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Rizvi SMD, Almazni IA, Moawadh MS, Alharbi ZM, Helmi N, Alqahtani LS, Hussain T, Alafnan A, Moin A, Elkhalifa AO, Awadelkareem AM, Khalid M, Tiwari RK. Targeting NF-κB signaling cascades of glioblastoma by a natural benzophenone, garcinol, via in vitro and molecular docking approaches. Front Chem 2024; 12:1352009. [PMID: 38435669 PMCID: PMC10904546 DOI: 10.3389/fchem.2024.1352009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 01/03/2024] [Indexed: 03/05/2024] Open
Abstract
Glioblastoma multiforme (GBM) is regarded as the most aggressive form of brain tumor delineated by high cellular heterogeneity; it is resistant to conventional therapeutic regimens. In this study, the anti-cancer potential of garcinol, a naturally derived benzophenone, was assessed against GBM. During the analysis, we observed a reduction in the viability of rat glioblastoma C6 cells at a concentration of 30 µM of the extract (p < 0.001). Exposure to garcinol also induced nuclear fragmentation and condensation, as evidenced by DAPI-stained photomicrographs of C6 cells. The dissipation of mitochondrial membrane potential in a dose-dependent fashion was linked to the activation of caspases. Furthermore, it was observed that garcinol mediated the inhibition of NF-κB (p < 0.001) and decreased the expression of genes associated with cell survival (Bcl-XL, Bcl-2, and survivin) and proliferation (cyclin D1). Moreover, garcinol showed interaction with NF-κB through some important amino acid residues, such as Pro275, Trp258, Glu225, and Gly259 during molecular docking analysis. Comparative analysis with positive control (temozolomide) was also performed. We found that garcinol induced apoptotic cell death via inhibiting NF-κB activity in C6 cells, thus implicating it as a plausible therapeutic agent for GBM.
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Affiliation(s)
- Syed Mohd Danish Rizvi
- Department of Pharmaceutics, College of Pharmacy, University of Ha’il, Ha’il, Saudi Arabia
| | - Ibrahim A. Almazni
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran, Saudi Arabia
| | - Mamdoh S. Moawadh
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk, Saudi Arabia
| | - Zeyad M. Alharbi
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk, Saudi Arabia
| | - Nawal Helmi
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Leena S. Alqahtani
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Talib Hussain
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Ha’il, Ha’il, Saudi Arabia
| | - Ahmed Alafnan
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Ha’il, Ha’il, Saudi Arabia
| | - Afrasim Moin
- Department of Pharmaceutics, College of Pharmacy, University of Ha’il, Ha’il, Saudi Arabia
| | - AbdElmoneim O. Elkhalifa
- Department of Clinical Nutrition, College of Applied Medical Sciences, University of Hail, Ha’il, Saudi Arabia
| | - Amir Mahgoub Awadelkareem
- Department of Clinical Nutrition, College of Applied Medical Sciences, University of Hail, Ha’il, Saudi Arabia
| | - Mohammad Khalid
- Department of Pharmacognosy, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Rohit Kumar Tiwari
- Department of Clinical Research, Sharda School of Allied Health Sciences, Sharda University, Gautam Budh Nagar, India
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2
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Xu MH, Wang CF, Liu YT, Cui QL. Co(II) coordination polymer: Treatment activity on the chronic obstructive pulmonary disease by reducing the inflammatory cytokines releasing. MAIN GROUP CHEMISTRY 2021. [DOI: 10.3233/mgc-210005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
In the current study, using a semi-flexible quadritopic N-donor ligand, 5,5′-bipyrimidine (bpym), a new azide-based coordination polymer, [Co(bpym)(N3)2]n (1), was synthesized and structurally characterized via the single crystal X-ray diffraction along with the elemental analysis. Its treatment activity on the chronic obstructive pulmonary disease (COPD) would be evaluated and the related mechanism was explored. Firstly, the ELISA (enzyme linked immunosorbent assay) detection assay was performed and the levels of the inflammatory cytokines were measured. In addition to this, the NF-κB signaling pathway activation in the lung epithelial cells was measured with the real time RT-PCR (reverse transcription-polymerase chain reaction). Both six-membered rings containing nitrogen and the azide group on the designed drug molecule were confirmed by molecular docking simulation to have activities to the NF-kappaB.
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Affiliation(s)
- Mei-Hua Xu
- Department of Pharmacy, Traditional Chinese Medical Hospital of Huangdao District, Qingdao, Shandong, China
| | - Cui-Feng Wang
- Department of Pulmonary Diseases, Huangdao District Chinese Medicine Hospital, Qingdao, Shandong, China
| | - Yan-Tao Liu
- Qingdao Center for Disease Control and Prevention, Qingdao, Shandong, China
| | - Qiu-Lian Cui
- Department of Health Management, Chinese Medicine Hospital of Huangdao District, Qingdao, Shandong, China
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3
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Mulero MC, Wang VYF, Huxford T, Ghosh G. Genome reading by the NF-κB transcription factors. Nucleic Acids Res 2019; 47:9967-9989. [PMID: 31501881 PMCID: PMC6821244 DOI: 10.1093/nar/gkz739] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 08/05/2019] [Accepted: 08/21/2019] [Indexed: 12/25/2022] Open
Abstract
The NF-κB family of dimeric transcription factors regulates transcription by selectively binding to DNA response elements present within promoters or enhancers of target genes. The DNA response elements, collectively known as κB sites or κB DNA, share the consensus 5'-GGGRNNNYCC-3' (where R, Y and N are purine, pyrimidine and any nucleotide base, respectively). In addition, several DNA sequences that deviate significantly from the consensus have been shown to accommodate binding by NF-κB dimers. X-ray crystal structures of NF-κB in complex with diverse κB DNA have helped elucidate the chemical principles that underlie target selection in vitro. However, NF-κB dimers encounter additional impediments to selective DNA binding in vivo. Work carried out during the past decades has identified some of the barriers to sequence selective DNA target binding within the context of chromatin and suggests possible mechanisms by which NF-κB might overcome these obstacles. In this review, we first highlight structural features of NF-κB:DNA complexes and how distinctive features of NF-κB proteins and DNA sequences contribute to specific complex formation. We then discuss how native NF-κB dimers identify DNA binding targets in the nucleus with support from additional factors and how post-translational modifications enable NF-κB to selectively bind κB sites in vivo.
