1
|
Gabler T, Dali A, Bellei M, Sebastiani F, Becucci M, Battistuzzi G, Furtmüller PG, Smulevich G, Hofbauer S. Revisiting catalytic His and Glu residues in coproporphyrin ferrochelatase - unexpected activities of active site variants. FEBS J 2024. [PMID: 38390750 DOI: 10.1111/febs.17101] [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] [Received: 12/13/2023] [Revised: 01/17/2024] [Accepted: 02/13/2024] [Indexed: 02/24/2024]
Abstract
The identification of the coproporphyrin-dependent heme biosynthetic pathway, which is used almost exclusively by monoderm bacteria in 2015 by Dailey et al. triggered studies aimed at investigating the enzymes involved in this pathway that were originally assigned to the protoporphyrin-dependent heme biosynthetic pathway. Here, we revisit the active site of coproporphyrin ferrochelatase by a biophysical and biochemical investigation using the physiological substrate coproporphyrin III, which in contrast to the previously used substrate protoporphyrin IX has four propionate substituents and no vinyl groups. In particular, we have compared the reactivity of wild-type coproporphyrin ferrochelatase from the firmicute Listeria monocytogenes with those of variants, namely, His182Ala (H182A) and Glu263Gln (E263Q), involving two key active site residues. Interestingly, both variants are active only toward the physiological substrate coproporphyrin III but inactive toward protoporphyrin IX. In addition, E263 exchange impairs the final oxidation step from ferrous coproheme to ferric coproheme. The characteristics of the active site in the context of the residues involved and the substrate binding properties are discussed here using structural and functional means, providing a further contribution to the deciphering of this enigmatic reaction mechanism.
Collapse
Affiliation(s)
- Thomas Gabler
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Andrea Dali
- Department of Chemistry "Ugo Schiff" (DICUS), University of Florence, Sesto Fiorentino, Italy
| | - Marzia Bellei
- Department of Life Sciences, University of Modena and Reggio Emilia, Italy
| | - Federico Sebastiani
- Department of Chemistry "Ugo Schiff" (DICUS), University of Florence, Sesto Fiorentino, Italy
| | - Maurizio Becucci
- Department of Chemistry "Ugo Schiff" (DICUS), University of Florence, Sesto Fiorentino, Italy
| | - Gianantonio Battistuzzi
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Paul Georg Furtmüller
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Giulietta Smulevich
- Department of Chemistry "Ugo Schiff" (DICUS), University of Florence, Sesto Fiorentino, Italy
- INSTM Research Unit of Firenze, Sesto Fiorentino, Italy
| | - Stefan Hofbauer
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| |
Collapse
|
2
|
Gabler T, Dali A, Sebastiani F, Furtmüller PG, Becucci M, Hofbauer S, Smulevich G. Iron insertion into coproporphyrin III-ferrochelatase complex: Evidence for an intermediate distorted catalytic species. Protein Sci 2023; 32:e4788. [PMID: 37743577 PMCID: PMC10578119 DOI: 10.1002/pro.4788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/07/2023] [Accepted: 09/20/2023] [Indexed: 09/26/2023]
Abstract
Understanding the reaction mechanism of enzymes at the molecular level is generally a difficult task, since many parameters affect the turnover. Often, due to high reactivity and formation of transient species or intermediates, detailed information on enzymatic catalysis is obtained by means of model substrates. Whenever possible, it is essential to confirm a reaction mechanism based on substrate analogues or model systems by using the physiological substrates. Here we disclose the ferrous iron incorporation mechanism, in solution, and in crystallo, by the coproporphyrin III-coproporphyrin ferrochelatase complex from the firmicute, pathogen, and antibiotic resistant, Listeria monocytogenes. Coproporphyrin ferrochelatase plays an important physiological role as the metalation represents the penultimate reaction step in the prokaryotic coproporphyrin-dependent heme biosynthetic pathway, yielding coproheme (ferric coproporphyrin III). By following the metal titration with resonance Raman spectroscopy and x-ray crystallography, we prove that upon metalation the saddling distortion becomes predominant both in the crystal and in solution. This is a consequence of the readjustment of hydrogen bond interactions of the propionates with the protein scaffold during the enzymatic catalysis. Once the propionates have established the interactions typical of the coproheme complex, the distortion slowly decreases, to reach the almost planar final product.
Collapse
Affiliation(s)
- Thomas Gabler
- Department of ChemistryInstitute of Biochemistry, University of Natural Resources and Life SciencesViennaAustria
| | - Andrea Dali
- Dipartimento di Chimica “Ugo Schiff”—DICUSUniversità di FirenzeSesto FiorentinoItaly
| | - Federico Sebastiani
- Dipartimento di Chimica “Ugo Schiff”—DICUSUniversità di FirenzeSesto FiorentinoItaly
| | - Paul Georg Furtmüller
- Department of ChemistryInstitute of Biochemistry, University of Natural Resources and Life SciencesViennaAustria
| | - Maurizio Becucci
- Dipartimento di Chimica “Ugo Schiff”—DICUSUniversità di FirenzeSesto FiorentinoItaly
| | - Stefan Hofbauer
- Department of ChemistryInstitute of Biochemistry, University of Natural Resources and Life SciencesViennaAustria
| | - Giulietta Smulevich
- Dipartimento di Chimica “Ugo Schiff”—DICUSUniversità di FirenzeSesto FiorentinoItaly
- INSTM Research Unit of FirenzeSesto FiorentinoItaly
| |
Collapse
|
3
|
Yaghoobi A, Seyedmirzaei H, Ala M. Genome- and Exome-Wide Association Studies Revealed Candidate Genes Associated with DaTscan Imaging Features. PARKINSON'S DISEASE 2023; 2023:2893662. [PMID: 37664790 PMCID: PMC10468272 DOI: 10.1155/2023/2893662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 07/02/2023] [Accepted: 08/16/2023] [Indexed: 09/05/2023]
Abstract
Introduction Despite remarkable progress in identifying Parkinson's disease (PD) genetic risk loci, the genetic basis of PD remains largely unknown. With the help of the endophenotype approach and using data from dopamine transporter single-photon emission computerized tomography (DaTscan), we identified potentially involved genes in PD. Method We conducted an imaging genetic study by performing exome-wide association study (EWAS) and genome-wide association study (GWAS) on the specific binding ratio (SBR) of six DaTscan anatomical areas between 489 and 559 subjects of Parkinson's progression markers initiative (PPMI) cohort and 83,623 and 36,845 single-nucleotide polymorphisms (SNPs)/insertion-deletion mutations (INDELs). We also investigated the association of cerebrospinal fluid (CSF) protein concentration of our significant genes with PD progression using PPMI CSF proteome data. Results Among 83,623 SNPs/INDELs in EWAS, one SNP (rs201465075) on 1 q32.1 locus was significantly (P value = 4.03 × 10-7) associated with left caudate DaTscan SBR, and 33 SNPs were suggestive. Among 36,845 SNPs in GWAS, one SNP (rs12450112) on 17 p.12 locus was significantly (P value = 1.34 × 10-6) associated with right anterior putamen DaTscan SBR, and 39 SNPs were suggestive among which 8 SNPs were intergenic. We found that rs201465075 and rs12450112 are most likely related to IGFN1 and MAP2K4 genes. The protein level of MAP2K4 in the CSF was significantly associated with PD progression in the PPMI cohort; however, proteomic data were not available for the IGFN1 gene. Conclusion We have shown that particular variants of IGFN1 and MAP2K4 genes may be associated with PD. Since DaTscan imaging could be positive in other Parkinsonian syndromes, caution should be taken when interpreting our results. Future experimental studies are also needed to verify these findings.
Collapse
Affiliation(s)
- Arash Yaghoobi
- Institute for Research in Fundamental Sciences (IPM), School of Biological Sciences, Tehran, Iran
| | - Homa Seyedmirzaei
- Interdisciplinary Neuroscience Research Program (INRP), Tehran University of Medical Sciences, Tehran, Iran
- Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Moein Ala
- Experimental Research Center, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| |
Collapse
|
4
|
Falb N, Patil G, Furtmüller PG, Gabler T, Hofbauer S. Structural aspects of enzymes involved in prokaryotic Gram-positive heme biosynthesis. Comput Struct Biotechnol J 2023; 21:3933-3945. [PMID: 37593721 PMCID: PMC10427985 DOI: 10.1016/j.csbj.2023.07.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/19/2023] [Accepted: 07/19/2023] [Indexed: 08/19/2023] Open
Abstract
The coproporphyrin dependent heme biosynthesis pathway is almost exclusively utilized by Gram-positive bacteria. This fact makes it a worthwhile topic for basic research, since a fundamental understanding of a metabolic pathway is necessary to translate the focus towards medical biotechnology, which is very relevant in this specific case, considering the need for new antibiotic targets to counteract the pathogenicity of Gram-positive superbugs. Over the years a lot of structural data on the set of enzymes acting in Gram-positive heme biosynthesis has accumulated in the Protein Database (www.pdb.org). One major challenge is to filter and analyze all available structural information in sufficient detail in order to be helpful and to draw conclusions. Here we pursued to give a holistic overview of structural information on enzymes involved in the coproporphyrin dependent heme biosynthesis pathway. There are many aspects to be extracted from experimentally determined structures regarding the reaction mechanisms, where the smallest variation of the position of an amino acid residue might be important, but also on a larger level regarding protein-protein interactions, where the focus has to be on surface characteristics and subunit (secondary) structural elements and oligomerization. This review delivers a status quo, highlights still missing information, and formulates future research endeavors in order to better understand prokaryotic heme biosynthesis.
Collapse
Affiliation(s)
- Nikolaus Falb
- University of Natural Resources and Life Sciences, Vienna, Department of Chemistry, Institute of Biochemistry, Muthgasse 18, A-1190 Vienna, Austria
| | - Gaurav Patil
- University of Natural Resources and Life Sciences, Vienna, Department of Chemistry, Institute of Biochemistry, Muthgasse 18, A-1190 Vienna, Austria
| | - Paul G. Furtmüller
- University of Natural Resources and Life Sciences, Vienna, Department of Chemistry, Institute of Biochemistry, Muthgasse 18, A-1190 Vienna, Austria
| | - Thomas Gabler
- University of Natural Resources and Life Sciences, Vienna, Department of Chemistry, Institute of Biochemistry, Muthgasse 18, A-1190 Vienna, Austria
| | - Stefan Hofbauer
- University of Natural Resources and Life Sciences, Vienna, Department of Chemistry, Institute of Biochemistry, Muthgasse 18, A-1190 Vienna, Austria
| |
Collapse
|
5
|
Ushimaru R, Lyu J, Abe I. Diverse enzymatic chemistry for propionate side chain cleavages in tetrapyrrole biosynthesis. J Ind Microbiol Biotechnol 2023; 50:kuad016. [PMID: 37422437 PMCID: PMC10548856 DOI: 10.1093/jimb/kuad016] [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] [Received: 05/03/2023] [Accepted: 07/07/2023] [Indexed: 07/10/2023]
Abstract
Tetrapyrroles represent a unique class of natural products that possess diverse chemical architectures and exhibit a broad range of biological functions. Accordingly, they attract keen attention from the natural product community. Many metal-chelating tetrapyrroles serve as enzyme cofactors essential for life, while certain organisms produce metal-free porphyrin metabolites with biological activities potentially beneficial for the producing organisms and for human use. The unique properties of tetrapyrrole natural products derive from their extensively modified and highly conjugated macrocyclic core structures. Most of these various tetrapyrrole natural products biosynthetically originate from a branching point precursor, uroporphyrinogen III, which contains propionate and acetate side chains on its macrocycle. Over the past few decades, many modification enzymes with unique catalytic activities, and the diverse enzymatic chemistries employed to cleave the propionate side chains from the macrocycles, have been identified. In this review, we highlight the tetrapyrrole biosynthetic enzymes required for the propionate side chain removal processes and discuss their various chemical mechanisms. ONE-SENTENCE SUMMARY This mini-review describes various enzymes involved in the propionate side chain cleavages during the biosynthesis of tetrapyrrole cofactors and secondary metabolites.
