101
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van Dijk ADJ, Morabito G, Fiers M, van Ham RCHJ, Angenent GC, Immink RGH. Sequence motifs in MADS transcription factors responsible for specificity and diversification of protein-protein interaction. PLoS Comput Biol 2010; 6:e1001017. [PMID: 21124869 PMCID: PMC2991254 DOI: 10.1371/journal.pcbi.1001017] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2010] [Accepted: 10/27/2010] [Indexed: 11/18/2022] Open
Abstract
Protein sequences encompass tertiary structures and contain information about specific molecular interactions, which in turn determine biological functions of proteins. Knowledge about how protein sequences define interaction specificity is largely missing, in particular for paralogous protein families with high sequence similarity, such as the plant MADS domain transcription factor family. In comparison to the situation in mammalian species, this important family of transcription regulators has expanded enormously in plant species and contains over 100 members in the model plant species Arabidopsis thaliana. Here, we provide insight into the mechanisms that determine protein-protein interaction specificity for the Arabidopsis MADS domain transcription factor family, using an integrated computational and experimental approach. Plant MADS proteins have highly similar amino acid sequences, but their dimerization patterns vary substantially. Our computational analysis uncovered small sequence regions that explain observed differences in dimerization patterns with reasonable accuracy. Furthermore, we show the usefulness of the method for prediction of MADS domain transcription factor interaction networks in other plant species. Introduction of mutations in the predicted interaction motifs demonstrated that single amino acid mutations can have a large effect and lead to loss or gain of specific interactions. In addition, various performed bioinformatics analyses shed light on the way evolution has shaped MADS domain transcription factor interaction specificity. Identified protein-protein interaction motifs appeared to be strongly conserved among orthologs, indicating their evolutionary importance. We also provide evidence that mutations in these motifs can be a source for sub- or neo-functionalization. The analyses presented here take us a step forward in understanding protein-protein interactions and the interplay between protein sequences and network evolution.
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Affiliation(s)
| | | | - Martijn Fiers
- Plant Research International, Bioscience, Wageningen, The Netherlands
| | | | - Gerco C. Angenent
- Plant Research International, Bioscience, Wageningen, The Netherlands
- Centre for BioSystems Genomics (CBSG), Wageningen, The Netherlands
| | - Richard G. H. Immink
- Plant Research International, Bioscience, Wageningen, The Netherlands
- Centre for BioSystems Genomics (CBSG), Wageningen, The Netherlands
- * E-mail:
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102
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Xiao J, Hamilton BS, Tolbert TJ. Synthesis of N-terminally linked protein and peptide dimers by native chemical ligation. Bioconjug Chem 2010; 21:1943-7. [PMID: 20973495 DOI: 10.1021/bc100370j] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Dimerization can be utilized to double the molecular weight of proteins and peptides and potentially increase their avidity of binding to target receptors. These dimerization effects may be utilized to increase in vivo half-lives in a manner similar to PEGylation and may also improve biological activity. In this paper, we report a new strategy for the synthesis of N-terminally linked protein and peptide homodimers utilizing native chemical ligation to conjugate a short dithioester linker to the N-terminal cysteines of protein and peptide monomers to form dimers in a single step. This strategy is general and has been applied to the production of dimers from three recombinantly expressed polypeptides, the IgG binding domain Protein G, an HIV entry inhibitor peptide C37H6, and human interleukin-1 receptor antagonist (IL-1ra). The biological activities of the C37H6 and IL-1ra dimers produced by these methods were retained or even slightly increased when compared to their corresponding monomers.
