1
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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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Targeting protein self-association in drug design. Drug Discov Today 2021; 26:1148-1163. [PMID: 33548462 DOI: 10.1016/j.drudis.2021.01.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/24/2020] [Accepted: 01/26/2021] [Indexed: 01/05/2023]
Abstract
Protein self-association is a universal phenomenon essential for stability and molecular recognition. Disrupting constitutive homomers constitutes an original and emerging strategy in drug design. Inhibition of homomeric proteins can be achieved through direct complex disruption, subunit intercalation, or by promoting inactive oligomeric states. Targeting self-interaction grants several advantages over active site inhibition because of the stimulation of protein degradation, the enhancement of selectivity, substoichiometric inhibition, and by-pass of compensatory mechanisms. This new landscape in protein inhibition is driven by the development of biophysical and biochemical tools suited for the study of homomeric proteins, such as differential scanning fluorimetry (DSF), native mass spectrometry (MS), Förster resonance energy transfer (FRET) spectroscopy, 2D nuclear magnetic resonance (NMR), and X-ray crystallography. In this review, we discuss the different aspects of this new paradigm in drug design.
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3
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Liu G, Sil D, Maio N, Tong WH, Bollinger JM, Krebs C, Rouault TA. Heme biosynthesis depends on previously unrecognized acquisition of iron-sulfur cofactors in human amino-levulinic acid dehydratase. Nat Commun 2020; 11:6310. [PMID: 33298951 PMCID: PMC7725820 DOI: 10.1038/s41467-020-20145-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 11/06/2020] [Indexed: 12/18/2022] Open
Abstract
Heme biosynthesis and iron-sulfur cluster (ISC) biogenesis are two major mammalian metabolic pathways that require iron. It has long been known that these two pathways interconnect, but the previously described interactions do not fully explain why heme biosynthesis depends on intact ISC biogenesis. Herein we identify a previously unrecognized connection between these two pathways through our discovery that human aminolevulinic acid dehydratase (ALAD), which catalyzes the second step of heme biosynthesis, is an Fe-S protein. We find that several highly conserved cysteines and an Ala306-Phe307-Arg308 motif of human ALAD are important for [Fe4S4] cluster acquisition and coordination. The enzymatic activity of human ALAD is greatly reduced upon loss of its Fe-S cluster, which results in reduced heme biosynthesis in human cells. As ALAD provides an early Fe-S-dependent checkpoint in the heme biosynthetic pathway, our findings help explain why heme biosynthesis depends on intact ISC biogenesis. Heme biosynthesis depends on iron-sulfur (Fe-S) cluster biogenesis but the molecular connection between these pathways is not fully understood. Here, the authors show that the heme biosynthesis enzyme ALAD contains an Fe-S cluster, disruption of which reduces ALAD activity and heme production in human cells.
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Affiliation(s)
- Gang Liu
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Debangsu Sil
- Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Nunziata Maio
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Wing-Hang Tong
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - J Martin Bollinger
- Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, USA.,Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Carsten Krebs
- Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, USA. .,Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA.
| | - Tracey Ann Rouault
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
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4
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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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5
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Vimal A, Kumar A. The morpheein model of allosterism: a remedial step for targeting virulent l -asparaginase. Drug Discov Today 2017; 22:814-822. [DOI: 10.1016/j.drudis.2016.10.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 09/02/2016] [Accepted: 10/03/2016] [Indexed: 11/15/2022]
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6
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Ramirez UD, Nikonova AS, Liu H, Pecherskaya A, Lawrence SH, Serebriiskii IG, Zhou Y, Robinson MK, Einarson MB, Golemis EA, Jaffe EK. Compounds identified by virtual docking to a tetrameric EGFR extracellular domain can modulate Grb2 internalization. BMC Cancer 2015; 15:436. [PMID: 26016476 PMCID: PMC4451962 DOI: 10.1186/s12885-015-1415-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Accepted: 05/05/2015] [Indexed: 01/27/2023] Open
Abstract