Collapse
Affiliation(s)
- Richiro Ushimaru
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Jiaqi Lyu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| |
Collapse
|
6
|
Dali A, Gabler T, Sebastiani F, Destinger A, Furtmüller PG, Pfanzagl V, Becucci M, Smulevich G, Hofbauer S. Active site architecture of coproporphyrin ferrochelatase with its physiological substrate coproporphyrin III: Propionate interactions and porphyrin core deformation. Protein Sci 2023; 32:e4534. [PMID: 36479958 PMCID: PMC9794026 DOI: 10.1002/pro.4534] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/29/2022] [Accepted: 12/03/2022] [Indexed: 12/13/2022]
Abstract
Coproporphyrin ferrochelatases (CpfCs) are enzymes catalyzing the penultimate step in the coproporphyrin-dependent (CPD) heme biosynthesis pathway, which is mainly utilized by monoderm bacteria. Ferrochelatases insert ferrous iron into a porphyrin macrocycle and have been studied for many decades, nevertheless many mechanistic questions remain unanswered to date. Especially CpfCs, which are found in the CPD pathway, are currently in the spotlight of research. This pathway was identified in 2015 and revealed that the correct substrate for these ferrochelatases is coproporphyrin III (cpIII) instead of protoporphyrin IX, as believed prior the discovery of the CPD pathway. The chemistry of cpIII, which has four propionates, differs significantly from protoporphyrin IX, which features two propionate and two vinyl groups. These findings let us to thoroughly describe the physiological cpIII-ferrochelatase complex in solution and in the crystal phase. Here, we present the first crystallographic structure of the CpfC from the representative monoderm pathogen Listeria monocytogenes bound to its physiological substrate, cpIII, together with the in-solution data obtained by resonance Raman and UV-vis spectroscopy, for wild-type ferrochelatase and variants, analyzing propionate interactions. The results allow us to evaluate the porphyrin distortion and provide an in-depth characterization of the catalytically-relevant binding mode of cpIII prior to iron insertion. Our findings are discussed in the light of the observed structural restraints and necessities for this porphyrin-enzyme complex to catalyze the iron insertion process. Knowledge about this initial situation is essential for understanding the preconditions for iron insertion in CpfCs and builds the basis for future studies.
Collapse
Affiliation(s)
- Andrea Dali
- Dipartimento di Chimica “Ugo Schiff” – DICUSUniversità di FirenzeSesto Fiorentino (FI)Italy
| | - Thomas Gabler
- Department of ChemistryInstitute of Biochemistry, University of Natural Resources and Life SciencesViennaAustria
| | - Federico Sebastiani
- Dipartimento di Chimica “Ugo Schiff” – DICUSUniversità di FirenzeSesto Fiorentino (FI)Italy
| | - Alina Destinger
- Department of ChemistryInstitute of Biochemistry, University of Natural Resources and Life SciencesViennaAustria
| | - Paul Georg Furtmüller
- Department of ChemistryInstitute of Biochemistry, University of Natural Resources and Life SciencesViennaAustria
| | - Vera Pfanzagl
- Department of ChemistryInstitute of Biochemistry, University of Natural Resources and Life SciencesViennaAustria
| | - Maurizio Becucci
- Dipartimento di Chimica “Ugo Schiff” – DICUSUniversità di FirenzeSesto Fiorentino (FI)Italy
| | - Giulietta Smulevich
- Dipartimento di Chimica “Ugo Schiff” – DICUSUniversità di FirenzeSesto Fiorentino (FI)Italy,INSTM Research Unit of FirenzeSesto Fiorentino (Fi)Italy
| | - Stefan Hofbauer
- Department of ChemistryInstitute of Biochemistry, University of Natural Resources and Life SciencesViennaAustria
| |
Collapse
|
7
|
Tahir N, Ashraf A, Waqar SHB, Rafae A, Kantamneni L, Sheikh T, Khan R. Copper deficiency, a rare but correctable cause of pancytopenia: a review of literature. Expert Rev Hematol 2022; 15:999-1008. [PMID: 36314081 DOI: 10.1080/17474086.2022.2142113] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
INTRODUCTION Copper is increasingly being recognized as a vital mineral required by both animals and humans. It plays a vital role in many metabolic processes such as cellular respiration, iron oxidation, and hemoglobin synthesis. Copper deficiency, which can be hereditary or acquired, can lead to a wide spectrum of disease processes such as ringed sideroblastic anemia, myelodysplasia, and pancytopenia. Timely identification and management of copper deficiency is necessary to prevent irreversible complications. AREAS COVERED Our study focuses on prevalence, etiology, pathophysiology, complications, and treatment of copper deficiency. EXPERT OPINION Copper deficiency is frequently underrecognized as the cause of anemia, neutropenia, and bone marrow dysplasia. As it is potentially treatable, it should always be kept in the differentials when patients present with neurological and hematological abnormalities.
Collapse
Affiliation(s)
- Nayha Tahir
- Department of Hematology and Oncology, Kaiser Permanente, San Francisco, CA, USA
| | - Aqsa Ashraf
- Department of Internal Medicine, Zucker School of Medicine, Hofstra/Northwell, Mather Hospital, Port Jefferson, NY, USA
| | - Syed Hamza Bin Waqar
- Department of Internal Medicine, State University of New York, Downstate Medical Center Brooklyn, Brooklyn, NY, USA
| | - Abdul Rafae
- Department of Hematology and Oncology, University of Arkansas for Medical Sciences (UAMS), Little Rock, AR, USA
| | - Leela Kantamneni
- Department of Internal Medicine, Huntsville Regional Medical Campus, University of Alabama, Birmingham, AL, USA
| | - Taha Sheikh
- Department of Hematology and Oncology, University of Toledo, Toledo, OH, USA
| | - Rafiullah Khan
- Division of Hematology Oncology, The Christ Hospital Network Physicians, Cincinnati, OH, USA
| |
Collapse
|
8
|
Abstract
Heme (protoheme IX) is an essential cofactor for a large variety of proteins whose functions vary from one electron reactions to binding gases. While not ubiquitous, heme is found in the great majority of known life forms. Unlike most cofactors that are acquired from dietary sources, the vast majority of organisms that utilize heme possess a complete pathway to synthesize the compound. Indeed, dietary heme is most frequently utilized as an iron source and not as a source of heme. In Nature there are now known to exist three pathways to synthesize heme. These are the siroheme dependent (SHD) pathway which is the most ancient, but least common of the three; the coproporphyrin dependent (CPD) pathway which with one known exception is found only in gram positive bacteria; and the protoporphyrin dependent (PPD) pathway which is found in gram negative bacteria and all eukaryotes. All three pathways share a core set of enzymes to convert the first committed intermediate, 5-aminolevulinate (ALA) into uroporphyrinogen III. In the current review all three pathways are reviewed as well as the two known pathways to synthesize ALA. In addition, interesting features of some heme biosynthesis enzymes are discussed as are the regulation and disorders of heme biosynthesis.
Collapse
Affiliation(s)
- Harry A Dailey
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602-1111, USA
- Department of Microbiology, University of Georgia, Athens, GA 30602-1111, USA
| | - Amy E Medlock
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602-1111, USA
- Augusta University/University of Georgia Medical Partnership, University of Georgia, Athens, GA, USA
| |
Collapse
|
9
|
Hunter GA, Ferreira GC. Metal ion coordination sites in ferrochelatase. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2022.214464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
10
|
Armillotta F, D'Incecco E, Corva M, Stredansky M, Gallet J, Bournel F, Goldoni A, Morgante A, Vesselli E, Verdini A. Self‐Metalation of Porphyrins at the Solid–Gas Interface. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202111932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Francesco Armillotta
- Physics Department University of Trieste via Valerio 2 34127 Trieste Italy
- CNR-IOM, Area Science Park S.S. 14 km 163.5 34149 Basovizza Trieste Italy
| | - Enrico D'Incecco
- Physics Department University of Trieste via Valerio 2 34127 Trieste Italy
| | - Manuel Corva
- Physics Department University of Trieste via Valerio 2 34127 Trieste Italy
- CNR-IOM, Area Science Park S.S. 14 km 163.5 34149 Basovizza Trieste Italy
| | - Matus Stredansky
- Physics Department University of Trieste via Valerio 2 34127 Trieste Italy
- CNR-IOM, Area Science Park S.S. 14 km 163.5 34149 Basovizza Trieste Italy
| | - Jean‐Jacques Gallet
- Sorbonne Université CNRS UMR7614 Laboratoire de Chimie Physique Matière et Rayonnement 4 place Jussieu 75005 Paris France
- Synchrotron SOLEIL L'Orme des Merisiers, Saint-Aubin—BP 4891192 Gif-sur-Yvette CEDEX France
| | - Fabrice Bournel
- Sorbonne Université CNRS UMR7614 Laboratoire de Chimie Physique Matière et Rayonnement 4 place Jussieu 75005 Paris France
- Synchrotron SOLEIL L'Orme des Merisiers, Saint-Aubin—BP 4891192 Gif-sur-Yvette CEDEX France
| | - Andrea Goldoni
- Elettra Sincrotrone Trieste S.S. 14 km 163.5 34149 Basovizza Trieste Italy
| | - Alberto Morgante
- Physics Department University of Trieste via Valerio 2 34127 Trieste Italy
- CNR-IOM, Area Science Park S.S. 14 km 163.5 34149 Basovizza Trieste Italy
| | - Erik Vesselli
- Physics Department University of Trieste via Valerio 2 34127 Trieste Italy
- CNR-IOM, Area Science Park S.S. 14 km 163.5 34149 Basovizza Trieste Italy
| | - Alberto Verdini
- CNR-IOM, Area Science Park S.S. 14 km 163.5 34149 Basovizza Trieste Italy
| |
Collapse
|
11
|
Armillotta F, D'Incecco E, Corva M, Stredansky M, Gallet JJ, Bournel F, Goldoni A, Morgante A, Vesselli E, Verdini A. Self-Metalation of Porphyrins at the Solid-Gas Interface. Angew Chem Int Ed Engl 2021; 60:25988-25993. [PMID: 34591358 PMCID: PMC9299001 DOI: 10.1002/anie.202111932] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Indexed: 11/30/2022]
Abstract
Self‐metalation is a promising route to include a single metal atom in a tetrapyrrolic macrocycle in organic frameworks supported by metal surfaces. The molecule–surface interaction may provide the charge transfer and the geometric distortion of the molecular plane necessary for metal inclusion. However, at a metal surface the presence of an activation barrier can represent an obstacle that cannot be compensated by a higher substrate temperature without affecting the layer integrity. The formation of the intermediate state can be facilitated in some cases by oxygen pre‐adsorption at the supporting metal surface, like in the case of 2H‐TPP/Pd(100). In such cases, the activation barrier can be overcome by mild annealing, yielding the formation of desorbing products and of the metalated tetrapyrrole. We show here that the self‐metalation of 2H‐TPP at the Pd(100) surface can be promoted already at room temperature by the presence of an oxygen gas phase at close‐to‐ambient conditions via an Eley–Rideal mechanism.