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Affiliation(s)
- Junpeng Xiao
- Department of Chemistry, Indiana University, Bloomington, 47405, United States
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103
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Fegan A, White B, Carlson JCT, Wagner CR. Chemically controlled protein assembly: techniques and applications. Chem Rev 2010; 110:3315-36. [PMID: 20353181 DOI: 10.1021/cr8002888] [Citation(s) in RCA: 236] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Adrian Fegan
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA
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104
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Nanomolecular HLA-DR10 antibody mimics: A potent system for molecular targeted therapy and imaging. Cancer Biother Radiopharm 2010; 23:783-96. [PMID: 20443696 DOI: 10.1089/cbr.2008.0589] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
To mimic the molecular specificity and cell selectivity of monoclonal antibody (mAb) binding while decreasing size, nanomolecules (selective high-affinity ligands; SHALs), based on in silico modeling, have been created to bind to human leukocyte antigen-DR (HLA-DR10), a signaling receptor protein upregulated on the malignant B-lymphocytes of non-Hodgkin's lymphoma and chronic lymphocytic leukemia. SHALs were synthesized with a biotin or DOTA chelate (1,4,7,10-tetraazacyclododecane-N,N',N'',N'''-tetraacetic acid), using a solid-phase lysine-polyethyleneglycol backbone to link sets of ligands shown previously to bind to HLA-DR10. Using cell-binding and death assays and confocal microscopy, SHAL uptake, residualization, and cytocidal activity were evaluated in HLA-DR10 expressing and nonexpressing live, human lymphoma cell lines. All of the SHALs tested were selective for, and accumulated in, expressing cells. Reflecting binding to HLA-DR10 inside the cells, SHALs having the Ct ligand (3-(2-([3-chloro-5-trifluoromethyl)-2-pyridinyl]oxy)-anilino)-3-oxopropanionic acid) residualized in expressing cells greater than 179 times more than accountable by cell-surface membrane HLA-DR10. Confocal microscopy confirmed the intracellular residualization of these SHALs. Importantly, SHALs with a Ct ligand had direct cytocidal activity, similar in potency to that of Lym-1 mAb and rituximab, selectively for HLA-DR10 expressing lymphoma cells and xenografts. The results show that SHALs containing the Ct ligand residualize intracellularly and have cytocidal effects mediated by HLA-DR10. These SHALs have extraordinary potential as novel molecules for the selective targeting of lymphoma and leukemia for molecular therapy and imaging. Further, these SHALs can be used to transport and residualize cytotoxic agents near critical sites inside these malignant cells.
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105
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Sigalov AB. The SCHOOL of nature: III. From mechanistic understanding to novel therapies. SELF/NONSELF 2010; 1:192-224. [PMID: 21487477 PMCID: PMC3047783 DOI: 10.4161/self.1.3.12794] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2010] [Revised: 06/10/2010] [Accepted: 06/11/2010] [Indexed: 11/19/2022]
Abstract
Protein-protein interactions play a central role in biological processes and thus represent an appealing target for innovative drug design and development. They can be targeted by small molecule inhibitors, modulatory peptides and peptidomimetics, which represent a superior alternative to protein therapeutics that carry many disadvantages. Considering that transmembrane signal transduction is an attractive process to therapeutically control multiple diseases, it is fundamentally and clinically important to mechanistically understand how signal transduction occurs. Uncovering specific protein-protein interactions critical for signal transduction, a general platform for receptor-mediated signaling, the signaling chain homooligomerization (SCHOOL) platform, suggests these interactions as universal therapeutic targets. Within the platform, the general principles of signaling are similar for a variety of functionally unrelated receptors. This suggests that global therapeutic strategies targeting key protein-protein interactions involved in receptor triggering and transmembrane signal transduction may be used to treat a diverse set of diseases. This also assumes that clinical knowledge and therapeutic strategies can be transferred between seemingly disparate disorders, such as T cell-mediated skin diseases and platelet disorders or combined to develop novel pharmacological approaches. Intriguingly, human viruses use the SCHOOL-like strategies to modulate and/or escape the host immune response. These viral mechanisms are highly optimized over the millennia, and the lessons learned from viral pathogenesis can be used practically for rational drug design. Proof of the SCHOOL concept in the development of novel therapies for atopic dermatitis, rheumatoid arthritis, cancer, platelet disorders and other multiple indications with unmet needs opens new horizons in therapeutics.
