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Wittmann D, Wang C, Grimm B. More indications for redox-sensitive cysteine residues of the Arabidopsis 5-aminolevulinate dehydratase. FRONTIERS IN PLANT SCIENCE 2024; 14:1294802. [PMID: 38317833 PMCID: PMC10839789 DOI: 10.3389/fpls.2023.1294802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/28/2023] [Indexed: 02/07/2024]
Abstract
Redox-dependent thiol-disulfide switches of cysteine residues are one of the significant posttranslational modifications of proteins to control rapidly their stability, activity, and protein interaction. Redox control also modulates the tetrapyrrole biosynthesis (TBS). Among the redox-dependent TBS enzymes, 5-aminolevulinic acid dehydratase (ALAD) was previously recognized to interact with reductants, such a thioredoxins or NADPH-dependent thioredoxin reductase C. In this report, we aim to verify the redox sensitivity of ALAD and identify the redox-reactive cysteine residues among the six cysteines of the mature protein form Arabidopsis. Based on structural modelling and comparative studies of wild-type ALAD and ALAD mutants with single and double Cys➔Ser substitutions under oxidizing and reducing conditions, we aim to predict the dimerization and oligomerisation of ALAD as well as the crucial Cys residues for disulfide bridge formation and enzyme activity. The Cys404Ser mutation led to a drastic inactivation of ALAD and redox-dependent properties of ALAD were severely impaired, when Cys71 was simultaneously mutated with Cys152 or Cys251. Cys71 is located in a flexible N-terminal arm of ALAD, which could allow intramolecular disulfide bridges with Cys residues at the surface of the remaining globule ALAD structure. As a result, we propose different roles of Cys residues for redox control, catalytic activity and Mg2+-dependent assembly.
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Affiliation(s)
- Daniel Wittmann
- Institute of Biology/Plant Physiology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Chao Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Bernhard Grimm
- Institute of Biology/Plant Physiology, Humboldt-Universität zu Berlin, Berlin, Germany
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
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2
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Jaffe EK. Wrangling Shape-Shifting Morpheeins to Tackle Disease and Approach Drug Discovery. Front Mol Biosci 2020; 7:582966. [PMID: 33330623 PMCID: PMC7729013 DOI: 10.3389/fmolb.2020.582966] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 10/26/2020] [Indexed: 12/15/2022] Open
Abstract
Homo-multimeric proteins that can come apart, change shape, and reassemble differently with functional consequences have been called morpheeins and/or transformers; these provide a largely unexplored context for understanding disease and developing allosteric therapeutics. This article describes such proteins within the context of protein structure dynamics, provides one detailed example related to an inborn error of metabolism and potential herbicide development, and describes the context for applying these ideas for understanding disease and designing bioactive molecules, such as therapeutics.
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Affiliation(s)
- Eileen K Jaffe
- Fox Chase Cancer Center, Philadelphia, PA, United States
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Porphobilinogen synthase: An equilibrium of different assemblies in human health. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2019; 169:85-104. [PMID: 31952692 DOI: 10.1016/bs.pmbts.2019.11.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Porphobilinogen synthase (PBGS) is an essential enzyme that catalyzes an early step in heme biosynthesis. An unexpected human PBGS quaternary structure dynamic drove the definition of morpheeins, which are protein multimers that dissociate, change shape, and re-assemble differently with functional consequences. Each PBGS monomer has two domains that can reposition through a hinge motion. Human PBGS exists in an equilibrium among high activity octamer, low activity hexamer, and low mole-fraction dimer in which the hinge motion occurs. The dimer conformation dictates the multimer architecture. An octamer-specific inter-subunit interaction responds to pH, resulting in a pH-dependence to the octamer-hexamer equilibrium. An inborn error of metabolism, ALAD porphyria, is caused by single amino acid substitutions that stabilize the hexamer relative to octamer. Drugs that stabilize the PBGS hexamer result in a drug side effect that can exacerbate porphyria. PBGS is essential for all organisms that require respiration, photosynthesis, or methanogenesis. Consequently, phylogenetic variation in PBGS multimerization equilibria provides insight into how Nature has harnessed oligomeric variation in the control of protein function. The dynamic multimerization of PBGS revealed the morpheein mechanism for allostery, a structural basis for inborn errors of metabolism, a quaternary structure focus for drug discovery and/or drug side effects, and a pathway toward new antibiotics or herbicides. The fortuitous discovery of PBGS quaternary structure dynamics arose from characterization of a low-activity single amino acid variant that dramatically stabilized the hexamer, whose existence had previously gone unnoticed.
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Towards Initial Indications for a Thiol-Based Redox Control of Arabidopsis 5-Aminolevulinic Acid Dehydratase. Antioxidants (Basel) 2018; 7:antiox7110152. [PMID: 30384439 PMCID: PMC6262466 DOI: 10.3390/antiox7110152] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 10/26/2018] [Accepted: 10/28/2018] [Indexed: 12/15/2022] Open
Abstract
Thiol-based redox control is one of the important posttranslational mechanisms of the tetrapyrrole biosynthesis pathway. Many enzymes of the pathway have been shown to interact with thioredoxin (TRX) and Nicotinamide adenine dinucleotide phosphate (NADPH)-dependent thioredoxin reductase C (NTRC). We examined the redox-dependency of 5-aminolevulinic acid dehydratase (ALAD), which catalyzed the conjugation of two 5-aminolevulinic acid (ALA) molecules to porphobilinogen. ALAD interacted with TRX f, TRX m and NTRC in chloroplasts. Consequently, less ALAD protein accumulated in the trx f1, ntrc and trx f1/ntrc mutants compared to wild-type control resulting in decreased ALAD activity. In a polyacrylamide gel under non-reducing conditions, ALAD monomers turned out to be present in reduced and two oxidized forms. The reduced and oxidized forms of ALAD differed in their catalytic activity. The addition of TRX stimulated ALAD activity. From our results it was concluded that (i) deficiency of the reducing power mainly affected the in planta stability of ALAD; and (ii) the reduced form of ALAD displayed increased enzymatic activity.