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Affiliation(s)
- Maria Carmen Mulero
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Vivien Ya-Fan Wang
- Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau SAR, China
| | - Tom Huxford
- Structural Biochemistry Laboratory, Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA
| | - Gourisankar Ghosh
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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4
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Mulero MC, Huxford T, Ghosh G. NF-κB, IκB, and IKK: Integral Components of Immune System Signaling. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1172:207-226. [PMID: 31628658 DOI: 10.1007/978-981-13-9367-9_10] [Citation(s) in RCA: 137] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The NF-κB (Nuclear Factor kappa B) transcription factor plays crucial roles in the regulation of numerous biological processes including development of the immune system, inflammation, and innate and adaptive immune responses. Control over the immune cell functions of NF-κB results from signaling through one of two different routes: the canonical and noncanonical NF-κB signaling pathways. Present at the end of both pathways are the proteins NF-κB, IκB, and the IκB kinase (IKK). These proteins work together to deliver the myriad outcomes that influence context-dependent transcriptional control in immune cells. In the present chapter, we review the structural information available on NF-κB, IκB, and IKK, the critical terminal components of the NF-κB signaling, in relation to their physiological function.
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Affiliation(s)
- Maria Carmen Mulero
- Department of Chemistry & Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Tom Huxford
- Structural Biochemistry Laboratory, Department of Chemistry & Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA
| | - Gourisankar Ghosh
- Department of Chemistry & Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
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Li N, Xin WY, Yao BR, Cong W, Wang CH, Hou GG. N-phenylsulfonyl-3,5-bis(arylidene)-4-piperidone derivatives as activation NF-κB inhibitors in hepatic carcinoma cell lines. Eur J Med Chem 2018; 155:531-544. [DOI: 10.1016/j.ejmech.2018.06.027] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 06/08/2018] [Accepted: 06/10/2018] [Indexed: 01/28/2023]
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6
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Ashkenazi S, Plotnikov A, Bahat A, Dikstein R. Effective cell-free drug screening protocol for protein-protein interaction. Anal Biochem 2017; 532:53-59. [PMID: 28579488 DOI: 10.1016/j.ab.2017.05.030] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Revised: 05/18/2017] [Accepted: 05/31/2017] [Indexed: 11/18/2022]
Abstract
Specific protein-protein interaction (PPI) is an essential feature of many cellular processes however, targeting these interactions by small molecules is highly challenging due to the nature of the interaction interface. Thus, screening for PPI inhibitors requires enormous number of compounds. Here we describe a simple and improved protocol designed for a search of direct PPI inhibitors. We engineered a bacterial expression system for the split-Renilla luciferase (RL) complementation assay that monitors PPI. This enables production of large quantities of the RL fusion proteins in a simple and cost effective manner that is suitable for very large screens. Subsequently, inhibitory compounds are analyzed in a similar complementation assay in living cultured mammalian cells to select for those that can penetrate cells. We applied this method to NF-κB, a family of dimeric transcription factors that plays central roles in immune responses, cell survival and aging, and its dysregulation is linked to many pathological states. This strategy led to the identification of several direct NF-κB inhibitors. As the described protocol is very straightforward and robust it may be suitable for many pairs of interacting proteins.
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Affiliation(s)
- Shaked Ashkenazi
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Alexander Plotnikov
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Anat Bahat
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Rivka Dikstein
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel.
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7
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The "Sticky Patch" Model of Crystallization and Modification of Proteins for Enhanced Crystallizability. Methods Mol Biol 2017; 1607:77-115. [PMID: 28573570 DOI: 10.1007/978-1-4939-7000-1_4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Crystallization of macromolecules has long been perceived as a stochastic process, which cannot be predicted or controlled. This is consistent with another popular notion that the interactions of molecules within the crystal, i.e., crystal contacts, are essentially random and devoid of specific physicochemical features. In contrast, functionally relevant surfaces, such as oligomerization interfaces and specific protein-protein interaction sites, are under evolutionary pressures so their amino acid composition, structure, and topology are distinct. However, current theoretical and experimental studies are significantly changing our understanding of the nature of crystallization. The increasingly popular "sticky patch" model, derived from soft matter physics, describes crystallization as a process driven by interactions between select, specific surface patches, with properties thermodynamically favorable for cohesive interactions. Independent support for this model comes from various sources including structural studies and bioinformatics. Proteins that are recalcitrant to crystallization can be modified for enhanced crystallizability through chemical or mutational modification of their surface to effectively engineer "sticky patches" which would drive crystallization. Here, we discuss the current state of knowledge of the relationship between the microscopic properties of the target macromolecule and its crystallizability, focusing on the "sticky patch" model. We discuss state-of-the-art in silico methods that evaluate the propensity of a given target protein to form crystals based on these relationships, with the objective to design variants with modified molecular surface properties and enhanced crystallization propensity. We illustrate this discussion with specific cases where these approaches allowed to generate crystals suitable for structural analysis.
