1
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Brennan A, Leech JT, Kad NM, Mason JM. An Approach to Derive Functional Peptide Inhibitors of Transcription Factor Activity. JACS AU 2022; 2:996-1006. [PMID: 35557753 PMCID: PMC9088798 DOI: 10.1021/jacsau.2c00105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/01/2022] [Accepted: 03/01/2022] [Indexed: 06/15/2023]
Abstract
We report the development of a high-throughput, intracellular "transcription block survival" (TBS) screening platform to derive functional transcription factor antagonists. TBS is demonstrated using the oncogenic transcriptional regulator cJun, with the development of antagonists that bind cJun and prevent both dimerization and, more importantly, DNA binding remaining a primary challenge. In TBS, cognate TRE sites are introduced into the coding region of the essential gene, dihydrofolate reductase (DHFR). Introduction of cJun leads to TRE binding, preventing DHFR expression by directly blocking RNA polymerase gene transcription to abrogate cell proliferation. Peptide library screening identified a sequence that both binds cJun and antagonizes function by preventing DNA binding, as demonstrated by restored cell viability and subsequent in vitro hit validation. TBS is an entirely tag-free genotype-to-phenotype approach, selecting desirable attributes such as high solubility, target specificity, and low toxicity within a complex cellular environment. TBS facilitates rapid library screening to accelerate the identification of therapeutically valuable sequences.
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Affiliation(s)
- Andrew Brennan
- Department
of Biology & Biochemistry, University
of Bath, Bath BA2 7AY, U.K.
| | - James T. Leech
- School
of Biosciences, University of Kent, Canterbury CT2 7NH, U.K.
| | - Neil M. Kad
- School
of Biosciences, University of Kent, Canterbury CT2 7NH, U.K.
| | - Jody M. Mason
- Department
of Biology & Biochemistry, University
of Bath, Bath BA2 7AY, U.K.
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2
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Rieu M, Krutyholowa R, Taylor NMI, Berry RM. A new class of biological ion-driven rotary molecular motors with 5:2 symmetry. Front Microbiol 2022; 13:948383. [PMID: 35992645 PMCID: PMC9389320 DOI: 10.3389/fmicb.2022.948383] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 07/04/2022] [Indexed: 11/15/2022] Open
Abstract
Several new structures of three types of protein complexes, obtained by cryo-electron microscopy (cryo-EM) and published between 2019 and 2021, identify a new family of natural molecular wheels, the "5:2 rotary motors." These span the cytoplasmic membranes of bacteria, and their rotation is driven by ion flow into the cell. They consist of a pentameric wheel encircling a dimeric axle within the cytoplasmic membrane of both Gram-positive and gram-negative bacteria. The axles extend into the periplasm, and the wheels extend into the cytoplasm. Rotation of these wheels has never been observed directly; it is inferred from the symmetry of the complexes and from the roles they play within the larger systems that they are known to power. In particular, the new structure of the stator complex of the Bacterial Flagellar Motor, MotA5B2, is consistent with a "wheels within wheels" model of the motor. Other 5:2 rotary motors are believed to share the core rotary function and mechanism, driven by ion-motive force at the cytoplasmic membrane. Their structures diverge in their periplasmic and cytoplasmic parts, reflecting the variety of roles that they perform. This review focuses on the structures of 5:2 rotary motors and their proposed mechanisms and functions. We also discuss molecular rotation in general and its relation to the rotational symmetry of molecular complexes.
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Affiliation(s)
- Martin Rieu
- Department of Physics, University of Oxford, Oxford, United Kingdom
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building University of Oxford, Oxford, United Kingdom
| | - Roscislaw Krutyholowa
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Nicholas M. I. Taylor
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
- Nicholas M. I. Taylor,
| | - Richard M. Berry
- Department of Physics, University of Oxford, Oxford, United Kingdom
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building University of Oxford, Oxford, United Kingdom
- *Correspondence: Richard M. Berry,
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3
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Fan F, Podar K. The Role of AP-1 Transcription Factors in Plasma Cell Biology and Multiple Myeloma Pathophysiology. Cancers (Basel) 2021; 13:2326. [PMID: 34066181 PMCID: PMC8151277 DOI: 10.3390/cancers13102326] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/02/2021] [Accepted: 05/06/2021] [Indexed: 12/19/2022] Open
Abstract
Multiple myeloma (MM) is an incurable hematologic malignancy characterized by the clonal expansion of malignant plasma cells within the bone marrow. Activator Protein-1 (AP-1) transcription factors (TFs), comprised of the JUN, FOS, ATF and MAF multigene families, are implicated in a plethora of physiologic processes and tumorigenesis including plasma cell differentiation and MM pathogenesis. Depending on the genetic background, the tumor stage, and cues of the tumor microenvironment, specific dimeric AP-1 complexes are formed. For example, AP-1 complexes containing Fra-1, Fra-2 and B-ATF play central roles in the transcriptional control of B cell development and plasma cell differentiation, while dysregulation of AP-1 family members c-Maf, c-Jun, and JunB is associated with MM cell proliferation, survival, drug resistance, bone marrow angiogenesis, and bone disease. The present review article summarizes our up-to-date knowledge on the role of AP-1 family members in plasma cell differentiation and MM pathophysiology. Moreover, it discusses novel, rationally derived approaches to therapeutically target AP-1 TFs, including protein-protein and protein-DNA binding inhibitors, epigenetic modifiers and natural products.
