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Pierson E, De Pol F, Fillet M, Wouters J. A morpheein equilibrium regulates catalysis in phosphoserine phosphatase SerB2 from Mycobacterium tuberculosis. Commun Biol 2023; 6:1024. [PMID: 37817000 PMCID: PMC10564941 DOI: 10.1038/s42003-023-05402-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 09/29/2023] [Indexed: 10/12/2023] Open
Abstract
Mycobacterium tuberculosis phosphoserine phosphatase MtSerB2 is of interest as a new antituberculosis target due to its essential metabolic role in L-serine biosynthesis and effector functions in infected cells. Previous works indicated that MtSerB2 is regulated through an oligomeric transition induced by L-Ser that could serve as a basis for the design of selective allosteric inhibitors. However, the mechanism underlying this transition remains highly elusive due to the lack of experimental structural data. Here we describe a structural, biophysical, and enzymological characterisation of MtSerB2 oligomerisation in the presence and absence of L-Ser. We show that MtSerB2 coexists in dimeric, trimeric, and tetrameric forms of different activity levels interconverting through a conformationally flexible monomeric state, which is not observed in two near-identical mycobacterial orthologs. This morpheein behaviour exhibited by MtSerB2 lays the foundation for future allosteric drug discovery and provides a starting point to the understanding of its peculiar multifunctional moonlighting properties.
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Affiliation(s)
- Elise Pierson
- Laboratoire de Chimie Biologique Structurale (CBS), Namur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), 5000, Namur, Belgium
| | - Florian De Pol
- Laboratoire de Chimie Biologique Structurale (CBS), Namur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), 5000, Namur, Belgium
| | - Marianne Fillet
- Laboratory for the Analysis of Medicines (LAM), Center for Interdisciplinary Research on Medicines (CIRM), University of Liège (ULiège), 4000, Liège, Belgium
| | - Johan Wouters
- Laboratoire de Chimie Biologique Structurale (CBS), Namur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), 5000, Namur, Belgium.
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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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Abstract
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Since
the proposal of Anfinsen’s thermodynamic hypothesis
in 1963, our understanding of protein folding and dynamics has gained
significant appreciation of its nuance and complexity. Intrinsically
disordered proteins, chameleonic sequences, morpheeins, and metamorphic
proteins have broadened the protein folding paradigm. Here, we discuss
noncanonical protein folding patterns, with an emphasis on metamorphic
proteins, and we review known metamorphic proteins that occur naturally
and that have been engineered in the laboratory. Finally, we discuss
research areas surrounding metamorphic proteins that are primed for
future exploration, including evolution, drug discovery, and the quest
for previously unrecognized metamorphs. As we enter an age where we
are capable of complex bioinformatic searches and de novo protein design, we are primed to search for previously unrecognized
metamorphic proteins and to design our own metamorphs to act as targeted,
switchable drugs; biosensors; and more.
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Affiliation(s)
- Acacia F. Dishman
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Brian F. Volkman
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
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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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Stadler AM, Ramírez J, Lehn JM, Vincent B. Supramolecular reactions of metallo-architectures: Ag 2-double-helicate/Zn 4-grid, Pb 4-grid/Zn 4-grid interconversions, and Ag 2-double-helicate fusion. Chem Sci 2016; 7:3689-3693. [PMID: 30008998 PMCID: PMC6008726 DOI: 10.1039/c5sc04403k] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 02/03/2016] [Indexed: 01/29/2023] Open
Abstract
Supramolecular reactions are of importance in many fields. We report herein three examples where complexes of hydrazone-based ligands are involved. A Ag2-double-helicate was converted, by treatment with Zn(OTf)2, into a Zn4-grid (exchange of metal ions and change of the nature of the initial complex). A Pb4-grid was converted, upon reaction with ZnCl2 or ZnBr2, into a Zn4-grid (exchange of metal ions, but conservation of the nature of the initial complex). The reverse conversions were also achieved. The fusion of a Ag2-double-helicate with another Ag2-double-helicate was performed (exchange of ligands, but conservation of the nature of the complexes) and resulted in a mixture of three helicates (two homostranded ones and one heterostranded one).