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5
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Abstract
Porphobilinogen synthase (PBGS), also known as 5-aminolevulinate dehydratase, is an essential enzyme in the biosynthesis of all tetrapyrroles, which function in respiration, photosynthesis, and methanogenesis. Throughout evolution, PBGS adapted to a diversity of cellular niches and evolved to use an unusual variety of metal ions both for catalytic function and to control protein multimerization. With regard to the active site, some PBGSs require Zn2+; a subset of those, including human PBGS, contain a constellation of cysteine residues that acts as a sink for the environmental toxin Pb2+. PBGSs that do not require the soft metal ion Zn2+ at the active site instead are suspected of using the hard metal Mg2+. The most unexpected property of the PBGS family of enzymes is a dissociative allosteric mechanism that utilizes an equilibrium of architecturally and functionally distinct protein assemblies. The high-activity assembly is an octamer in which intersubunit interactions modulate active-site lid motion. This octamer can dissociate to dimer, the dimer can undergo a hinge twist, and the twisted dimer can assemble to a low-activity hexamer. The hexamer does not have the intersubunit interactions required to stabilize a closed conformation of the active site lid. PBGS active site chemistry benefits from a closed lid because porphobilinogen biosynthesis includes Schiff base formation, which requires deprotonated lysine amino groups. N-terminal and C-terminal sequence extensions dictate whether a specific species of PBGS can sample the hexameric assembly. The bulk of species (nearly all except animals and yeasts) use Mg2+ as an allosteric activator. Mg2+ functions allosterically by binding to an intersubunit interface that is present in the octamer but absent in the hexamer. This conformational selection allosteric mechanism is purported to be essential to avoid the untimely accumulation of phototoxic chlorophyll precursors in plants. For those PBGSs that do not use the allosteric Mg2+, there is a spatially equivalent arginine-derived guanidium group. Deprotonation of this residue promotes formation of the hexamer and accounts for the basic arm of the bell-shaped pH vs activity profile of human PBGS. A human inborn error of metabolism known as ALAD porphyria is attributed to PBGS variants that favor the hexameric assembly. The existence of one such variant, F12L, which dramatically stabilizes the human PBGS hexamer, allowed crystal structure determination for the hexamer. Without this crystal structure and octameric PBGS structures containing the allosteric Mg2+, it would have been difficult to decipher the structural basis for PBGS allostery. The requirement for multimer dissociation as an intermediate step in PBGS allostery was established by monitoring subunit disproportionation during the turnover-dependent transition of heteromeric PBGS (comprised of human wild type and F12L) from hexamer to octamer. One outcome of these studies was the definition of the dissociative morpheein model of protein allostery. The phylogenetically variable time scales for PBGS multimer interconversion result in atypical kinetic and biophysical behaviors. These behaviors can serve to identify other proteins that use the morpheein model of protein allostery.
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Affiliation(s)
- Eileen K. Jaffe
- Fox Chase Cancer Center, Temple University Health System, 333 Cottman Avenue, Philadelphia, Pennsylvania 19111, United States
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Mishra S, Alfeld M, Sobotka R, Andresen E, Falkenberg G, Küpper H. Analysis of sublethal arsenic toxicity to Ceratophyllum demersum: subcellular distribution of arsenic and inhibition of chlorophyll biosynthesis. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:4639-46. [PMID: 27340233 PMCID: PMC4973734 DOI: 10.1093/jxb/erw238] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Arsenic (As) pollution is a serious concern worldwide. Recent studies under environmentally relevant conditions revealed that, in the aquatic plant Ceratophyllum demersum, pigments are the first observable target of toxicity, prior to any effect on photosynthetic parameters or to oxidative stress. Lethal toxicity was initiated by a change of As species and their distribution pattern in various tissues. Here, the localization of As was investigated at the subcellular level through X-ray fluorescence using a submicron beam and a Maia detector. Further, it was possible to obtain useful tissue structural information from the ratio of the tomogram of photon flux behind the sample to the tomogram of Compton scattering. The micro-X-ray fluorescence tomograms showed that As predominantly accumulated in the nucleus of the epidermal cells in young mature leaves exposed to sublethal 1 µM As. This suggests that As may exert toxic effects in the nucleus, for example, by interfering with nucleic acid synthesis by replacing phosphorous with As. At higher cellular concentrations, As was mainly stored in the vacuole, particularly in mature leaves. An analysis of precursors of chlorophyll and degradation metabolites revealed that the observed decrease in chlorophyll concentration was associated with hindered biosynthesis, and was not due to degradation. Coproporphyrinogen III could not be detected after exposure to only 0.5 µM As. Levels of subsequent precursors, for example, protoporphyrin IX, Mg-protoporphyrin, Mg-protoporphyrin methyl ester, and divinyl protochlorophyllide, were significantly decreased at this concentration as well, indicating that the pathway was blocked upstream of tetrapyrrole synthesis.
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Affiliation(s)
- Seema Mishra
- CSIR-National Botanical Research Institute, Plant Ecology & Environmental Science Division, Rana Pratap Marg, Lucknow 226 001 (U.P.), India Universität Konstanz, Mathematisch-Naturwissenschaftliche Sektion, Fachbereich Biologie, Postfach M665, D-78457 Konstanz, Germany
| | - Matthias Alfeld
- Deutsches Elektronen-Synchrotron (DESY), Photon Science, Notkestr. 85, 22603 Hamburg, Germany
| | - Roman Sobotka
- Centre Algatech, Institute of Microbiology, Academy of Sciences of the Czech Republic, CZ-379 81 Třeboň, Czech Republic Institute of Plant Molecular Biology, Department of Biophysics and Biochemistry of Plants, Biology Centre of the AS CR, Branišovská 31/1160, CZ-370 05 České Budějovice, Czech Republic
| | - Elisa Andresen
- Universität Konstanz, Mathematisch-Naturwissenschaftliche Sektion, Fachbereich Biologie, Postfach M665, D-78457 Konstanz, Germany University of South Bohemia, Faculty of Science, Branišovská 31, CZ-370 05 České Budejovice, Czech Republic
| | - Gerald Falkenberg
- Deutsches Elektronen-Synchrotron (DESY), Photon Science, Notkestr. 85, 22603 Hamburg, Germany
| | - Hendrik Küpper
- Universität Konstanz, Mathematisch-Naturwissenschaftliche Sektion, Fachbereich Biologie, Postfach M665, D-78457 Konstanz, Germany Institute of Plant Molecular Biology, Department of Biophysics and Biochemistry of Plants, Biology Centre of the AS CR, Branišovská 31/1160, CZ-370 05 České Budějovice, Czech Republic University of South Bohemia, Faculty of Science, Branišovská 31, CZ-370 05 České Budejovice, Czech Republic
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Lentz C, Halls VS, Hannam JS, Strassel S, Lawrence SH, Jaffe EK, Famulok M, Hoerauf A, Pfarr KM. wALADin benzimidazoles differentially modulate the function of porphobilinogen synthase orthologs. J Med Chem 2014; 57:2498-510. [PMID: 24568185 PMCID: PMC3983392 DOI: 10.1021/jm401785n] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Indexed: 01/05/2023]
Abstract
The heme biosynthesis enzyme porphobilinogen synthase (PBGS) is a potential drug target in several human pathogens. wALADin1 benzimidazoles have emerged as species-selective PBGS inhibitors against Wolbachia endobacteria of filarial worms. In the present study, we have systematically tested wALADins against PBGS orthologs from bacteria, protozoa, metazoa, and plants to elucidate the inhibitory spectrum. However, the effect of wALADin1 on different PBGS orthologs was not limited to inhibition: several orthologs were stimulated by wALADin1; others remained unaffected. We demonstrate that wALADins allosterically modulate the PBGS homooligomeric equilibrium with inhibition mediated by favoring low-activity oligomers, while 5-aminolevulinic acid, Mg(2+), or K(+) stabilized high-activity oligomers. Pseudomonas aeruginosa PBGS could be inhibited or stimulated by wALADin1 depending on these factors and pH. We have defined the wALADin chemotypes responsible for either inhibition or stimulation, facilitating the design of tailored PBGS modulators for potential application as antimicrobial agents, herbicides, or drugs for porphyric disorders.