Collapse
Affiliation(s)
- Francesco Armillotta
- Physics Department, University of Trieste, via Valerio 2, 34127, Trieste, Italy.,CNR-IOM, Area Science Park, S.S. 14 km 163.5, 34149 Basovizza, Trieste, Italy
| | - Enrico D'Incecco
- Physics Department, University of Trieste, via Valerio 2, 34127, Trieste, Italy
| | - Manuel Corva
- Physics Department, University of Trieste, via Valerio 2, 34127, Trieste, Italy.,CNR-IOM, Area Science Park, S.S. 14 km 163.5, 34149 Basovizza, Trieste, Italy
| | - Matus Stredansky
- Physics Department, University of Trieste, via Valerio 2, 34127, Trieste, Italy.,CNR-IOM, Area Science Park, S.S. 14 km 163.5, 34149 Basovizza, Trieste, Italy
| | - Jean-Jacques Gallet
- Sorbonne Université, CNRS UMR7614, Laboratoire de Chimie Physique Matière et Rayonnement, 4 place Jussieu, 75005, Paris, France.,Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin-BP, 4891192, Gif-sur-Yvette CEDEX, France
| | - Fabrice Bournel
- Sorbonne Université, CNRS UMR7614, Laboratoire de Chimie Physique Matière et Rayonnement, 4 place Jussieu, 75005, Paris, France.,Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin-BP, 4891192, Gif-sur-Yvette CEDEX, France
| | - Andrea Goldoni
- Elettra Sincrotrone Trieste, S.S. 14 km 163.5, 34149 Basovizza, Trieste, Italy
| | - Alberto Morgante
- Physics Department, University of Trieste, via Valerio 2, 34127, Trieste, Italy.,CNR-IOM, Area Science Park, S.S. 14 km 163.5, 34149 Basovizza, Trieste, Italy
| | - Erik Vesselli
- Physics Department, University of Trieste, via Valerio 2, 34127, Trieste, Italy.,CNR-IOM, Area Science Park, S.S. 14 km 163.5, 34149 Basovizza, Trieste, Italy
| | - Alberto Verdini
- CNR-IOM, Area Science Park, S.S. 14 km 163.5, 34149 Basovizza, Trieste, Italy
| |
Collapse
|
12
|
Gabler T, Sebastiani F, Helm J, Dali A, Obinger C, Furtmüller PG, Smulevich G, Hofbauer S. Substrate specificity and complex stability of coproporphyrin ferrochelatase is governed by hydrogen-bonding interactions of the four propionate groups. FEBS J 2021; 289:1680-1699. [PMID: 34719106 DOI: 10.1111/febs.16257] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/19/2021] [Accepted: 10/28/2021] [Indexed: 11/24/2022]
Abstract
Coproporpyhrin III is the substrate of coproporphyrin ferrochelatases (CpfCs). These enzymes catalyse the insertion of ferrous iron into the porphyrin ring. This is the penultimate step within the coproporphyrin-dependent haeme biosynthesis pathway. This pathway was discovered in 2015 and is mainly utilised by monoderm bacteria. Prior to this discovery, monoderm bacteria were believed to utilise the protoporphyrin-dependent pathway, analogously to diderm bacteria, where the substrate for the respective ferrochelatase is protoporphyrin IX, which has two propionate groups at positions 6 and 7 and two vinyl groups at positions 2 and 4. In this work, we describe for the first time the interactions of the four-propionate substrate, coproporphyrin III, and the four-propionate product, iron coproporphyrin III (coproheme), with the CpfC from Listeria monocytogenes and pin down differences with respect to the protoporphyrin IX and haeme b complexes in the wild-type (WT) enzyme. We further created seven LmCpfC variants aiming at altering substrate and product coordination. The WT enzyme and all the variants were comparatively studied by spectroscopic, thermodynamic and kinetic means to investigate in detail the H-bonding interactions, which govern complex stability and substrate specificity. We identified a tyrosine residue (Y124 in LmCpfC), coordinating the propionate at position 2, which is conserved in monoderm CpfCs, to be highly important for binding and stabilisation. Importantly, we also describe a tyrosine-serine-threonine triad, which coordinates the propionate at position 4. The study of the triad variants indicates structural differences between the coproporphyrin III and the coproheme complexes. ENZYME: EC 4.99.1.9.
Collapse
Affiliation(s)
- Thomas Gabler
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Federico Sebastiani
- Dipartimento di Chimica 'Ugo Schiff' (DICUS), Università di Firenze, Sesto Fiorentino, Italy
| | - Johannes Helm
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Andrea Dali
- Dipartimento di Chimica 'Ugo Schiff' (DICUS), Università di Firenze, Sesto Fiorentino, Italy
| | - Christian Obinger
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Paul G Furtmüller
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Giulietta Smulevich
- Dipartimento di Chimica 'Ugo Schiff' (DICUS), Università di Firenze, Sesto Fiorentino, Italy.,INSTM Research Unit of Firenze, Sesto Fiorentino, Italy
| | - Stefan Hofbauer
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| |
Collapse
|
13
|
Abstract
In this review, DNA and nanomaterial based catalysts for porphyrin metalation reactions are summarized, including the selection of DNAzymes, choice of nanomaterials, their catalytic mechanisms, and applications of the reactions.
Collapse
Affiliation(s)
- Hualin Yang
- College of Life Science
- Yangtze University
- Jingzhou
- China
- Department of Chemistry
| | - Yu Zhou
- College of Life Science
- Yangtze University
- Jingzhou
- China
- College of Animal Science
| | - Juewen Liu
- Department of Chemistry
- Waterloo Institute for Nanotechnology
- University of Waterloo
- Waterloo
- Canada
| |
Collapse
|
14
|
Lin LY, McCarthy S, Powell BM, Manurung Y, Xiang IM, Dean WL, Chaires B, Yatsunyk LA. Biophysical and X-ray structural studies of the (GGGTT)3GGG G-quadruplex in complex with N-methyl mesoporphyrin IX. PLoS One 2020; 15:e0241513. [PMID: 33206666 PMCID: PMC7673559 DOI: 10.1371/journal.pone.0241513] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 10/15/2020] [Indexed: 01/21/2023] Open
Abstract
The G-quadruplex (GQ) is a well-studied non-canonical DNA structure formed by G-rich sequences found at telomeres and gene promoters. Biological studies suggest that GQs may play roles in regulating gene expression, DNA replication, and DNA repair. Small molecule ligands were shown to alter GQ structure and stability and thereby serve as novel therapies, particularly against cancer. In this work, we investigate the interaction of a G-rich sequence, 5'-GGGTTGGGTTGGGTTGGG-3' (T1), with a water-soluble porphyrin, N-methyl mesoporphyrin IX (NMM) via biophysical and X-ray crystallographic studies. UV-vis and fluorescence titrations, as well as a Job plot, revealed a 1:1 binding stoichiometry with an impressively tight binding constant of 30-50 μM-1 and ΔG298 of -10.3 kcal/mol. Eight extended variants of T1 (named T2 -T9) were fully characterized and T7 was identified as a suitable candidate for crystallographic studies. We solved the crystal structures of the T1- and T7-NMM complexes at 2.39 and 2.34 Å resolution, respectively. Both complexes form a 5'-5' dimer of parallel GQs capped by NMM at the 3' G-quartet, supporting the 1:1 binding stoichiometry. Our work provides invaluable details about GQ-ligand binding interactions and informs the design of novel anticancer drugs that selectively recognize specific GQs and modulate their stability for therapeutic purposes.
Collapse
Affiliation(s)
- Linda Yingqi Lin
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania, United States of America
| | - Sawyer McCarthy
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania, United States of America
| | - Barrett M. Powell
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania, United States of America
| | - Yanti Manurung
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania, United States of America
| | - Irene M. Xiang
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania, United States of America
| | - William L. Dean
- Structural Biology Program JG Brown Cancer Center, University of Louisville, Louisville, Kentucky, United States of America
| | - Brad Chaires
- Structural Biology Program JG Brown Cancer Center, University of Louisville, Louisville, Kentucky, United States of America
| | - Liliya A. Yatsunyk
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania, United States of America
| |
Collapse
|
15
|
Hofbauer S, Helm J, Obinger C, Djinović-Carugo K, Furtmüller PG. Crystal structures and calorimetry reveal catalytically relevant binding mode of coproporphyrin and coproheme in coproporphyrin ferrochelatase. FEBS J 2020; 287:2779-2796. [PMID: 31794133 PMCID: PMC7340540 DOI: 10.1111/febs.15164] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 11/18/2019] [Accepted: 12/02/2019] [Indexed: 01/24/2023]
Abstract
Coproporphyrin ferrochelatases (CpfCs, EC 4.99.1.9) insert ferrous iron into coproporphyrin III yielding coproheme. CpfCs are utilized by prokaryotic, mainly monoderm (Gram-positive) bacteria within the recently detected coproporphyrin-dependent (CPD) heme biosynthesis pathway. Here, we present a comprehensive study on CpfC from Listeria monocytogenes (LmCpfC) including the first crystal structure of a coproheme-bound CpfC. Comparison of crystal structures of apo-LmCpfC and coproheme-LmCpfC allowed identification of structural rearrangements and of amino acids involved in tetrapyrrole macrocycle and Fe2+ binding. Differential scanning calorimetry of apo-, coproporphyrin III-, and coproheme-LmCpfC underline the pronounced noncovalent interaction of both coproporphyrin and coproheme with the protein (ΔTm = 11 °C compared to apo-LmCpfC), which includes the propionates (p2, p4, p6, p7) and the amino acids Arg29, Arg45, Tyr46, Ser53, and Tyr124. Furthermore, the thermodynamics and kinetics of coproporphyrin III and coproheme binding to apo-LmCpfC is presented as well as the kinetics of insertion of ferrous iron into coproporphyrin III-LmCpfC that immediately leads to formation of ferric coproheme-LmCpfC (kcat /KM = 4.7 × 105 m-1 ·s-1 ). We compare the crystal structure of coproheme-LmCpfC with available structures of CpfCs with artificial tetrapyrrole macrocycles and discuss our data on substrate binding, iron insertion and substrate release in the context of the CPD heme biosynthesis pathway. ENZYME: EC 4.99.1.9 DATABASE: pdb-codes of structural data in this work: 6RWV, 6SV3.
