1
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Karpurapu M, Kakarala KK, Chung S, Nie Y, Koley A, Dougherty P, Christman JW. Epigallocatechin gallate regulates the myeloid-specific transcription factor PU.1 in macrophages. PLoS One 2024; 19:e0301904. [PMID: 38662666 PMCID: PMC11045095 DOI: 10.1371/journal.pone.0301904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
Our previous research demonstrated that PU.1 regulates expression of the genes involved in inflammation in macrophages. Selective knockdown of PU.1 in macrophages ameliorated LPS-induced acute lung injury (ALI) in bone marrow chimera mice. Inhibitors that block the transcriptional activity of PU.1 in macrophages have the potential to mitigate the pathophysiology of LPS-induced ALI. However, complete inactivation of PU.1 gene disrupts normal myelopoiesis. Although the green tea polyphenol Epigallocatechin gallate (EGCG) has been shown to regulate inflammatory genes in various cell types, it is not known if EGCG alters the transcriptional activity of PU.1 protein. Using Schrodinger Glide docking, we have identified that EGCG binds with PU.1 protein, altering its DNA-binding and self-dimerization activity. In silico analysis shows that EGCG forms Hydrogen bonds with Glutamic Acid 209, Leucine 250 in DNA binding and Lysine 196, Tryptophan 193, and Leucine 182 in the self-dimerization domain of the PU.1 protein. Experimental validation using mouse bone marrow-derived macrophages (BMDM) confirmed that EGCG inhibits both DNA binding by PU.1 and self-dimerization. Importantly, EGCG had no impact on expression of the total PU.1 protein levels but significantly reduced expression of various inflammatory genes and generation of ROS. In summary, we report that EGCG acts as an inhibitor of the PU.1 transcription factor in macrophages.
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Affiliation(s)
- Manjula Karpurapu
- Division of Pulmonary, Davis Heart and Lung Research Institute, Critical Care and Sleep Medicine, Ohio State University Wexner Medical Center, Columbus, OH, United States of America
| | | | - Sangwoon Chung
- Division of Pulmonary, Davis Heart and Lung Research Institute, Critical Care and Sleep Medicine, Ohio State University Wexner Medical Center, Columbus, OH, United States of America
| | - Yunjuan Nie
- Division of Pulmonary, Davis Heart and Lung Research Institute, Critical Care and Sleep Medicine, Ohio State University Wexner Medical Center, Columbus, OH, United States of America
- Department of Basic Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, 214122, P.R. China
| | - Amritendu Koley
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, United States of America
| | - Patrick Dougherty
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, United States of America
| | - John W. Christman
- Division of Pulmonary, Davis Heart and Lung Research Institute, Critical Care and Sleep Medicine, Ohio State University Wexner Medical Center, Columbus, OH, United States of America
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2
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Ogbonna EN, Paul A, Ross Terrell J, Fang Z, Chen C, Poon GMK, Boykin DW, Wilson WD. Drug design and DNA structural research inspired by the Neidle laboratory: DNA minor groove binding and transcription factor inhibition by thiophene diamidines. Bioorg Med Chem 2022; 68:116861. [PMID: 35661929 DOI: 10.1016/j.bmc.2022.116861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/23/2022] [Accepted: 05/26/2022] [Indexed: 11/02/2022]
Abstract
The understanding of sequence-specific DNA minor groove interactions has recently made major steps forward and as a result, the goal of development of compounds that target the minor groove is an active research area. In an effort to develop biologically active minor groove agents, we are preparing and exploring the DNA interactions of diverse diamidine derivatives with a 5'-GAATTC-3' binding site using a powerful array of methods including, biosensor-SPR methods, and X-ray crystallography. The benzimidazole-thiophene module provides an excellent minor groove recognition component. A central thiophene in a benzimidazole-thiophene-phenyl aromatic system provides essentially optimum curvature for matching the shape of the minor groove. Comparison of that structure to one with the benzimidazole replaced with an indole shows that the two structures are very similar, but have some interesting and important differences in electrostatic potential maps, the DNA minor groove binding structure based on x-ray crystallographic analysis, and inhibition of the major groove binding PU.1 transcription factor complex. The binding KD for both compounds is under 10 nM and both form amidine H-bonds to DNA bases. They both have bifurcated H-bonds from the benzimidazole or indole groups to bases at the center of the -AATT- binding site. Analysis of the comparative results provides an excellent understanding of how thiophene compounds recognize the minor groove and can act as transcription factor inhibitors.
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Affiliation(s)
- Edwin N Ogbonna
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Ananya Paul
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA
| | - J Ross Terrell
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Ziyuan Fang
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Cen Chen
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Gregory M K Poon
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA
| | - David W Boykin
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA
| | - W David Wilson
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA.