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8
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A Novel Allosteric Mechanism of NF-κB Dimerization and DNA Binding Targeted by an Anti-Inflammatory Drug. Mol Cell Biol 2016; 36:1237-47. [PMID: 26830231 DOI: 10.1128/mcb.00895-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 01/25/2016] [Indexed: 11/20/2022] Open
Abstract
The NF-κB family plays key roles in immune and stress responses, and its deregulation contributes to several diseases. Therefore its modulation has become an important therapeutic target. Here, we used a high-throughput screen for small molecules that directly inhibit dimerization of the NF-κB protein p65. One of the identified inhibitors is withaferin A (WFA), a documented anticancer and anti-inflammatory compound. Computational modeling suggests that WFA contacts the dimerization interface on one subunit and surface residues E285 and Q287 on the other. Despite their locations far from the dimerization site, E285 and Q287 substitutions diminished both dimerization and the WFA effect. Further investigation revealed that their effects on dimerization are associated with their proximity to a conserved hydrophobic core domain (HCD) that is crucial for dimerization and DNA binding. Our findings established NF-κB dimerization as a drug target and uncovered an allosteric domain as a target of WFA action.
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9
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Csizmok V, Follis AV, Kriwacki RW, Forman-Kay JD. Dynamic Protein Interaction Networks and New Structural Paradigms in Signaling. Chem Rev 2016; 116:6424-62. [PMID: 26922996 DOI: 10.1021/acs.chemrev.5b00548] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Understanding signaling and other complex biological processes requires elucidating the critical roles of intrinsically disordered proteins (IDPs) and regions (IDRs), which represent ∼30% of the proteome and enable unique regulatory mechanisms. In this review, we describe the structural heterogeneity of disordered proteins that underpins these mechanisms and the latest progress in obtaining structural descriptions of conformational ensembles of disordered proteins that are needed for linking structure and dynamics to function. We describe the diverse interactions of IDPs that can have unusual characteristics such as "ultrasensitivity" and "regulated folding and unfolding". We also summarize the mounting data showing that large-scale assembly and protein phase separation occurs within a variety of signaling complexes and cellular structures. In addition, we discuss efforts to therapeutically target disordered proteins with small molecules. Overall, we interpret the remodeling of disordered state ensembles due to binding and post-translational modifications within an expanded framework for allostery that provides significant insights into how disordered proteins transmit biological information.
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Affiliation(s)
- Veronika Csizmok
- Molecular Structure & Function, The Hospital for Sick Children , Toronto, ON M5G 0A4, Canada
| | - Ariele Viacava Follis
- Department of Structural Biology, St. Jude Children's Research Hospital , Memphis, Tennessee 38105, United States
| | - Richard W Kriwacki
- Department of Structural Biology, St. Jude Children's Research Hospital , Memphis, Tennessee 38105, United States.,Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Sciences Center , Memphis, Tennessee 38163, United States
| | - Julie D Forman-Kay
- Molecular Structure & Function, The Hospital for Sick Children , Toronto, ON M5G 0A4, Canada.,Department of Biochemistry, University of Toronto , Toronto, ON M5S 1A8, Canada
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10
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Iacob RE, Krystek SR, Huang RYC, Wei H, Tao L, Lin Z, Morin PE, Doyle ML, Tymiak AA, Engen JR, Chen G. Hydrogen/deuterium exchange mass spectrometry applied to IL-23 interaction characteristics: potential impact for therapeutics. Expert Rev Proteomics 2015; 12:159-69. [PMID: 25711416 DOI: 10.1586/14789450.2015.1018897] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
IL-23 is an important therapeutic target for the treatment of inflammatory diseases. Adnectins are targeted protein therapeutics that are derived from domain III of human fibronectin and have a similar protein scaffold to antibodies. Adnectin 2 was found to bind to IL-23 and compete with the IL-23/IL-23R interaction, posing a potential protein therapeutic. Hydrogen/deuterium exchange mass spectrometry and computational methods were applied to probe the binding interactions between IL-23 and Adnectin 2 and to determine the correlation between the two orthogonal methods. This review summarizes the current structural knowledge about IL-23 and focuses on the applicability of hydrogen/deuterium exchange mass spectrometry to investigate the higher order structure of proteins, which plays an important role in the discovery of new and improved biotherapeutics.