Background Overexpression or mutation of the epidermal growth factor receptor (EGFR) potently enhances the growth of many solid tumors. Tumor cells frequently display resistance to mechanistically-distinct EGFR-directed therapeutic agents, making it valuable to develop therapeutics that work by additional mechanisms. Current EGFR-targeting therapeutics include antibodies targeting the extracellular domains, and small molecules inhibiting the intracellular kinase domain. Recent studies have identified a novel prone extracellular tetrameric EGFR configuration, which we identify as a potential target for drug discovery. Methods Our focus is on the prone EGFR tetramer, which contains a novel protein-protein interface involving extracellular domain III. This EGFR tetramer is computationally targeted for stabilization by small molecule ligand binding. This study performed virtual screening of a Life Chemicals, Inc. small molecule library of 345,232 drug-like compounds against a molecular dynamics simulation of protein-protein interfaces distinct to the novel tetramer. One hundred nine chemically diverse candidate molecules were selected and evaluated using a cell-based high-content imaging screen that directly assessed induced internalization of the EGFR effector protein Grb2. Positive hits were further evaluated for influence on phosphorylation of EGFR and its effector ERK1/2. Results Fourteen hit compounds affected internalization of Grb2, an adaptor responsive to EGFR activation. Most hits had limited effect on cell viability, and minimally influenced EGFR and ERK1/2 phosphorylation. Docked hit compound poses generally include Arg270 or neighboring residues, which are also involved in binding the effective therapeutic cetuximab, guiding further chemical optimization. Conclusions These data suggest that the EGFR tetrameric configuration offers a novel cancer drug target. Electronic supplementary material The online version of this article (doi:10.1186/s12885-015-1415-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ursula D Ramirez
- Molecular Therapeutics Program, Fox Chase Cancer Center, 333 Cottman Ave, Philadelphia, PA, 19111, USA.
| | - Anna S Nikonova
- Molecular Therapeutics Program, Fox Chase Cancer Center, 333 Cottman Ave, Philadelphia, PA, 19111, USA.
| | - Hanqing Liu
- Molecular Therapeutics Program, Fox Chase Cancer Center, 333 Cottman Ave, Philadelphia, PA, 19111, USA.
| | - Anna Pecherskaya
- Translational Facility, Fox Chase Cancer Center, 333 Cottman Ave, Philadelphia, PA, 19111, USA.
| | - Sarah H Lawrence
- Molecular Therapeutics Program, Fox Chase Cancer Center, 333 Cottman Ave, Philadelphia, PA, 19111, USA.
| | - Ilya G Serebriiskii
- Molecular Therapeutics Program, Fox Chase Cancer Center, 333 Cottman Ave, Philadelphia, PA, 19111, USA. .,Kazan Federal University, Kazan, Russia.
| | - Yan Zhou
- Biostatistics and Bioinformatics Facility, Fox Chase Cancer Center, 333 Cottman Ave, Philadelphia, PA, 19111, USA.
| | - Matthew K Robinson
- Molecular Therapeutics Program, Fox Chase Cancer Center, 333 Cottman Ave, Philadelphia, PA, 19111, USA.
| | - Margret B Einarson
- Translational Facility, Fox Chase Cancer Center, 333 Cottman Ave, Philadelphia, PA, 19111, USA.
| | - Erica A Golemis
- Molecular Therapeutics Program, Fox Chase Cancer Center, 333 Cottman Ave, Philadelphia, PA, 19111, USA.
| | - Eileen K Jaffe
- Molecular Therapeutics Program, Fox Chase Cancer Center, 333 Cottman Ave, Philadelphia, PA, 19111, USA.
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7
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Dingerdissen H, Weaver DS, Karp PD, Pan Y, Simonyan V, Mazumder R. A framework for application of metabolic modeling in yeast to predict the effects of nsSNV in human orthologs. Biol Direct 2014; 9:9. [PMID: 24894379 PMCID: PMC4057618 DOI: 10.1186/1745-6150-9-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 05/19/2014] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND We have previously suggested a method for proteome wide analysis of variation at functional residues wherein we identified the set of all human genes with nonsynonymous single nucleotide variation (nsSNV) in the active site residue of the corresponding proteins. 34 of these proteins were shown to have a 1:1:1 enzyme:pathway:reaction relationship, making these proteins ideal candidates for laboratory validation through creation and observation of specific yeast active site knock-outs and downstream targeted metabolomics experiments. Here we present the next step in the workflow toward using yeast metabolic modeling to predict human metabolic behavior resulting from nsSNV. RESULTS For the previously identified candidate proteins, we used the reciprocal best BLAST hits method followed by manual alignment and pathway comparison to identify 6 human proteins with yeast orthologs which were suitable for flux balance analysis (FBA). 5 of these proteins are known to be associated with diseases, including ribose 5-phosphate isomerase deficiency, myopathy with lactic acidosis and sideroblastic anaemia, anemia due to disorders of glutathione metabolism, and two porphyrias, and we suspect the sixth enzyme to have disease associations which are not yet classified or understood based on the work described herein. CONCLUSIONS Preliminary findings using the Yeast 7.0 FBA model show lack of growth for only one enzyme, but augmentation of the Yeast 7.0 biomass function to better simulate knockout of certain genes suggested physiological relevance of variations in three additional proteins. Thus, we suggest the following four proteins for laboratory validation: delta-aminolevulinic acid dehydratase, ferrochelatase, ribose-5 phosphate isomerase and mitochondrial tyrosyl-tRNA synthetase. This study indicates that the predictive ability of this method will improve as more advanced, comprehensive models are developed. Moreover, these findings will be useful in the development of simple downstream biochemical or mass-spectrometric assays to corroborate these predictions and detect presence of certain known nsSNVs with deleterious outcomes. Results may also be useful in predicting as yet unknown outcomes of active site nsSNVs for enzymes that are not yet well classified or annotated.