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3
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Vo TD, Schneider AL, Poon GMK, Wilson WD. DNA-facilitated target search by nucleoproteins: Extension of a biosensor-surface plasmon resonance method. Anal Biochem 2021; 629:114298. [PMID: 34252439 PMCID: PMC8427768 DOI: 10.1016/j.ab.2021.114298] [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: 04/18/2021] [Accepted: 06/30/2021] [Indexed: 10/20/2022]
Abstract
To extend the value of biosensor-SPR in the characterization of DNA recognition by nucleoproteins, we report a comparative analysis of DNA-facilitated target search by two ETS-family transcription factors: Elk1 and ETV6. ETS domains represent an attractive system for developing biosensor-based techniques due to a broad range of physicochemical properties encoded within a highly conserved DNA-binding motif. Building on a biosensor approach in which the protein is quantitatively sequestered and presented to immobilized cognate DNA as nonspecific complexes, we assessed the impact of intrinsic cognate and nonspecific affinities on long-range (intersegmental) target search. The equilibrium constants of DNA-facilitated binding were sensitive to the intrinsic binding properties of the proteins such that their relative specificity for cognate DNA were reinforced when binding occurred by transfer vs. without nonspecific DNA. Direct measurement of association and dissociation kinetics revealed ionic features of the activated complex that evidenced DNA-facilitated dissociation, even though Elk1 and ETV6 harbor only a single DNA-binding surface. At salt concentrations that masked the effects of nonspecific pre-binding at equilibrium, the dissociation kinetics of cognate binding were nevertheless distinct from conditions under which nonspecific DNA was absent. These results further strengthen the significance of long-range DNA-facilitated translocation in the physiologic environment.
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Affiliation(s)
- Tam D Vo
- Department of Chemistry, Georgia State University, USA
| | | | - Gregory M K Poon
- Department of Chemistry, Georgia State University, USA; Center for Diagnostics and Therapeutics, Georgia State University, USA.
| | - W David Wilson
- Department of Chemistry, Georgia State University, USA; Center for Diagnostics and Therapeutics, Georgia State University, USA.
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4
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Vo TD, Schneider AL, Wilson WD, Poon GMK. Salt bridge dynamics in protein/DNA recognition: a comparative analysis of Elk1 and ETV6. Phys Chem Chem Phys 2021; 23:13490-13502. [PMID: 34120158 PMCID: PMC8233815 DOI: 10.1039/d1cp01568k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electrostatic protein/DNA interactions arise from the neutralization of the DNA phosphodiester backbone as well as coupled exchanges by charged protein residues as salt bridges or with mobile ions. Much focus has been and continues to be paid to interfacial ion pairs with DNA. The role of extra-interfacial ionic interactions, particularly as dynamic drivers of DNA sequence selectivity, remain poorly known. The ETS family of transcription factors represents an attractive model for addressing this knowledge gap given their diverse ionic composition in primary structures that fold to a tightly conserved DNA-binding motif. To probe the importance of extra-interfacial salt bridges in DNA recognition, we compared the salt-dependent binding by Elk1 with ETV6, two ETS homologs differing markedly in ionic composition. While both proteins exhibit salt-dependent binding with cognate DNA that corresponds to interfacial phosphate contacts, their nonspecific binding diverges from cognate binding as well as each other. Molecular dynamics simulations in explicit solvent, which generated ionic interactions in agreement with the experimental binding data, revealed distinct salt-bridge dynamics in the nonspecific complexes formed by the two proteins. Impaired DNA contact by ETV6 resulted in fewer backbone contacts in the nonspecific complex, while Elk1 exhibited a redistribution of extra-interfacial salt bridges via residues that are non-conserved between the two ETS relatives. Thus, primary structure variation in ionic residues can encode highly differentiated specificity mechanisms in a highly conserved DNA-binding motif.
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Affiliation(s)
- Tam D Vo
- Department of Chemistry, Georgia State University, P.O. Box 3965, Atlanta, GA 30303, USA.
| | - Amelia L Schneider
- Department of Chemistry, Georgia State University, P.O. Box 3965, Atlanta, GA 30303, USA.
| | - W David Wilson
- Department of Chemistry, Georgia State University, P.O. Box 3965, Atlanta, GA 30303, USA. and Center for Diagnostics and Therapeutics, Georgia State University, P.O. Box 3965, Atlanta, GA 30303, USA
| | - Gregory M K Poon
- Department of Chemistry, Georgia State University, P.O. Box 3965, Atlanta, GA 30303, USA. and Center for Diagnostics and Therapeutics, Georgia State University, P.O. Box 3965, Atlanta, GA 30303, USA
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5
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Shashikala HBM, Chakravorty A, Alexov E. Modeling Electrostatic Force in Protein-Protein Recognition. Front Mol Biosci 2019; 6:94. [PMID: 31608289 PMCID: PMC6774301 DOI: 10.3389/fmolb.2019.00094] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 09/11/2019] [Indexed: 12/25/2022] Open
Abstract
Electrostatic interactions are important for understanding molecular interactions, since they are long-range interactions and can guide binding partners to their correct binding positions. To investigate the role of electrostatic forces in molecular recognition, we calculated electrostatic forces between binding partners separated at various distances. The investigation was done on a large set of 275 protein complexes using recently developed DelPhiForce tool and in parallel, evaluating the total electrostatic force via electrostatic association energy. To accomplish the goal, we developed a method to find an appropriate direction to move one chain of protein complex away from its bound position and then calculate the corresponding electrostatic force as a function of separation distance. It is demonstrated that at large distances between the partners, the electrostatic force (magnitude and direction) is consistent among the protocols used and the main factors contributing to it are the net charge of the partners and their interfaces. However, at short distances, where partners form specific pair-wise interactions or de-solvation penalty becomes significant, the outcome depends on the precise balance of these factors. Based on the electrostatic force profile (force as a function of distance), we group the cases into four distinctive categories, among which the most intriguing is the case termed "soft landing." In this case, the electrostatic force at large distances is favorable assisting the partners to come together, while at short distance it opposes binding, and thus slows down the approach of the partners toward their physical binding.