Collapse
Affiliation(s)
- Stefan Hofbauer
- Department of Chemistry, Institute of Biochemistry, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria
| | - Johannes Helm
- Department of Chemistry, Institute of Biochemistry, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria
| | - Christian Obinger
- Department of Chemistry, Institute of Biochemistry, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria
| | - Kristina Djinović-Carugo
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Austria
- Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Slovenia
| | - Paul G Furtmüller
- Department of Chemistry, Institute of Biochemistry, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria
| |
Collapse
|
16
|
Laraia L, Garivet G, Foley DJ, Kaiser N, Müller S, Zinken S, Pinkert T, Wilke J, Corkery D, Pahl A, Sievers S, Janning P, Arenz C, Wu Y, Rodriguez R, Waldmann H. Image‐Based Morphological Profiling Identifies a Lysosomotropic, Iron‐Sequestering Autophagy Inhibitor. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201913712] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Luca Laraia
- Department of Chemical Biology Max-Planck-Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
- current address: Technical University of Denmark Department of Chemistry Kemitorvet 207 2800 Kgs. Lyngby Denmark
| | - Guillaume Garivet
- Department of Chemical Biology Max-Planck-Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Faculty of Chemistry and Chemical Biology TU Dortmund Otto-Hahn-Strasse 6 44227 Dortmund Germany
| | - Daniel J. Foley
- Department of Chemical Biology Max-Planck-Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
- current address: School of Physical and Chemical Sciences University of Canterbury Christchurch New Zealand
| | - Nadine Kaiser
- Department of Chemical Biology Max-Planck-Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Faculty of Chemistry and Chemical Biology TU Dortmund Otto-Hahn-Strasse 6 44227 Dortmund Germany
| | - Sebastian Müller
- Institut Curie CNRS UMR 3666 INSERM U1143 PSL University Paris Chemical Cell Biology Group 26 Rue d'Ulm 75248 Paris Cedex 05 France
| | - Sarah Zinken
- Department of Chemical Biology Max-Planck-Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Faculty of Chemistry and Chemical Biology TU Dortmund Otto-Hahn-Strasse 6 44227 Dortmund Germany
| | - Thomas Pinkert
- Institut für Chemie der Humboldt-Universität zu Berlin Brook-Taylor-Str. 2 (R 1'102) 12489 Berlin Germany
| | - Julian Wilke
- Department of Chemical Biology Max-Planck-Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Faculty of Chemistry and Chemical Biology TU Dortmund Otto-Hahn-Strasse 6 44227 Dortmund Germany
| | - Dale Corkery
- Department of Chemistry Umeå Universitet KB.A4, Linnaeus väg 10 (rum: A4.35.07) 90187 Umeå Sweden
| | - Axel Pahl
- Compound Management and Screening Center, Dortmund Otto-Hahn-Str. 11 44227 Dortmund Germany
| | - Sonja Sievers
- Compound Management and Screening Center, Dortmund Otto-Hahn-Str. 11 44227 Dortmund Germany
| | - Petra Janning
- Department of Chemical Biology Max-Planck-Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Faculty of Chemistry and Chemical Biology TU Dortmund Otto-Hahn-Strasse 6 44227 Dortmund Germany
| | - Christoph Arenz
- Institut für Chemie der Humboldt-Universität zu Berlin Brook-Taylor-Str. 2 (R 1'102) 12489 Berlin Germany
| | - Yaowen Wu
- Department of Chemistry Umeå Universitet KB.A4, Linnaeus väg 10 (rum: A4.35.07) 90187 Umeå Sweden
| | - Raphaël Rodriguez
- Institut Curie CNRS UMR 3666 INSERM U1143 PSL University Paris Chemical Cell Biology Group 26 Rue d'Ulm 75248 Paris Cedex 05 France
| | - Herbert Waldmann
- Department of Chemical Biology Max-Planck-Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Faculty of Chemistry and Chemical Biology TU Dortmund Otto-Hahn-Strasse 6 44227 Dortmund Germany
| |
Collapse
|
17
|
Laraia L, Garivet G, Foley DJ, Kaiser N, Müller S, Zinken S, Pinkert T, Wilke J, Corkery D, Pahl A, Sievers S, Janning P, Arenz C, Wu Y, Rodriguez R, Waldmann H. Image-Based Morphological Profiling Identifies a Lysosomotropic, Iron-Sequestering Autophagy Inhibitor. Angew Chem Int Ed Engl 2020; 59:5721-5729. [PMID: 31769920 PMCID: PMC7154763 DOI: 10.1002/anie.201913712] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Indexed: 01/15/2023]
Abstract
Chemical proteomics is widely applied in small-molecule target identification. However, in general it does not identify non-protein small-molecule targets, and thus, alternative methods for target identification are in high demand. We report the discovery of the autophagy inhibitor autoquin and the identification of its molecular mode of action using image-based morphological profiling in the cell painting assay. A compound-induced fingerprint representing changes in 579 cellular parameters revealed that autoquin accumulates in lysosomes and inhibits their fusion with autophagosomes. In addition, autoquin sequesters Fe2+ in lysosomes, resulting in an increase of lysosomal reactive oxygen species and ultimately cell death. Such a mechanism of action would have been challenging to unravel by current methods. This work demonstrates the potential of the cell painting assay to deconvolute modes of action of small molecules, warranting wider application in chemical biology.
Collapse
Affiliation(s)
- Luca Laraia
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany.,current address: Technical University of Denmark, Department of Chemistry, Kemitorvet 207, 2800 Kgs., Lyngby, Denmark
| | - Guillaume Garivet
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany.,Faculty of Chemistry and Chemical Biology, TU Dortmund, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
| | - Daniel J Foley
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany.,current address: School of Physical and Chemical Sciences, University of Canterbury, Christchurch, New Zealand
| | - Nadine Kaiser
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany.,Faculty of Chemistry and Chemical Biology, TU Dortmund, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
| | - Sebastian Müller
- Institut Curie, CNRS UMR 3666, INSERM U1143, PSL University Paris, Chemical Cell Biology Group, 26 Rue d'Ulm, 75248, Paris Cedex 05, France
| | - Sarah Zinken
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany.,Faculty of Chemistry and Chemical Biology, TU Dortmund, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
| | - Thomas Pinkert
- Institut für Chemie der, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2 (R 1'102), 12489, Berlin, Germany
| | - Julian Wilke
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany.,Faculty of Chemistry and Chemical Biology, TU Dortmund, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
| | - Dale Corkery
- Department of Chemistry, Umeå Universitet, KB.A4, Linnaeus väg 10 (rum: A4.35.07), 90187, Umeå, Sweden
| | - Axel Pahl
- Compound Management and Screening Center, Dortmund, Otto-Hahn-Str. 11, 44227, Dortmund, Germany
| | - Sonja Sievers
- Compound Management and Screening Center, Dortmund, Otto-Hahn-Str. 11, 44227, Dortmund, Germany
| | - Petra Janning
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany.,Faculty of Chemistry and Chemical Biology, TU Dortmund, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
| | - Christoph Arenz
- Institut für Chemie der, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2 (R 1'102), 12489, Berlin, Germany
| | - Yaowen Wu
- Department of Chemistry, Umeå Universitet, KB.A4, Linnaeus väg 10 (rum: A4.35.07), 90187, Umeå, Sweden
| | - Raphaël Rodriguez
- Institut Curie, CNRS UMR 3666, INSERM U1143, PSL University Paris, Chemical Cell Biology Group, 26 Rue d'Ulm, 75248, Paris Cedex 05, France
| | - Herbert Waldmann
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany.,Faculty of Chemistry and Chemical Biology, TU Dortmund, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
| |
Collapse
|
18
|
Yett A, Lin LY, Beseiso D, Miao J, Yatsunyk LA. N-methyl mesoporphyrin IX as a highly selective light-up probe for G-quadruplex DNA. J PORPHYR PHTHALOCYA 2019; 23:1195-1215. [PMID: 34385812 PMCID: PMC8356643 DOI: 10.1142/s1088424619300179] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
N-methyl mesoporphyrin IX (NMM) is a water-soluble, non-symmetric porphyrin with excellent optical properties and unparalleled selectivity for G-quadruplex (GQ) DNA. G-quadruplexes are non-canonical DNA structures formed by guanine-rich sequences. They are implicated in genomic stability, longevity, and cancer. The ability of NMM to selectively recognize GQ structures makes it a valuable scaffold for designing novel GQ binders. In this review, we survey the literature describing the GQ-binding properties of NMM as well as its wide utility in chemistry and biology. We start with the discovery of the GQ-binding properties of NMM and the development of NMM-binding aptamers. We then discuss the optical properties of NMM, focusing on the light-switch effect - high fluorescence of NMM induced upon its binding to GQ DNA. Additionally, we examine the affinity and selectivity of NMM for GQs, as well as its ability to stabilize GQ structures and favor parallel GQ conformations. Furthermore, a portion of the review is dedicated to the applications of NMM-GQ complexes as biosensors for heavy metals, small molecules (e.g. ATP and pesticides), DNA, and proteins. Finally and importantly, we discuss the utility of NMM as a probe to investigate the roles of GQs in biological processes.
Collapse
Affiliation(s)
- Ariana Yett
- Swarthmore College, Department of Chemistry and Biochemistry, 500 College Ave, Swarthmore, PA 19081, USA
| | - Linda Yingqi Lin
- Swarthmore College, Department of Chemistry and Biochemistry, 500 College Ave, Swarthmore, PA 19081, USA
| | - Dana Beseiso
- Swarthmore College, Department of Chemistry and Biochemistry, 500 College Ave, Swarthmore, PA 19081, USA
| | - Joanne Miao
- Swarthmore College, Department of Chemistry and Biochemistry, 500 College Ave, Swarthmore, PA 19081, USA
| | - Liliya A. Yatsunyk
- Correspondence to: Liliya A. Yatsunyk, Swarthmore College, 500 College Ave, Swarthmore, PA 19081, USA. tel.: 610-328-8558,
| |
Collapse
|
19
|
|
20
|
Yadav P, Kumar M, Bansal R, Kaur P, Ethayathulla AS. Structure model of ferrochelatase from Salmonella Typhi elucidating metalation mechanism. Int J Biol Macromol 2019; 127:585-593. [PMID: 30660563 DOI: 10.1016/j.ijbiomac.2019.01.066] [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: 11/29/2018] [Revised: 01/15/2019] [Accepted: 01/15/2019] [Indexed: 11/16/2022]
Abstract
A homology model of ferrochelatase (HemH), the heme biosynthesis terminal step enzyme from Salmonella Typhi was generated to understand the mechanism of metal insertion into protoporphyrin IX for heme biosynthesis. The overall fold of membrane associated ferrochelatase (StFc) from S. Typhi is similar to human and Yeast ferrochelatase than Bacillus subtilis, and Bacillus anthracis. An insertion of 16 amino acid residues in helical switch having hydrophobic patch proposed to interact with membrane lipids and in opening and closing of heme binding cleft. The sequence analysis and the docking study revealed that the protoporphyrin binding site in StFc has a crucial replacement of Tyr/Met to Leu13 unique in comparison to other known structures, where Tyr13 observed in B. subtilis/B. anthracis while Met76 in human/yeast play important role in holding protoporphyrin in optimal orientation for metalation. A sitting-a-top (SAT) complex mechanism for metalation is proposed with His194 and Glu264 lie at the bottom and Leu13 on the top of the porphyrin ring. In addition, an entry and exit mechanism is also proposed for protoporphyrin binding into cavity by opening and closing of helical switch using molecular dynamics simulation studies of Apo and heme complexed model structure of S. Typhi HemH.
Collapse
Affiliation(s)
| | - Manoj Kumar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Rohit Bansal
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Punit Kaur
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Abdul S Ethayathulla
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India.
| |
Collapse
|
21
|
Alavi FS, Gheidi M, Zahedi M, Safari N, Ryde U. A novel mechanism of heme degradation to biliverdin studied by QM/MM and QM calculations. Dalton Trans 2018; 47:8283-8291. [DOI: 10.1039/c8dt00064f] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Heme degradation by heme oxygenase enzymes is important for maintaining iron homeostasis and prevention of oxidative stress.