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Affiliation(s)
- Christian
S. Lentz
- Institute
of Medical Microbiology, Immunology and Parasitology, University Hospital of Bonn, Sigmund-Freud Strasse 25, 53127 Bonn, Germany
| | - Victoria S. Halls
- Chemical
Biology and Medicinal Chemistry Unit, LIMES Institute, University of Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
| | - Jeffrey S. Hannam
- Chemical
Biology and Medicinal Chemistry Unit, LIMES Institute, University of Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
| | - Silke Strassel
- Institute
of Medical Microbiology, Immunology and Parasitology, University Hospital of Bonn, Sigmund-Freud Strasse 25, 53127 Bonn, Germany
| | - Sarah H. Lawrence
- Fox
Chase Cancer Center, Temple University Health
System, 333 Cottman Avenue, Philadelphia, Pennsylvania, 19111, United States
| | - Eileen K. Jaffe
- Fox
Chase Cancer Center, Temple University Health
System, 333 Cottman Avenue, Philadelphia, Pennsylvania, 19111, United States
| | - Michael Famulok
- Chemical
Biology and Medicinal Chemistry Unit, LIMES Institute, University of Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
| | - Achim Hoerauf
- Institute
of Medical Microbiology, Immunology and Parasitology, University Hospital of Bonn, Sigmund-Freud Strasse 25, 53127 Bonn, Germany
| | - Kenneth M. Pfarr
- Institute
of Medical Microbiology, Immunology and Parasitology, University Hospital of Bonn, Sigmund-Freud Strasse 25, 53127 Bonn, Germany
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8
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Lentz CS, Halls V, Hannam JS, Niebel B, Strübing U, Mayer G, Hoerauf A, Famulok M, Pfarr KM. A selective inhibitor of heme biosynthesis in endosymbiotic bacteria elicits antifilarial activity in vitro. ACTA ACUST UNITED AC 2013; 20:177-87. [PMID: 23438747 DOI: 10.1016/j.chembiol.2012.11.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Revised: 11/19/2012] [Accepted: 11/21/2012] [Indexed: 12/19/2022]
Abstract
Lymphatic filariasis and onchocerciasis are severe diseases caused by filarial worms and affect more than 150 million people worldwide. Endosymbiotic α-proteobacteria Wolbachia are essential for these parasites throughout their life cycle. Using a high-throughput chemical screen, we identified a benzimidazole compound, wALADin1, that selectively targets the δ-aminolevulinic acid dehydratase (ALAD) of Wolbachia (wALAD) and exhibits macrofilaricidal effects on Wolbachia-containing filarial worms in vitro. wALADin1 is a mixed competitive/noncompetitive inhibitor that interferes with the Mg(2+)-induced activation of wALAD. This mechanism inherently excludes activity against the Zn(2+)-dependent human ortholog and might be translatable to Mg(2+)-responsive orthologs of other bacterial or protozoan pathogens. The specificity profile of wALADin1 derivatives reveals chemical features responsible for inhibitory potency and species selectivity. Our findings validate wALADins as a basis for developing potent leads that meet current requirements for antifilarial drugs.
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Affiliation(s)
- Christian S Lentz
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Sigmund-Freud Strasse 25, 53127 Bonn, Germany
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9
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Gupta P, Jain M, Sarangthem J, Gadre R. Inhibition of 5-aminolevulinic acid dehydratase by mercury in excised greening maize leaf segments. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2013. [PMID: 23191957 DOI: 10.1016/j.plaphy.2012.10.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Mercury (Hg), a potent metallic toxicant, is known for having inhibitory effect on chlorophyll biosynthesis. In vivo supply of HgCl(2) inhibited 5-aminolevulinic acid dehydratase (ALAD, EC 4.2.1.24) activity in excised greening maize (Zea mays) leaf segments. The inhibition caused by Hg was alleviated by addition of KNO(3). Amongst the nutrients and metabolites tested, NH(4)Cl and sucrose increased the inhibitory effect of Hg on enzyme activity, while glutamine and glutathione decreased it. The inhibitors, levulinic acid and 5,5' dithio bis 2-nitrobenzoic acid, also reduced the % inhibition of enzyme activity caused by Hg supply. In vitro inclusion of Hg during assay of the enzyme preparations obtained from the tissue treated without Hg (-Hg enzyme) and with Hg (+Hg enzyme) caused the inhibition of -Hg enzyme but activation of +Hg enzyme. Almost similar trend was observed for the in vitro inclusion of Hg in the presence of levulinic acid. It is suggested that two forms of enzyme exist in Hg-treated tissue, i.e. the usual Mg dependent form and an unusual Hg modified form. Kinetic studies for the two enzymes, -Hg enzyme and +Hg enzyme, involving the effect of varying concentrations of δ-aminolevulinic acid yielded distinct apparent K(m) and apparent V(max) values being 532 μM and 118 units g(-1) fr. wt., respectively, for -Hg enzyme and 347 μM and 52 units g(-1) fr. wt., respectively, for +Hg enzyme indicating that +Hg enzyme has higher affinity for δ-aminolevulinic acid but lower activity as compared to the -Hg enzyme.