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106
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Zhou CY, Li J, Peddibhotla S, Romo D. Mild Arming and Derivatization of Natural Products via an In(OTf)3-Catalyzed Arene Iodination. Org Lett 2010; 12:2104-7. [DOI: 10.1021/ol100587j] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Cong-Ying Zhou
- Department of Chemistry, P.O. Box 30012, Texas A&M University, College Station, Texas 77842-3012
| | - Jing Li
- Department of Chemistry, P.O. Box 30012, Texas A&M University, College Station, Texas 77842-3012
| | | | - Daniel Romo
- Department of Chemistry, P.O. Box 30012, Texas A&M University, College Station, Texas 77842-3012
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107
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Abstract
Proteins are the most versatile among the various biological building blocks and a mature field of protein engineering has lead to many industrial and biomedical applications. But the strength of proteins—their versatility, dynamics and interactions—also complicates and hinders systems engineering. Therefore, the design of more sophisticated, multi-component protein systems appears to lag behind, in particular, when compared to the engineering of gene regulatory networks. Yet, synthetic biologists have started to tinker with the information flow through natural signaling networks or integrated protein switches. A successful strategy common to most of these experiments is their focus on modular interactions between protein domains or domains and peptide motifs. Such modular interaction swapping has rewired signaling in yeast, put mammalian cell morphology under the control of light, or increased the flux through a synthetic metabolic pathway. Based on this experience, we outline an engineering framework for the connection of reusable protein interaction devices into self-sufficient circuits. Such a framework should help to ‘refacture’ protein complexity into well-defined exchangeable devices for predictive engineering. We review the foundations and initial success stories of protein synthetic biology and discuss the challenges and promises on the way from protein- to protein systems design.
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Affiliation(s)
- Raik Grünberg
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), UPF, 08003 Barcelona, Spain.
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108
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Sigalov AB. The SCHOOL of nature: II. Protein order, disorder and oligomericity in transmembrane signaling. SELF/NONSELF 2010; 1:89-102. [PMID: 21487511 PMCID: PMC3065667 DOI: 10.4161/self.1.2.11590] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Revised: 02/20/2010] [Accepted: 02/22/2010] [Indexed: 11/19/2022]
Abstract
Recent reports have revealed that many proteins that do not adopt globular structures under native conditions, thus termed intrinsically disordered proteins (IDPs), are involved in cell signaling. Intriguingly, physiologically relevant oligomerization of IDPs has been recently observed and shown to exhibit unique biophysical characteristics, including the lack of significant changes in chemical shift and peak intensity upon binding. In this work, I summarize several distinct features of protein disorder that are especially important as related to receptor-mediated transmembrane signal transduction. I also hypothesize that interactions of IDPs with their protein or lipid partners represent a general biphasic process with the "no disorder-to-order" fast interaction which, depending on the interacting partner, may or may not be accompanied by the slow formation of a secondary structure. Further, I suggest signaling-related functional connections between protein order, disorder, and oligomericity and hypothesize that receptor oligomerization induced or tuned upon ligand binding outside the cell is translated across the membrane into protein oligomerization inside the cell, thus providing a general platform, the Signaling Chain HOmoOLigomerization (SCHOOL) platform, for receptor-mediated signaling. This structures our current multidisciplinary knowledge and views of the mechanisms governing the coupling of recognition to signal transduction and cell response. Importantly, this approach not only reveals previously unrecognized striking similarities in the basic mechanistic principles of function of numerous functionally diverse and unrelated surface membrane receptors, but also suggests the similarity between therapeutic targets, thus opening new horizons for both fundamental and clinically relevant studies.
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109
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Min L, Wu W, Joseph RE, Fulton DB, Berg L, Andreotti AH. Disrupting the intermolecular self-association of Itk enhances T cell signaling. THE JOURNAL OF IMMUNOLOGY 2010; 184:4228-35. [PMID: 20237289 DOI: 10.4049/jimmunol.0901908] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The Tec family tyrosine kinase (Itk), is a key component of the TCR signaling pathway. Biochemical studies have shown that Itk activation requires recruitment of Itk to the membrane via its pleckstrin homology domain, phosphorylation of Itk by the Src kinase, Lck, and binding of Itk to the SLP-76/LAT adapter complex. However, the regulation of Itk enzymatic activity by Itk domain interactions is not yet well understood. In this study, we show that full-length Itk self-associates in an intermolecular fashion. Using this information, we have designed an Itk variant that exhibits reduced self-association but maintains normal binding to exogenous ligands via each of its regulatory domains. When expressed in insect cells, the Itk substrate phospholipase Cgamma1 is phosphorylated more efficiently by the Itk variant than by wild-type Itk. Furthermore, expression of the Itk variant in primary murine T cells induced higher ERK activation and increased calcium flux following TCR stimulation compared with that of wild-type Itk. Our results indicate that the Tec kinase Itk is negatively regulated by intermolecular clustering and that disruption of this clustering leads to increased Itk kinase activity following TCR stimulation.