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6
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Liu B, Bashkin JK, Poon GMK, Wang S, Wang S, Wilson WD. Modulating DNA by polyamides to regulate transcription factor PU.1-DNA binding interactions. Biochimie 2019; 167:1-11. [PMID: 31445072 DOI: 10.1016/j.biochi.2019.08.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 08/20/2019] [Indexed: 12/17/2022]
Abstract
Hairpin polyamides are synthetic small molecules that bind DNA minor groove sequence-selectively and, in many sequences, induce widening of the minor groove and compression of the major groove. The structural distortion of DNA caused by polyamides has enhanced our understanding of the regulation of DNA-binding proteins via polyamides. Polyamides have DNA binding affinities that are comparable to those proteins, therefore, can potentially be used as therapeutic agents to treat diseases caused by aberrant gene expression. In fact, many diseases are characterized by over- or under-expressed genes. PU.1 is a transcription factor that regulates many immune system genes. Aberrant expression of PU.1 has been associated with the development of acute myeloid leukemia (AML). We have, therefore, designed and synthesized ten hairpin polyamides to investigate their capacity in controlling the PU.1-DNA interaction. Our results showed that nine of the polyamides disrupt PU.1-DNA binding and the inhibition capacity strongly correlates with binding affinity. One molecule, FH1024, was observed forming a FH1024-PU.1-DNA ternary complex instead of inhibiting PU.1-DNA binding. This is the first report of a small molecule that is potentially a weak agonist that recruits PU.1 to DNA. This finding sheds light on the design of polyamides that exhibit novel regulatory mechanisms on protein-DNA binding.
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Affiliation(s)
- Beibei Liu
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA
| | - James K Bashkin
- Department of Chemistry & Biochemistry, Center for Nanoscience, University of Missouri-St. Louis, St. Louis, MO, 63121, USA
| | - Gregory M K Poon
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA
| | - Shuo Wang
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA
| | - Siming Wang
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA
| | - W David Wilson
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA.
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7
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A New Generation of Minor-Groove-Binding-Heterocyclic Diamidines That Recognize G·C Base Pairs in an AT Sequence Context. Molecules 2019; 24:molecules24050946. [PMID: 30866557 PMCID: PMC6429135 DOI: 10.3390/molecules24050946] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 02/28/2019] [Accepted: 03/01/2019] [Indexed: 12/17/2022] Open
Abstract
We review the preparation of new compounds with good solution and cell uptake properties that can selectively recognize mixed A·T and G·C bp sequences of DNA. Our underlying aim is to show that these new compounds provide important new biotechnology reagents as well as a new class of therapeutic candidates with better properties and development potential than other currently available agents. In this review, entirely different ways to recognize mixed sequences of DNA by modifying AT selective heterocyclic cations are described. To selectively recognize a G·C base pair an H-bond acceptor must be incorporated with AT recognizing groups as with netropsin. We have used pyridine, azabenzimidazole and thiophene-N-methylbenzimidazole GC recognition units in modules crafted with both rational design and empirical optimization. These modules can selectively and strongly recognize a single G·C base pair in an AT sequence context. In some cases, a relatively simple change in substituents can convert a heterocyclic module from AT to GC recognition selectivity. Synthesis and DNA interaction results for initial example lead modules are described for single G·C base pair recognition compounds. The review concludes with a description of the initial efforts to prepare larger compounds to recognize sequences of DNA with more than one G·C base pairs. The challenges and initial successes are described along with future directions.
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8
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Lambert M, Jambon S, Depauw S, David-Cordonnier MH. Targeting Transcription Factors for Cancer Treatment. Molecules 2018; 23:molecules23061479. [PMID: 29921764 PMCID: PMC6100431 DOI: 10.3390/molecules23061479] [Citation(s) in RCA: 229] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 06/11/2018] [Accepted: 06/15/2018] [Indexed: 12/15/2022] Open
Abstract
Transcription factors are involved in a large number of human diseases such as cancers for which they account for about 20% of all oncogenes identified so far. For long time, with the exception of ligand-inducible nuclear receptors, transcription factors were considered as “undruggable” targets. Advances knowledge of these transcription factors, in terms of structure, function (expression, degradation, interaction with co-factors and other proteins) and the dynamics of their mode of binding to DNA has changed this postulate and paved the way for new therapies targeted against transcription factors. Here, we discuss various ways to target transcription factors in cancer models: by modulating their expression or degradation, by blocking protein/protein interactions, by targeting the transcription factor itself to prevent its DNA binding either through a binding pocket or at the DNA-interacting site, some of these inhibitors being currently used or evaluated for cancer treatment. Such different targeting of transcription factors by small molecules is facilitated by modern chemistry developing a wide variety of original molecules designed to specifically abort transcription factor and by an increased knowledge of their pathological implication through the use of new technologies in order to make it possible to improve therapeutic control of transcription factor oncogenic functions.