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Affiliation(s)
- Priyanka Gupta
- School of Biochemistry, Devi Ahilya University, Takshashila Campus, Khandwa Road, Indore 452 017, Madhya Pradesh, India
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10
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Selwood T, Jaffe EK. Dynamic dissociating homo-oligomers and the control of protein function. Arch Biochem Biophys 2012; 519:131-43. [PMID: 22182754 PMCID: PMC3298769 DOI: 10.1016/j.abb.2011.11.020] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Revised: 11/16/2011] [Accepted: 11/28/2011] [Indexed: 11/20/2022]
Abstract
Homo-oligomeric protein assemblies are known to participate in dynamic association/disassociation equilibria under native conditions, thus creating an equilibrium of assembly states. Such quaternary structure equilibria may be influenced in a physiologically significant manner either by covalent modification or by the non-covalent binding of ligands. This review follows the evolution of ideas about homo-oligomeric equilibria through the 20th and into the 21st centuries and the relationship of these equilibria to allosteric regulation by the non-covalent binding of ligands. A dynamic quaternary structure equilibria is described where the dissociated state can have alternate conformations that cannot reassociate to the original multimer; the alternate conformations dictate assembly to functionally distinct alternate multimers of finite stoichiometry. The functional distinction between different assemblies provides a mechanism for allostery. The requirement for dissociation distinguishes this morpheein model of allosteric regulation from the classical MWC concerted and KNF sequential models. These models are described alongside earlier dissociating allosteric models. The identification of proteins that exist as an equilibrium of diverse native quaternary structure assemblies has the potential to define new targets for allosteric modulation with significant consequences for further understanding and/or controlling protein structure and function. Thus, a rationale for identifying proteins that may use the morpheein model of allostery is presented and a selection of proteins for which published data suggests this mechanism may be operative are listed.
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Affiliation(s)
- Trevor Selwood
- Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111
| | - Eileen K. Jaffe
- Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111
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12
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Jaffe EK, Lawrence SH. The morpheein model of allostery: evaluating proteins as potential morpheeins. Methods Mol Biol 2012; 796:217-31. [PMID: 22052493 PMCID: PMC3256758 DOI: 10.1007/978-1-61779-334-9_12] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
An equilibrium mixture of alternate quaternary structure assemblies can form a basis for allostery. The morpheein model of allostery is a concerted dissociative model that describes an equilibrium of alternate quaternary structure assemblies whose architectures are dictated by alternate conformations in the dissociated state. Kinetic and biophysical anomalies that suggest that the morpheein model of allostery applies for a given protein of interest are briefly described. Two methods are presented for evaluating proteins as potential morpheeins. One is a subunit interchange method that uses chromatography, dialysis, and mass spectroscopy to monitor changes in multimer composition. The other is a two-dimensional native gel electrophoresis method to monitor ligand-induced changes in an equilibrium of alternate multimeric assemblies.
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13
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Jaffe EK, Lawrence SH. Allostery and the dynamic oligomerization of porphobilinogen synthase. Arch Biochem Biophys 2011; 519:144-53. [PMID: 22037356 DOI: 10.1016/j.abb.2011.10.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Revised: 10/12/2011] [Accepted: 10/13/2011] [Indexed: 10/16/2022]
Abstract
The structural basis for allosteric regulation of porphobilinogen synthase (PBGS) is modulation of a quaternary structure equilibrium between octamer and hexamer (via dimers), which is represented schematically as 8mer ⇔ 2mer ⇔ 2mer∗⇔ 6mer∗. The "∗" represents a reorientation between two domains of each subunit that occurs in the dissociated state because it is sterically forbidden in the larger multimers. Allosteric effectors of PBGS are both intrinsic and extrinsic and are phylogenetically variable. In some species this equilibrium is modulated intrinsically by magnesium which binds at a site specific to the 8mer. In other species this equilibrium is modulated intrinsically by pH with the guanidinium group of an arginine being spatially equivalent to the allosteric magnesium ion. In humans, disease associated variants all shift the equilibrium toward the 6mer∗ relative to wild type. The 6mer∗ has a surface cavity that is not present in the 8mer and is proposed as a small molecule allosteric binding site. In silico and in vitro approaches have revealed species-specific allosteric PBGS inhibitors that stabilize the 6mer∗. Some of these inhibitors are drugs in clinical use leading to the hypothesis that extrinsic allosteric inhibition of human PBGS could be a mechanism for drug side effects.
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Affiliation(s)
- Eileen K Jaffe
- Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA.
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14
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Pereira LB, Mazzanti CMDA, Gonçalves JF, Cargnelutti D, Tabaldi LA, Becker AG, Calgaroto NS, Farias JG, Battisti V, Bohrer D, Nicoloso FT, Morsch VM, Schetinger MRC. Aluminum-induced oxidative stress in cucumber. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2010; 48:683-9. [PMID: 20554214 DOI: 10.1016/j.plaphy.2010.04.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2009] [Revised: 04/22/2010] [Accepted: 04/23/2010] [Indexed: 05/19/2023]
Abstract
Aluminum (Al) is one of the most abundant elements of the planet and exposure to this metal can cause oxidative stress and lead to various signs of toxicity in plants. Plants are essential organisms for the environment as well as food for humans and animals. The toxic effect of aluminum is the major cause of decreased crop productivity. Thus, the objective of the present study was to analyze the effects of aluminum on the activity of antioxidant enzymes such as catalase (CAT - E.C. 1.11.1.6), superoxide dismutase (SOD - E.C.1.15.1.1) and ascorbate peroxidase (APX - E.C. 1.11.1.11), and on lipid peroxidation, electrolyte leakage percentage (ELP) and chlorophyll and protein oxidation levels in Cucumis sativus L. (cv. Aodai). Seedlings were grown at different concentrations of aluminum ranging from 1 to 2000 microM for 10 days. The increase in ELP and H(2)O(2) production observed in the seedlings may be related to the decreased efficiency of the antioxidant system at higher aluminum concentrations. The antioxidant system was unable to overcome toxicity resulting in negative effects such as lipid peroxidation, protein oxidation and a decrease in the growth of Cucumis seedlings. Aluminum toxicity triggered alterations in the antioxidant and physiological status of growing cucumber seedlings.
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Affiliation(s)
- Luciane Belmonte Pereira
- Departamento de Química, Centro de Ciências Naturais e Exatas, Universidade Federal de Santa Maria, 97105-900 Santa Maria, RS, Brazil
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Shanmugam D, Wu B, Ramirez U, Jaffe EK, Roos DS. Plastid-associated porphobilinogen synthase from Toxoplasma gondii: kinetic and structural properties validate therapeutic potential. J Biol Chem 2010; 285:22122-31. [PMID: 20442414 DOI: 10.1074/jbc.m110.107243] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Apicomplexan parasites (including Plasmodium spp. and Toxoplasma gondii) employ a four-carbon pathway for de novo heme biosynthesis, but this pathway is distinct from the animal/fungal C4 pathway in that it is distributed between three compartments: the mitochondrion, cytosol, and apicoplast, a plastid acquired by secondary endosymbiosis of an alga. Parasite porphobilinogen synthase (PBGS) resides within the apicoplast, and phylogenetic analysis indicates a plant origin. The PBGS family exhibits a complex use of metal ions (Zn(2+) and Mg(2+)) and oligomeric states (dimers, hexamers, and octamers). Recombinant T. gondii PBGS (TgPBGS) was purified as a stable approximately 320-kDa octamer, and low levels of dimers but no hexamers were also observed. The enzyme displays a broad activity peak (pH 7-8.5), with a K(m) for aminolevulinic acid of approximately 150 microM and specific activity of approximately 24 micromol of porphobilinogen/mg of protein/h. Like the plant enzyme, TgPBGS responds to Mg(2+) but not Zn(2+) and shows two Mg(2+) affinities, interpreted as tight binding at both the active and allosteric sites. Unlike other Mg(2+)-binding PBGS, however, metal ions are not required for TgPBGS octamer stability. A mutant enzyme lacking the C-terminal 13 amino acids distinguishing parasite PBGS from plant and animal enzymes purified as a dimer, suggesting that the C terminus is required for octamer stability. Parasite heme biosynthesis is inhibited (and parasites are killed) by succinylacetone, an active site-directed suicide substrate. The distinct phylogenetic, enzymatic, and structural features of apicomplexan PBGS offer scope for developing selective inhibitors of the parasite enzyme based on its quaternary structure characteristics.