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Affiliation(s)
- Lie Min
- Department of Biochemistry, Iowa State University, Ames, IA 50011, USA
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110
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Prinsell MR, Everson DA, Weix DJ. Nickel-catalyzed, sodium iodide-promoted reductive dimerization of alkyl halides, alkyl pseudohalides, and allylic acetates. Chem Commun (Camb) 2010; 46:5743-5. [DOI: 10.1039/c0cc01716g] [Citation(s) in RCA: 144] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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111
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Sigalov AB. The SCHOOL of nature: I. Transmembrane signaling. SELF/NONSELF 2010; 1:4-39. [PMID: 21559175 PMCID: PMC3091606 DOI: 10.4161/self.1.1.10832] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2009] [Revised: 11/30/2009] [Accepted: 12/01/2009] [Indexed: 11/19/2022]
Abstract
Receptor-mediated transmembrane signaling plays an important role in health and disease. Recent significant advances in our understanding of the molecular mechanisms linking ligand binding to receptor activation revealed previously unrecognized striking similarities in the basic structural principles of function of numerous cell surface receptors. In this work, I demonstrate that the Signaling Chain Homooligomerization (SCHOOL)-based mechanism represents a general biological mechanism of transmembrane signal transduction mediated by a variety of functionally unrelated single- and multichain activating receptors. within the SCHOOL platform, ligand binding-induced receptor clustering is translated across the membrane into protein oligomerization in cytoplasmic milieu. This platform resolves a long-standing puzzle in transmembrane signal transduction and reveals the major driving forces coupling recognition and activation functions at the level of protein-protein interactions-biochemical processes that can be influenced and controlled. The basic principles of transmembrane signaling learned from the SCHOOL model can be used in different fields of immunology, virology, molecular and cell biology and others to describe, explain and predict various phenomena and processes mediated by a variety of functionally diverse and unrelated receptors. Beyond providing novel perspectives for fundamental research, the platform opens new avenues for drug discovery and development.
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Affiliation(s)
- Alexander B Sigalov
- Department of Pathology; University of Massachusetts Medical School; Worcester, MA USA
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112
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Sigalov AB. Protein intrinsic disorder and oligomericity in cell signaling. ACTA ACUST UNITED AC 2010; 6:451-61. [DOI: 10.1039/b916030m] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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113
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Baeza JL, Gerona-Navarro G, Thompson K, Pérez de Vega MJ, Infantes L, García-López MT, González-Muñiz R, Martín-Martínez M. Further Evidence for 2-Alkyl-2-carboxyazetidines as γ-Turn Inducers. J Org Chem 2009; 74:8203-11. [DOI: 10.1021/jo901712x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- José Luis Baeza
- Instituto de Química Médica (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | | | - Kevin Thompson
- Instituto de Química Médica (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | | | - Lourdes Infantes
- Instituto de Química Física Rocasolano (CSIC), Serrano 119, 28006 Madrid, Spain
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114
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Uhlenheuer D, Wasserberg D, Nguyen H, Zhang L, Blum C, Subramaniam V, Brunsveld L. Modulation of Protein Dimerization by a Supramolecular Host-Guest System. Chemistry 2009; 15:8779-90. [DOI: 10.1002/chem.200900462] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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115
