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Insertion of unnatural metal ligand in the heme pocket of nitrophorin through protein semi-synthesis: toward biomimicking binuclear active sites. CHINESE CHEM LETT 2023. [DOI: 10.1016/j.cclet.2023.108251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
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2
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Huang S, Deng WH, Liao RZ, He C. Repurposing a Nitric Oxide Transport Hemoprotein Nitrophorin 2 for Olefin Cyclopropanation. ACS Catal 2022. [DOI: 10.1021/acscatal.2c03515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Shunzhi Huang
- School of Chemistry and Chemical Engineering, South China University of Technology, 510640 Guangzhou, China
| | - Wen-Hao Deng
- School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, 430074 Wuhan, China
| | - Rong-Zhen Liao
- School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, 430074 Wuhan, China
| | - Chunmao He
- School of Chemistry and Chemical Engineering, South China University of Technology, 510640 Guangzhou, China
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3
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De Simone G, di Masi A, Vita GM, Polticelli F, Pesce A, Nardini M, Bolognesi M, Ciaccio C, Coletta M, Turilli ES, Fasano M, Tognaccini L, Smulevich G, Abbruzzetti S, Viappiani C, Bruno S, Ascenzi P. Mycobacterial and Human Nitrobindins: Structure and Function. Antioxid Redox Signal 2020; 33:229-246. [PMID: 32295384 DOI: 10.1089/ars.2019.7874] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Aims: Nitrobindins (Nbs) are evolutionary conserved all-β-barrel heme-proteins displaying a highly solvent-exposed heme-Fe(III) atom. The physiological role(s) of Nbs is almost unknown. Here, the structural and functional properties of ferric Mycobacterium tuberculosis Nb (Mt-Nb(III)) and ferric Homo sapiens Nb (Hs-Nb(III)) have been investigated and compared with those of ferric Arabidopsis thaliana Nb (At-Nb(III), Rhodnius prolixus nitrophorins (Rp-NP(III)s), and mammalian myoglobins. Results: Data here reported demonstrate that Mt-Nb(III), At-Nb(III), and Hs-Nb(III) share with Rp-NP(III)s the capability to bind selectively nitric oxide, but display a very low reactivity, if any, toward histamine. Data obtained overexpressing Hs-Nb in human embryonic kidney 293 cells indicate that Hs-Nb localizes mainly in the cytoplasm and partially in the nucleus, thanks to a nuclear localization sequence encompassing residues Glu124-Leu154. Human Hs-Nb corresponds to the C-terminal domain of the human nuclear protein THAP4 suggesting that Nb may act as a sensor possibly modulating the THAP4 transcriptional activity residing in the N-terminal region. Finally, we provide strong evidence that both Mt-Nb(III) and Hs-Nb(III) are able to scavenge peroxynitrite and to protect free l-tyrosine against peroxynitrite-mediated nitration. Innovation: Data here reported suggest an evolutionarily conserved function of Nbs related to their role as nitric oxide sensors and components of antioxidant systems. Conclusion: Human THAP4 may act as a sensing protein that couples the heme-based Nb(III) reactivity with gene transcription. Mt-Nb(III) seems to be part of the pool of proteins required to scavenge reactive nitrogen and oxygen species produced by the host during the immunity response.