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Affiliation(s)
- Roxana E Iacob
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
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11
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Iacob RE, Chen G, Ahn J, Houel S, Wei H, Mo J, Tao L, Cohen D, Xie D, Lin Z, Morin PE, Doyle ML, Tymiak AA, Engen JR. The influence of adnectin binding on the extracellular domain of epidermal growth factor receptor. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:2093-2102. [PMID: 25223306 PMCID: PMC4224629 DOI: 10.1007/s13361-014-0973-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 07/29/2014] [Accepted: 08/03/2014] [Indexed: 06/03/2023]
Abstract
The precise and unambiguous elucidation and characterization of interactions between a high affinity recognition entity and its cognate protein provides important insights for the design and development of drugs with optimized properties and efficacy. In oncology, one important target protein has been shown to be the epidermal growth factor receptor (EGFR) through the development of therapeutic anticancer antibodies that are selective inhibitors of EGFR activity. More recently, smaller protein derived from the 10th type III domain of human fibronectin termed an adnectin has also been shown to inhibit EGFR in clinical studies. The mechanism of EGFR inhibition by either an adnectin or an antibody results from specific binding of the high affinity protein to the extracellular portion of EGFR (exEGFR) in a manner that prevents phosphorylation of the intracellular kinase domain of the receptor and thereby blocks intracellular signaling. Here, the structural changes induced upon binding were studied by probing the solution conformations of full length exEGFR alone and bound to a cognate adnectin through hydrogen/deuterium exchange mass spectrometry (HDX MS). The effects of binding in solution were identified and compared with the structure of a bound complex determined by X-ray crystallography.ᅟ
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Affiliation(s)
- Roxana E. Iacob
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA USA
| | - Guodong Chen
- Bioanalytical and Discovery Analytical Sciences, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Joomi Ahn
- Waters Corporation, Milford, MA, USA
| | | | - Hui Wei
- Bioanalytical and Discovery Analytical Sciences, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Jingjie Mo
- Bioanalytical and Discovery Analytical Sciences, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Li Tao
- Biologics Manufacturing and Process Development, Global Manufacturing and Supply, Bristol-Myers Squibb Company, Hopewell, NJ, USA
| | - Daniel Cohen
- Protein Science, Research and Development, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Dianlin Xie
- Protein Science, Research and Development, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Zheng Lin
- Protein Science, Research and Development, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Paul E. Morin
- Protein Science, Research and Development, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Michael L. Doyle
- Protein Science, Research and Development, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Adrienne A. Tymiak
- Bioanalytical and Discovery Analytical Sciences, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - John R. Engen
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA USA
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12
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Dyson HJ, Komives EA. Role of disorder in IκB-NFκB interaction. IUBMB Life 2012; 64:499-505. [PMID: 22573609 DOI: 10.1002/iub.1044] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Accepted: 04/04/2012] [Indexed: 01/22/2023]
Abstract
The paradigmatic transcription factors of the NFκB family provide an increasingly complex view of the mechanism of signal-mediated transcriptional activation. Although the primary event, phosphorylation and subsequent ubiquitin-dependent degradation of IκBα, the inhibitor of the canonical NFκB (p50/p65), is reasonably well understood, the means whereby the activation is turned off by postinduction repression are less well understood. Recent work highlighted in this review suggests that the inhibitor IκBα participates in the "stripping" of NFκB from the DNA, and that this process relies heavily on the disordered and weakly ordered segments of IκBα. Kinetic and equilibrium measurements in vitro as well as genetic screens in vivo convincingly demonstrate not only that IκBα greatly increases the dissociation rate of NFκB from DNA but also that further control of the process is mediated by the extremely short half-life of free IκBα, doubtless a result of the overall weakly folded nature of the free protein. These studies illustrate the versatility of protein systems that use not only well-structured proteins and protein complexes but also the full range of available weakly structured and disordered states to maximize functional efficiency and metabolic control.
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Affiliation(s)
- H Jane Dyson
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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13
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Rowe AJ. Ultra-weak reversible protein–protein interactions. Methods 2011; 54:157-66. [DOI: 10.1016/j.ymeth.2011.02.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2010] [Revised: 01/15/2011] [Accepted: 02/07/2011] [Indexed: 10/18/2022] Open
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Manavalan B, Basith S, Choi YM, Lee G, Choi S. Structure-function relationship of cytoplasmic and nuclear IκB proteins: an in silico analysis. PLoS One 2010; 5:e15782. [PMID: 21203422 PMCID: PMC3009747 DOI: 10.1371/journal.pone.0015782] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Accepted: 11/23/2010] [Indexed: 12/31/2022] Open
Abstract
Cytoplasmic IκB proteins are primary regulators that interact with NF-κB subunits in the cytoplasm of unstimulated cells. Upon stimulation, these IκB proteins are rapidly degraded, thus allowing NF-κB to translocate into the nucleus and activate the transcription of genes encoding various immune mediators. Subsequent to translocation, nuclear IκB proteins play an important role in the regulation of NF-κB transcriptional activity by acting either as activators or inhibitors. To date, molecular basis for the binding of IκBα, IκBβ and IκBζ along with their partners is known; however, the activation and inhibition mechanism of the remaining IκB (IκBNS, IκBε and Bcl-3) proteins remains elusive. Moreover, even though IκB proteins are structurally similar, it is difficult to determine the exact specificities of IκB proteins towards their respective binding partners. The three-dimensional structures of IκBNS, IκBζ and IκBε were modeled. Subsequently, we used an explicit solvent method to perform detailed molecular dynamic simulations of these proteins along with their known crystal structures (IκBα, IκBβ and Bcl-3) in order to investigate the flexibility of the ankyrin repeat domains (ARDs). Furthermore, the refined models of IκBNS, IκBε and Bcl-3 were used for multiple protein-protein docking studies for the identification of IκBNS-p50/p50, IκBε-p50/p65 and Bcl-3-p50/p50 complexes in order to study the structural basis of their activation and inhibition. The docking experiments revealed that IκBε masked the nuclear localization signal (NLS) of the p50/p65 subunits, thereby preventing its translocation into the nucleus. For the Bcl-3- and IκBNS-p50/p50 complexes, the results show that Bcl-3 mediated transcription through its transactivation domain (TAD) while IκBNS inhibited transcription due to its lack of a TAD, which is consistent with biochemical studies. Additionally, the numbers of identified flexible residues were equal in number among all IκB proteins, although they were not conserved. This could be the primary reason for their binding partner specificities.