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Affiliation(s)
- Fengjuan Fan
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Avenue 1277, Wuhan 430022, China;
| | - Klaus Podar
- Department of Internal Medicine II, University Hospital Krems, Mitterweg 10, 3500 Krems an der Donau, Austria
- Molecular Oncology and Hematology Unit, Karl Landsteiner University of Health Sciences, Dr.-Karl-Dorrek-Strasse 30, 3500 Krems an der Donau, Austria
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4
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Inamoto I, Sheoran I, Popa SC, Hussain M, Shin JA. Combining Rational Design and Continuous Evolution on Minimalist Proteins That Target the E-box DNA Site. ACS Chem Biol 2021; 16:35-44. [PMID: 33370105 DOI: 10.1021/acschembio.0c00684] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Protein-based therapeutics are part of the next-generation arsenal of drugs being developed against proto-oncoprotein Myc. We designed protein MEF to mimic the basic region/helix-loop-helix/leucine zipper (bHLHZ) domain of Max and Myc, which bind to the E-box motif (enhancer box, CACGTG). To make MEF, we started with our rationally designed ME47, a hybrid of the Max basic region and E47 HLH, that effectively inhibited tumor growth in a mouse model of breast cancer. We used phage-assisted continuous evolution (PACE), which uncovered mutations at Arg12 that contact the DNA phosphodiester backbone. The Arg12 mutations improved ME47's stability. We replaced Cys29 with Ala to eliminate potential undesired disulfide formation and fused the designed FosW leucine zipper to mutated ME47 to increase the dimerization interface and E-box targeting activity. This "franken-protein" MEF comprises the Max basic region, E47 HLH, and FosW leucine zipper. Compared with ME47, MEF gives 2-fold stronger binding to E-box and 4-fold increased specificity for E-box over nonspecific DNA. The synergistic combination of rational design and PACE allowed us to make MEF and demonstrates the power and utility of our two-pronged approach toward development of promising protein drugs with robust structure and DNA-binding function.
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Affiliation(s)
- Ichiro Inamoto
- Department of Chemistry, University of Toronto, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada
| | - Inder Sheoran
- Department of Chemistry, University of Toronto, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada
| | - Serban C. Popa
- Department of Chemistry, University of Toronto, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada
| | - Montdher Hussain
- Department of Chemistry, University of Toronto, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada
| | - Jumi A. Shin
- Department of Chemistry, University of Toronto, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada
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5
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Brennan A, Leech JT, Kad NM, Mason JM. Selective antagonism of cJun for cancer therapy. J Exp Clin Cancer Res 2020; 39:184. [PMID: 32917236 PMCID: PMC7488417 DOI: 10.1186/s13046-020-01686-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 08/20/2020] [Indexed: 01/10/2023] Open
Abstract
The activator protein-1 (AP-1) family of transcription factors modulate a diverse range of cellular signalling pathways into outputs which can be oncogenic or anti-oncogenic. The transcription of relevant genes is controlled by the cellular context, and in particular by the dimeric composition of AP-1. Here, we describe the evidence linking cJun in particular to a range of cancers. This includes correlative studies of protein levels in patient tumour samples and mechanistic understanding of the role of cJun in cancer cell models. This develops an understanding of cJun as a focal point of cancer-altered signalling which has the potential for therapeutic antagonism. Significant work has produced a range of small molecules and peptides which have been summarised here and categorised according to the binding surface they target within the cJun-DNA complex. We highlight the importance of selectively targeting a single AP-1 family member to antagonise known oncogenic function and avoid antagonism of anti-oncogenic function.