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Affiliation(s)
| | | | | | - Fabio Polticelli
- Dipartimento di Scienze, Università Roma Tre, Roma, Italy.,Istituto Nazionale di Fisica Nucleare, Sezione di Roma Tre, Roma, Italy
| | | | - Marco Nardini
- Dipartimento di Bioscienze, Università di Milano, Milano, Italy
| | - Martino Bolognesi
- Dipartimento di Bioscienze, Università di Milano, Milano, Italy.,Centro di Ricerche Pediatriche R.E. Invernizzi, Università di Milano, Milano, Italy
| | - Chiara Ciaccio
- Dipartimento di Scienze Cliniche e Medicina Traslazionale, Università di Roma Tor Vergata, Roma, Italy
| | - Massimo Coletta
- Dipartimento di Scienze Cliniche e Medicina Traslazionale, Università di Roma Tor Vergata, Roma, Italy
| | - Emily Samuela Turilli
- Dipartimento di Scienza ed Alta Tecnologia, Università dell'Insubria, Busto Arsizio, Italy
| | - Mauro Fasano
- Dipartimento di Scienza ed Alta Tecnologia, Università dell'Insubria, Busto Arsizio, Italy
| | - Lorenzo Tognaccini
- Dipartimento di Chimica Ugo Schiff, Università di Firenze, Sesto Fiorentino, Italy
| | - Giulietta Smulevich
- Dipartimento di Chimica Ugo Schiff, Università di Firenze, Sesto Fiorentino, Italy
| | - Stefania Abbruzzetti
- Dipartimento di Scienze Matematiche, Fisiche e Informatiche, Università di Parma, Parma, Italy
| | - Cristiano Viappiani
- Dipartimento di Scienze Matematiche, Fisiche e Informatiche, Università di Parma, Parma, Italy
| | - Stefano Bruno
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università di Parma, Parma, Italy
| | - Paolo Ascenzi
- Dipartimento di Scienze, Università Roma Tre, Roma, Italy
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Frydenvang K, Verkade-Vreeker MCA, Dohmen F, Commandeur JNM, Rafiq M, Mirza O, Jørgensen FS, Geerke DP. Structural analysis of Cytochrome P450 BM3 mutant M11 in complex with dithiothreitol. PLoS One 2019; 14:e0217292. [PMID: 31125381 PMCID: PMC6534296 DOI: 10.1371/journal.pone.0217292] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 05/08/2019] [Indexed: 11/18/2022] Open
Abstract
The bacterial Cytochrome P450 (CYP) BM3 (CYP102A1) is one of the most active CYP isoforms. BM3 mutants can serve as a model for human drug-metabolizing CYPs and/or as biocatalyst for selective formation of drug metabolites. Hence, molecular and computational biologists have in the last two decades shown strong interest in the discovery and design of novel BM3 variants with optimized activity and selectivity for substrate conversion. This led e.g. to the discovery of mutant M11 that is able to metabolize a variety of drugs and drug-like compounds with relatively high activity. In order to further improve our understanding of CYP binding and reactions, we performed a co-crystallization study of mutant M11 and report here the three-dimensional structure M11 in complex with dithiothreitol (DTT) at a resolution of 2.16 Å. The structure shows that DTT can coordinate to the Fe atom in the heme group. UV/Vis spectroscopy and molecular dynamics simulation studies underline this finding and as first structure of the CYP BM3 mutant M11 in complex with a ligand, it offers a basis for structure-based design of novel mutants.
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Affiliation(s)
- Karla Frydenvang
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Marlies C. A. Verkade-Vreeker
- AIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit, Amsterdam, the Netherlands
| | - Floor Dohmen
- AIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit, Amsterdam, the Netherlands
| | - Jan N. M. Commandeur
- AIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit, Amsterdam, the Netherlands
| | - Maria Rafiq
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Osman Mirza
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Flemming Steen Jørgensen
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
- * E-mail: (FSJ); (DPG)
| | - Daan P. Geerke
- AIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit, Amsterdam, the Netherlands
- * E-mail: (FSJ); (DPG)
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Walker AA, Weirauch C, Fry BG, King GF. Venoms of Heteropteran Insects: A Treasure Trove of Diverse Pharmacological Toolkits. Toxins (Basel) 2016; 8:43. [PMID: 26907342 PMCID: PMC4773796 DOI: 10.3390/toxins8020043] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 01/25/2016] [Accepted: 01/26/2016] [Indexed: 11/16/2022] Open
Abstract
The piercing-sucking mouthparts of the true bugs (Insecta: Hemiptera: Heteroptera) have allowed diversification from a plant-feeding ancestor into a wide range of trophic strategies that include predation and blood-feeding. Crucial to the success of each of these strategies is the injection of venom. Here we review the current state of knowledge with regard to heteropteran venoms. Predaceous species produce venoms that induce rapid paralysis and liquefaction. These venoms are powerfully insecticidal, and may cause paralysis or death when injected into vertebrates. Disulfide-rich peptides, bioactive phospholipids, small molecules such as N,N-dimethylaniline and 1,2,5-trithiepane, and toxic enzymes such as phospholipase A2, have been reported in predatory venoms. However, the detailed composition and molecular targets of predatory venoms are largely unknown. In contrast, recent research into blood-feeding heteropterans has revealed the structure and function of many protein and non-protein components that facilitate acquisition of blood meals. Blood-feeding venoms lack paralytic or liquefying activity but instead are cocktails of pharmacological modulators that disable the host haemostatic systems simultaneously at multiple points. The multiple ways venom is used by heteropterans suggests that further study will reveal heteropteran venom components with a wide range of bioactivities that may be recruited for use as bioinsecticides, human therapeutics, and pharmacological tools.