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Neuroligin-1 performs neurexin-dependent and neurexin-independent functions in synapse validation. EMBO J 2009; 28:3244-55. [PMID: 19730411 DOI: 10.1038/emboj.2009.249] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2009] [Accepted: 07/30/2009] [Indexed: 12/28/2022] Open
Abstract
Postsynaptic neuroligins are thought to perform essential functions in synapse validation and synaptic transmission by binding to, and dimerizing, presynaptic alpha- and beta-neurexins. To test this hypothesis, we examined the functional effects of neuroligin-1 mutations that impair only alpha-neurexin binding, block both alpha- and beta-neurexin binding, or abolish neuroligin-1 dimerization. Abolishing alpha-neurexin binding abrogated neuroligin-induced generation of neuronal synapses onto transfected non-neuronal cells in the so-called artificial synapse-formation assay, even though beta-neurexin binding was retained. Thus, in this assay, neuroligin-1 induces apparent synapse formation by binding to presynaptic alpha-neurexins. In transfected neurons, however, neither alpha- nor beta-neurexin binding was essential for the ability of postsynaptic neuroligin-1 to dramatically increase synapse density, suggesting a neurexin-independent mechanism of synapse formation. Moreover, neuroligin-1 dimerization was not required for either the non-neuronal or the neuronal synapse-formation assay. Nevertheless, both alpha-neurexin binding and neuroligin-1 dimerization were essential for the increase in apparent synapse size that is induced by neuroligin-1 in transfected neurons. Thus, neuroligin-1 performs diverse synaptic functions by mechanisms that include as essential components of alpha-neurexin binding and neuroligin dimerization, but extend beyond these activities.
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116
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BLASINI ANAM, RODRíGUEZ MARTA. ALTERED SIGNALING TRIGGERED BY LIGATION OF THE TCR/CD3 RECEPTOR IN T LYMPHOCYTES FROM PATIENTS WITH SYSTEMIC LUPUS ERYTHEMATOSUS: THE ROAD FROM ANERGY TO AUTOIMMUNITY. Int Rev Immunol 2009. [DOI: 10.1080/08830180490452594-17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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117
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Chung HS, Howe GA. A critical role for the TIFY motif in repression of jasmonate signaling by a stabilized splice variant of the JASMONATE ZIM-domain protein JAZ10 in Arabidopsis. THE PLANT CELL 2009; 21:131-45. [PMID: 19151223 PMCID: PMC2648087 DOI: 10.1105/tpc.108.064097] [Citation(s) in RCA: 311] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2008] [Revised: 12/22/2008] [Accepted: 01/02/2009] [Indexed: 05/17/2023]
Abstract
JASMONATE ZIM-domain (JAZ) proteins act as repressors of jasmonate (JA) signaling. Perception of bioactive JAs by the F-box protein CORONATINE INSENSITIVE1 (COI1) causes degradation of JAZs via the ubiquitin-proteasome pathway, which in turn activates the expression of genes involved in plant growth, development, and defense. JAZ proteins contain two highly conserved sequence regions: the Jas domain that interacts with COI1 to destabilize the repressor and the ZIM domain of unknown function. Here, we show that the conserved TIFY motif (TIFF/YXG) within the ZIM domain mediates homo- and heteromeric interactions between most Arabidopsis thaliana JAZs. We have also identified an alternatively spliced form (JAZ10.4) of JAZ10 that lacks the Jas domain and, as a consequence, is highly resistant to JA-induced degradation. Strong JA-insensitive phenotypes conferred by overexpression of JAZ10.4 were suppressed by mutations in the TIFY motif that block JAZ10.4-JAZ interactions. We conclude that JAZ10.4 functions to attenuate signal output in the presence of JA and further suggest that the dominant-negative action of this splice variant involves protein-protein interaction through the ZIM/TIFY domain. The ability of JAZ10.4 to interact with MYC2 is consistent with a model in which a JAZ10.4-containing protein complex directly represses the activity of transcription factors that promote expression of JA response genes.