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Affiliation(s)
- Andrew Brennan
- Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - James T Leech
- School of Biosciences, University of Kent, Canterbury, CT2 7NH, UK
| | - Neil M Kad
- School of Biosciences, University of Kent, Canterbury, CT2 7NH, UK
| | - Jody M Mason
- Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK.
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6
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Lee HS, Hua HS, Wang CH, Yu MC, Chen BC, Lin CH. Mycobacterium tuberculosis induces connective tissue growth factor expression through the TLR2-JNK-AP-1 pathway in human lung fibroblasts. FASEB J 2019; 33:12554-12564. [PMID: 31451010 DOI: 10.1096/fj.201900487r] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Mycobacterium tuberculosis (M.tb) infection in lung causes pulmonary fibrosis, which leads to the irreversible reduction of pulmonary function. Fibrotic protein connective tissue growth factor (CTGF) expression has been confirmed to play a crucial role in lung fibrosis. However, the underlying signal pathway and effect of M.tb on CTGF expression in human lung fibroblasts are unclear. Our results revaled that M.tb caused time- and concentration-dependent increases in CTGF expression in human lung fibroblasts. A mechanistic investigation revealed that M.tb induced CTGF expression through TLR2 but not TLR4. The promoter activity assay indicated that M.tb-induced CTGF activity was mainly controlled by the promoter region at -747 to -184 bp, which contained signal transducer and activator of transcription 3 and activator protein 1 (AP-1) binding sites. Moreover, curcumin (AP-1 inhibitor) restrained M.tb-induced CTGF expression. M.tb also induced increases in AP-1 luciferase activity and DNA binding activity of c-Jun and c-Fos on the CTGF promoter. Furthermore, the knockdown of c-Jun by small interfering RNA attenuated M.tb-induced CTGF expression and AP-1 luciferase activity. A JNK inhibitor (SP600125) and a JNK dominant-negative mutant suppressed M.tb-induced CTGF expression. We also discovered that M.tb could induce the phosphorylation of JNK and c-Jun. Furthermore, SP600125 inhibited M.tb-induced c-Jun phosphorylation and AP-1- luciferase activity. M.tb-induced fibronectin expression was inhibited by anti-CTGF antibody. These results demonstrate that M.tb is activated through TLR2 to induce JNK activation, further increasing the DNA binding activity of c-Jun and c-Fos and finally inducing CTGF expression and extracellular matrix production.-Lee, H.-S., Hua, H.-S., Wang, C.-H., Yu, M.-C., Chen, B.-C., Lin, C.-H. Mycobacterium tuberculosis induces connective tissue growth factor expression through the TLR2-JNK-AP-1 pathway in human lung fibroblasts.
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Affiliation(s)
- Hong-Sheng Lee
- Graduate Institute of Medical Sciences, Taipei Medical University, Taipei, Taiwan
| | - Hung-Sheng Hua
- Graduate Institute of Medical Sciences, Taipei Medical University, Taipei, Taiwan
| | - Cheng-Hui Wang
- Department of Laboratory Medicine, Wanfang Hospital, Taipei Medical University, Taipei, Taiwan.,Pulmonary Research Center, Wanfang Hospital, Taipei Medical University, Taipei, Taiwan
| | - Ming-Chih Yu
- Pulmonary Research Center, Wanfang Hospital, Taipei Medical University, Taipei, Taiwan.,School of Respiratory Therapy, Taipei Medical University, Taipei, Taiwan.,Division of Pulmonary Medicine, Department of Internal Medicine, Wanfang Hospital, Taipei Medical University, Taipei, Taiwan
| | - Bing-Chang Chen
- School of Respiratory Therapy, Taipei Medical University, Taipei, Taiwan.,Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Chien-Huang Lin
- Graduate Institute of Medical Sciences, Taipei Medical University, Taipei, Taiwan
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7
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Lathbridge A, Mason JM. Combining Constrained Heptapeptide Cassettes with Computational Design To Create Coiled-Coil Targeting Helical Peptides. ACS Chem Biol 2019; 14:1293-1304. [PMID: 31117396 DOI: 10.1021/acschembio.9b00265] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A total of 32 heptapeptides have been synthesized and characterized to establish the effect of K → D (i → i + 4) lactamization upon their ability to adopt a helical conformation. Because most parallel and dimeric coiled-coil sequences can be deconvoluted into gabcdef repeats, we have introduced fixed solvent exposed b → f (K → D) constraints into this design scaffold. Interfacial " a" hydrophobic (L/I/V/N) and " e/g" electrostatic (E/K) options (4 × 2 × 2 = 16 cassettes) were introduced as core drivers of coiled-coil stability and specificity. All present as random coils when linear but adopt a helical conformation upon lactamization. Helicity varied in magnitude from 34 to 68%, indicating different levels of constraint tolerance within the context of a sequence required to be helical for function. Using the oncogenic transcription factor cJun as an exemplar, we next utilized our bCIPA coiled-coil screening engine to select four cassettes of highest predicted affinity when paired with four gabcdef cassettes within the full-length cJun target counterpart (164 = 65 536 combinations). This information was coupled with observed helicity for each constrained cassette to select for the best balance of predicted affinity when linear and experimentally validated helicity when constrained. As a control, the same approach was taken using cassettes of high predicted target affinity but with lower experimentally validated helicity. The approach provides a novel platform of modular heptapeptide cassettes experimentally validated and separated by helical content. Appropriate cassettes can be selected and conjugated to produce longer peptides, in which constraints impart appropriate helicity such that a wide range of targets can be engaged with high affinity and selectivity.