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Affiliation(s)
- Hayley Dingerdissen
- Department of Biochemistry and Molecular Biology, The George Washington University Medical Center, Ross Hall, Room 540, 2300 Eye Street NW, Washington, DC 20037, USA
| | - Daniel S Weaver
- Bioinformatics Research Group, Artificial Intelligence Center, SRI International Menlo Park, Menlo Park, CA 94025, USA
| | - Peter D Karp
- Bioinformatics Research Group, Artificial Intelligence Center, SRI International Menlo Park, Menlo Park, CA 94025, USA
| | - Yang Pan
- Department of Biochemistry and Molecular Biology, The George Washington University Medical Center, Ross Hall, Room 540, 2300 Eye Street NW, Washington, DC 20037, USA
| | - Vahan Simonyan
- Center for Biologics Evaluation and Research, US Food and Drug Administration, 1451 Rockville Pike, Rockville, MD 20852, USA
| | - Raja Mazumder
- Department of Biochemistry and Molecular Biology, The George Washington University Medical Center, Ross Hall, Room 540, 2300 Eye Street NW, Washington, DC 20037, USA
- McCormick Genomic and Proteomic Center, George Washington University, Washington, DC 20037, USA
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8
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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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9
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Ma B, Nussinov R. Druggable orthosteric and allosteric hot spots to target protein-protein interactions. Curr Pharm Des 2014; 20:1293-301. [PMID: 23713780 PMCID: PMC6361532 DOI: 10.2174/13816128113199990073] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Accepted: 05/21/2013] [Indexed: 11/22/2022]
Abstract
Drug designing targeting protein-protein interactions is challenging. Because structural elucidation and computational analysis have revealed the importance of hot spot residues in stabilizing these interactions, there have been on-going efforts to develop drugs which bind the hot spots and out-compete the native protein partners. The question arises as to what are the key 'druggable' properties of hot spots in protein-protein interactions and whether these mimic the general hot spot definition. Identification of orthosteric (at the protein- protein interaction site) and allosteric (elsewhere) druggable hot spots is expected to help in discovering compounds that can more effectively modulate protein-protein interactions. For example, are there any other significant features beyond their location in pockets in the interface? The interactions of protein-protein hot spots are coupled with conformational dynamics of protein complexes. Currently increasing efforts focus on the allosteric drug discovery. Allosteric drugs bind away from the native binding site and can modulate the native interactions. We propose that identification of allosteric hot spots could similarly help in more effective allosteric drug discovery. While detection of allosteric hot spots is challenging, targeting drugs to these residues has the potential of greatly increasing the hot spot and protein druggability.
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Affiliation(s)
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, NCIFrederick, Frederick, MD 21702.