Collapse
Affiliation(s)
- Fatemeh Sadat Alavi
- Department of Chemistry
- Faculty of Sciences
- Shahid Beheshti University
- Tehran
- Iran
| | - Mahin Gheidi
- Department of Chemistry
- Faculty of Sciences
- Shahid Beheshti University
- Tehran
- Iran
| | - Mansour Zahedi
- Department of Chemistry
- Faculty of Sciences
- Shahid Beheshti University
- Tehran
- Iran
| | - Nasser Safari
- Department of Chemistry
- Faculty of Sciences
- Shahid Beheshti University
- Tehran
- Iran
| | - Ulf Ryde
- Department of Theoretical Chemistry
- Lund University
- Chemical Centre
- SE-221 00 Lund
- Sweden
| |
Collapse
|
22
|
Mamardashvili GM, Zhdanova DY, Mamardashvili NZ, Koifman OI, Dehaen W. Catalytic and inhibiting effect of amino acids on the porphyrin metallation reactions. J PORPHYR PHTHALOCYA 2017. [DOI: 10.1142/s1088424617500663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
In the present work, using the interaction of tetra-(4-sulfophenyl)porphyrin with copper(II) chloride as an example, it has been shown how different amino acid additives (glycine, valine, leucine and tryptophan) catalyze or inhibit the formation of Cu-porphyrin as a function of the chemical environment (borate buffer (pH7.4), DMSO) and the concentration of the additive. It has been demonstrated that the type of amino acid affects the complexation reaction rate. Possible mechanisms of metalloporphyrin formation and the ways of their acceleration are discussed.
Collapse
Affiliation(s)
- Galina M. Mamardashvili
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, Academicheskay st. 1, Ivanovo, 153045, Russia
| | - Daria Yu. Zhdanova
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, Academicheskay st. 1, Ivanovo, 153045, Russia
| | - Nugzar Zh. Mamardashvili
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, Academicheskay st. 1, Ivanovo, 153045, Russia
| | - Oskar I. Koifman
- Research Institute of Macroheterocycles, Ivanovo State University of Chemistry and Technology, Sheremetevskiy Av. 7, Ivanovo 153000, Russia
| | - Wim Dehaen
- Molecular Design and Synthesis, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Leuven, B-3001, Belgium
| |
Collapse
|
23
|
Alavi FS, Zahedi M, Safari N, Ryde U. QM/MM Study of the Conversion of Oxophlorin into Verdoheme by Heme Oxygenase. J Phys Chem B 2017; 121:11427-11436. [PMID: 29090581 DOI: 10.1021/acs.jpcb.7b08332] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Heme oxygenase is an enzyme that degrades heme, thereby recycling iron in most organisms, including humans. Pervious density functional theory (DFT) calculations have suggested that iron(III) hydroxyheme, an intermediate generated in the first step of heme degradation by heme oxygenase, is converted to iron(III) superoxo oxophlorin in the presence of dioxygen. In this article, we have studied the detailed mechanism of conversion of iron(III) superoxo oxophlorin to verdoheme by using combined quantum mechanics and molecular mechanics (QM/MM) calculations. The calculations employed the B3LYP method and the def2-QZVP basis set, considering dispersion effects with the DFT-D3 approach, obtaining accurate energies with large QM regions of almost 1000 atoms. The reaction was found to be exothermic by -35 kcal/mol, with a rate-determining barrier of 19 kcal/mol in the doublet state. The protein environment and especially water in the enzyme pocket significantly affects the reaction by decreasing the reaction activation energies and changing the structures by providing strategic hydrogen bonds.
Collapse
Affiliation(s)
- Fatemeh Sadat Alavi
- Department of Chemistry, Faculty of Sciences, Shahid Beheshti University , G.C., Evin, 19839-6313 Tehran, Iran
| | - Mansour Zahedi
- Department of Chemistry, Faculty of Sciences, Shahid Beheshti University , G.C., Evin, 19839-6313 Tehran, Iran
| | - Nasser Safari
- Department of Chemistry, Faculty of Sciences, Shahid Beheshti University , G.C., Evin, 19839-6313 Tehran, Iran
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University , Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| |
Collapse
|
24
|
Sciortino G, Rodríguez-Guerra Pedregal J, Lledós A, Garribba E, Maréchal JD. Prediction of the interaction of metallic moieties with proteins: An update for protein-ligand docking techniques. J Comput Chem 2017; 39:42-51. [PMID: 29076256 DOI: 10.1002/jcc.25080] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 08/31/2017] [Accepted: 09/25/2017] [Indexed: 12/16/2022]
Abstract
In this article, we present a new approach to expand the range of application of protein-ligand docking methods in the prediction of the interaction of coordination complexes (i.e., metallodrugs, natural and artificial cofactors, etc.) with proteins. To do so, we assume that, from a pure computational point of view, hydrogen bond functions could be an adequate model for the coordination bonds as both share directionality and polarity aspects. In this model, docking of metalloligands can be performed without using any geometrical constraints or energy restraints. The hard work consists in generating the convenient atom types and scoring functions. To test this approach, we applied our model to 39 high-quality X-ray structures with transition and main group metal complexes bound via a unique coordination bond to a protein. This concept was implemented in the protein-ligand docking program GOLD. The results are in very good agreement with the experimental structures: the percentage for which the RMSD of the simulated pose is smaller than the X-ray spectra resolution is 92.3% and the mean value of RMSD is < 1.0 Å. Such results also show the viability of the method to predict metal complexes-proteins interactions when the X-ray structure is not available. This work could be the first step for novel applicability of docking techniques in medicinal and bioinorganic chemistry and appears generalizable enough to be implemented in most protein-ligand docking programs nowadays available. © 2017 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Giuseppe Sciortino
- Departament de Química, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallés, Barcelona, Spain.,Dipartimento di Chimica e Farmacia, Università di Sassari, Via Vienna 2, I-07100, Sassari, Italy
| | | | - Agustí Lledós
- Departament de Química, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallés, Barcelona, Spain
| | - Eugenio Garribba
- Dipartimento di Chimica e Farmacia, Università di Sassari, Via Vienna 2, I-07100, Sassari, Italy
| | - Jean-Didier Maréchal
- Departament de Química, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallés, Barcelona, Spain
| |
Collapse
|
25
|
The coproporphyrin ferrochelatase of Staphylococcus aureus: mechanistic insights into a regulatory iron-binding site. Biochem J 2017; 474:3513-3522. [PMID: 28864672 PMCID: PMC5633918 DOI: 10.1042/bcj20170362] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 08/24/2017] [Accepted: 08/29/2017] [Indexed: 11/21/2022]
Abstract
The majority of characterised ferrochelatase enzymes catalyse the final step of classical haem synthesis, inserting ferrous iron into protoporphyrin IX. However, for the recently discovered coproporphyrin-dependent pathway, ferrochelatase catalyses the penultimate reaction where ferrous iron is inserted into coproporphyrin III. Ferrochelatase enzymes from the bacterial phyla Firmicutes and Actinobacteria have previously been shown to insert iron into coproporphyrin, and those from Bacillus subtilis and Staphylococcus aureus are known to be inhibited by elevated iron concentrations. The work herein reports a Km (coproporphyrin III) for S. aureus ferrochelatase of 1.5 µM and it is shown that elevating the iron concentration increases the Km for coproporphyrin III, providing a potential explanation for the observed iron-mediated substrate inhibition. Together, structural modelling, site-directed mutagenesis, and kinetic analyses confirm residue Glu271 as being essential for the binding of iron to the inhibitory regulatory site on S. aureus ferrochelatase, providing a molecular explanation for the observed substrate inhibition patterns. This work therefore has implications for how haem biosynthesis in S. aureus is regulated by iron availability.
Collapse
|
26
|
Dailey HA, Dailey TA, Gerdes S, Jahn D, Jahn M, O'Brian MR, Warren MJ. Prokaryotic Heme Biosynthesis: Multiple Pathways to a Common Essential Product. Microbiol Mol Biol Rev 2017; 81:e00048-16. [PMID: 28123057 PMCID: PMC5312243 DOI: 10.1128/mmbr.00048-16] [Citation(s) in RCA: 185] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The advent of heme during evolution allowed organisms possessing this compound to safely and efficiently carry out a variety of chemical reactions that otherwise were difficult or impossible. While it was long assumed that a single heme biosynthetic pathway existed in nature, over the past decade, it has become clear that there are three distinct pathways among prokaryotes, although all three pathways utilize a common initial core of three enzymes to produce the intermediate uroporphyrinogen III. The most ancient pathway and the only one found in the Archaea converts siroheme to protoheme via an oxygen-independent four-enzyme-step process. Bacteria utilize the initial core pathway but then add one additional common step to produce coproporphyrinogen III. Following this step, Gram-positive organisms oxidize coproporphyrinogen III to coproporphyrin III, insert iron to make coproheme, and finally decarboxylate coproheme to protoheme, whereas Gram-negative bacteria first decarboxylate coproporphyrinogen III to protoporphyrinogen IX and then oxidize this to protoporphyrin IX prior to metal insertion to make protoheme. In order to adapt to oxygen-deficient conditions, two steps in the bacterial pathways have multiple forms to accommodate oxidative reactions in an anaerobic environment. The regulation of these pathways reflects the diversity of bacterial metabolism. This diversity, along with the late recognition that three pathways exist, has significantly slowed advances in this field such that no single organism's heme synthesis pathway regulation is currently completely characterized.
Collapse
Affiliation(s)
- Harry A Dailey
- Department of Microbiology, Department of Biochemistry and Molecular Biology, and Biomedical and Health Sciences Institute, University of Georgia, Athens, Georgia, USA
| | - Tamara A Dailey
- Department of Microbiology, Department of Biochemistry and Molecular Biology, and Biomedical and Health Sciences Institute, University of Georgia, Athens, Georgia, USA
| | - Svetlana Gerdes
- Fellowship for Interpretation of Genomes, Burr Ridge, Illinois, USA
| | - Dieter Jahn
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universitaet Braunschweig, Braunschweig, Germany
| | - Martina Jahn
- Institute of Microbiology, Technische Universitaet Braunschweig, Braunschweig, Germany
| | - Mark R O'Brian
- Department of Biochemistry, University at Buffalo, The State University of New York, Buffalo, New York, USA
| | - Martin J Warren
- Department of Biosciences, University of Kent, Canterbury, Kent, United Kingdom
| |
Collapse
|
27
|
Wu J, Wen S, Zhou Y, Chao H, Shen Y. Human Ferrochelatase: Insights for the Mechanism of Ferrous Iron Approaching Protoporphyrin IX by QM/MM and QTCP Free Energy Studies. J Chem Inf Model 2016; 56:2421-2433. [PMID: 27801584 DOI: 10.1021/acs.jcim.6b00216] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ferrochelatase catalyzes the insertion of ferrous iron into protoporphyrin IX, the terminal step in heme biosynthesis. Some disputes in its mechanism remain unsolved, especially for human ferrochelatase. In this paper, high-level quantum mechanical/molecular mechanics (QM/MM) and free-energy studies were performed to address these controversial issues including the iron-binding site, the optimal reaction path, the substrate porphyrin distortion, and the presence of the sitting-atop (SAT) complex. Our results reveal that the ferrous iron is probably at the binding site coordinating with Met76, and His263 plays the role of proton acceptor. The rate-determining step is either the first proton removed by His263 or the proton transition within the porphyrin with an energy barrier of 14.99 or 14.87 kcal/mol by the quantum mechanical thermodynamic cycle perturbation (QTCP) calculations, respectively. The fast deprotonation step with the conservative residues rather than porphyrin deformation found in solution provides the driving force for biochelation. The SAT complex is not a necessity for the catalysis though it induces a modest distortion on the porphyrin ring.
