhr , Germany . ;
| | - Hideaki Ogata
- Max Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36 , D-45470 , Mülheim an der Ruhr , Germany . ;
| | - Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36 , D-45470 , Mülheim an der Ruhr , Germany . ;
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He C, Kulkarni SS, Thuaud F, Bode JW. Chemical Synthesis of the 20 kDa Heme Protein Nitrophorin 4 by α-Ketoacid-Hydroxylamine (KAHA) Ligation. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201505379] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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He C, Kulkarni SS, Thuaud F, Bode JW. Chemical Synthesis of the 20 kDa Heme Protein Nitrophorin 4 by α‐Ketoacid‐Hydroxylamine (KAHA) Ligation. Angew Chem Int Ed Engl 2015; 54:12996-3001. [DOI: 10.1002/anie.201505379] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 07/27/2015] [Indexed: 11/09/2022]
Affiliation(s)
- Chunmao He
- Institute of Transformative Bio‐Molecules (WPI‐ITbM), Nagoya University, Chikusa, Nagoya 464‐8602 (Japan)
| | - Sameer S. Kulkarni
- Institute of Transformative Bio‐Molecules (WPI‐ITbM), Nagoya University, Chikusa, Nagoya 464‐8602 (Japan)
| | - Frédéric Thuaud
- Institute of Transformative Bio‐Molecules (WPI‐ITbM), Nagoya University, Chikusa, Nagoya 464‐8602 (Japan)
- Laboratorium für Organische Chemie, ETH Zurich, 8093 Zurich (Switzerland) http://www.bode.ethz.ch/
| | - Jeffrey W. Bode
- Institute of Transformative Bio‐Molecules (WPI‐ITbM), Nagoya University, Chikusa, Nagoya 464‐8602 (Japan)
- Laboratorium für Organische Chemie, ETH Zurich, 8093 Zurich (Switzerland) http://www.bode.ethz.ch/
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Knipp M, Ogata H, Soavi G, Cerullo G, Allegri A, Abbruzzetti S, Bruno S, Viappiani C, Bidon-Chanal A, Luque FJ. Structure and dynamics of the membrane attaching nitric oxide transporter nitrophorin 7. F1000Res 2015; 4:45. [PMID: 26167269 PMCID: PMC4482215 DOI: 10.12688/f1000research.6060.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/28/2015] [Indexed: 11/20/2022] Open
Abstract
Nitrophorins represent a unique class of heme proteins that are able to perform the delicate transportation and release of the free-radical gaseous messenger nitric oxide (NO) in a pH-triggered manner. Besides its ability to bind to phospholipid membranes, the N-terminus contains an additional Leu-Pro-Gly stretch, which is a unique sequence trait, and the heme cavity is significantly altered with respect to other nitrophorins. These distinctive features encouraged us to solve the X-ray crystallographic structures of NP7 at low and high pH and bound with different heme ligands (nitric oxide, histamine, imidazole). The overall fold of the lipocalin motif is well preserved in the different X-ray structures and resembles the fold of other nitrophorins. However, a chain-like arrangement in the crystal lattice due to a number of head-to-tail electrostatic stabilizing interactions is found in NP7. Furthermore, the X-ray structures also reveal ligand-dependent changes in the orientation of the heme, as well as in specific interactions between the A-B and G-H loops, which are considered to be relevant for the biological function of nitrophorins. Fast and ultrafast laser triggered ligand rebinding experiments demonstrate the pH-dependent ligand migration within the cavities and the exit route. Finally, the topological distribution of pockets located around the heme as well as from inner cavities present at the rear of the protein provides a distinctive feature in NP7, so that while a loop gated exit mechanism to the solvent has been proposed for most nitrophorins, a more complex mechanism that involves several interconnected gas hosting cavities is proposed for NP7.
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Affiliation(s)
- Markus Knipp
- Max-Planck-Institut für Chemische Energiekonversion, Mülheim an der Ruhr, 45470, Germany
| | - Hideaki Ogata
- Max-Planck-Institut für Chemische Energiekonversion, Mülheim an der Ruhr, 45470, Germany
| | - Giancarlo Soavi
- Dipartimento di Fisica, Politecnico di Milano, Milano, 20133, Italy
| | - Giulio Cerullo
- Dipartimento di Fisica, Politecnico di Milano, Milano, 20133, Italy
| | - Alessandro Allegri
- Dipartimento di Fisica e Scienze della Terra, Università di Parma, Parma, 43124, Italy
| | - Stefania Abbruzzetti
- Dipartimento di Bioscienze, Università di Parma, Parma, 43124, Italy ; NEST, Istituto Nanoscienze, Consiglio Nazionale delle Ricerche, Pisa, 56127, Italy
| | - Stefano Bruno
- Dipartimento di Farmacia, Università di Parma, Parma, 43124, Italy
| | - Cristiano Viappiani
- Dipartimento di Fisica e Scienze della Terra, Università di Parma, Parma, 43124, Italy ; NEST, Istituto Nanoscienze, Consiglio Nazionale delle Ricerche, Pisa, 56127, Italy
| | - Axel Bidon-Chanal
- Departament de Fisicoquímica, Facultat de Farmàcia and Institute of Biomedicine, Universitat de Barcelona, Santa Coloma de Gramenet, E-08921, Spain
| | - F Javier Luque
- Departament de Fisicoquímica, Facultat de Farmàcia and Institute of Biomedicine, Universitat de Barcelona, Santa Coloma de Gramenet, E-08921, Spain
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Dworkowski FSN, Hough MA, Pompidor G, Fuchs MR. Challenges and solutions for the analysis of in situ, in crystallo micro-spectrophotometric data. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:27-35. [PMID: 25615857 PMCID: PMC4304683 DOI: 10.1107/s1399004714015107] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 06/26/2014] [Indexed: 11/22/2022]
Abstract
Combining macromolecular crystallography with in crystallo micro-spectrophotometry yields valuable complementary information on the sample, including the redox states of metal cofactors, the identification of bound ligands and the onset and strength of undesired photochemistry, also known as radiation damage. However, the analysis and processing of the resulting data differs significantly from the approaches used for solution spectrophotometric data. The varying size and shape of the sample, together with the suboptimal sample environment, the lack of proper reference signals and the general influence of the X-ray beam on the sample have to be considered and carefully corrected for. In the present article, how to characterize and treat these sample-dependent artefacts in a reproducible manner is discussed and the SLS-APE in situ, in crystallo optical spectroscopy data-analysis toolbox is demonstrated.