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Affiliation(s)
- Mélanie Lambert
- INSERM UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), Lille University and Hospital Center (CHU-Lille), Institut pour la Recherche sur le Cancer de Lille (IRCL), Place de Verdun, F-59045 Lille, France.
| | - Samy Jambon
- INSERM UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), Lille University and Hospital Center (CHU-Lille), Institut pour la Recherche sur le Cancer de Lille (IRCL), Place de Verdun, F-59045 Lille, France.
| | - Sabine Depauw
- INSERM UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), Lille University and Hospital Center (CHU-Lille), Institut pour la Recherche sur le Cancer de Lille (IRCL), Place de Verdun, F-59045 Lille, France.
| | - Marie-Hélène David-Cordonnier
- INSERM UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), Lille University and Hospital Center (CHU-Lille), Institut pour la Recherche sur le Cancer de Lille (IRCL), Place de Verdun, F-59045 Lille, France.
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9
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Tan C, Takada S. Dynamic and Structural Modeling of the Specificity in Protein–DNA Interactions Guided by Binding Assay and Structure Data. J Chem Theory Comput 2018; 14:3877-3889. [DOI: 10.1021/acs.jctc.8b00299] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Cheng Tan
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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10
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Paul A, Kumar A, Nanjunda R, Farahat AA, Boykin DW, Wilson WD. Systematic synthetic and biophysical development of mixed sequence DNA binding agents. Org Biomol Chem 2018; 15:827-835. [PMID: 27995240 DOI: 10.1039/c6ob02390h] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
It is now well established that, although only about 5% of the human genome codes for protein, most of the DNA has some function, such as synthesis of specific, functional RNAs and/or control of gene expression. These functional sequences open immense possibilities in both biotechnology and therapeutics for the use of cell-permeable, small molecules that can bind mixed-base pair sequences of DNA for regulation of genomic functions. Unfortunately very few types of modules have been designed to recognize mixed DNA sequences and for progress in targeting specific genes, it is essential to have additional classes of compounds. Compounds that can be rationally designed from established modules and which can bind strongly to mixed base pair DNA sequences are especially attractive. Based on extensive experience in design of minor-groove agents for AT recognition, a small library of compounds with two AT specific binding modules, connected through linkers which can recognize the G·C base pairs, were prepared. The compound-DNA interactions were evaluated with a powerful array of biophysical methods and the results show that some pyridyl-linked compounds bind with the target sequence with sub-nanomolar KD, with very slow dissociation kinetics and 200 times selectivity over the related sequence without a G·C base pair. Interestingly, a set of compounds with AT module connected by different linkers shows cooperative dimer recognition of related sequences. This type of design approach can be expanded to additional modules for recognition of a wide variety of sequences.
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Affiliation(s)
- Ananya Paul
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA.
| | - Arvind Kumar
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA.
| | - Rupesh Nanjunda
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA. and Janssen Research and Development, 1400 McKean Rd, Spring House, PA 19477, USA
| | - Abdelbasset A Farahat
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA. and Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - David W Boykin
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA.
| | - W David Wilson
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA.
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11
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Antony-Debré I, Paul A, Leite J, Mitchell K, Kim HM, Carvajal LA, Todorova TI, Huang K, Kumar A, Farahat AA, Bartholdy B, Narayanagari SR, Chen J, Ambesi-Impiombato A, Ferrando AA, Mantzaris I, Gavathiotis E, Verma A, Will B, Boykin DW, Wilson WD, Poon GM, Steidl U. Pharmacological inhibition of the transcription factor PU.1 in leukemia. J Clin Invest 2017; 127:4297-4313. [PMID: 29083320 DOI: 10.1172/jci92504] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 09/21/2017] [Indexed: 11/17/2022] Open
Abstract
The transcription factor PU.1 is often impaired in patients with acute myeloid leukemia (AML). Here, we used AML cells that already had low PU.1 levels and further inhibited PU.1 using either RNA interference or, to our knowledge, first-in-class small-molecule inhibitors of PU.1 that we developed specifically to allosterically interfere with PU.1-chromatin binding through interaction with the DNA minor groove that flanks PU.1-binding motifs. These small molecules of the heterocyclic diamidine family disrupted the interaction of PU.1 with target gene promoters and led to downregulation of canonical PU.1 transcriptional targets. shRNA or small-molecule inhibition of PU.1 in AML cells from either PU.1lo mutant mice or human patients with AML-inhibited cell growth and clonogenicity and induced apoptosis. In murine and human AML (xeno)transplantation models, treatment with our PU.1 inhibitors decreased tumor burden and resulted in increased survival. Thus, our study provides proof of concept that PU.1 inhibition has potential as a therapeutic strategy for the treatment of AML and for the development of small-molecule inhibitors of PU.1.