Collapse
Affiliation(s)
- Jingheng Wu
- School of Chemistry, Sun Yat-sen University , 510275 Guangzhou, P R China
| | - Sixiang Wen
- School of Chemistry, Sun Yat-sen University , 510275 Guangzhou, P R China
| | - Yiwei Zhou
- School of Chemistry, Sun Yat-sen University , 510275 Guangzhou, P R China
| | - Hui Chao
- School of Chemistry, Sun Yat-sen University , 510275 Guangzhou, P R China
| | - Yong Shen
- School of Chemistry, Sun Yat-sen University , 510275 Guangzhou, P R China
| |
Collapse
|
28
|
Senge MO, MacGowan SA, O'Brien JM. Conformational control of cofactors in nature - the influence of protein-induced macrocycle distortion on the biological function of tetrapyrroles. Chem Commun (Camb) 2016; 51:17031-63. [PMID: 26482230 DOI: 10.1039/c5cc06254c] [Citation(s) in RCA: 135] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Tetrapyrrole-containing proteins are one of the most fundamental classes of enzymes in nature and it remains an open question to give a chemical rationale for the multitude of biological reactions that can be catalyzed by these pigment-protein complexes. There are many fundamental processes where the same (i.e., chemically identical) porphyrin cofactor is involved in chemically quite distinct reactions. For example, heme is the active cofactor for oxygen transport and storage (hemoglobin, myoglobin) and for the incorporation of molecular oxygen in organic substrates (cytochrome P450). It is involved in the terminal oxidation (cytochrome c oxidase) and the metabolism of H2O2 (catalases and peroxidases) and catalyzes various electron transfer reactions in cytochromes. Likewise, in photosynthesis the same chlorophyll cofactor may function as a reaction center pigment (charge separation) or as an accessory pigment (exciton transfer) in light harvesting complexes (e.g., chlorophyll a). Whilst differences in the apoprotein sequences alone cannot explain the often drastic differences in physicochemical properties encountered for the same cofactor in diverse protein complexes, a critical factor for all biological functions must be the close structural interplay between bound cofactors and the respective apoprotein in addition to factors such as hydrogen bonding or electronic effects. Here, we explore how nature can use the same chemical molecule as a cofactor for chemically distinct reactions using the concept of conformational flexibility of tetrapyrroles. The multifaceted roles of tetrapyrroles are discussed in the context of the current knowledge on distorted porphyrins. Contemporary analytical methods now allow a more quantitative look at cofactors in protein complexes and the development of the field is illustrated by case studies on hemeproteins and photosynthetic complexes. Specific tetrapyrrole conformations are now used to prepare bioengineered designer proteins with specific catalytic or photochemical properties.
Collapse
Affiliation(s)
- Mathias O Senge
- School of Chemistry, SFI Tetrapyrrole Laboratory, Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse Street, Dublin 2, Ireland and Medicinal Chemistry, Institute of Molecular Medicine, Trinity Centre for Health Sciences, Trinity College Dublin, St. James's Hospital, Dublin 8, Ireland.
| | - Stuart A MacGowan
- School of Chemistry, SFI Tetrapyrrole Laboratory, Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Jessica M O'Brien
- Medicinal Chemistry, Institute of Molecular Medicine, Trinity Centre for Health Sciences, Trinity College Dublin, St. James's Hospital, Dublin 8, Ireland.
| |
Collapse
|
29
|
Combined use of optical spectroscopy and computational methods to study the binding and the photoinduced conformational modification of proteins when NMR and X-ray structural determinations are not an option. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2016. [PMID: 24018324 DOI: 10.1016/b978-0-12-416596-0.00004-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register]
Abstract
The functions of proteins depend on their interactions with various ligands and these interactions are controlled by the structure of the polypeptides. If one can manipulate the structure of proteins, their functions can in principle be modulated. The issue of protein structure-function relationship is not only a central problem in biophysics, but is becoming clear that the ability to "artificially" modify the structure of proteins could be relevant in fields beyond the biomedical area to provide, for instance, light responses in proteins which would not possess such properties in their native state. This chapter presents an overview of the combination of optical electronic and vibrational spectroscopy with various computational methods to investigate the binding between photoactive ligands and proteins.
Collapse
|
30
|
McMicken B, Parker JE, Thomas RJ, Brancaleon L. Resonance Raman and vibrational mode analysis used to predict ligand geometry for docking simulations of a water soluble porphyrin and tubulin. J Biomol Struct Dyn 2015; 34:1998-2010. [PMID: 26431467 DOI: 10.1080/07391102.2015.1102082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The ability to modify the conformation of a protein by controlled partial unfolding may have practical applications such as inhibiting its function or providing non-native photosensitive properties. A water-soluble porphyrin, meso-tetrakis (p-sulfonatophenyl) porphyrin (TSPP), non-covalently bound to tubulin can be used as a photosensitizer, which upon irradiation can lead to conformational changes of the protein. To fully understand the mechanism responsible for this partial unfolding and determine the amino acid residues and atoms involved, it is essential to find the most likely binding location and the configuration of the ligand and protein. Techniques typically used to analyze atomic position details, such as nuclear magnetic resonance and X-ray crystallography, require large concentrations, which are incompatible with the dilute conditions required in experiments for photoinduced mechanisms. Instead, we develop an atomistic description of the TSPP-tubulin complex using vibrational mode analysis from density functional theory calculations correlated to resonance Raman spectra of the porphyrin paired with docking simulations. Changes in the Raman peaks of the porphyrin molecule correlate with changes in its structural vibrational modes when bound to tubulin. The data allow us to construct the relative geometry of the porphyrin when bound to protein, which are then used with docking simulations to find the most likely configuration of the TSPP-tubulin complex.
Collapse
Affiliation(s)
- Brady McMicken
- a Department of Physics and Astronomy , The University of Texas at San Antonio , San Antonio , TX 78249 , USA.,c Optical Radiation Bioeffects Branch, Bioeffects Division, Human Effectiveness Directorate, 711th Human Performance Wing , Air Force Research Laboratory , JBSA Fort Sam Houston, TX 78234 , USA
| | - James E Parker
- a Department of Physics and Astronomy , The University of Texas at San Antonio , San Antonio , TX 78249 , USA.,b General Dynamics Information Technology , JBSA Fort Sam Houston, TX 78234 , USA
| | - Robert J Thomas
- c Optical Radiation Bioeffects Branch, Bioeffects Division, Human Effectiveness Directorate, 711th Human Performance Wing , Air Force Research Laboratory , JBSA Fort Sam Houston, TX 78234 , USA
| | - Lorenzo Brancaleon
- a Department of Physics and Astronomy , The University of Texas at San Antonio , San Antonio , TX 78249 , USA
| |
Collapse
|
31
|
Chen X, Pu H, Wang X, Long W, Lin R, Liu L. Crystal Structures of GUN4 in Complex with Porphyrins. MOLECULAR PLANT 2015; 8:1125-7. [PMID: 25958236 DOI: 10.1016/j.molp.2015.04.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 04/17/2015] [Accepted: 04/30/2015] [Indexed: 05/08/2023]
Affiliation(s)
- Xuemin Chen
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Haidian District, Beijing 100093, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Haidian District, Beijing 100049, China
| | - Hua Pu
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Haidian District, Beijing 100093, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Haidian District, Beijing 100049, China
| | - Xiao Wang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Haidian District, Beijing 100093, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Haidian District, Beijing 100049, China
| | - Weiwei Long
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Haidian District, Beijing 100093, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Haidian District, Beijing 100049, China
| | - Rongcheng Lin
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Haidian District, Beijing 100093, China
| | - Lin Liu
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Haidian District, Beijing 100093, China.
| |
Collapse
|
32
|
Nicoludis JM, Miller ST, Jeffrey PD, Barrett SP, Rablen PR, Lawton TJ, Yatsunyk LA. Optimized end-stacking provides specificity of N-methyl mesoporphyrin IX for human telomeric G-quadruplex DNA. J Am Chem Soc 2012. [PMID: 23181361 DOI: 10.1021/ja3088746] [Citation(s) in RCA: 156] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
N-methyl mesoporphyrin IX (NMM) is exceptionally selective for G-quadruplexes (GQ) relative to duplex DNA and, as such, has found a wide range of applications in biology and chemistry. In addition, NMM is selective for parallel versus antiparallel GQ folds, as was recently demonstrated in our laboratory. Here, we present the X-ray crystal structure of a complex between NMM and human telomeric DNA dAGGG(TTAGGG)(3), Tel22, determined in two space groups, P2(1)2(1)2 and P6, at 1.65 and 2.15 Å resolution, respectively. The former is the highest resolution structure of the human telomeric GQ DNA reported to date. The biological unit contains a Tel22 dimer of 5'-5' stacked parallel-stranded quadruplexes capped on both ends with NMM, supporting the spectroscopically determined 1:1 stoichiometry. NMM is capable of adjusting its macrocycle geometry to closely match that of the terminal G-tetrad required for efficient π-π stacking. The out-of-plane N-methyl group of NMM fits perfectly into the center of the parallel GQ core where it aligns with potassium ions. In contrast, the interaction of the N-methyl group with duplex DNA or antiparallel GQ would lead to steric clashes that prevent NMM from binding to these structures, thus explaining its unique selectivity. On the basis of the biochemical data, binding of NMM to Tel22 does not rely on relatively nonspecific electrostatic interactions, which characterize most canonical GQ ligands, but rather it is hydrophobic in nature. The structural features observed in the NMM-Tel22 complex described here will serve as guidelines for developing new quadruplex ligands that have excellent affinity and precisely defined selectivity.
Collapse
Affiliation(s)
- John M Nicoludis
- Department of Chemistry and Biochemistry, Swarthmore College, 500 College Avenue, Swarthmore, Pennsylvania 19081, United States
| | | | | | | | | | | | | |
Collapse
|
33
|
Wang Y, Shen Y. Is it possible for Fe2+ to approach protoporphyrin IX from the side of Tyr-13 in Bacillus subtilis ferrochelatase? An answer from QM/MM study. J Mol Model 2012; 19:963-71. [DOI: 10.1007/s00894-012-1627-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2012] [Accepted: 10/03/2012] [Indexed: 11/28/2022]
|
34
|
Asuru AP, An M, Busenlehner LS. Dissection of Porphyrin-Induced Conformational Dynamics in the Heme Biosynthesis Enzyme Ferrochelatase. Biochemistry 2012; 51:7116-27. [DOI: 10.1021/bi300704c] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Awuri P. Asuru
- Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Mier An
- Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Laura S. Busenlehner
- Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| |
Collapse
|
35
|
Parker JE, Thomas RJ, Morisson D, Brancaleon L. Combination of Resonance Raman Spectroscopy and Docking Simulations to Study the Nonspecific Binding of a Free-Base Porphyrin to a Globular Protein. J Phys Chem B 2012; 116:11032-40. [DOI: 10.1021/jp304310z] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- James E. Parker
- General Dynamics Information Technology, San Antonio, Texas 78234, United
States
- Department of Physics
and Astronomy, The University of Texas at San Antonio, San Antonio,
Texas 78249, United States
| | - Robert J. Thomas
- Optical Radiation Bioeffects Branch,
Bioeffects Division, Air Force Research Laboratory, Fort Sam Houston, Texas 78234, United States
| | - Dayla Morisson
- Department of Physics, The University of Texas at Arlington, Arlington, Texas
76019, United States
| | - Lorenzo Brancaleon
- Department of Physics
and Astronomy, The University of Texas at San Antonio, San Antonio,
Texas 78249, United States
| |
Collapse
|
36
|
Medlock AE, Najahi-Missaoui W, Ross TA, Dailey TA, Burch J, O'Brien JR, Lanzilotta WN, Dailey HA. Identification and characterization of solvent-filled channels in human ferrochelatase. Biochemistry 2012; 51:5422-33. [PMID: 22712763 DOI: 10.1021/bi300598g] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ferrochelatase catalyzes the formation of protoheme from two potentially cytotoxic products, iron and protoporphyrin IX. While much is known from structural and kinetic studies on human ferrochelatase of the dynamic nature of the enzyme during catalysis and the binding of protoporphyrin IX and heme, little is known about how metal is delivered to the active site and how chelation occurs. Analysis of all ferrochelatase structures available to date reveals the existence of several solvent-filled channels that originate at the protein surface and continue to the active site. These channels have been proposed to provide a route for substrate entry, water entry, and proton exit during the catalytic cycle. To begin to understand the functions of these channels, we investigated in vitro and in vivo a number of variants that line these solvent-filled channels. Data presented herein support the role of one of these channels, which originates at the surface residue H240, in the delivery of iron to the active site. Structural studies of the arginyl variant of the conserved residue F337, which resides at the back of the active site pocket, suggest that it not only regulates the opening and closing of active site channels but also plays a role in regulating the enzyme mechanism. These data provide insight into the movement of the substrate and water into and out of the active site and how this movement is coordinated with the reaction mechanism.