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Affiliation(s)
- Balachandran Manavalan
- Department of Molecular Science and Technology, Ajou University, Suwon, Republic of Korea
| | - Shaherin Basith
- Department of Molecular Science and Technology, Ajou University, Suwon, Republic of Korea
| | - Yong-Min Choi
- Department of Molecular Science and Technology, Ajou University, Suwon, Republic of Korea
| | - Gwang Lee
- Department of Molecular Science and Technology, Ajou University, Suwon, Republic of Korea
- Institute for Medical Sciences, School of Medicine, Ajou University, Republic of Korea
| | - Sangdun Choi
- Department of Molecular Science and Technology, Ajou University, Suwon, Republic of Korea
- * E-mail:
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15
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Ferreiro DU, Komives EA. Molecular mechanisms of system control of NF-kappaB signaling by IkappaBalpha. Biochemistry 2010; 49:1560-7. [PMID: 20055496 DOI: 10.1021/bi901948j] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The NF-kappaB family of transcription factors responds to inflammatory cytokines with rapid transcriptional activation and subsequent signal repression. Much of the system control depends on the unique characteristics of its major inhibitor, IkappaBalpha, which appears to have folding dynamics that underlie the biophysical properties of its activity. Theoretical folding studies followed by experiments have shown that a portion of the ankyrin repeat domain of IkappaBalpha folds on binding. In resting cells, IkappaBalpha is constantly being synthesized, but most of it is rapidly degraded, leaving only a very small pool of free IkappaBalpha. Nearly all of the NF-kappaB is bound to IkappaBalpha, resulting in near-complete inhibition of nuclear localization and transcriptional activation. Combined solution biophysical measurements and quantitative protein half-life measurements inside cells have allowed us to understand how the inhibition occurs, why IkappaBalpha can be degraded quickly in the free state but remain extremely stable in the bound state, and how signal activation and repression can be tuned by IkappaB folding dynamics. This review summarizes results of in vitro and in vivo experiments that converge demonstrating the effective interplay between biophysics and cell biology in understanding transcriptional control by the NF-kappaB signaling module.
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Affiliation(s)
- Diego U Ferreiro
- Laboratorio de Expresion y Plegado de Proteinas, Universidad Nacional de Quilmes, Roque Saenz Pena 352,B1876BXD Bernal, Buenos Aires, Argentina
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16
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Scott FL, Stec B, Pop C, Dobaczewska MK, Lee JJ, Monosov E, Robinson H, Salvesen GS, Schwarzenbacher R, Riedl SJ. The Fas-FADD death domain complex structure unravels signalling by receptor clustering. Nature 2008; 457:1019-22. [PMID: 19118384 PMCID: PMC2661029 DOI: 10.1038/nature07606] [Citation(s) in RCA: 271] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2008] [Accepted: 10/30/2008] [Indexed: 12/24/2022]
Abstract
The Death Inducing Signaling Complex (DISC) formed by Fas receptor, FADD and caspase-8 is a pivotal trigger of apoptosis1-3. The Fas/FADD DISC represents a receptor platform, which once assembled initiates the induction of programmed cell death. A highly oligomeric network of homotypic protein interactions comprised of the death domains (DD) of Fas and FADD is at the center of DISC formation4, 5. Thus characterising the mechanistic basis for the Fas/FADD interaction is paramount for understanding DISC signaling but has remained enigmatic largely due to a lack of structural data. We have successfully formed and isolated the Fas/FADD DD complex and here we report the 2.7 Å crystal structure. The complex shows a tetrameric arrangement of four FADD DDs bound to four Fas DDs. We show that an opening of the Fas DD exposes the FADD binding site and simultaneously generates a Fas/Fas bridge. The result is a regulatory Fas/FADD complex bridge governed by weak protein:protein interactions revealing a model where the complex functions as a mechanistic switch. This switch prevents accidental DISC assembly, yet allows for highly processive DISC formation and clustering upon a sufficient stimulus. Thus besides depicting a previously unknown mode of death domain interactions, these results further uncover a mechanism for receptor signaling solely by oligomerization and clustering events.
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Affiliation(s)
- Fiona L Scott
- Program in Apoptosis and Cell Death Research, The Burnham Institute for Medical Research, La Jolla, California 92037, USA
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17
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Bergqvist S, Ghosh G, Komives EA. The IkappaBalpha/NF-kappaB complex has two hot spots, one at either end of the interface. Protein Sci 2008; 17:2051-8. [PMID: 18824506 DOI: 10.1110/ps.037481.108] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
IkappaBalpha binds to and inhibits the transcriptional activity of NF-kappaB family members via its ankyrin repeat (AR) domain. The binding affinity of IkappaBalpha with NF-kappaB(p50/p65) heterodimers and NF-kappaB(p65/65) homodimers is in the picomolar range, and in the cell, this results in long half-lives of the complexes. Direct binding experiments have been performed using surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC) on a series of truncations and mutations in order to understand what regions of the interface are most important for the tight binding affinity of this complex. We previously showed that interactions between residues 305 and 321 of NF-kappaB(p65) with the first AR of IkappaBalpha are critical for the binding energy. Interactions in this region are responsible for more than 7 kcal/mol of the binding energy. Here we show equally drastic consequences for the binding energy occur upon truncation of even a few residues at the C terminus of IkappaBalpha. Thus, the interface actually has two hot spots, one at either end of the elongated and large surface of interaction. These results suggest a "squeeze" mechanism that leads to the extremely high affinity of the IkappaBalpha*NF-kappaB complex through stabilization of the ankyrin repeat domain.
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Affiliation(s)
- Simon Bergqvist
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0378, USA
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18
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Sue SC, Cervantes C, Komives EA, Dyson HJ. Transfer of flexibility between ankyrin repeats in IkappaB* upon formation of the NF-kappaB complex. J Mol Biol 2008; 380:917-31. [PMID: 18565540 DOI: 10.1016/j.jmb.2008.05.048] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2008] [Revised: 05/16/2008] [Accepted: 05/21/2008] [Indexed: 12/01/2022]
Abstract
The mechanism of inhibition of the transcriptional activator nuclear factor kappaB (NF-kappaB) by the inhibitor IkappaB* is central to the understanding of the control of transcriptional activity via this widely employed pathway. Previous studies suggested that IkappaB* , a modular protein with an NF-kappaB binding domain consisting of six ankyrin repeat domains (ANKs), shows differential flexibility, with ANK 1-4 apparently more rigid in solution in the absence of NF-kappaB than ANK 5 and 6. Here we report NMR studies that confirm the enhanced flexibility of ANK 5 and 6 in free IkappaB* . Upon binding of NF-kappaB, ANK 5 and 6 become well structured and rigid, but, somewhat surprisingly, other domains of the IkappaB* , which were relatively rigid in the free protein, become significantly more flexible. Due to the high molecular masses of the component proteins and the complexes, we employ a hierarchical experimental plan to maximize the available information on local flexibility in the ankyrin repeat domains. Backbone resonances of the 221-residue IkappaB* protein were assigned firstly in a smaller construct consisting of ankyrin repeats 1-4. These assignments could be readily transferred to the spectra of the construct containing six repeats, both free and complexed with various combinations of the NF-kappaB p50 and p65 domains. Transverse relaxation optimized spectroscopy-type NMR experiments on differentially labeled proteins enabled information on backbone structure and dynamics to be obtained, even in complexes with molecular masses approaching 100 kDa. Changes in the flexibility and stability of the various ankyrin repeat domains of IkappaB* complex formation take a variety of forms depending on the position of the domain in the complex, providing a variety of examples of the structural and functional utility of intrinsically unstructured or partly folded protein domains.