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Affiliation(s)
- Iléana Antony-Debré
- Department of Cell Biology, Albert Einstein College of Medicine, New York, New York, USA
| | - Ananya Paul
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA
| | - Joana Leite
- Department of Cell Biology, Albert Einstein College of Medicine, New York, New York, USA
| | - Kelly Mitchell
- Department of Cell Biology, Albert Einstein College of Medicine, New York, New York, USA
| | - Hye Mi Kim
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA
| | - Luis A Carvajal
- Department of Cell Biology, Albert Einstein College of Medicine, New York, New York, USA
| | - Tihomira I Todorova
- Department of Cell Biology, Albert Einstein College of Medicine, New York, New York, USA
| | - Kenneth Huang
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA
| | - Arvind Kumar
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA
| | - Abdelbasset A Farahat
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA.,Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Boris Bartholdy
- Department of Cell Biology, Albert Einstein College of Medicine, New York, New York, USA
| | | | - Jiahao Chen
- Department of Cell Biology, Albert Einstein College of Medicine, New York, New York, USA
| | | | - Adolfo A Ferrando
- Institute for Cancer Genetics, Columbia University, New York, New York, USA
| | - Ioannis Mantzaris
- Department of Medicine (Oncology), Division of Hemato-Oncology, Albert Einstein College of Medicine-Montefiore Medical Center, New York, New York, USA
| | - Evripidis Gavathiotis
- Department of Biochemistry.,Albert Einstein Cancer Center, and.,Ruth L. and David S. Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, New York, New York, USA
| | - Amit Verma
- Department of Medicine (Oncology), Division of Hemato-Oncology, Albert Einstein College of Medicine-Montefiore Medical Center, New York, New York, USA.,Albert Einstein Cancer Center, and.,Ruth L. and David S. Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, New York, New York, USA
| | - Britta Will
- Department of Cell Biology, Albert Einstein College of Medicine, New York, New York, USA.,Albert Einstein Cancer Center, and.,Ruth L. and David S. Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, New York, New York, USA
| | - David W Boykin
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA
| | - W David Wilson
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA
| | - Gregory Mk Poon
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA
| | - Ulrich Steidl
- Department of Cell Biology, Albert Einstein College of Medicine, New York, New York, USA.,Department of Medicine (Oncology), Division of Hemato-Oncology, Albert Einstein College of Medicine-Montefiore Medical Center, New York, New York, USA.,Albert Einstein Cancer Center, and.,Ruth L. and David S. Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, New York, New York, USA
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12
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Tiwari N, Srivastava A, Kundu B, Munde M. Biophysical insight into the heparin-peptide interaction and its modulation by a small molecule. J Mol Recognit 2017; 31. [DOI: 10.1002/jmr.2674] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 08/28/2017] [Accepted: 09/03/2017] [Indexed: 12/21/2022]
Affiliation(s)
- Neha Tiwari
- School of Physical Sciences; Jawaharlal Nehru University; New Delhi India
| | - Ankit Srivastava
- School of Biological Sciences; Indian Institute of Technology; New Delhi India
| | - Bishwajit Kundu
- School of Biological Sciences; Indian Institute of Technology; New Delhi India
| | - Manoj Munde
- School of Physical Sciences; Jawaharlal Nehru University; New Delhi India
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13
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Vo T, Wang S, Poon GMK, Wilson WD. Electrostatic control of DNA intersegmental translocation by the ETS transcription factor ETV6. J Biol Chem 2017; 292:13187-13196. [PMID: 28592487 PMCID: PMC5555182 DOI: 10.1074/jbc.m117.792887] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Revised: 06/06/2017] [Indexed: 01/22/2023] Open
Abstract
To find their DNA target sites in complex solution environments containing excess heterogeneous DNA, sequence-specific DNA-binding proteins execute various translocation mechanisms known collectively as facilitated diffusion. For proteins harboring a single DNA contact surface, long-range translocation occurs by jumping between widely spaced DNA segments. We have configured biosensor-based surface plasmon resonance to directly measure the affinity and kinetics of this intersegmental jumping by the ETS-family transcription factor ETS variant 6 (ETV6). To isolate intersegmental target binding in a functionally defined manner, we pre-equilibrated ETV6 with excess salmon sperm DNA, a heterogeneous polymer, before exposing the nonspecifically bound protein to immobilized oligomeric DNA harboring a high-affinity ETV6 site. In this way, the mechanism of ETV6-target association could be toggled electrostatically through varying NaCl concentration in the bulk solution. Direct measurements of association and dissociation kinetics of the site-specific complex indicated that 1) freely diffusive binding by ETV6 proceeds through a nonspecific-like intermediate, 2) intersegmental jumping is rate-limited by dissociation from the nonspecific polymer, and 3) dissociation of the specific complex is independent of the history of complex formation. These results show that target searches by proteins with an ETS domain, such as ETV6, whose single DNA-binding domain cannot contact both source and destination sites simultaneously, are nonetheless strongly modulated by intersegmental jumping in heterogeneous site environments. Our findings establish biosensors as a general technique for directly and specifically measuring target site search by DNA-binding proteins via intersegmental translocation.
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Affiliation(s)
- Tam Vo
- From the Department of Chemistry and
| | - Shuo Wang
- From the Department of Chemistry and
| | - Gregory M K Poon
- From the Department of Chemistry and
- Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303
| | - W David Wilson
- From the Department of Chemistry and
- Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303
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14
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Xhani S, Esaki S, Huang K, Erlitzki N, Poon GMK. Distinct Roles for Interfacial Hydration in Site-Specific DNA Recognition by ETS-Family Transcription Factors. J Phys Chem B 2017; 121:2748-2758. [PMID: 28296403 DOI: 10.1021/acs.jpcb.7b00325] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ETS family of transcription factors is a functionally heterogeneous group of gene regulators that share a structurally conserved, eponymous DNA-binding domain. Unlike other ETS homologues, such as Ets-1, DNA recognition by PU.1 is highly sensitive to its osmotic environment due to excess interfacial hydration in the complex. To investigate interfacial hydration in the two homologues, we mutated a conserved tyrosine residue, which is exclusively engaged in coordinating a well-defined water contact between the protein and DNA among ETS proteins, to phenylalanine. The loss of this water-mediated contact blunted the osmotic sensitivity of PU.1/DNA binding, but did not alter binding under normo-osmotic conditions, suggesting that PU.1 has evolved to maximize osmotic sensitivity. The homologous mutation in Ets-1, which was minimally sensitive to osmotic stress due to a sparsely hydrated interface, reduced DNA-binding affinity at normal osmolality but the complex became stabilized by osmotic stress. Molecular dynamics simulations of wildtype and mutant PU.1 and Ets-1 in their free and DNA-bound states, which recapitulated experimental features of the proteins, showed that abrogation of this tyrosine-mediated water contact perturbed the Ets-1/DNA complex not through disruption of interfacial hydration, but by inhibiting local dynamics induced specifically in the bound state. Thus, a configurationally identical water-mediated contact plays mechanistically distinct roles in mediating DNA recognition by structurally homologous ETS transcription factors.