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Affiliation(s)
- Dhanasekaran Shanmugam
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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16
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Calgaroto NS, Castro GY, Cargnelutti D, Pereira LB, Gonçalves JF, Rossato LV, Antes FG, Dressler VL, Flores EMM, Schetinger MRC, Nicoloso FT. Antioxidant system activation by mercury in Pfaffia glomerata plantlets. Biometals 2010; 23:295-305. [DOI: 10.1007/s10534-009-9287-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Accepted: 12/22/2009] [Indexed: 10/20/2022]
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17
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Photosynthetic pigments content, δ-aminolevulinic acid dehydratase and acid phosphatase activities and mineral nutrients concentration in cadmium-exposed Cucumis sativus L. Biologia (Bratisl) 2009. [DOI: 10.2478/s11756-009-0034-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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18
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Skrebsky EC, Tabaldi LA, Pereira LB, Rauber R, Maldaner J, Cargnelutti D, Gonçalves JF, Castro GY, Shetinger MR, Nicoloso FT. Effect of cadmium on growth, micronutrient concentration, and δ-aminolevulinic acid dehydratase and acid phosphatase activities in plants of Pfaffia glomerata. ACTA ACUST UNITED AC 2008. [DOI: 10.1590/s1677-04202008000400004] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Pfaffia glomerata (Spreng.) Pedersen plantlets were grown under different cadmium (Cd) concentrations (0, 20, 40, 60 and 80 μM) in a hydroponic system during 7 d. Plant growth, micronutrient, chlorophyll and carotenoid concentrations, as well as δ-aminolevulinic acid dehydratase (ALA-D; E.C.4.2.1.24) and acid phosphatase (AP; E.C.3.1.3.2) activities were then analysed. Cadmium concentration in both shoots and roots increased with increasing external Cd levels. Metal concentration was on average 12-fold greater in root than in shoot tissues. Root length was unaffected by Cd treatments. In contrast, dry weight of both shoot and roots increased significantly upon addition of 20 and 40 μM Cd. Moreover, shoot and total plant dry weight was only reduced in plants treated with 80 μM Cd. Conversely, root dry weight decreased significantly upon addition of Cd concentrations above 40 μM. A micronutrient- and organ-dependent response to Cd toxicity was observed. Zinc and Cu concentrations in both shoot and roots did not alter upon treatment with Cd. Cadmium stress reduced Mn uptake but not its translocation within the plant. A synergistic effect of Cd on Fe concentration in root at 20 μM and 80 μM Cd levels was observed. The activity of AP, and especially that of ALA-D, was reduced with increasing Cd levels. At those these Cd levels, chlorophyll concentration was also reduced. There was a positive correlation between concentrations of carotenoids and chlorophylls. Our results indicate that P. glomerata seems to have some degree of Cd tolerance.
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Affiliation(s)
| | | | | | | | - Joseila Maldaner
- Departamento de Biologia; Programa de Pós-Graduação em Agronomia
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19
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Kokona B, Rigotti DJ, Wasson AS, Lawrence SH, Jaffe EK, Fairman R. Probing the oligomeric assemblies of pea porphobilinogen synthase by analytical ultracentrifugation. Biochemistry 2008; 47:10649-56. [PMID: 18795796 DOI: 10.1021/bi801128d] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The enzyme porphobilinogen synthase (PBGS) can exist in different nonadditive homooligomeric assemblies, and under appropriate conditions, the distribution of these assemblies can respond to ligands such as metals or substrate. PBGS from most organisms was believed to be octameric until work on a rare allele of human PBGS revealed an alternate hexameric assembly, which is also available to the wild-type enzyme at elevated pH [Breinig, S., et al. (2003) Nat. Struct. Biol. 10, 757-763]. Herein, we establish that the distribution of pea PBGS quaternary structures also contains octamers and hexamers, using both sedimentation velocity and sedimentation equilibrium experiments. We report results in which the octamer dominates under purification conditions and discuss conditions that influence the octamer:hexamer ratio. As predicted by PBGS crystal structures from related organisms, in the absence of magnesium, the octameric assembly is significantly destabilized, and the oligomeric distribution is dominated largely by the hexameric assembly. Although the PBGS hexamer-to-octamer oligomeric rearrangement is well documented under some conditions, both assemblies are very stable (under AU conditions) in the time frame of our ultracentrifuge experiments.
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Affiliation(s)
- Bashkim Kokona
- Department of Biology, Haverford College, 370 Lancaster Avenue, Haverford, Pennsylvania 19041, USA
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20
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Lawrence SH, Ramirez UD, Tang L, Fazliyez F, Kundrat L, Markham GD, Jaffe EK. Shape shifting leads to small-molecule allosteric drug discovery. ACTA ACUST UNITED AC 2008; 15:586-96. [PMID: 18559269 DOI: 10.1016/j.chembiol.2008.04.012] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2007] [Revised: 04/17/2008] [Accepted: 04/21/2008] [Indexed: 11/19/2022]
Abstract
Enzymes that regulate their activity by modulating an equilibrium of alternate, nonadditive, functionally distinct oligomeric assemblies (morpheeins) constitute a recently described mode of allostery. The oligomeric equilibrium for porphobilinogen synthase (PBGS) consists of high-activity octamers, low-activity hexamers, and two dimer conformations. A phylogenetically diverse allosteric site specific to hexamers is proposed as an inhibitor binding site. Inhibitor binding is predicted to draw the oligomeric equilibrium toward the low-activity hexamer. In silico docking enriched a selection from a small-molecule library for compounds predicted to bind to this allosteric site. In vitro testing of selected compounds identified one compound whose inhibition mechanism is species-specific conversion of PBGS octamers to hexamers. We propose that this strategy for inhibitor discovery can be applied to other proteins that use the morpheein model for allosteric regulation.