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Affiliation(s)
- Shih-Che Sue
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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19
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Trinh DV, Zhu N, Farhang G, Kim BJ, Huxford T. The nuclear I kappaB protein I kappaB zeta specifically binds NF-kappaB p50 homodimers and forms a ternary complex on kappaB DNA. J Mol Biol 2008; 379:122-35. [PMID: 18436238 DOI: 10.1016/j.jmb.2008.03.060] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2008] [Revised: 03/25/2008] [Accepted: 03/25/2008] [Indexed: 11/17/2022]
Abstract
Although they share sequence homology to classical cytoplasmic I kappaB inhibitors of transcription factor NF-kappaB, the proteins I kappaB zeta, Bcl-3, and I kappa BNS function in the nucleus as factors that influence NF-kappaB-dependent gene expression profiles. Through the use of purified recombinant proteins and by comparison with the classical I kappaB protein I kappaB alpha, we have discovered mechanistic details of the interaction between I kappaB zeta and functional NF-kappaB dimers. Whereas I kappaB alpha and other classical I kappaB proteins bind tightly to NF-kappaB dimers that possess the p65 subunit, I kappaB zeta binds preferentially to NF-kappaB p50 homodimers. This altered specificity is particularly interesting in light of the fact that both NF-kappaB subunits exhibit high sequence and structural homology, while the I kappaB alpha and I kappaB zeta proteins are also conserved in primary amino acid sequence. We further show that I kappaB zeta is capable of forming a stable ternary complex with the NF-kappaB p50 homodimer and kappaB DNA. Again, this is a stark contrast from I kappaB alpha, which inhibits NF-kappaB p65 homodimer binding to NF-kappaB target DNA sequences. Removal of the DNA sequences flanking the NF-kappaB binding site does not directly affect the interaction of p50 and I kappaB zeta. Rather, we have discovered that the carboxy-terminal glycine-rich region of the NF-kappaB p50 homodimer is involved in mediating high-affinity binding of I kappaB zeta and NF-kappaB p50. We conclude that the NF-kappaB p50 homodimer functions as a legitimate activator of gene expression through formation of a ternary complex between itself, I kappaB zeta, and DNA. The requirement for formation of this complex could explain why the nuclear I kappaB protein I kappaB zeta is absolutely required for expression of the pluripotent pro-inflammatory cytokine interleukin-6 in peritoneal macrophages.
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Affiliation(s)
- Dan V Trinh
- Structural Biochemistry Laboratory, Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182-1030, USA
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20
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Yakovlev VA, Barani IJ, Rabender CS, Black SM, Leach JK, Graves PR, Kellogg GE, Mikkelsen RB. Tyrosine nitration of IkappaBalpha: a novel mechanism for NF-kappaB activation. Biochemistry 2007; 46:11671-83. [PMID: 17910475 PMCID: PMC2678910 DOI: 10.1021/bi701107z] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The NF-kappaB family of transcription factors is an important component of stress-activated cytoprotective signal transduction pathways. Previous studies demonstrated that some activation mechanisms require phosphorylation, ubiquitination, and degradation of the inhibitor protein, IkappaBalpha. Herein, it is demonstrated that ionizing radiation in the therapeutic dose range stimulates NF-kappaB activity by a mechanism in which IkappaBalpha tyrosine 181 is nitrated as a consequence of constitutive NO* synthase activation, leading to dissociation of intact IkappaBalpha from NF-kappaB. This mechanism does not appear to require IkappaBalpha kinase-dependent phosphorylation or proteolytic degradation of IkappaBalpha. Tyrosine 181 is involved in several noncovalent interactions with the p50 subunit of NF-kappaB stabilizing the IkappaBalpha-NF-kappaB complex. Evaluation of hydropathic interactions of the IkappaBalpha-p50 complex on the basis of the crystal structure of the complex is consistent with nitration disrupting these interactions and dissociating the IkappaBalpha-NF-kappaB complex. Tyrosine nitration is not commonly studied in the context of signal transduction. However, these results indicate that tyrosine nitration is an important post-translational regulatory modification for NF-kappaB activation and possibly for other signaling molecules modulated by mild and transient oxidative and nitrosative stresses.