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8
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De Franceschi N, Miihkinen M, Hamidi H, Alanko J, Mai A, Picas L, Guzmán C, Lévy D, Mattjus P, Goult BT, Goud B, Ivaska J. ProLIF - quantitative integrin protein-protein interactions and synergistic membrane effects on proteoliposomes. J Cell Sci 2018; 132:jcs.214270. [PMID: 30072441 DOI: 10.1242/jcs.214270] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 07/07/2018] [Indexed: 01/23/2023] Open
Abstract
Integrin transmembrane receptors control a wide range of biological interactions by triggering the assembly of large multiprotein complexes at their cytoplasmic interface. Diverse methods have been used to investigate interactions between integrins and intracellular proteins, and predominantly include peptide-based pulldowns and biochemical immuno-isolations from detergent-solubilised cell lysates. However, quantitative methods to probe integrin-protein interactions in a more biologically relevant context where the integrin is embedded within a lipid bilayer have been lacking. Here, we describe 'protein-liposome interactions by flow cytometry' (denoted ProLIF), a technique to reconstitute recombinant integrin transmembrane domains (TMDs) and cytoplasmic tail (CT) fragments in liposomes as individual subunits or as αβ heterodimers and, via flow cytometry, allow rapid and quantitative measurement of protein interactions with these membrane-embedded integrins. Importantly, the assay can analyse binding of fluorescent proteins directly from cell lysates without further purification steps. Moreover, the effect of membrane composition, such as PI(4,5)P2 incorporation, on protein recruitment to the integrin CTs can be analysed. ProLIF requires no specific instrumentation and can be applied to measure a broad range of membrane-dependent protein-protein interactions with the potential for high-throughput/multiplex analyses.This article has associated First Person interviews with the first authors of the paper (see doi: 10.1242/jcs.223644 and doi: 10.1242/jcs.223719).
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Affiliation(s)
- Nicola De Franceschi
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, 20520 Turku, Finland.,Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR 168, 75005 Paris, France.,Sorbonne Universités, UPMC, 75005 Paris, France
| | - Mitro Miihkinen
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | - Hellyeh Hamidi
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | - Jonna Alanko
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | - Anja Mai
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | - Laura Picas
- Institut Curie, PSL Research University, UMR 168, Centre de Recherche, 75248 Paris, France
| | - Camilo Guzmán
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | - Daniel Lévy
- Institut Curie, PSL Research University, UMR 168, Centre de Recherche, 75248 Paris, France
| | - Peter Mattjus
- Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland
| | - Benjamin T Goult
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
| | - Bruno Goud
- Institut Curie, PSL Research University, UMR 168, Centre de Recherche, 75248 Paris, France
| | - Johanna Ivaska
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, 20520 Turku, Finland .,Department of Biochemistry, University of Turku, 20520 Turku, Finland
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9