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21
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Selwood T, Tang L, Lawrence SH, Anokhina Y, Jaffe EK. Kinetics and Thermodynamics of the Interchange of the Morpheein Forms of Human Porphobilinogen Synthase. Biochemistry 2008; 47:3245-57. [DOI: 10.1021/bi702113z] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Trevor Selwood
- Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, Pennsylvania 19111
| | - Lei Tang
- Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, Pennsylvania 19111
| | - Sarah H. Lawrence
- Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, Pennsylvania 19111
| | - Yana Anokhina
- Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, Pennsylvania 19111
| | - Eileen K. Jaffe
- Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, Pennsylvania 19111
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22
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Segarra G, Casanova E, Bellido D, Odena MA, Oliveira E, Trillas I. Proteome, salicylic acid, and jasmonic acid changes in cucumber plants inoculated with Trichoderma asperellum strain T34. Proteomics 2008; 7:3943-52. [PMID: 17902191 DOI: 10.1002/pmic.200700173] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Trichoderma spp. is one of the most commonly used biological control agents against plant pathogens. This fungus produces changes in plant metabolism, thus increasing growth and enhancing resistance to biotic and abiotic stresses. However, its modes of action remain to be defined. In the first hours of interaction between cucumber plant roots and Trichoderma asperellum strain T34, salicylic and jasmonic acid levels and typical antipathogenic peroxidase activity increase in the cotyledons to different degrees depending on the applied concentration of the fungi. The use of 2-DE protein profiling and MS analysis allowed us to identify 28 proteins whose expression was affected in cotyledons after cucumber root colonization by Trichoderma applied at high concentrations: 17 were found to be up-regulated while 11 were down-regulated. Proteins involved in ROS scavenging, stress response, isoprenoid and ethylene biosynthesis, and in photosynthesis, photorespiration, and carbohydrate metabolism were differentially regulated by Trichoderma. The proteome changes found in this study help to give an understanding of how Trichoderma-treated plants become more resistant to pathogen attacks through the changes in expression of a set of defence-oriented proteins which can directly protect the plant or switch the metabolism to a defensive, nonassimilatory state.
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Affiliation(s)
- Guillem Segarra
- Departament de Biologia Vegetal, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain.
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23
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Lawrence SH, Jaffe EK. Expanding the Concepts in Protein Structure-Function Relationships and Enzyme Kinetics: Teaching using Morpheeins. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2008; 36:274-283. [PMID: 19578473 PMCID: PMC2575429 DOI: 10.1002/bmb.20211] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A morpheein is a homo-oligomeric protein that can exist as an ensemble of physiologically significant and functionally different alternate quaternary assemblies. Morpheeins exist in nature and utilize conformational equilibria between different tertiary structures to form distinct oligomers as a means of regulating their function. Notably, alternate morpheeins are not misfolded forms of a protein; they are differently assembled native states that contain alternate subunit conformations. Transitions between alternate morpheein assemblies involve oligomer dissociation, conformational change in the dissociated state, and reassembly to a different oligomer. These transitions occur in response to the protein's environment, e.g., effector molecules, and represent a new model of allosteric regulation. The unique features of morpheeins are being revealed through detailed characterization of the prototype enzyme, porphobilinogen synthase, which exists in a dynamic equilibrium of a high activity octamer, a low activity hexamer, and two dimer conformations. Morpheeins are likely far more common than previously appreciated. There are, however, both intellectual and experimental barriers to recognizing proteins as morpheeins. These barriers derive from the way we were taught and continue to teach about protein folding, protein purification, protein structure-function relationships, and enzyme kinetics. This article explores some of these limitations and encourages incorporation of morpheeins into both introductory and advanced biochemistry classes.
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24
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Jaffe EK. Morpheeins--a new structural paradigm for allosteric regulation. Trends Biochem Sci 2005; 30:490-7. [PMID: 16023348 DOI: 10.1016/j.tibs.2005.07.003] [Citation(s) in RCA: 112] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2005] [Revised: 05/20/2005] [Accepted: 07/04/2005] [Indexed: 11/16/2022]
Abstract
Classic models for the allosteric regulation of protein function consider an equilibrium among protein structures of constant oligomeric multiplicity. The morpheein (mor-phee'-in) concept expands this model to include a dynamic equilibrium of protein structures wherein a protein monomer can exist in more than one conformation and each monomer conformation dictates a different quaternary structure of finite multiplicity and different functionality. The morpheein concept provides a new framework for understanding allosteric regulation, kinetic cooperativity and hysteresis. Porphobilinogen synthase constitutes a prototype morpheein ensemble comprising several interconverting quaternary structure isoforms; one monomer conformation dictates assembly of a high-activity octamer, whereas an alternative monomer conformation dictates assembly of a low-activity hexamer. It is proposed here that the behavior of some other allosteric enzymes reflect dynamic morpheein equilibrium systems and six candidate proteins are enumerated.
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Affiliation(s)
- Eileen K Jaffe
- BioMolecular Structure and Function Group, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA.
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25
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Peltier JB, Cai Y, Sun Q, Zabrouskov V, Giacomelli L, Rudella A, Ytterberg AJ, Rutschow H, van Wijk KJ. The oligomeric stromal proteome of Arabidopsis thaliana chloroplasts. Mol Cell Proteomics 2005; 5:114-33. [PMID: 16207701 DOI: 10.1074/mcp.m500180-mcp200] [Citation(s) in RCA: 269] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
This study presents an analysis of the stromal proteome in its oligomeric state extracted from highly purified chloroplasts of Arabidopsis thaliana. 241 proteins (88% with predicted cTP), mostly assembled in oligomeric complexes, were identified by mass spectrometry with emphasis on distinguishing between paralogues. This is critical because different paralogues in a gene family often have different subcellular localizations and/or different expression patterns and functions. The native protein masses were determined for all identified proteins. Comparison with the few well characterized stromal complexes from A. thaliana confirmed the accuracy of the native mass determination, and by extension, the usefulness of the native mass data for future in-depth protein interaction studies. Resolved protein interactions are discussed and compared with an extensive collection of native mass data of orthologues in other plants and bacteria. Relative protein expression levels were estimated from spot intensities and also provided estimates of relative concentrations of individual proteins. No such quantification has been reported so far. Surprisingly proteins dedicated to chloroplast protein synthesis, biogenesis, and fate represented nearly 10% of the total stroma protein mass. Oxidative pentose phosphate pathway, glycolysis, and Calvin cycle represented together about 75%, nitrogen assimilation represented 5-7%, and all other pathways such as biosynthesis of e.g. fatty acids, amino acids, nucleotides, tetrapyrroles, and vitamins B(1) and B(2) each represented less than 1% of total protein mass. Several proteins with diverse functions outside primary carbon metabolism, such as the isomerase ROC4, lipoxygenase 2 involved in jasmonic acid biosynthesis, and a carbonic anhydrase (CA1), were surprisingly abundant in the range of 0.75-1.5% of the total stromal mass. Native images with associated information are available via the Plastid Proteome Database.