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Affiliation(s)
- Andrew A Walker
- Institute for Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia.
| | - Christiane Weirauch
- Department of Entomology, University of California, Riverside, CA 92521, USA.
| | - Bryan G Fry
- School of Biological Sciences, The University of Queensland, St Lucia, QLD 4072, Australia.
| | - Glenn F King
- Institute for Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia.
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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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7
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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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Tang K, Knipp M, Liu BB, Cox N, Stabel R, He Q, Zhou M, Scheer H, Zhao KH, Gärtner W. Redox-dependent Ligand Switching in a Sensory Heme-binding GAF Domain of the Cyanobacterium Nostoc sp. PCC7120. J Biol Chem 2015; 290:19067-80. [PMID: 26063806 DOI: 10.1074/jbc.m115.654087] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Indexed: 11/06/2022] Open
Abstract
The genome of the cyanobacterium Nostoc sp. PCC7120 carries three genes (all4978, all7016, and alr7522) encoding putative heme-binding GAF (cGMP-specific phosphodiesterases, adenylyl cyclases, and FhlA) proteins that were annotated as transcriptional regulators. They are composed of an N-terminal cofactor domain and a C-terminal helix-turn-helix motif. All4978 showed the highest affinity for protoheme binding. The heme binding capability of All7016 was moderate, and Alr7522 did not bind heme at all. The "as isolated" form of All4978, identified by Soret band (λmax = 427 nm), was assigned by electronic absorption, EPR, and resonance Raman spectroscopy as a hexa-coordinated low spin Fe(III) heme with a distal cysteine ligand (absorption of δ-band around 360 nm). The protoheme cofactor is noncovalently incorporated. Reduction of the heme could be accomplished by chemically using sodium dithionite and electrospectrochemically; this latter method yielded remarkably low midpoint potentials of -445 and -453 mV (following Soret and α-band absorption changes, respectively). The reduced form of the heme (Fe(II) state) binds both NO and CO. Cysteine coordination of the as isolated Fe(III) protein is unambiguous, but interestingly, the reduced heme instead displays spectral features indicative of histidine coordination. Cys-His ligand switches have been reported as putative signaling mechanisms in other heme-binding proteins; however, these novel cyanobacterial proteins are the first where such a ligand-switch mechanism has been observed in a GAF domain. DNA binding of the helix-turn-helix domain was investigated using a DNA sequence motif from its own promoter region. Formation of a protein-DNA complex preferentially formed in ferric state of the protein.
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Affiliation(s)
- Kun Tang
- From the State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China, the Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim, Germany
| | - Markus Knipp
- the Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim, Germany, Resolv, Faculty for Chemistry and Biochemistry, Ruhr University Bochum, D-44780 Bochum, Germany, and
| | - Bing-Bing Liu
- From the State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Nicholas Cox
- the Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim, Germany
| | - Robert Stabel
- the Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim, Germany
| | - Qi He
- From the State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ming Zhou
- From the State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Hugo Scheer
- the Department of Biologie I, Ludwig-Maximilians-Universität, Menzinger Strasse 67, D-80638 München, Germany
| | - Kai-Hong Zhao
- From the State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China,
| | - Wolfgang Gärtner
- the Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim, Germany,
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9
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Smith AT, Pazicni S, Marvin KA, Stevens DJ, Paulsen KM, Burstyn JN. Functional divergence of heme-thiolate proteins: a classification based on spectroscopic attributes. Chem Rev 2015; 115:2532-58. [PMID: 25763468 DOI: 10.1021/cr500056m] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Aaron T Smith
- †Department of Molecular Biosciences, Northwestern University, 2205 Tech Drive, Evanston, Illinois 60208, United States
| | - Samuel Pazicni
- ‡Department of Chemistry, University of New Hampshire, 23 Academic Way, Durham, New Hampshire 03824, United States
| | - Katherine A Marvin
- §Department of Chemistry, Hendrix College, 1600 Washington Avenue, Conway, Arkansas 72032, United States
| | - Daniel J Stevens
- ∥Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Katherine M Paulsen
- ∥Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Judith N Burstyn
- ∥Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
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Kabbua T, Anwised P, Boonmee A, Subedi BP, Pierce BS, Thammasirirak S. Autoinduction, purification, and characterization of soluble α-globin chains of crocodile (Crocodylus siamensis) hemoglobin in Escherichia coli. Protein Expr Purif 2014; 103:56-63. [DOI: 10.1016/j.pep.2014.08.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 08/19/2014] [Accepted: 08/20/2014] [Indexed: 01/30/2023]
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