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10
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Jaffe EK. Impact of quaternary structure dynamics on allosteric drug discovery. Curr Top Med Chem 2013; 13:55-63. [PMID: 23409765 DOI: 10.2174/1568026611313010006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 11/29/2012] [Accepted: 11/30/2012] [Indexed: 11/22/2022]
Abstract
The morpheein model of allosteric regulation draws attention to proteins that can exist as an equilibrium of functionally distinct assemblies where: one subunit conformation assembles into one multimer; a different subunit conformation assembles into a different multimer; and the various multimers are in a dynamic equilibrium whose position can be modulated by ligands that bind to a multimer-specific ligand binding site. The case study of porphobilinogen synthase (PBGS) illustrates how such an equilibrium holds lessons for disease mechanisms, drug discovery, understanding drug side effects, and identifying proteins wherein drug discovery efforts might focus on quaternary structure dynamics. The morpheein model of allostery has been proposed as applicable for a wide assortment of disease-associated proteins (Selwood, T., Jaffe, E., (2012) Arch. Bioch. Biophys, 519:131-143). Herein we discuss quaternary structure dynamics aspects to drug discovery for the disease-associated putative morpheeins phenylalanine hydroxylase, HIV integrase, pyruvate kinase, and tumor necrosis factor α. Also highlighted is the quaternary structure equilibrium of transthyretin and successful drug discovery efforts focused on controlling its quaternary structure dynamics.
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Affiliation(s)
- Eileen K Jaffe
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA.
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11
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Gray TA, Murray E, Nowicki MW, Remnant L, Scherl A, Muller P, Vojtesek B, Hupp TR. Development of a fluorescent monoclonal antibody-based assay to measure the allosteric effects of synthetic peptides on self-oligomerization of AGR2 protein. Protein Sci 2013; 22:1266-78. [PMID: 23780840 DOI: 10.1002/pro.2299] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Revised: 06/10/2013] [Accepted: 06/10/2013] [Indexed: 11/12/2022]
Abstract
Many regulatory proteins are homo-oligomeric and designing assays that measure self-assembly will provide novel approaches to study protein allostery and screen for novel small molecule modulators of protein interactions. We present an assay to begin to define the biochemical determinants that regulate dimerization of the cancer-associated oncoprotein AGR2. A two site-sandwich microtiter assay ((2S) MTA) was designed using a DyLight800-labeled monoclonal antibody that binds to an epitope in AGR2 to screen for synthetic self-peptides that might regulate dimer stability. Peptides derived from the intrinsically disordered N-terminal region of AGR2 increase in trans oligomer stability as defined using the (2S) MTA assay. A DSS-crosslinking assay that traps the AGR2 dimer through K95-K95 adducts confirmed that Δ45-AGR2 was a more stable dimer using denaturing gel electrophoresis. A titration of wt-AGR2, Δ45-AGR2 (more stable dimer), and monomeric AGR2(E60A) revealed that Δ45-AGR2 was more active in binding to Reptin than either wt-AGR2 or the AGR2(E60A) mutant. Our data have defined a functional role for the AGR2 dimer in the binding to its most well characterized interacting protein, Reptin. The ability to regulate AGR2 oligomerization in trans opens the possibility for developing small molecules that regulate its' biochemical activity as potential cancer therapeutics. The data also highlight the utility of this oligomerization assay to screen chemical libraries for ligands that could regulate AGR2 dimer stability and its' oncogenic potential.
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Affiliation(s)
- Terry A Gray
- Institute of Genetics and Molecular Medicine, Cell Signaling Unit, University of Edinburgh, United Kingdom
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12
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Jaffe EK, Stith L, Lawrence SH, Andrake M, Dunbrack RL. A new model for allosteric regulation of phenylalanine hydroxylase: implications for disease and therapeutics. Arch Biochem Biophys 2013; 530:73-82. [PMID: 23296088 PMCID: PMC3580015 DOI: 10.1016/j.abb.2012.12.017] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Revised: 12/07/2012] [Accepted: 12/19/2012] [Indexed: 02/06/2023]
Abstract
The structural basis for allosteric regulation of phenylalanine hydroxylase (PAH), whose dysfunction causes phenylketonuria (PKU), is poorly understood. A new morpheein model for PAH allostery is proposed to consist of a dissociative equilibrium between two architecturally different tetramers whose interconversion requires a ∼90° rotation between the PAH catalytic and regulatory domains, the latter of which contains an ACT domain. This unprecedented model is supported by in vitro data on purified full length rat and human PAH. The conformational change is both predicted to and shown to render the tetramers chromatographically separable using ion exchange methods. One novel aspect of the activated tetramer model is an allosteric phenylalanine binding site at the intersubunit interface of ACT domains. Amino acid ligand-stabilized ACT domain dimerization follows the multimerization and ligand binding behavior of ACT domains present in other proteins in the PDB. Spectroscopic, chromatographic, and electrophoretic methods demonstrate a PAH equilibrium consisting of two architecturally distinct tetramers as well as dimers. We postulate that PKU-associated mutations may shift the PAH quaternary structure equilibrium in favor of the low activity assemblies. Pharmacological chaperones that stabilize the ACT:ACT interface can potentially provide PKU patients with a novel small molecule therapeutic.