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Baxter D, Ullman CG, Frigotto L, Mason JM. Exploiting Overlapping Advantages of In Vitro and In Cellulo Selection Systems to Isolate a Novel High-Affinity cJun Antagonist. ACS Chem Biol 2017; 12:2579-2588. [PMID: 28880076 DOI: 10.1021/acschembio.7b00693] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We have combined two peptide library-screening systems, exploiting the benefits offered by both to select novel antagonistic agents of cJun. CIS display is an in vitro cell-free system that allows very large libraries (≤1014) to be interrogated. However, affinity-based screening conditions can poorly reflect those relevant to therapeutic application, particularly for difficult intracellular targets, and can lead to false positives. In contrast, an in cellulo screening system such as the Protein-fragment Complementation Assay (PCA) selects peptides with high target affinity while additionally profiling for target specificity, protease resistance, solubility, and lack of toxicity in a more relevant context. A disadvantage is the necessity to transform cells, limiting library sizes that can be screened to ≤106. However, by combining both cell-free and cell-based systems, we isolated a peptide (CPW) from a ∼1010 member library, which forms a highly stable interaction with cJun (Tm = 63 °C, Kd = 750 nM, ΔG = -8.2 kcal/mol) using the oncogenic transcriptional regulator Activator Protein-1 (AP-1) as our exemplar target. In contrast, CIS display alone selected a peptide with low affinity for cJun (Tm = 34 °C, Kd = 25 μM, ΔG = -6.2 kcal/mol), highlighting the benefit of CIS → PCA. Furthermore, increased library size with CIS → PCA vs PCA alone allows the freedom to introduce noncanonical options, such as interfacial aromatics, and solvent exposed options that may allow the molecule to explore alternative structures and interact with greater affinity and efficacy with the target. CIS → PCA therefore offers significant potential as a peptide-library screening platform by synergistically combining the relative attributes of both assays to generate therapeutically interesting compounds that may otherwise not be identified.
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Affiliation(s)
- Daniel Baxter
- Dept
of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
- Isogenica Ltd., Chesterford Research
Park, Little Chesterford, Essex CB10 1XL, United Kingdom
| | - Christopher G. Ullman
- Isogenica Ltd., Chesterford Research
Park, Little Chesterford, Essex CB10 1XL, United Kingdom
| | - Laura Frigotto
- Isogenica Ltd., Chesterford Research
Park, Little Chesterford, Essex CB10 1XL, United Kingdom
| | - Jody M. Mason
- Dept
of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
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10
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Baxter D, Perry SR, Hill TA, Kok WM, Zaccai NR, Brady RL, Fairlie DP, Mason JM. Downsizing Proto-oncogene cFos to Short Helix-Constrained Peptides That Bind Jun. ACS Chem Biol 2017. [PMID: 28636317 DOI: 10.1021/acschembio.7b00303] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The oncogenic transcription factor activator protein-1 (AP-1) is a DNA-binding protein that assembles through dimerization of Fos and Jun protein subunits, their leucine-rich helical sequences entwining into a coiled-coil structure. This study reports on downsizing the proto-oncogene cFos protein (380 residues) to shorter peptides (37-25 residues) modified with helix-inducing constraints to enhance binding to Jun. A crystal structure is reported for a 37-residue Fos-derived peptide (FosW) bound to Jun. This guided iterative downsizing of FosW to shorter peptide sequences that were constrained into stable water-soluble α-helices by connecting amino acid side chains to form cyclic pentapeptide components. Structural integrity in the presence and absence of Jun was assessed by circular dichroism spectroscopy, while the thermodynamics of binding to cFos was measured by isothermal titration calorimetry. A 25-residue constrained peptide, one-third shorter yet 25% more helical than the structurally characterized 37-residue Fos-derived peptide, retained 80% of the binding free energy as a result of preorganization in a Jun-binding helix conformation, with the entropy gain (TΔS = +3.2 kcal/mol) compensating for the enthalpy loss. Attaching a cell-penetrating peptide (TAT48-57) and a nuclear localization signal (SV40) promoted cell uptake, localization to the nucleus, and inhibition of the proliferation of two breast cancer cell lines.