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Affiliation(s)
- Vasily A. Yakovlev
- Department of Radiation Oncology, Massey Cancer Center, Virginia Commonwealth University, Richmond VA 23298
| | - Igor J. Barani
- Department of Radiation Oncology, Massey Cancer Center, Virginia Commonwealth University, Richmond VA 23298
| | - Christopher S. Rabender
- Department of Radiation Oncology, Massey Cancer Center, Virginia Commonwealth University, Richmond VA 23298
| | - Stephen M. Black
- Vascular Biology Center, Medical College of Georgia, Augusta, GA 30912
| | - J. Kevin Leach
- Drug Metabolism and Pharmacokinetics, Merck Research Laboratories, Boston, MA 02115
| | - Paul R. Graves
- Department of Radiation Oncology, Massey Cancer Center, Virginia Commonwealth University, Richmond VA 23298
| | - Glen E. Kellogg
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA23298
| | - Ross B. Mikkelsen
- Department of Radiation Oncology, Massey Cancer Center, Virginia Commonwealth University, Richmond VA 23298
- To whom correspondence should be addressed: Ross B. Mikkelsen, Department of Radiation Oncology, Massey Cancer Center, 401 College St., Richmond, VA 23298, Tel.: (804) 628-0857; Fax: (804) 828-6042; E-Mail:
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21
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Ferreiro DU, Cervantes CF, Truhlar SME, Cho SS, Wolynes PG, Komives EA. Stabilizing IkappaBalpha by "consensus" design. J Mol Biol 2006; 365:1201-16. [PMID: 17174335 PMCID: PMC1866275 DOI: 10.1016/j.jmb.2006.11.044] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2006] [Revised: 09/27/2006] [Accepted: 11/10/2006] [Indexed: 01/21/2023]
Abstract
IkappaBalpha is the major regulator of transcription factor NF-kappaB function. The ankyrin repeat region of IkappaBalpha mediates specific interactions with NF-kappaB dimers, but ankyrin repeats 1, 5 and 6 display a highly dynamic character when not in complex with NF-kappaB. Using chemical denaturation, we show here that IkappaBalpha displays two folding transitions: a non-cooperative conversion under weak perturbation, and a major cooperative folding phase upon stronger insult. Taking advantage of a native Trp residue in ankyrin repeat (AR) 6 and engineered Trp residues in AR2, AR4 and AR5, we show that the cooperative transition involves AR2 and AR3, while the non-cooperative transition involves AR5 and AR6. The major structural transition can be affected by single amino acid substitutions converging to the "consensus" ankyrin repeat sequence, increasing the native state stability significantly. We further characterized the structural and dynamic properties of the native state ensemble of IkappaBalpha and the stabilized mutants by H/(2)H exchange mass spectrometry and NMR. The solution experiments were complemented with molecular dynamics simulations to elucidate the microscopic origins of the stabilizing effect of the consensus substitutions, which can be traced to the fast conformational dynamics of the folded ensemble.
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Affiliation(s)
- Diego U Ferreiro
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0359, USA
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22
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Bergqvist S, Croy CH, Kjaergaard M, Huxford T, Ghosh G, Komives EA. Thermodynamics reveal that helix four in the NLS of NF-kappaB p65 anchors IkappaBalpha, forming a very stable complex. J Mol Biol 2006; 360:421-34. [PMID: 16756995 PMCID: PMC2680085 DOI: 10.1016/j.jmb.2006.05.014] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2006] [Revised: 04/05/2006] [Accepted: 05/05/2006] [Indexed: 10/24/2022]
Abstract
IkappaBalpha is an ankyrin repeat protein that inhibits NF-kappaB transcriptional activity by sequestering NF-kappaB outside of the nucleus in resting cells. We have characterized the binding thermodynamics and kinetics of the IkappaBalpha ankyrin repeat domain to NF-kappaB(p50/p65) using surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC). SPR data showed that the IkappaBalpha and NF-kappaB associate rapidly but dissociate very slowly, leading to an extremely stable complex with a K(D,obs) of approximately 40 pM at 37 degrees C. As reported previously, the amino-terminal DNA-binding domain of p65 contributes little to the overall binding affinity. Conversely, helix four of p65, which forms part of the nuclear localization sequence, was essential for high-affinity binding. This was surprising, given the small size of the binding interface formed by this part of p65. The NF-kappaB(p50/p65) heterodimer and p65 homodimer bound IkappaBalpha with almost indistinguishable thermodynamics, except that the NF-kappaB p65 homodimer was characterized by a more favorable DeltaH(obs) relative to the NF-kappaB(p50/p65) heterodimer. Both interactions were characterized by a large negative heat capacity change (DeltaC(P,obs)), approximately half of which was contributed by the p65 helix four that was necessary for tight binding. This could not be accounted for readily by the small loss of buried non-polar surface area and we hypothesize that the observed effect is due to additional folding of some regions of the complex.
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Affiliation(s)
- Simon Bergqvist
- Department of Chemistry and Biochemistry, University of California, San Diego 9500 Gilman Dr. La Jolla, CA 92093-0378
| | - Carrie H. Croy
- Department of Chemistry, University of Colorado, Boulder, Boulder, CO 80309-0215
| | - Magnus Kjaergaard
- Department of Chemistry and Biochemistry, University of California, San Diego 9500 Gilman Dr. La Jolla, CA 92093-0378
| | - Tom Huxford
- Department of Chemistry, San Diego State University, San Diego, CA 92182
| | - Gourisankar Ghosh
- Department of Chemistry and Biochemistry, University of California, San Diego 9500 Gilman Dr. La Jolla, CA 92093-0378
| | - Elizabeth A. Komives
- Department of Chemistry and Biochemistry, University of California, San Diego 9500 Gilman Dr. La Jolla, CA 92093-0378
- To whom correspondence should be addressed: ph: (858) 534-3058 FAX: (858) 534-6174
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23
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Desrosiers DC, Peng ZY. A Binding Free Energy Hot Spot in the Ankyrin Repeat Protein GABPβ Mediated Protein–Protein Interaction. J Mol Biol 2005; 354:375-84. [PMID: 16243355 DOI: 10.1016/j.jmb.2005.09.045] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2005] [Revised: 09/07/2005] [Accepted: 09/16/2005] [Indexed: 11/17/2022]
Abstract
The frequently observed ankyrin repeat motif represents a structural scaffold evolved for mediating protein-protein interactions. As such, these repeats modulate a diverse range of cellular functions. We thermodynamically characterized the heterodimeric GA-binding protein (GABP) alphabeta complex and focused specifically on the interaction mediated by the ankyrin repeat domain of the GABPbeta. Our isothermal titration calorimetric analysis of the interaction between the GABP subunits determined an association constant (K(A)) of 6.0 x 10(8) M(-1) and that the association is favorably driven by a significant change in enthalpy (DeltaH) and a minor change in entropy (-TDeltaS). A total of 16 GABPbeta interface residues were chosen for alanine scanning mutagenesis. The calorimetrically measured differences in the free energy of binding were compared to computationally calculated values resulting in a correlation coefficient r = 0.71. We identified three spatially contiguous hydrophobic and aromatic residues that form a binding free energy hot spot (DeltaDeltaG > 2.0 kcal/mol). One residue provides structural support to the hot spot residues. Three non-hot spot residues are intermediate contributors (DeltaDeltaG approximately 1.0 kcal/mol) and create a canopy-like structure over the hot spot residues to possibly occlude solvent and orientate the subunits. The remaining interface residues are located peripherally and have weak contributions. Finally, our mutational analysis revealed a significant entropy-enthalpy compensation for this interaction.