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Affiliation(s)
- Eileen K Jaffe
- Developmental Therapeutics, Institute for Cancer Research, Fox Chase Cancer Center, Temple Health, 333 Cottman Ave., Philadelphia, PA 19111, USA.
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13
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Thompson AD, Dugan A, Gestwicki JE, Mapp AK. Fine-tuning multiprotein complexes using small molecules. ACS Chem Biol 2012; 7:1311-20. [PMID: 22725693 DOI: 10.1021/cb300255p] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Multiprotein complexes such as the transcriptional machinery, signaling hubs, and protein folding machines are typically composed of at least one enzyme combined with multiple non-enzymes. Often the components of these complexes are incorporated in a combinatorial manner, in which the ultimate composition of the system helps dictate the type, location, or duration of cellular activities. Although drugs and chemical probes have traditionally targeted the enzyme components, emerging strategies call for controlling the function of protein complexes by modulation of protein-protein interactions (PPIs). However, the challenges of targeting PPIs have been well documented, and the diversity of PPIs makes a "one-size-fits-all" solution highly unlikely. These hurdles are particularly daunting for PPIs that encompass large buried surface areas and those with weak affinities. In this Review, we discuss lessons from natural systems, in which allostery and other mechanisms are used to overcome the challenge of regulating the most difficult PPIs. These systems may provide a blueprint for identifying small molecules that target challenging PPIs and affecting molecular decision-making within multiprotein systems.
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Affiliation(s)
- Andrea D. Thompson
- Program
in Chemical Biology, ‡Departments of Pathology and Biological Chemistry and the Life Sciences
Institute, and §Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Amanda Dugan
- Program
in Chemical Biology, ‡Departments of Pathology and Biological Chemistry and the Life Sciences
Institute, and §Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jason E. Gestwicki
- Program
in Chemical Biology, ‡Departments of Pathology and Biological Chemistry and the Life Sciences
Institute, and §Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Anna K. Mapp
- Program
in Chemical Biology, ‡Departments of Pathology and Biological Chemistry and the Life Sciences
Institute, and §Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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14
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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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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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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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17
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Jaffe EK, Shanmugam D, Gardberg A, Dieterich S, Sankaran B, Stewart LJ, Myler PJ, Roos DS. Crystal structure of Toxoplasma gondii porphobilinogen synthase: insights on octameric structure and porphobilinogen formation. J Biol Chem 2011; 286:15298-307. [PMID: 21383008 PMCID: PMC3083160 DOI: 10.1074/jbc.m111.226225] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Revised: 03/03/2011] [Indexed: 11/06/2022] Open
Abstract
Porphobilinogen synthase (PBGS) is essential for heme biosynthesis, but the enzyme of the protozoan parasite Toxoplasma gondii (TgPBGS) differs from that of its human host in several important respects, including subcellular localization, metal ion dependence, and quaternary structural dynamics. We have solved the crystal structure of TgPBGS, which contains an octamer in the crystallographic asymmetric unit. Crystallized in the presence of substrate, each active site contains one molecule of the product porphobilinogen. Unlike prior structures containing a substrate-derived heterocycle directly bound to an active site zinc ion, the product-bound TgPBGS active site contains neither zinc nor magnesium, placing in question the common notion that all PBGS enzymes require an active site metal ion. Unlike human PBGS, the TgPBGS octamer contains magnesium ions at the intersections between pro-octamer dimers, which are presumed to function in allosteric regulation. TgPBGS includes N- and C-terminal regions that differ considerably from previously solved crystal structures. In particular, the C-terminal extension found in all apicomplexan PBGS enzymes forms an intersubunit β-sheet, stabilizing a pro-octamer dimer and preventing formation of hexamers that can form in human PBGS. The TgPBGS structure suggests strategies for the development of parasite-selective PBGS inhibitors.