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Affiliation(s)
- Jean-Benoit Peltier
- Department of Plant Biology, Cornell Theory Center, Cornell University, Ithaca, New York 14853, USA
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26
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Tang L, Stith L, Jaffe EK. Substrate-induced interconversion of protein quaternary structure isoforms. J Biol Chem 2005; 280:15786-93. [PMID: 15710608 DOI: 10.1074/jbc.m500218200] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human porphobilinogen synthase (PBGS) can exist in two dramatically different quaternary structure isoforms, which have been proposed to be in dynamic equilibrium. The quaternary structure isoforms of PBGS result from two alternative conformations of the monomer; one monomer structure assembles into a high activity octamer, whereas the other monomer structure assembles into a low activity hexamer. The kinetic behavior of these oligomers led to the hypothesis that turnover facilitates the interconversion of the oligomeric structures. The current work demonstrates that the interactions of ligands at the enzyme active site promote the structural interconversion between human PBGS quaternary structure isoforms, favoring formation of the octamer. This observation illustrates that the assembly and disassembly of oligomeric proteins can be facilitated by the protein motions that accompany enzymatic catalysis.
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Affiliation(s)
- Lei Tang
- Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
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27
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Bollivar DW, Clauson C, Lighthall R, Forbes S, Kokona B, Fairman R, Kundrat L, Jaffe EK. Rhodobacter capsulatus porphobilinogen synthase, a high activity metal ion independent hexamer. BMC BIOCHEMISTRY 2004; 5:17. [PMID: 15555082 PMCID: PMC535902 DOI: 10.1186/1471-2091-5-17] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2004] [Accepted: 11/22/2004] [Indexed: 12/02/2022]
Abstract
Background The enzyme porphobilinogen synthase (PBGS), which is central to the biosynthesis of heme, chlorophyll and cobalamins, has long been known to use a variety of metal ions and has recently been shown able to exist in two very different quaternary forms that are related to metal ion usage. This paper reports new information on the metal ion independence and quaternary structure of PBGS from the photosynthetic bacterium Rhodobacter capsulatus. Results The gene for R. capsulatus PBGS was amplified from genomic DNA and sequencing revealed errors in the sequence database. R. capsulatus PBGS was heterologously expressed in E. coli and purified to homogeneity. Analysis of an unusual phylogenetic variation in metal ion usage by PBGS enzymes predicts that R. capsulatus PBGS does not utilize metal ions such as Zn2+, or Mg2+, which have been shown to act in other PBGS at either catalytic or allosteric sites. Studies with these ions and chelators confirm the predictions. A broad pH optimum was determined to be independent of monovalent cations, approximately 8.5, and the Km value shows an acidic pKa of ~6. Because the metal ions of other PBGS affect the quaternary structure, gel permeation chromatography and analytical ultracentrifugation experiments were performed to examine the quaternary structure of metal ion independent R. capsulatus PBGS. The enzyme was found to be predominantly hexameric, in contrast with most other PBGS, which are octameric. A protein concentration dependence to the specific activity suggests that the hexameric R. capsulatus PBGS is very active and can dissociate to smaller, less active, species. A homology model of hexameric R. capsulatus PBGS is presented and discussed. Conclusion The evidence presented in this paper supports the unusual position of the R. capsulatus PBGS as not requiring any metal ions for function. Unlike other wild-type PBGS, the R. capsulatus protein is a hexamer with an unusually high specific activity when compared to other octameric PBGS proteins.
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Affiliation(s)
- David W Bollivar
- Department of Biology, Illinois Wesleyan University, P.O. Box 2900, Bloomington, IL 61702-2900, USA
| | - Cheryl Clauson
- Department of Biology, Illinois Wesleyan University, P.O. Box 2900, Bloomington, IL 61702-2900, USA
| | - Rachel Lighthall
- Department of Biology, Illinois Wesleyan University, P.O. Box 2900, Bloomington, IL 61702-2900, USA
| | - Siiri Forbes
- Department of Biology, Illinois Wesleyan University, P.O. Box 2900, Bloomington, IL 61702-2900, USA
| | - Bashkim Kokona
- Biology Department, Haverford College, Haverford, PA 19041, USA
| | - Robert Fairman
- Biology Department, Haverford College, Haverford, PA 19041, USA
| | - Lenka Kundrat
- Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
| | - Eileen K Jaffe
- Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
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28
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Breinig S, Kervinen J, Stith L, Wasson AS, Fairman R, Wlodawer A, Zdanov A, Jaffe EK. Control of tetrapyrrole biosynthesis by alternate quaternary forms of porphobilinogen synthase. Nat Struct Mol Biol 2003; 10:757-63. [PMID: 12897770 DOI: 10.1038/nsb963] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2003] [Accepted: 07/15/2003] [Indexed: 11/09/2022]
Abstract
Porphobilinogen synthase (PBGS) catalyzes the first common step in the biosynthesis of tetrapyrroles (such as heme and chlorophyll). Although the predominant oligomeric form of this enzyme, as inferred from many crystal structures, is that of a homo-octamer, a rare human PBGS allele, F12L, reveals the presence of a hexameric form. Rearrangement of an N-terminal arm is responsible for this oligomeric switch, which results in profound changes in kinetic behavior. The structural transition between octamer and hexamer must proceed through an unparalleled equilibrium containing two different dimer structures. The allosteric magnesium, present in most PBGS, has a binding site in the octamer but not in the hexamer. The unprecedented structural rearrangement reported here relates to the allosteric regulation of PBGS and suggests that alternative PBGS oligomers may function in a magnesium-dependent regulation of tetrapyrrole biosynthesis in plants and some bacteria.