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Affiliation(s)
- Suela Xhani
- Department of Chemistry, Georgia State University , Atlanta, Georgia 30303, United States
| | - Shingo Esaki
- Department of Chemistry, Georgia State University , Atlanta, Georgia 30303, United States
| | - Kenneth Huang
- Department of Chemistry, Georgia State University , Atlanta, Georgia 30303, United States
| | - Noa Erlitzki
- Department of Chemistry, Georgia State University , Atlanta, Georgia 30303, United States
| | - Gregory M K Poon
- Department of Chemistry, Georgia State University , Atlanta, Georgia 30303, United States.,Center for Diagnostics and Therapeutics, Georgia State University , Atlanta, Georgia 30303, United States
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15
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Chakravorty A, Jia Z, Li L, Alexov E. A New DelPhi Feature for Modeling Electrostatic Potential around Proteins: Role of Bound Ions and Implications for Zeta-Potential. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:2283-2295. [PMID: 28181811 PMCID: PMC9831612 DOI: 10.1021/acs.langmuir.6b04430] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A new feature of the popular software DelPhi is developed and reported, allowing for computing the surface averaged electrostatic potential (SAEP) of macromolecules. The user is given the option to specify the distance from the van der Waals surface where the electrostatic potential will be outputted. In conjunction with DelPhiPKa and the BION server, the user can adjust the charges of titratable groups according to specific pH values, and add explicit ions bound to the macromolecular surface. This approach is applied to a set of four proteins with "experimentally" delivered zeta (ζ)-potentials at different pH values and salt concentrations. It has been demonstrated that the protocol is capable of predicting ζ-potentials in the case of proteins with relatively large net charges. This protocol has been less successful for proteins with low net charges. The work demonstrates that in the case of proteins with large net charges, the electrostatic potential should be collected at distances about 4 Å away from the vdW surface and explicit ions should be added at a binding energy cutoff larger than 1-2kT, in order to accurately predict ζ-potentials. The low salt conditions substantiate this effect of ions on SAEP.
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Affiliation(s)
- Arghya Chakravorty
- Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University , Clemson, South Carolina 29634, United States
| | - Zhe Jia
- Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University , Clemson, South Carolina 29634, United States
| | - Lin Li
- Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University , Clemson, South Carolina 29634, United States
| | - Emil Alexov
- Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University , Clemson, South Carolina 29634, United States
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16
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Stephens DC, Kim HM, Kumar A, Farahat AA, Boykin DW, Poon GM. Pharmacologic efficacy of PU.1 inhibition by heterocyclic dications: a mechanistic analysis. Nucleic Acids Res 2016; 44:4005-13. [PMID: 27079976 PMCID: PMC4872103 DOI: 10.1093/nar/gkw229] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 03/29/2016] [Indexed: 12/11/2022] Open
Abstract
Heterocyclic dications are receiving increasing attention as targeted inhibitors of transcription factors. While many dications act as purely competitive inhibitors, some fail to displace protein efficiently at drug concentrations expected to saturate their DNA target. To achieve a mechanistic understanding of these non-competitive effects, we used a combination of dications, which are intrinsically fluorescent and spectrally-separated fluorescently labeled DNA to dissect complex interactions in multi-component drug/DNA/protein systems. Specifically, we interrogated site-specific binding by the transcription factor PU.1 and its perturbation by DB270, a furan-bisbenzimidazole-diamidine that strongly targets PU.1 binding sites yet poorly inhibits PU.1/DNA complexes. By titrating DB270 and/or cyanine-labeled DNA with protein or unlabeled DNA, and following the changes in their fluorescence polarization, we found direct evidence that DB270 bound protein independently of their mutual affinities for sequence-specific DNA. Each of the three species competed for the other two, and this interplay of mutually dependent equilibria abrogated DB270's inhibitory activity, which was substantively restored under conditions that attenuated DB270/PU.1 binding. PU.1 binding was consistent with DB270's poor inhibitory efficacy of PU.1 in vivo, while its isosteric selenophene analog (DB1976), which did not bind PU.1 and strongly inhibited the PU.1/DNA complex in vitro, fully antagonized PU.1-dependent transactivation in vivo.