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Affiliation(s)
- Daniel Baxter
- Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, U.K
| | - Samuel R. Perry
- Division
of Chemistry and Structural Biology, Australian Research Council Centre
of Excellence in Advanced Molecular Imaging, Institute for Molecular
Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Timothy A. Hill
- Division
of Chemistry and Structural Biology, Australian Research Council Centre
of Excellence in Advanced Molecular Imaging, Institute for Molecular
Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
| | - W. Mei Kok
- Division
of Chemistry and Structural Biology, Australian Research Council Centre
of Excellence in Advanced Molecular Imaging, Institute for Molecular
Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Nathan R. Zaccai
- School
of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, U.K
| | - R. Leo Brady
- School
of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, U.K
| | - David P. Fairlie
- Division
of Chemistry and Structural Biology, Australian Research Council Centre
of Excellence in Advanced Molecular Imaging, Institute for Molecular
Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Jody M. Mason
- Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, U.K
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11
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Non-covalent modification of granulocyte-colony stimulating factor (G-CSF) by coiled-coil technology. Int J Pharm 2016; 511:98-103. [PMID: 27363936 DOI: 10.1016/j.ijpharm.2016.06.122] [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: 03/30/2016] [Revised: 06/21/2016] [Accepted: 06/26/2016] [Indexed: 11/21/2022]
Abstract
We present here an approach to non-covalently combine an engineered model protein with a PEGylated peptide via coiled-coil binding. To this end a fusion protein of G-CSF and the peptide sequence (JunB) was created-one sequence of JunB was expressed at the N-terminal of GCSF. JunB is able to bind to the peptide sequence cFos, which was in turn covalently linked to a chain of poly(ethylene glycol) (PEG). The selected peptide sequences are leucine zipper motives from transcription factors and are known to bind to each other specifically by formation of a super secondary structure called coiled-coil. The binding between PEGylated peptides of various molecular weights and the modified protein was assessed by isothermal calorimetry (ITC), dynamic light scattering (DLS), circular dichroism (CD), and fluorescence anisotropy. Our findings show that the attachment of 2 and 5kDa PEG does not interfere with coiled-coil formation and thus binding of peptide to fusion protein. With this work we successfully demonstrate the non-covalent binding of a model moiety (PEG) to a protein through coiled-coil interaction.
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12
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Rezaei Araghi R, Keating AE. Designing helical peptide inhibitors of protein-protein interactions. Curr Opin Struct Biol 2016; 39:27-38. [PMID: 27123812 DOI: 10.1016/j.sbi.2016.04.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 03/28/2016] [Accepted: 04/03/2016] [Indexed: 02/04/2023]
Abstract
Short helical peptides combine characteristics of small molecules and large proteins and provide an exciting area of opportunity in protein design. A growing number of studies report novel helical peptide inhibitors of protein-protein interactions. New techniques have been developed for peptide design and for chemically stabilizing peptides in a helical conformation, which frequently improves protease resistance and cell permeability. We summarize advances in peptide crosslinking chemistry and give examples of peptide design studies targeting coiled-coil transcription factors, Bcl-2 family proteins, MDM2/MDMX, and HIV gp41, among other targets.
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Affiliation(s)
- Raheleh Rezaei Araghi
- MIT Department of Biology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Amy E Keating
- MIT Department of Biology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States; MIT Department of Biological Engineering, 77 Massachusetts Avenue, Cambridge, MA 02139, United States.
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13
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Pazos E, Portela C, Penas C, Vázquez ME, Mascareñas JL. Peptide-DNA conjugates as tailored bivalent binders of the oncoprotein c-Jun. Org Biomol Chem 2016; 13:5385-90. [PMID: 25778494 DOI: 10.1039/c5ob00318k] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
We describe a ds-oligonucleotide-peptide conjugate that is able to efficiently dismount preformed DNA complexes of the bZIP regions of oncoproteins c-Fos and c-Jun (AP-1), and therefore might be useful as disrupters of AP-1-mediated gene expression pathways.
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Affiliation(s)
- Elena Pazos
- Departamento de Química Orgánica and Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Universidade de Santiago de Compostela, C/Jenaro de la Fuente s/n, Campus Vida, 15782 Santiago de Compostela, Spain.