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Affiliation(s)
- Eileen K. Jaffe
- From the Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111
| | | | - Anna Gardberg
- Emerald BioStructures, Inc., Bainbridge Island, Washington 98110
- the Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington 98109
| | - Shellie Dieterich
- Emerald BioStructures, Inc., Bainbridge Island, Washington 98110
- the Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington 98109
| | | | - Lance J. Stewart
- Emerald BioStructures, Inc., Bainbridge Island, Washington 98110
- the Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington 98109
| | - Peter J. Myler
- the Seattle Biomedical Research Institute, Seattle, Washington 98109 and the Departments of Global Health and Medical Education & Biomedical Informatics, University of Washington, Seattle, Washington 98195, and
- the Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington 98109
| | - David S. Roos
- the Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
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Lawrence SH, Selwood T, Jaffe EK. Diverse clinical compounds alter the quaternary structure and inhibit the activity of an essential enzyme. ChemMedChem 2011; 6:1067-73. [PMID: 21506274 DOI: 10.1002/cmdc.201100009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Revised: 02/24/2011] [Indexed: 11/10/2022]
Abstract
An in vitro evaluation of the Johns Hopkins Clinical Compound Library demonstrates that certain drugs can alter the quaternary structure of an essential human protein. Human porphobilinogen synthase (HsPBGS) is an essential enzyme involved in heme biosynthesis; it exists as an equilibrium of high-activity octamers, low-activity hexamers, and alternate dimer configurations that dictate the stoichiometry and architecture of further assembly. Decreased HsPBGS activity is implicated in toxicities associated with lead poisoning and 5-aminolevulinate dehydratase (ALAD) porphyria, the latter of which involves hexamer-favoring HsPBGS variants. A medium-throughput native PAGE mobility-shift screen coupled with evaluation of hits as HsPBGS inhibitors revealed 12 drugs that stabilize the HsPBGS hexamer and inhibit HsPBGS activity in vitro. A detailed characterization of these effects is presented. Drug inhibition of HsPBGS in vivo by inducing hexamer formation would constitute an unprecedented mechanism for side effects. We suggest that small-molecule perturbation of quaternary structure equilibria be considered as a general mechanism for drug action and side effects.
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Affiliation(s)
- Sarah H Lawrence
- Developmental Therapeutics, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
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Lu Q, Ma J, Rong H, Fan J, Yuan Y, Li K, Gao Y, Zhang X, Teng M, Niu L. Cloning, expression, purification, crystallization and preliminary crystallographic analysis of 5-aminolaevulinic acid dehydratase from Bacillus subtilis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:1053-5. [PMID: 20823524 PMCID: PMC2935225 DOI: 10.1107/s1744309110027582] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2010] [Accepted: 07/12/2010] [Indexed: 11/10/2022]
Abstract
5-aminolaevulinic acid dehydratase (ALAD), a crucial enzyme in the biosynthesis of tetrapyrrole, catalyses the condensation of two 5-aminolaevulinic acid (ALA) molecules to form porphobilinogen (PBG). The gene encoding ALAD was amplified from genomic DNA of Bacillus subtilis and the protein was overexpressed in Escherichia coli strain BL21 (DE3). The protein was purified and crystallized with an additional MGSSHHHHHHSSGLVPRGSH- tag at the N-terminus of the target protein. Diffraction-quality single crystals were obtained by the hanging-drop vapour-diffusion method. An X-ray diffraction data set was collected at a resolution of 2.7 A.
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Affiliation(s)
- Qianda Lu
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230027, People’s Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, 96 Jinzhai Road, Hefei, Anhui 230027, People’s Republic of China
| | - Jinming Ma
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230027, People’s Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, 96 Jinzhai Road, Hefei, Anhui 230027, People’s Republic of China
| | - Hui Rong
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230027, People’s Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, 96 Jinzhai Road, Hefei, Anhui 230027, People’s Republic of China
| | - Jun Fan
- School of Life Sciences, Anhui Agricultural University, 130 West Changjiang Road, Hefei, Anhui 230036, People’s Republic of China
| | - Ye Yuan
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230027, People’s Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, 96 Jinzhai Road, Hefei, Anhui 230027, People’s Republic of China
| | - Kuai Li
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230027, People’s Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, 96 Jinzhai Road, Hefei, Anhui 230027, People’s Republic of China
| | - Yongxiang Gao
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230027, People’s Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, 96 Jinzhai Road, Hefei, Anhui 230027, People’s Republic of China
| | - Xiao Zhang
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230027, People’s Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, 96 Jinzhai Road, Hefei, Anhui 230027, People’s Republic of China
| | - Maikun Teng
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230027, People’s Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, 96 Jinzhai Road, Hefei, Anhui 230027, People’s Republic of China
| | - Liwen Niu
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230027, People’s Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, 96 Jinzhai Road, Hefei, Anhui 230027, People’s Republic of China
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Abstract
The morpheein model of allosteric regulation can be applied as a novel approach to the discovery of small molecule allosteric modulators of protein function. Morpheeins are homo-oligomeric proteins where, under physiological conditions, the oligomer can dissociate, the dissociated units can change conformation, and the altered conformational state can reassociate to a structurally and functionally distinct oligomer. This phenomenon serves as a basis for allostery, as a basis for conformational diseases, as a basis for drug discovery, and may be applicable to personalized medicine such as in the prediction of drug side effects. Each of these relationships has been established for the prototype morpheein, porphobilinogen synthase, where the conformational disease is a porphyria and the drug application is in antimicrobial discovery. These data are presented along with a discussion of other drug targets for which the morpheein model of allostery may apply. Such targets include HIV integrase, TNFα, β-tryptase, and p53.