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Affiliation(s)
- Adrian-Mihail Stadler
- Université de Strasbourg , CNRS , UMR 7006 , ISIS , 8 Allée G. Monge , Strasbourg , France .
- Institute of Nanotechnology (INT) , Karlsruhe Institute of Technolgoy (KIT) , 76344 , Eggenstein-Leopoldshafen , Germany
| | - Juan Ramírez
- Institut Pasteur Paris , 28 Rue du Docteur Roux , 75015 Paris , France
| | - Jean-Marie Lehn
- Université de Strasbourg , CNRS , UMR 7006 , ISIS , 8 Allée G. Monge , Strasbourg , France .
| | - Bruno Vincent
- Service de RMN , Faculté de Chimie , 1 Rue B. Pascal , Strasbourg , France
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Ahmad MF, Huff SE, Pink J, Alam I, Zhang A, Perry K, Harris ME, Misko T, Porwal SK, Oleinick NL, Miyagi M, Viswanathan R, Dealwis CG. Identification of Non-nucleoside Human Ribonucleotide Reductase Modulators. J Med Chem 2015; 58:9498-509. [PMID: 26488902 DOI: 10.1021/acs.jmedchem.5b00929] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ribonucleotide reductase (RR) catalyzes the rate-limiting step of dNTP synthesis and is an established cancer target. Drugs targeting RR are mainly nucleoside in nature. In this study, we sought to identify non-nucleoside small-molecule inhibitors of RR. Using virtual screening, binding affinity, inhibition, and cell toxicity, we have discovered a class of small molecules that alter the equilibrium of inactive hexamers of RR, leading to its inhibition. Several unique chemical categories, including a phthalimide derivative, show micromolar IC50s and KDs while demonstrating cytotoxicity. A crystal structure of an active phthalimide binding at the targeted interface supports the noncompetitive mode of inhibition determined by kinetic studies. Furthermore, the phthalimide shifts the equilibrium from dimer to hexamer. Together, these data identify several novel non-nucleoside inhibitors of human RR which act by stabilizing the inactive form of the enzyme.
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Affiliation(s)
- Md Faiz Ahmad
- Department of Pharmacology, School of Medicine, Case Western Reserve University , Cleveland, Ohio 44106, United States
| | - Sarah E Huff
- Department of Chemistry, Case Western Reserve University , Cleveland, Ohio 44106, United States
| | - John Pink
- Case Comprehensive Cancer Center, Case Western Reserve University , Cleveland, Ohio 44106, United States
| | - Intekhab Alam
- Department of Pharmacology, School of Medicine, Case Western Reserve University , Cleveland, Ohio 44106, United States
| | - Andrew Zhang
- Department of Pharmacology, School of Medicine, Case Western Reserve University , Cleveland, Ohio 44106, United States
| | - Kay Perry
- Northeastern-CAT at the Advanced Photon Source, Argonne National Laboratory , Argonne, Illinois 60439, United States
| | - Michael E Harris
- Department of Biochemistry, School of Medicine, Case Western Reserve University , Cleveland, Ohio 44106, United States
| | - Tessianna Misko
- Department of Pharmacology, School of Medicine, Case Western Reserve University , Cleveland, Ohio 44106, United States
| | - Suheel K Porwal
- Department of Chemistry, Dehradun Institute of Technology, University of Deharadun , Dehradun 248197, India
| | - Nancy L Oleinick
- Case Comprehensive Cancer Center, Case Western Reserve University , Cleveland, Ohio 44106, United States.,Department of Radiation Oncology, School of Medicine, Case Western Reserve University , Cleveland, Ohio 44106, United States
| | - Masaru Miyagi
- Center for Proteomics and Bioinformatics, Case Western Reserve University , Cleveland, Ohio 44106, United States
| | - Rajesh Viswanathan
- Department of Chemistry, Case Western Reserve University , Cleveland, Ohio 44106, United States
| | - Chris Godfrey Dealwis
- Department of Pharmacology, School of Medicine, Case Western Reserve University , Cleveland, Ohio 44106, United States.,Center for Proteomics and the Department of Chemistry, Case Western Reserve University , Cleveland, Ohio 44106, United States
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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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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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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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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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