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Affiliation(s)
| | - Michael A. Hough
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
| | - Guillaume Pompidor
- European Molecular Biology Laboratory Hamburg, c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany
| | - Martin R. Fuchs
- Photon Sciences, Brookhaven National Laboratory, Mail Stop 745, Upton, NY 11973, USA
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Rauf MK, Imtiaz-ud-Din, Badshah A. Novel approaches to screening guanidine derivatives. Expert Opin Drug Discov 2013; 9:39-53. [PMID: 24261559 DOI: 10.1517/17460441.2013.857308] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Compounds containing guanidine moiety, originating both from natural and synthetic sources, have found potential applications in both synthetic and medicinal chemistry. Indeed, guanidine functionality can be found in many natural and pharmaceutical products as well as in cosmetic ingredients produced by synthetic methods. AREAS COVERED This review covers the latest developments in the research undertaken for the therapeutic application of newly synthesized guanidine derivatives including: small peptides and peptidomimetics. This article encompasses the selected literature published in the last three decades with a focus on the novel approaches for screening of lead drug candidates with their pharmacological action. EXPERT OPINION Guanidines, as they are both organically based and also hydrophilic in nature, have undergone a mammoth amount of screening and testing to discover promising lead structures with a CN3 core, appropriate for potential future drug development. The compounds have the potential to be neurodegenerative therapeutic options, as well as: anti-inflammatory, anti-protozoal, anti-HIV, chemotherapeutic, anti-diabetic agents and so on. It is true that guanidine-based compounds of natural sources also, like synthetic and virtually designed drugs, have been of significant interest and have the potential to be useful therapeutic options in the future. As for now, however, there is not sufficient data to support their use in a number of the suggested areas, and further studies are required.
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Pompidor G, Dworkowski FSN, Thominet V, Schulze-Briese C, Fuchs MR. A new on-axis micro-spectrophotometer for combining Raman, fluorescence and UV/Vis absorption spectroscopy with macromolecular crystallography at the Swiss Light Source. JOURNAL OF SYNCHROTRON RADIATION 2013; 20:765-76. [PMID: 23955041 PMCID: PMC3747950 DOI: 10.1107/s0909049513016063] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 06/10/2013] [Indexed: 05/08/2023]
Abstract
The combination of X-ray diffraction experiments with optical methods such as Raman, UV/Vis absorption and fluorescence spectroscopy greatly enhances and complements the specificity of the obtained information. The upgraded version of the in situ on-axis micro-spectrophotometer, MS2, at the macromolecular crystallography beamline X10SA of the Swiss Light Source is presented. The instrument newly supports Raman and resonance Raman spectroscopy, in addition to the previously available UV/Vis absorption and fluorescence modes. With the recent upgrades of the spectral bandwidth, instrument stability, detection efficiency and control software, the application range of the instrument and its ease of operation were greatly improved. Its on-axis geometry with collinear X-ray and optical axes to ensure optimal control of the overlap of sample volumes probed by each technique is still unique amongst comparable facilities worldwide and the instrument has now been in general user operation for over two years.
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Affiliation(s)
| | | | | | | | - Martin R. Fuchs
- Paul Scherrer Institut, CH-5232 Villigen, Switzerland
- Correspondence e-mail:
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Complexes of ferriheme nitrophorin 4 with low-molecular weight thiol(ate)s occurring in blood plasma. J Inorg Biochem 2013; 122:38-48. [DOI: 10.1016/j.jinorgbio.2013.01.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Revised: 01/14/2013] [Accepted: 01/14/2013] [Indexed: 11/17/2022]
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He C, Ogata H, Knipp M. Insertion of an H-Bonding Residue into the Distal Pocket of the Ferriheme Protein Nitrophorin 4: Effect on NitriteIron Coordination and Nitrite Disproportionation. Chem Biodivers 2012; 9:1761-75. [DOI: 10.1002/cbdv.201100401] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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