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14
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Lin CH, Shih CH, Tseng CC, Yu CC, Tsai YJ, Bien MY, Chen BC. CXCL12 induces connective tissue growth factor expression in human lung fibroblasts through the Rac1/ERK, JNK, and AP-1 pathways. PLoS One 2014; 9:e104746. [PMID: 25121739 PMCID: PMC4133236 DOI: 10.1371/journal.pone.0104746] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 07/01/2014] [Indexed: 01/31/2023] Open
Abstract
CXCL12 (stromal cell-derived factor-1, SDF-1) is a potent chemokine for homing of CXCR4+ fibrocytes to injury sites of lung tissue, which contributes to pulmonary fibrosis. Overexpression of connective tissue growth factor (CTGF) plays a critical role in pulmonary fibrosis. In this study, we investigated the roles of Rac1, extracellular signal-regulated kinase (ERK), c-Jun N-terminal kinase (JNK), and activator protein-1 (AP-1) in CXCL12-induced CTGF expression in human lung fibroblasts. CXCL12 caused concentration- and time-dependent increases in CTGF expression and CTGF-luciferase activity. CXCL12-induced CTGF expression was inhibited by a CXCR4 antagonist (AMD3100), small interfering RNA of CXCR4 (CXCR4 siRNA), a dominant negative mutant of Rac1 (RacN17), a mitogen-activated protein kinase (MAPK) kinase (MEK) inhibitor (PD98059), a JNK inhibitor (SP600125), a p21-activated kinase inhibitor (PAK18), c-Jun siRNA, and an AP-1 inhibitor (curcumin). Treatment of cells with CXCL12 caused activations of Rac1, Rho, ERK, and c-Jun. The CXCL12-induced increase in ERK phosphorylation was inhibited by RacN17. Treatment of cells with PD98059 and SP600125 both inhibited CXCL12-induced c-Jun phosphorylation. CXCL12 caused the recruitment of c-Jun and c-Fos binding to the CTGF promoter. Furthermore, CXCL12 induced an increase in α-smooth muscle actin (α-SMA) expression, a myofibroblastic phenotype, and actin stress fiber formation. CXCL12-induced actin stress fiber formation and α-SMA expression were respectively inhibited by AMD3100 and CTGF siRNA. Taken together, our results suggest that CXCL12, acting through CXCR4, activates the Rac/ERK and JNK signaling pathways, which in turn initiates c-Jun phosphorylation, and recruits c-Jun and c-Fos to the CTGF promoter and ultimately induces CTGF expression in human lung fibroblasts. Moreover, overexpression of CTGF mediates CXCL12-induced α-SMA expression.
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Affiliation(s)
- Chien-Huang Lin
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Chung-Huang Shih
- School of Respiratory Therapy, College of Medicine, Taipei Medical University, Taipei, Taiwan
- Division of Pulmonary Medicine, Department of Internal Medicine, Taipei Medical University Hospital, Taipei, Taiwan
| | - Chih-Chieh Tseng
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Chung-Chi Yu
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Yuan-Jhih Tsai
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Mauo-Ying Bien
- School of Respiratory Therapy, College of Medicine, Taipei Medical University, Taipei, Taiwan
- Division of Pulmonary Medicine, Department of Internal Medicine, Taipei Medical University Hospital, Taipei, Taiwan
| | - Bing-Chang Chen
- School of Respiratory Therapy, College of Medicine, Taipei Medical University, Taipei, Taiwan
- * E-mail:
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Lin CH, Yu MC, Tung WH, Chen TT, Yu CC, Weng CM, Tsai YJ, Bai KJ, Hong CY, Chien MH, Chen BC. Connective tissue growth factor induces collagen I expression in human lung fibroblasts through the Rac1/MLK3/JNK/AP-1 pathway. BIOCHIMICA ET BIOPHYSICA ACTA 2013; 1833:2823-2833. [PMID: 23906792 DOI: 10.1016/j.bbamcr.2013.07.016] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Revised: 07/03/2013] [Accepted: 07/17/2013] [Indexed: 01/05/2023]
Abstract
Connective tissue growth factor (CTGF) plays an important role in lung fibrosis. In this study, we investigated the role of Rac1, mixed-lineage kinase 3 (MLK3), c-Jun N-terminal kinase (JNK), and activator protein-1 (AP-1) in CTGF-induced collagen I expression in human lung fibroblasts. CTGF caused concentration- and time-dependent increases in collagen I expression. CTGF-induced collagen I expression was inhibited by the dominant negative mutant (DN) of Rac1 (RacN17), MLK3DN, MLK3 inhibitor (K252a), JNK1DN, JNK2DN, a JNK inhibitor (SP600125), and an AP-1 inhibitor (curcumin). Treatment of cells with CTGF caused activation of Rac1, MLK3, JNK, and AP-1. The CTGF-induced increase in MLK3 phosphorylation was inhibited by RacN17. Treatment with RacN17 and the MLK3DN inhibited CTGF-induced JNK phosphorylation. CTGF caused increases in c-Jun phosphorylation and the recruitment of c-Jun and c-Fos to the collagen I promoter. Furthermore, stimulation of cells with the CTGF resulted in increases in AP-1-luciferase activity; this effect was inhibited by Rac1N17, MLK3DN, JNK1DN, and JNK2DN. Moreover, CTGF-induced α-smooth muscle actin (α-SMA) expression was inhibited by the procollagen I small interfering RNA (siRNA). These results suggest for the first time that CTGF acting through Rac1 activates the MLK3/JNK signaling pathway, which in turn initiates AP-1 activation and recruitment of c-Jun and c-Fos to the collagen I promoter and ultimately induces collagen I expression in human lung fibroblasts.