Collapse
Affiliation(s)
- Amy E Medlock
- Biomedical and Health Sciences Institute, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, 30602, United States.
| | | | | | | | | | | | | | | |
Collapse
|
37
|
Hunter GA, Al-Karadaghi S, Ferreira GC. FERROCHELATASE: THE CONVERGENCE OF THE PORPHYRIN BIOSYNTHESIS AND IRON TRANSPORT PATHWAYS. J PORPHYR PHTHALOCYA 2012; 15:350-356. [PMID: 21852895 DOI: 10.1142/s108842461100332x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Ferrochelatase (also known as PPIX ferrochelatase; Enzyme Commission number 4.9.9.1.1) catalyzes the insertion of ferrous iron into PPIX to form heme. This reaction unites the biochemically synchronized pathways of porphyrin synthesis and iron transport in nearly all living organisms. The ferrochelatases are an evolutionarily diverse family of enzymes with no more than six active site residues known to be perfectly conserved. The availability of over thirty different crystal structures, including many with bound metal ions or porphyrins, has added tremendously to our understanding of ferrochelatase structure and function. It is generally believed that ferrous iron is directly channeled to ferrochelatase in vivo, but the identity of the suspected chaperone remains uncertain despite much recent progress in this area. Identification of a conserved metal ion binding site at the base of the active site cleft may be an important clue as to how ferrochelatases acquire iron, and catalyze desolvation during transport to the catalytic site to complete heme synthesis.
Collapse
Affiliation(s)
- Gregory A Hunter
- Department of Molecular Medicine, College of Medicine, University of South Florida, Tampa, Florida, 33620
| | | | | |
Collapse
|
38
|
Franco R, Al-Karadaghi S, Ferreira GC. Resonance Raman Spectroscopic Examination of Ferrochelatase-induced Porphyrin Distortion. J PORPHYR PHTHALOCYA 2012; 15:357-363. [PMID: 21776189 DOI: 10.1142/s1088424611003380] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Ferrochelatase, the terminal enzyme of the heme biosynthetic pathway, catalyzes the insertion of ferrous iron into protoporphyrin IX to give heme. Resonance Raman spectroscopy has been instrumental in defining the distortion (mode and extent) of the porphyrin substrate, which is a critical step in the catalytic mechanism of ferrochelatase. Saddling is the predominant porphyrin out-of-plane deformation induced upon binding to ferrochelatase. Our analysis demonstrated that the intensity of the γ(15) line, which is assigned to an out-of-plane porphyrin vibration, in resonance Raman spectra obtained for wild-type- and variant ferrochelatase-bound porphyrin, correlates with the saddling deformation undergone by the porphyrin substrate. Further analysis of the three dimensional X-ray structures of bacterial, human and yeast ferrochelatases and the type and extent of distortion of the protein-bound porphyrin substrate and inhibitors using normal structure decomposition, support the view that ferrochelatase catalysis involves binding of a distorted porphyrin substrate and releasing of a flatter, metalated porphyrin.
Collapse
Affiliation(s)
- Ricardo Franco
- REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | | | | |
Collapse
|
39
|
Miethke M, Hou J, Marahiel MA. The siderophore-interacting protein YqjH acts as a ferric reductase in different iron assimilation pathways of Escherichia coli. Biochemistry 2011; 50:10951-64. [PMID: 22098718 DOI: 10.1021/bi201517h] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Siderophore-interacting proteins (SIPs), such as YqjH from Escherichia coli, are widespread among bacteria and commonly associated with iron-dependent induction and siderophore utilization. In this study, we show by detailed biochemical and genetic analyses the reaction mechanism by which the YqjH protein is able to catalyze the release of iron from a variety of iron chelators, including ferric triscatecholates and ferric dicitrate, displaying the highest efficiency for the hydrolyzed ferric enterobactin complex ferric (2,3-dihydroxybenzoylserine)(3). Site-directed mutagenesis revealed that residues K55 and R130 of YqjH are crucial for both substrate binding and reductase activity. The NADPH-dependent iron reduction was found to proceed via single-electron transfer in a double-displacement-type reaction through formation of a transient flavosemiquinone. The capacity to reduce substrates with extremely negative redox potentials, though at low catalytic rates, was studied by displacing the native FAD cofactor with 5-deaza-5-carba-FAD, which is restricted to a two-electron transfer. In the presence of the reconstituted noncatalytic protein, the ferric enterobactin midpoint potential increased remarkably and partially overlapped with the effective E(1) redox range. Concurrently, the observed molar ratios of generated Fe(II) versus NADPH were found to be ~1.5-fold higher for hydrolyzed ferric triscatecholates and ferric dicitrate than for ferric enterobactin. Further, combination of a chromosomal yqjH deletion with entC single- and entC fes double-deletion backgrounds showed the impact of yqjH on growth during supplementation with ferric siderophore substrates. Thus, YqjH enhances siderophore utilization in different iron acquisition pathways, including assimilation of low-potential ferric substrates that are not reduced by common cellular cofactors.
Collapse
Affiliation(s)
- Marcus Miethke
- Department of Chemistry/Biochemistry, Philipps University Marburg, Hans Meerwein Strasse, D-35032 Marburg, Germany.
| | | | | |
Collapse
|
40
|
McIntyre NR, Franco R, Shelnutt JA, Ferreira GC. Nickel(II) chelatase variants directly evolved from murine ferrochelatase: porphyrin distortion and kinetic mechanism. Biochemistry 2011; 50:1535-44. [PMID: 21222436 DOI: 10.1021/bi101170p] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The heme biosynthetic pathway culminates with the ferrochelatase-catalyzed ferrous iron chelation into protoporphyrin IX to form protoheme. The catalytic mechanism of ferrochelatase has been proposed to involve the stabilization of a nonplanar porphyrin to present the pyrrole nitrogens to the metal ion substrate. Previously, we hypothesized that the ferrochelatase-induced nonplanar distortions of the porphyrin substrate impose selectivity for the divalent metal ion incorporated into the porphyrin ring and facilitate the release of the metalated porphyrin through its reduced affinity for the enzyme. Using resonance Raman spectroscopy, the structural properties of porphyrins bound to the active site of directly evolved Ni(2+)-chelatase variants are now examined with regard to the mode and extent of porphyrin deformation and related to the catalytic properties of the enzymes. The Ni(2+)-chelatase variants (S143T, F323L, and S143T/F323L), which were directly evolved to exhibit an enhanced Ni(2+)-chelatase activity over that of the parent wild-type ferrochelatase, induced a weaker saddling deformation of the porphyrin substrate. Steady-state kinetic parameters of the evolved variants for Ni(2+)- and Fe(2+)-chelatase activities increased compared to those of wild-type ferrochelatase. In particular, the reduced porphyrin saddling deformation correlated with increased catalytic efficiency toward the metal ion substrate (Ni(2+) or Fe(2+)). The results lead us to propose that the decrease in the induced protoporphyrin IX saddling mode is associated with a less stringent metal ion preference by ferrochelatase and a slower porphyrin chelation step.
Collapse
Affiliation(s)
- Neil R McIntyre
- Department of Molecular Medicine, College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | | | | | | |
Collapse
|
41
|
Doyle CM, Krasnikov SA, Sergeeva NN, Preobrajenski AB, Vinogradov NA, Sergeeva YN, Senge MO, Cafolla AA. Evidence for the formation of an intermediate complex in the direct metalation of tetra(4-bromophenyl)-porphyrin on the Cu(111) surface. Chem Commun (Camb) 2011; 47:12134-6. [DOI: 10.1039/c1cc15241f] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
42
|
Evolution in a family of chelatases facilitated by the introduction of active site asymmetry and protein oligomerization. Proc Natl Acad Sci U S A 2010; 108:97-102. [PMID: 21173279 DOI: 10.1073/pnas.1014298108] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The class II chelatases associated with heme, siroheme, and cobalamin biosynthesis are structurally related enzymes that insert a specific metal ion (Fe(2+) or Co(2+)) into the center of a modified tetrapyrrole (protoporphyrin or sirohydrochlorin). The structures of two related class II enzymes, CbiX(S) from Archaeoglobus fulgidus and CbiK from Salmonella enterica, that are responsible for the insertion of cobalt along the cobalamin biosynthesis pathway are presented in complex with their metallated product. A further structure of a CbiK from Desulfovibrio vulgaris Hildenborough reveals how cobalt is bound at the active site. The crystal structures show that the binding of sirohydrochlorin is distinctly different to porphyrin binding in the protoporphyrin ferrochelatases and provide a molecular overview of the mechanism of chelation. The structures also give insights into the evolution of chelatase form and function. Finally, the structure of a periplasmic form of Desulfovibrio vulgaris Hildenborough CbiK reveals a novel tetrameric arrangement of its subunits that are stabilized by the presence of a heme b cofactor. Whereas retaining colbaltochelatase activity, this protein has acquired a central cavity with the potential to chaperone or transport metals across the periplasmic space, thereby evolving a new use for an ancient protein subunit.
Collapse
|
43
|
Hansson MD, Karlberg T, Söderberg CAG, Rajan S, Warren MJ, Al-Karadaghi S, Rigby SEJ, Hansson M. Bacterial ferrochelatase turns human: Tyr13 determines the apparent metal specificity of Bacillus subtilis ferrochelatase. J Biol Inorg Chem 2010; 16:235-42. [DOI: 10.1007/s00775-010-0720-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2010] [Accepted: 10/09/2010] [Indexed: 10/18/2022]
|
44
|
Dailey TA, Boynton TO, Albetel AN, Gerdes S, Johnson MK, Dailey HA. Discovery and Characterization of HemQ: an essential heme biosynthetic pathway component. J Biol Chem 2010; 285:25978-86. [PMID: 20543190 DOI: 10.1074/jbc.m110.142604] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Here we identify a previously undescribed protein, HemQ, that is required for heme synthesis in Gram-positive bacteria. We have characterized HemQ from Bacillus subtilis and a number of Actinobacteria. HemQ is a multimeric heme-binding protein. Spectroscopic studies indicate that this heme is high spin ferric iron and is ligated by a conserved histidine with the sixth coordination site available for binding a small molecule. The presence of HemQ along with the terminal two pathway enzymes, protoporphyrinogen oxidase (HemY) and ferrochelatase, is required to synthesize heme in vivo and in vitro. Although the exact role played by HemQ remains to be characterized, to be fully functional in vitro it requires the presence of a bound heme. HemQ possesses minimal peroxidase activity, but as a catalase it has a turnover of over 10(4) min(-1). We propose that this activity may be required to eliminate hydrogen peroxide that is generated by each turnover of HemY. Given the essential nature of heme synthesis and the restricted distribution of HemQ, this protein is a potential antimicrobial target for pathogens such as Mycobacterium tuberculosis.