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Affiliation(s)
- Daniel C Desrosiers
- Department of Molecular, Microbial and Structural Biology, University of Connecticut Health Center, Farmington, CT 06032, USA.
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24
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Ferreiro DU, Cho SS, Komives EA, Wolynes PG. The energy landscape of modular repeat proteins: topology determines folding mechanism in the ankyrin family. J Mol Biol 2005; 354:679-92. [PMID: 16257414 DOI: 10.1016/j.jmb.2005.09.078] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2004] [Revised: 09/13/2005] [Accepted: 09/27/2005] [Indexed: 10/25/2022]
Abstract
Proteins consisting of repeating amino acid motifs are abundant in all kingdoms of life, especially in higher eukaryotes. Repeat-containing proteins self-organize into elongated non-globular structures. Do the same general underlying principles that dictate the folding of globular domains apply also to these extended topologies? Using a simplified structure-based model capturing a perfectly funneled energy landscape, we surveyed the predicted mechanism of folding for ankyrin repeat containing proteins. The ankyrin family is one of the most extensively studied classes of non-globular folds. The model based only on native contacts reproduces most of the experimental observations on the folding of these proteins, including a folding mechanism that is reminiscent of a nucleation propagation growth. The confluence of simulation and experimental results suggests that the folding of non-globular proteins is accurately described by a funneled energy landscape, in which topology plays a determinant role in the folding mechanism.
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Affiliation(s)
- Diego U Ferreiro
- Center for Theoretical Biological Physics, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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25
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Vaynberg J, Fukuda T, Chen K, Vinogradova O, Velyvis A, Tu Y, Ng L, Wu C, Qin J. Structure of an Ultraweak Protein-Protein Complex and Its Crucial Role in Regulation of Cell Morphology and Motility. Mol Cell 2005; 17:513-23. [PMID: 15721255 DOI: 10.1016/j.molcel.2004.12.031] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2004] [Revised: 08/13/2004] [Accepted: 12/29/2004] [Indexed: 10/25/2022]
Abstract
Weak protein-protein interactions (PPIs) (K(D) > 10(-6) M) are critical determinants of many biological processes. However, in contrast to a large growing number of well-characterized, strong PPIs, the weak PPIs, especially those with K(D) > 10(-4) M, are poorly explored. Genome wide, there exist few 3D structures of weak PPIs with K(D) > 10(-4) M, and none with K(D) > 10(-3) M. Here, we report the NMR structure of an extremely weak focal adhesion complex (K(D) approximately 3 x 10(-3) M) between Nck-2 SH3 domain and PINCH-1 LIM4 domain. The structure exhibits a remarkably small and polar interface with distinct binding modes for both SH3 and LIM domains. Such an interface suggests a transient Nck-2/PINCH-1 association process that may trigger rapid focal adhesion turnover during integrin signaling. Genetic rescue experiments demonstrate that this interface is indeed involved in mediating cell shape change and migration. Together, the data provide a molecular basis for an ultraweak PPI in regulating focal adhesion dynamics during integrin signaling.
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Affiliation(s)
- Julia Vaynberg
- Structural Biology Program, Lerner Research Institute, The Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, OH 44195, USA
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26
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Malek S, Huang DB, Huxford T, Ghosh S, Ghosh G. X-ray crystal structure of an IkappaBbeta x NF-kappaB p65 homodimer complex. J Biol Chem 2003; 278:23094-100. [PMID: 12686541 DOI: 10.1074/jbc.m301022200] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
We report the crystal structure of a murine IkappaBbeta x NF-kappaB p65 homodimer complex. Crystallographic models were determined for two triclinic crystalline systems and refined against data at 2.5 and 2.1 A. The overall complex structure is similar to that of the IkappaBalpha.NF-kappaB p50/p65 heterodimer complex. One NF-kappaB p65 subunit nuclear localization signal clearly contacts IkappaBbeta, whereas a homologous segment from the second subunit of the homodimer is mostly solvent-exposed. The unique 47-amino acid insertion between ankyrin repeats three and four of IkappaBbeta is mostly disordered in the structure. Primary sequence analysis and differences in the mode of binding at the IkappaBbeta sixth ankyrin repeat and NF-kappaB p65 homodimer suggest a model for nuclear IkappaBbeta.NF-kappaB.DNA ternary complex formation. These unique structural features of IkappaBbeta may contribute to its ability to mediate persistent NF-kappaB activation.
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Affiliation(s)
- Shiva Malek
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093-0359, USA
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