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Affiliation(s)
| | - Hye Mi Kim
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Arvind Kumar
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | | | - David W Boykin
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Gregory M Poon
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
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17
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He G, Tolic A, Bashkin JK, Poon GMK. Heterogeneous dynamics in DNA site discrimination by the structurally homologous DNA-binding domains of ETS-family transcription factors. Nucleic Acids Res 2015; 43:4322-31. [PMID: 25824951 PMCID: PMC4417174 DOI: 10.1093/nar/gkv267] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 03/05/2015] [Indexed: 01/09/2023] Open
Abstract
The ETS family of transcription factors exemplifies current uncertainty in how eukaryotic genetic regulators with overlapping DNA sequence preferences achieve target site specificity. PU.1 and Ets-1 represent archetypes for studying site discrimination by ETS proteins because their DNA-binding domains are the most divergent in sequence, yet they share remarkably superimposable DNA-bound structures. To gain insight into the contrasting thermodynamics and kinetics of DNA recognition by these two proteins, we investigated the structure and dynamics of site discrimination by their DNA-binding domains. Electrophoretic mobilities of complexes formed by the two homologs with circularly permuted binding sites showed significant dynamic differences only for DNA complexes of PU.1. Free solution measurements by dynamic light scattering showed PU.1 to be more dynamic than Ets-1; moreover, dynamic changes are strongly coupled to site discrimination by PU.1, but not Ets-1. Interrogation of the protein/DNA interface by DNA footprinting showed similar accessibility to dimethyl sulfate for PU.1/DNA and Ets-1/DNA complexes, indicating that the dynamics of PU.1/DNA complexes reside primarily outside that interface. An information-based analysis of the two homologs’ binding motifs suggests a role for dynamic coupling in PU.1's ability to enforce a more stringent sequence preference than Ets-1 and its proximal sequence homologs.
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Affiliation(s)
- Gaofei He
- Department of Chemistry and Biochemistry and Center for Nanoscience, University of Missouri - St. Louis, St. Louis, MO 63121, USA
| | - Ana Tolic
- College of Pharmacy, Washington State University, Spokane, WA 99210, USA
| | - James K Bashkin
- Department of Chemistry and Biochemistry and Center for Nanoscience, University of Missouri - St. Louis, St. Louis, MO 63121, USA
| | - Gregory M K Poon
- College of Pharmacy, Washington State University, Spokane, WA 99210, USA
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18
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Laughlin S, Wang S, Kumar A, Farahat AA, Boykin DW, Wilson WD. Resolution of mixed site DNA complexes with dimer-forming minor-groove binders by using electrospray ionization mass spectrometry: compound structure and DNA sequence effects. Chemistry 2015; 21:5528-39. [PMID: 25703690 PMCID: PMC4732565 DOI: 10.1002/chem.201406322] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Indexed: 12/18/2022]
Abstract
Small-molecule targeting of the DNA minor groove is a promising approach to modulate genomic processes necessary for normal cellular function. For instance, dicationic diamindines, a well-known class of minor groove binding compounds, have been shown to inhibit interactions of transcription factors binding to genomic DNA. The applications of these compounds could be significantly expanded if we understand sequence-specific recognition of DNA better and could use the information to design more sequence-specific compounds. Aside from polyamides, minor groove binders typically recognize DNA at A-tract or alternating AT base pair sites. Targeting sites with GC base pairs, referred to here as mixed base pair sequences, is much more difficult than those rich in AT base pairs. Compound 1 is the first dicationic diamidine reported to recognize a mixed base pair site. It binds in the minor groove of ATGA sequences as a dimer with positive cooperativity. Due to the well-characterized behavior of 1 with ATGA and AT rich sequences, it provides a paradigm for understanding the elements that are key for recognition of mixed sequence sites. Electrospray ionization mass spectrometry (ESI-MS) is a powerful method to screen DNA complexes formed by analogues of 1 for specific recognition. We also report a novel approach to determine patterns of recognition by 1 for cognate ATGA and ATGA-mutant sequences. We found that functional group modifications and mutating the DNA target site significantly affect binding and stacking, respectively. Both compound conformation and DNA sequence directionality are crucial for recognition.
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Affiliation(s)
- Sarah Laughlin
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303
| | - Siming Wang
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303
| | - Arvind Kumar
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303
| | - Abdelbasset A. Farahat
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt
| | - David W. Boykin
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303
| | - W. David Wilson
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303
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19
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Quantitative Investigation of Protein-Nucleic Acid Interactions by Biosensor Surface Plasmon Resonance. Methods Mol Biol 2015; 1334:313-32. [PMID: 26404159 DOI: 10.1007/978-1-4939-2877-4_20] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Biosensor-surface plasmon resonance (SPR) technology has emerged as a powerful label-free approach for the study of nucleic acid interactions in real time. The method provides simultaneous equilibrium and kinetic characterization for biomolecular interactions with low sample requirements and without the need for external probes. A detailed and practical guide for protein-DNA interaction analyses using biosensor-SPR methods is presented. Details of SPR technology and basic fundamentals are described with recommendations on the preparation of the SPR instrument, sensor chips and samples, experimental design, quantitative and qualitative data analyses and presentation. A specific example of the interaction of a transcription factor with DNA is provided with results evaluated by both kinetic and steady-state SPR methods.