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Affiliation(s)
- Chien-Huang Lin
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Ming-Chih Yu
- Department of Pulmonary Medicine, Taipei Medical University - Wanfang Hospital, Taipei, Taiwan; School of Respiratory Therapy, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Wan-Hsuan Tung
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Tzu-Ting Chen
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Chung-Chi Yu
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Chih-Ming Weng
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Yan-Jyu Tsai
- Department of Pharmacology, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Kua-Jen Bai
- Department of Pulmonary Medicine, Taipei Medical University - Wanfang Hospital, Taipei, Taiwan; School of Respiratory Therapy, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Chuang-Ye Hong
- Taipei Medical University Wangfang Hospital, Taipei, Taiwan
| | - Ming-Hsien Chien
- Taipei Medical University Wangfang Hospital, Taipei, Taiwan; Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Bing-Chang Chen
- School of Respiratory Therapy, College of Medicine, Taipei Medical University, Taipei, Taiwan.
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16
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De Jong AT. Effect of flanking bases on the DNA specificity of EmBP-1. Biochemistry 2013; 52:786-94. [PMID: 23305409 DOI: 10.1021/bi301404h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
EmBP-1 is a basic region leucine zipper (bZIP) protein found in many types of plants. In general, plant bZIP proteins bind selectively to DNA sequences containing ACGT core sequences with different immediate flanking nucleotides preferred by different proteins. I report that the distant flanking sequence also has a strong effect on the preference of EmBP-1 for internal bases and determine the residue governing this effect. EmBP-1 binds selectively to the 10 bp gcG-box palindrome GCCACGTGGC 18-fold more tightly than the gcC-box GTGACGTCAC, but when the outer flanking G/C residues were changed to A/T (i.e., ACCACGTGGT and ATGACGTCAT), an only 1.2-fold preference for G-box binding was observed. Analysis of a series of single-residue alanine mutants of EmBP-1 revealed that this effect is mediated by arginine 10. Mutation of this residue to alanine greatly reduces the affinity for the gcG-box while leaving the affinity for other sequences relatively unchanged. Partial retention of G-box specificity upon mutation of R10 to lysine indicates that the effect is reliant on the basic nature of the residue. Additional studies with other EmBP-1 protein mutants and with oligonucleotides containing the T/A and C/G flanking sequences demonstrate the complexity of the protein-DNA interaction and demonstrate that the mechanism of sequence selective DNA binding is highly dependent on the flanking sequence.
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Affiliation(s)
- Antonia T De Jong
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada.
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Zuo Z, Gandhi NS, Arndt KM, Mancera RL. Free energy calculations of the interactions of c-Jun-based synthetic peptides with the c-Fos protein. Biopolymers 2012; 97:899-909. [DOI: 10.1002/bip.22099] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Chen G, De Jong AT, Shin JA. Forced homodimerization of the c-Fos leucine zipper in designed bHLHZ-like hybrid proteins MaxbHLH-Fos and ArntbHLH-Fos. MOLECULAR BIOSYSTEMS 2012; 8:1286-96. [DOI: 10.1039/c2mb05354c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Crooks RO, Rao T, Mason JM. Truncation, randomization, and selection: generation of a reduced length c-Jun antagonist that retains high interaction stability. J Biol Chem 2011; 286:29470-9. [PMID: 21697091 PMCID: PMC3190987 DOI: 10.1074/jbc.m111.221267] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The DNA binding activity of the transcriptional regulator activator protein-1 shows considerable promise as a target in cancer therapy. A number of different strategies have been employed to inhibit the function of this protein with promise having been demonstrated both in vitro and in vivo. Peptide-based therapeutics have received renewed interest in the last few years, and a number of 37-amino acid peptides capable of binding to the coiled coil dimerization domain of Jun and Fos have been derived. Here, we demonstrate how truncation and semi-rational library design, followed by protein-fragment complementation, can be used to produce a leucine zipper binding peptide by iterative means. To this end, we have implemented this strategy on the FosW peptide to produce 4hFosW. This peptide is truncated by four residues with comparably favorable binding properties and demonstrates the possibility to design progressively shorter peptides to serve as leucine zipper antagonists while retaining many of the key features of the parent peptide. Whether or not the necessity for low molecular weight antagonists is required from the perspective of druggability and efficacy is subject to debate. However, antagonists of reduced length are worthy of perusal from the point of view of synthetic cost as well as identifying the smallest functional unit that is required for binding.
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Affiliation(s)
- Richard O Crooks
- Department of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, United Kingdom
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