Collapse
Affiliation(s)
- Tamara A Dailey
- Biomedical and Health Sciences Institute, University of Georgia, Athens, Georgia 30602, USA
| | | | | | | | | | | |
Collapse
|
45
|
Wang Y, Shen Y, Ryde U. QM/MM study of the insertion of metal ion into protoporphyrin IX by ferrochelatase. J Inorg Biochem 2009; 103:1680-6. [PMID: 19850353 DOI: 10.1016/j.jinorgbio.2009.09.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2009] [Revised: 09/16/2009] [Accepted: 09/18/2009] [Indexed: 11/16/2022]
Abstract
Ferrochelatase catalyzes the metallation of protoporphyrin IX in the terminal step of heme biosynthesis. Mutations in the ferrochelatase gene can lead to the disease erythropoietic porphyria. The catalyzing mechanism of ferrochelatase is still not fully understood. In this paper, we have studied the insertion of Fe(2+) into the protoporphyrin IX ring by Bacillussubtilis ferrochelatase using combined quantum mechanical and molecular mechanics (QM/MM) calculations. Geometries were optimized at the BP86/6-31G * level and energies were calculated at the B3LYP/TZVP level. The overall process involves the stepwise displacement of Glu-264, His-183, and a water molecule from Fe(2+), and the removal of two protons from the porphyrin ring. The rate-determining step is the cleavage of the bond between the oxygen atom of Glu-264 and Fe(2+), concomitant with the formation of the first Fe-N bond. It has an energy barrier of 57 kJ mol(-1). The porphyrin ring is only slightly distorted in the enzyme active site. The residue Tyr-13 plays a key role for the catalytic process extracting two protons from protoporphyrin IX.
Collapse
Affiliation(s)
- Yaxue Wang
- School of Chemistry and Chemical Engineering, Sun Yat-Sen University, 510275 Guangzhou, PR China
| | | | | |
Collapse
|
46
|
Davidson RE, Chesters CJ, Reid JD. Metal ion selectivity and substrate inhibition in the metal ion chelation catalyzed by human ferrochelatase. J Biol Chem 2009; 284:33795-9. [PMID: 19767646 DOI: 10.1074/jbc.m109.030205] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Protoporphyrin IX ferrochelatase (EC 4.99.1.1) catalyzes the terminal step in the heme biosynthetic pathway, the insertion of ferrous iron into protoporphyrin IX. Ferrochelatase shows specificity, in vitro, for multiple metal ion substrates and exhibits substrate inhibition in the case of zinc, copper, cobalt, and nickel. Zinc is the most biologically significant of these; when iron is depleted, zinc porphyrins are formed physiologically. Examining the k(cat)/K(m)(app) ratios for zinc and iron reveals that, in vitro, zinc is the preferred substrate at all concentrations of porphyrin. This is not the observed biological specificity, where zinc porphyrins are abnormal; these data argue for the existence of a specific iron delivery mechanism in vivo. We demonstrate that zinc acts as an uncompetitive substrate inhibitor, suggesting that ferrochelatase acts via an ordered pathway. Steady-state characterization demonstrates that the apparent k(cat) depends on zinc and shows substrate inhibition. Although porphyrin substrate is not inhibitory, zinc inhibition is enhanced by increasing porphyrin concentration. This indicates that zinc inhibits by binding to an enzyme-product complex (EZnD(IX)) and is likely to be the second substrate in an ordered mechanism. Our analysis shows that substrate inhibition by zinc is not a mechanism that can promote specificity for iron over zinc, but is instead one that will reduce the production of all metalloporphyrins in the presence of high concentrations of zinc.
Collapse
Affiliation(s)
- Ruth E Davidson
- Department of Chemistry, University of Sheffield, Sheffield S3 7HF, United Kingdom
| | | | | |
Collapse
|
47
|
Wu B, Novelli J, Foster J, Vaisvila R, Conway L, Ingram J, Ganatra M, Rao AU, Hamza I, Slatko B. The heme biosynthetic pathway of the obligate Wolbachia endosymbiont of Brugia malayi as a potential anti-filarial drug target. PLoS Negl Trop Dis 2009; 3:e475. [PMID: 19597542 PMCID: PMC2703803 DOI: 10.1371/journal.pntd.0000475] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2009] [Accepted: 06/02/2009] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Filarial parasites (e.g., Brugia malayi, Onchocerca volvulus, and Wuchereria bancrofti) are causative agents of lymphatic filariasis and onchocerciasis, which are among the most disabling of neglected tropical diseases. There is an urgent need to develop macro-filaricidal drugs, as current anti-filarial chemotherapy (e.g., diethylcarbamazine [DEC], ivermectin and albendazole) can interrupt transmission predominantly by killing microfilariae (mf) larvae, but is less effective on adult worms, which can live for decades in the human host. All medically relevant human filarial parasites appear to contain an obligate endosymbiotic bacterium, Wolbachia. This alpha-proteobacterial mutualist has been recognized as a potential target for filarial nematode life cycle intervention, as antibiotic treatments of filarial worms harboring Wolbachia result in the loss of worm fertility and viability upon antibiotic treatments both in vitro and in vivo. Human trials have confirmed this approach, although the length of treatments, high doses required and medical counter-indications for young children and pregnant women warrant the identification of additional anti-Wolbachia drugs. METHODS AND FINDINGS Genome sequence analysis indicated that enzymes involved in heme biosynthesis might constitute a potential anti-Wolbachia target set. We tested different heme biosynthetic pathway inhibitors in ex vivo B. malayi viability assays and report a specific effect of N-methyl mesoporphyrin (NMMP), which targets ferrochelatase (FC, the last step). Our phylogenetic analysis indicates evolutionarily significant divergence between Wolbachia heme genes and their human homologues. We therefore undertook the cloning, overexpression and analysis of several enzymes of this pathway alongside their human homologues, and prepared proteins for drug targeting. In vitro enzyme assays revealed a approximately 600-fold difference in drug sensitivities to succinyl acetone (SA) between Wolbachia and human 5'-aminolevulinic acid dehydratase (ALAD, the second step). Similarly, Escherichia coli hemH (FC) deficient strains transformed with human and Wolbachia FC homologues showed significantly different sensitivities to NMMP. This approach enables functional complementation in E. coli heme deficient mutants as an alternative E. coli-based method for drug screening. CONCLUSIONS Our studies indicate that the heme biosynthetic genes in the Wolbachia of B. malayi (wBm) might be essential for the filarial host survival. In addition, the results suggest they are likely candidate drug targets based upon significant differences in phylogenetic distance, biochemical properties and sensitivities to heme biosynthesis inhibitors, as compared to their human homologues.
Collapse
Affiliation(s)
- Bo Wu
- Division of Molecular Parasitology, New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Jacopo Novelli
- Division of Molecular Parasitology, New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Jeremy Foster
- Division of Molecular Parasitology, New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Romualdas Vaisvila
- Division of Molecular Parasitology, New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Leslie Conway
- Division of Molecular Parasitology, New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Jessica Ingram
- Division of Molecular Parasitology, New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Mehul Ganatra
- Division of Molecular Parasitology, New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Anita U. Rao
- Department of Animal and Avian Sciences and Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America
| | - Iqbal Hamza
- Department of Animal and Avian Sciences and Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America
| | - Barton Slatko
- Division of Molecular Parasitology, New England Biolabs, Ipswich, Massachusetts, United States of America
- * E-mail:
| |
Collapse
|
48
|
Szefczyk B, Cordeiro MNDS, Franco R, Gomes JANF. Molecular dynamics simulations of mouse ferrochelatase variants: what distorts and orientates the porphyrin? J Biol Inorg Chem 2009; 14:1119-28. [DOI: 10.1007/s00775-009-0556-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2009] [Accepted: 06/09/2009] [Indexed: 11/28/2022]
|
49
|
Masuda T. Recent overview of the Mg branch of the tetrapyrrole biosynthesis leading to chlorophylls. PHOTOSYNTHESIS RESEARCH 2008; 96:121-43. [PMID: 18273690 DOI: 10.1007/s11120-008-9291-4] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2007] [Accepted: 01/29/2008] [Indexed: 05/20/2023]
Abstract
In plants, chlorophylls (chlorophyll a and chlorophyll b) are the most abundant tetrapyrrole molecules and are essential for photosynthesis. The first committed step of chlorophyll biosynthesis is the insertion of Mg(2+) into protoporphyrin IX, and thus subsequent steps of the biosynthesis are called the Mg branch. As the Mg branch in higher plants is complex, it was not until the last decade--after many years of intensive research--that most of the genes encoding the enzymes for the pathway were identified. Biochemical and molecular genetic analyses have certainly modified the classic metabolic map of tetrapyrrole biosynthesis, and only recently have the molecular mechanisms of regulatory pathways governing chlorophyll metabolism been elucidated. As a result, novel functions of tetrapyrroles and biosynthetic enzymes have been proposed. In this review, I summarize the recent findings on enzymes involved in the Mg branch, mainly in higher plants.
Collapse
Affiliation(s)
- Tatsuru Masuda
- Graduate School of Arts and Sciences, The University of Tokyo, Komaba 3-8-1, Meguro-ku, Tokyo 153-8902, Japan.
| |
Collapse
|
50
|
Karlberg T, Hansson MD, Yengo RK, Johansson R, Thorvaldsen HO, Ferreira GC, Hansson M, Al-Karadaghi S. Porphyrin binding and distortion and substrate specificity in the ferrochelatase reaction: the role of active site residues. J Mol Biol 2008; 378:1074-83. [PMID: 18423489 DOI: 10.1016/j.jmb.2008.03.040] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2007] [Revised: 03/14/2008] [Accepted: 03/19/2008] [Indexed: 11/19/2022]
Abstract
The specific insertion of a divalent metal ion into tetrapyrrole macrocycles is catalyzed by a group of enzymes called chelatases. Distortion of the tetrapyrrole has been proposed to be an important component of the mechanism of metallation. We present the structures of two different inhibitor complexes: (1) N-methylmesoporphyrin (N-MeMP) with the His183Ala variant of Bacillus subtilis ferrochelatase; (2) the wild-type form of the same enzyme with deuteroporphyrin IX 2,4-disulfonic acid dihydrochloride (dSDP). Analysis of the structures showed that only one N-MeMP isomer out of the eight possible was bound to the protein and it was different from the isomer that was earlier found to bind to the wild-type enzyme. A comparison of the distortion of this porphyrin with other porphyrin complexes of ferrochelatase and a catalytic antibody with ferrochelatase activity using normal-coordinate structural decomposition reveals that certain types of distortion are predominant in all these complexes. On the other hand, dSDP, which binds closer to the protein surface compared to N-MeMP, does not undergo any distortion upon binding to the protein, underscoring that the position of the porphyrin within the active site pocket is crucial for generating the distortion required for metal insertion. In addition, in contrast to the wild-type enzyme, Cu(2+)-soaking of the His183Ala variant complex did not show any traces of porphyrin metallation. Collectively, these results provide new insights into the role of the active site residues of ferrochelatase in controlling stereospecificity, distortion and metallation.
Collapse
Affiliation(s)
- Tobias Karlberg
- Department of Molecular Biophysics, Centre for Molecular Protein Science, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
| | | | | | | | | | | | | | | |
Collapse
|