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Affiliation(s)
- Eileen K Jaffe
- Institute for Cancer Research, Fox Chase Cancer Center, 333 Cottman Ave, Philadelphia, PA 19111 U.S.A
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Reitz AB, Ramirez UD, Stith L, Du Y, Smith GR, Jaffe EK. Pseudomonas aeruginosa porphobilinogen synthase assembly state regulators: hit discovery and initial SAR studies. ARKIVOC 2010; 2010:175-188. [PMID: 21643541 PMCID: PMC3106444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023] Open
Abstract
Porphobilinogen synthase (PBGS) catalyzes the first common step in the biosynthesis of the essential heme, chlorophyll and vitamin B(12) heme pigments. PBGS activity is regulated by assembly state, with certain oligomers exhibiting biological activity and others either partially or completely inactive, affording an innovative means of allosteric drug action. Pseudomonas aeruginosa PBGS is functionally active as an octamer, and inactive as a dimer. We have identified a series of compounds that stabilize the inactive P. aeruginosa dimer by a computational prescreen followed by native PAGE gel mobility shift analysis. From those results, we have prepared related thiadiazoles and evaluated their ability to regulate P. aeruginosa PBGS assembly state.
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Affiliation(s)
- Allen B. Reitz
- Fox Chase Chemical Diversity Center, Inc., Pennsylvania Center for Drug Discovery, Pennsylvania Biotechnology Center, Doylestown, PA 18902 USA
| | - Ursula D. Ramirez
- Fox Chase Cancer Center, 333 Cottman Ave., Philadelphia, PA 19111 USA
| | - Linda Stith
- Fox Chase Cancer Center, 333 Cottman Ave., Philadelphia, PA 19111 USA
| | - Yanming Du
- Fox Chase Chemical Diversity Center, Inc., Pennsylvania Center for Drug Discovery, Pennsylvania Biotechnology Center, Doylestown, PA 18902 USA
| | - Garry R. Smith
- Fox Chase Chemical Diversity Center, Inc., Pennsylvania Center for Drug Discovery, Pennsylvania Biotechnology Center, Doylestown, PA 18902 USA
| | - Eileen K. Jaffe
- Fox Chase Cancer Center, 333 Cottman Ave., Philadelphia, PA 19111 USA
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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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Ramirez UD, Myachina F, Stith L, Jaffe EK. Docking to large allosteric binding sites on protein surfaces. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2010; 680:481-8. [PMID: 20865533 PMCID: PMC2946403 DOI: 10.1007/978-1-4419-5913-3_54] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The inactive porphobilinogen synthase (PBGS) hexamer has an oligomer-specific and phylogenetically variable surface cavity that is not present in the active octamer. The octamer and hexamer are components of a dynamic quaternary structure equilibrium characteristic of morpheeins. Small molecules that bind to the hexamer-specific surface cavity, which is at the interface of three subunits, are predicted to act as allosteric inhibitors that function by drawing the oligomeric equilibrium toward the hexamer. We used GLIDE as a tool to enrich a 250,000 molecule library for molecules with enhanced probability of acting as hexamer-stabilizing allosteric inhibitors of PBGS from Yersinia enterocolitica. Eighty-six compounds were tested in vitro and five showed hexamer stabilization. We discuss the application of computational docking to surface cavities as an approach to find allosteric modulators of protein function with specific reference to morpheeins that function as an equilibrium of non-additive quaternary structure assemblies.
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