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20
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Luo Y, North JA, Poirier MG. Single molecule fluorescence methodologies for investigating transcription factor binding kinetics to nucleosomes and DNA. Methods 2014; 70:108-18. [PMID: 25304387 DOI: 10.1016/j.ymeth.2014.09.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 09/03/2014] [Accepted: 09/30/2014] [Indexed: 11/20/2022] Open
Abstract
Site specific DNA binding complexes must bind their DNA target sites and then reside there for a sufficient amount of time for proper regulation of DNA processing including transcription, replication and DNA repair. In eukaryotes, the occupancy of DNA binding complexes at their target sites is regulated by chromatin structure and dynamics. Methodologies that probe both the binding and dissociation kinetics of DNA binding proteins with naked and nucleosomal DNA are essential for understanding the mechanisms by which these complexes function. Here, we describe single-molecule fluorescence methodologies for quantifying the binding and dissociation kinetics of transcription factors at a target site within DNA, nucleosomes and nucleosome arrays. This approach allowed for the unexpected observation that nucleosomes impact not only binding but also dissociation kinetics of transcription factors and is well-suited for the investigation of numerous DNA processing complexes that directly interact with DNA organized into chromatin.
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Affiliation(s)
- Yi Luo
- Department of Physics, The Ohio State University, Columbus, OH 43210-1117, United States; Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210-1117, United States
| | - Justin A North
- Department of Physics, The Ohio State University, Columbus, OH 43210-1117, United States
| | - Michael G Poirier
- Department of Physics, The Ohio State University, Columbus, OH 43210-1117, United States; Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210-1117, United States.
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21
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Wang S, Linde MH, Munde M, Carvalho VD, Wilson WD, Poon GMK. Mechanistic heterogeneity in site recognition by the structurally homologous DNA-binding domains of the ETS family transcription factors Ets-1 and PU.1. J Biol Chem 2014; 289:21605-16. [PMID: 24952944 DOI: 10.1074/jbc.m114.575340] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
ETS family transcription factors regulate diverse genes through binding at cognate DNA sites that overlap substantially in sequence. The DNA-binding domains of ETS proteins (ETS domains) are highly conserved structurally yet share limited amino acid homology. To define the mechanistic implications of sequence diversity within the ETS family, we characterized the thermodynamics and kinetics of DNA site recognition by the ETS domains of Ets-1 and PU.1, which represent the extremes in amino acid divergence among ETS proteins. Even though the two ETS domains bind their optimal sites with similar affinities under physiologic conditions, their nature of site recognition differs strikingly in terms of the role of hydration and counter ion release. The data suggest two distinct mechanisms wherein Ets-1 follows a "dry" mechanism that rapidly parses sites through electrostatic interactions and direct protein-DNA contacts, whereas PU.1 utilizes hydration to interrogate sequence-specific sites and form a long-lived complex relative to the Ets-1 counterpart. The kinetic persistence of the high affinity PU.1 · DNA complex may be relevant to an emerging role of PU.1, but not Ets-1, as a pioneer transcription factor in vivo. In addition, PU.1 activity is critical to the development and function of macrophages and lymphocytes, which present osmotically variable environments, and hydration-dependent specificity may represent an important regulatory mechanism in vivo, a hypothesis that finds support in gene expression profiles of primary murine macrophages.
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Affiliation(s)
- Shuo Wang
- From the Department of Chemistry, Georgia State University, Atlanta, Georgia 30303 and
| | - Miles H Linde
- the Department of Pharmaceutical Sciences, Washington State University, Spokane, Washington 99210-1495
| | - Manoj Munde
- From the Department of Chemistry, Georgia State University, Atlanta, Georgia 30303 and
| | - Victor D Carvalho
- the Department of Pharmaceutical Sciences, Washington State University, Spokane, Washington 99210-1495
| | - W David Wilson
- From the Department of Chemistry, Georgia State University, Atlanta, Georgia 30303 and
| | - Gregory M K Poon
- the Department of Pharmaceutical Sciences, Washington State University, Spokane, Washington 99210-1495
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22
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Munde M, Wang S, Kumar A, Stephens CE, Farahat AA, Boykin DW, Wilson WD, Poon GMK. Structure-dependent inhibition of the ETS-family transcription factor PU.1 by novel heterocyclic diamidines. Nucleic Acids Res 2013; 42:1379-90. [PMID: 24157839 PMCID: PMC3902942 DOI: 10.1093/nar/gkt955] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
ETS transcription factors mediate a wide array of cellular functions and are attractive targets for pharmacological control of gene regulation. We report the inhibition of the ETS-family member PU.1 with a panel of novel heterocyclic diamidines. These diamidines are derivatives of furamidine (DB75) in which the central furan has been replaced with selenophene and/or one or both of the bridging phenyl has been replaced with benzimidazole. Like all ETS proteins, PU.1 binds sequence specifically to 10-bp sites by inserting a recognition helix into the major groove of a 5′-GGAA-3′ consensus, accompanied by contacts with the flanking minor groove. We showed that diamidines target the minor groove of AT-rich sequences on one or both sides of the consensus and disrupt PU.1 binding. Although all of the diamidines bind to one or both of the expected sequences within the binding site, considerable heterogeneity exists in terms of stoichiometry, site–site interactions and induced DNA conformation. We also showed that these compounds accumulate in live cell nuclei and inhibit PU.1-dependent gene transactivation. This study demonstrates that heterocyclic diamidines are capable of inhibiting PU.1 by targeting the flanking sequences and supports future efforts to develop agents for inhibiting specific members of the ETS family.
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Affiliation(s)
- Manoj Munde
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA and Department of Pharmaceutical Sciences, Washington State University, Pullman, WA 99164-6534, USA
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