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Affiliation(s)
- Sabine Breinig
- Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, Pennsylvania 19111-2497, USA
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29
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Kundrat L, Martins J, Stith L, Dunbrack RL, Jaffe EK. A structural basis for half-of-the-sites metal binding revealed in Drosophila melanogaster porphobilinogen synthase. J Biol Chem 2003; 278:31325-30. [PMID: 12794073 DOI: 10.1074/jbc.m304124200] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Porphobilinogen synthase (PBGS) proteins fall into several distinct groups with different metal ion requirements. Drosophila melanogaster porphobilinogen synthase (DmPBGS) is the first non-mammalian metazoan PBGS to be characterized. The sequence shows the determinants for two zinc binding sites known to be present in both mammalian and yeast PBGS, proteins that differ in the exhibition of half-of-the-sites metal binding. The pH-dependent activity of DmPBGS is uniquely affected by zinc. A tight binding catalytic zinc binds at 0.5/subunit with a Kd well below microm. A second inhibitory zinc exhibits a Kd of approximately 5 microm and appears to bind at a stoichiometry of 1/subunit. A molecular model of DmPBGS suggests that the inhibitory zinc is located at a subunit interface using Cys-219 and His-10 as ligands. Zinc binding to this previously unknown inhibitory site is proposed to inhibit opening of the active site lid. As predicted, the DmPBGS mutant H10F is active but is not inhibited by zinc. H10F binds a catalytic zinc at 0.5/subunit and binds a second nonessential and noninhibitory zinc at 0.5/subunit. This result reveals a structural basis for half-of-the-sites metal binding that is consistent with a reciprocating motion model for function of oligomeric PBGS.
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Affiliation(s)
- Lenka Kundrat
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111-2497, USA
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30
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Griswold KE, Mahmood NA, Iverson BL, Georgiou G. Effects of codon usage versus putative 5'-mRNA structure on the expression of Fusarium solani cutinase in the Escherichia coli cytoplasm. Protein Expr Purif 2003; 27:134-42. [PMID: 12509995 DOI: 10.1016/s1046-5928(02)00578-8] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Matching the codon usage of recombinant genes to that of the expression host is a common strategy for increasing the expression of heterologous proteins in bacteria. However, while developing a cytoplasmic expression system for Fusarium solani cutinase in Escherichia coli, we found that altering codons to those preferred by E. coli led to significantly lower expression compared to the wild-type fungal gene, despite the presence of several rare E. coli codons in the fungal sequence. On the other hand, expression in the E. coli periplasm using a bacterial PhoA leader sequence resulted in high levels of expression for both the E. coli optimized and wild-type constructs. Sequence swapping experiments as well as calculations of predicted mRNA secondary structure provided support for the hypothesis that differential cytoplasmic expression of the E. coli optimized versus wild-type cutinase genes is due to differences in 5(') mRNA secondary structures. In particular, our results indicate that increased stability of 5(') mRNA secondary structures in the E. coli optimized transcript prevents efficient translation initiation in the absence of the phoA leader sequence. These results underscore the idea that potential 5(') mRNA secondary structures should be considered along with codon usage when designing a synthetic gene for high level expression in E. coli.
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Affiliation(s)
- Karl E Griswold
- Department of Chemistry and Biochemistry, University of Texas, Austin, TX 78712, USA
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31
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Jaffe EK. An unusual phylogenetic variation in the metal ion binding sites of porphobilinogen synthase. CHEMISTRY & BIOLOGY 2003; 10:25-34. [PMID: 12573695 DOI: 10.1016/s1074-5521(02)00296-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Porphobilinogen synthase (PBGS), which catalyzes the first common step in tetrapyrrole biosynthesis, contains a unique phylogenetic variation in the use of metal ions. Using sequence, structure, and enzymological information, this work codifies the phylogenetic segregation of metal utilization in PBGS from archaea, bacteria, and eucarya. All PBGS contain an active site metal binding sequence, determined herein to be either DXCXCX(Y/F)X(3)G(H/Q)CG or DXALDX(Y/F)X(3)G(H/Q)DG. The former dictates a requirement for zinc. Most PBGS that do not require zinc require magnesium and/or potassium instead. Most PBGS are also found to contain the binding determinants for an allosteric magnesium that resides outside the active site. The phylogenetic distribution of PBGS metal ion utilization suggests that the primordial PBGS required zinc and supports a hypothesis that the loss of the zinc site was concurrent with the advent of oxygenic photosynthesis.
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Affiliation(s)
- Eileen K Jaffe
- Institute for Cancer Research, Fox Chase Cancer Center, 7701 Burholme Avenue, Philadelphia, PA 19111, USA.
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32
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Jaffe EK, Kervinen J, Martins J, Stauffer F, Neier R, Wlodawer A, Zdanov A. Species-specific inhibition of porphobilinogen synthase by 4-oxosebacic acid. J Biol Chem 2002; 277:19792-9. [PMID: 11909869 DOI: 10.1074/jbc.m201486200] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Porphobilinogen synthase (PBGS) catalyzes the condensation of two molecules of 5-aminolevulinic acid (ALA), an essential step in tetrapyrrole biosynthesis. 4-Oxosebacic acid (4-OSA) and 4,7-dioxosebacic acid (4,7-DOSA) are bisubstrate reaction intermediate analogs for PBGS. We show that 4-OSA is an active site-directed irreversible inhibitor for Escherichia coli PBGS, whereas human, pea, Pseudomonas aeruginosa, and Bradyrhizobium japonicum PBGS are insensitive to inhibition by 4-OSA. Some variants of human PBGS (engineered to resemble E. coli PBGS) have increased sensitivity to inactivation by 4-OSA, suggesting a structural basis for the specificity. The specificity of 4-OSA as a PBGS inhibitor is significantly narrower than that of 4,7-DOSA. Comparison of the crystal structures for E. coli PBGS inactivated by 4-OSA versus 4,7-DOSA shows significant variation in the half of the inhibitor that mimics the second substrate molecule (A-side ALA). Compensatory changes occur in the structure of the active site lid, which suggests that similar changes normally occur to accommodate numerous hybridization changes that must occur at C3 of A-side ALA during the PBGS-catalyzed reaction. A comparison of these with other PBGS structures identifies highly conserved active site water molecules, which are isolated from bulk solvent and implicated as proton acceptors in the PBGS-catalyzed reaction.
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Affiliation(s)
- Eileen K Jaffe
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA.
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Vavilin DV, Vermaas WFJ. Regulation of the tetrapyrrole biosynthetic pathway leading to heme and chlorophyll in plants and cyanobacteria. PHYSIOLOGIA PLANTARUM 2002; 115:9-24. [PMID: 12010463 DOI: 10.1034/j.1399-3054.2002.1150102.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Photosynthetic organisms synthesize chlorophylls, hemes, and bilin pigments via a common tetrapyrrole biosynthetic pathway. This review summarizes current knowledge about the regulation of this pathway in plants, algae, and cyanobacteria. Particular emphasis is placed on the regulation of glutamate-1-semialdehyde formation and on the channelling of protoporphyrin IX into the heme and chlorophyll branches. The potential role of chlorophyll molecules that are not bound to photosynthetic pigment-protein complexes ('free chlorophylls') or of other Mg-containing porphyrins in regulation of tetrapyrrole synthesis is also discussed.
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Affiliation(s)
- Dmitrii V Vavilin
- Department of Plant Biology and Center for the Study of Early Events in Photosynthesis, Arizona State University, Box 871601, Tempe, AZ 85287-1601, USA
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