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Affiliation(s)
- Hoo Sun Chung
- Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824, USA
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118
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Characterization of the effects and functions of sumoylation through rapamycin-mediated heterodimerization. Methods Mol Biol 2008. [PMID: 19107416 DOI: 10.1007/978-1-59745-566-4_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Post-translational modification of proteins, such as phosphorylation, ubiquitination, and SUMO modification, is an important means of regulating a variety of cellular activities. SUMOs (Small Ubiquitin related Modifiers) are covalently conjugated to lysine residues of many proteins by a mechanism that parallels ubiquitination (1). The effects of sumoylation, however, are distinct from ubiquitination. Sumoylation does not directly control protein stability, but regulates proteins through various mechanisms that include modulation of protein-protein interactions, protein-nucleic acid interactions, subcellular protein localization, and enzymatic activity (1-4). There are many examples, however, where the molecular bases for the effects of sumoylation on protein function and on cellular processes remain unclear. Here, we outline the use of an inducible and reversible sumoylation system, based on rapamycin heterodimerization, as a novel tool to characterize the functions of sumoylation in mammalian cells.
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119
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Signaling Chain Homooligomerization (SCHOOL) Model. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2008; 640:121-63. [DOI: 10.1007/978-0-387-09789-3_12] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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120
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Detection of Homo- or Hetero-Association of Doks by Fluorescence Resonance Energy Transfer in Living Cells. Mol Imaging Biol 2008; 11:188-94. [DOI: 10.1007/s11307-008-0189-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2008] [Revised: 06/24/2008] [Accepted: 07/24/2008] [Indexed: 10/21/2022]
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121
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Howarth M, Ting AY. Imaging proteins in live mammalian cells with biotin ligase and monovalent streptavidin. Nat Protoc 2008; 3:534-45. [PMID: 18323822 DOI: 10.1038/nprot.2008.20] [Citation(s) in RCA: 185] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
This protocol describes a simple and efficient way to label specific cell surface proteins with biophysical probes on mammalian cells. Cell surface proteins tagged with a 15-amino acid peptide are biotinylated by Escherichia coli biotin ligase (BirA), whereas endogenous proteins are not modified. The biotin group then allows sensitive and stable binding by streptavidin conjugates. This protocol describes the optimal use of BirA and streptavidin for site-specific labeling and also how to produce BirA and monovalent streptavidin. Streptavidin is tetravalent and the cross-linking of biotinylated targets disrupts many of streptavidin's applications. Monovalent streptavidin has only a single functional biotin-binding site, but retains the femtomolar affinity, low off-rate and high thermostability of wild-type streptavidin. Site-specific biotinylation and streptavidin staining take only a few minutes, while expression of BirA takes 4 d and expression of monovalent streptavidin takes 8 d.
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Affiliation(s)
- Mark Howarth
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA.
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122
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Vera J, Millat T, Kolch W, Wolkenhauer O. Dynamics of receptor and protein transducer homodimerisation. BMC SYSTEMS BIOLOGY 2008; 2:92. [PMID: 18976473 PMCID: PMC2650691 DOI: 10.1186/1752-0509-2-92] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2007] [Accepted: 10/31/2008] [Indexed: 11/30/2022]
Abstract
Background Signalling pathways are complex systems in which not only simple monomeric molecules interact, but also more complex structures that include constitutive or induced protein assemblies. In particular, the hetero-and homo-dimerisation of proteins is a commonly encountered motif in signalling pathways. Several authors have suggested in recent times that dimerisation relates to a series of physical and biological outcomes used by the cell in the regulation of signal transduction. Results In this paper we investigate the role of homodimerisation in receptor-protein transducer interactions. Towards this end, mathematical modelling is used to analyse the features of such kind of interactions and to predict the behaviour of the system under different experimental conditions. A kinetic model in which the interaction between homodimers provokes a dual mechanism of activation (single and double protein transducer activation at the same time) is proposed. In addition, we analyse under which conditions the use of a power-law representation for the system is useful. Furthermore, we investigate the dynamical consequences of this dual mechanism and compare the performance of the system in different simulated experimental conditions. Conclusion The analysis of our mathematical model suggests that in receptor-protein interacting systems with dual mechanism there may be a shift between double and single activation in a way that intense double protein transducer activation could initiate and dominate the signal in the short term (getting a fast intense signal), while single protein activation could control the system in the medium and long term (when input signal is weaker and decreases slowly). Our investigation suggests that homodimerisation and oligomerisation are mechanisms used to enhance and regulate the dynamic properties of the initial steps in signalling pathways.
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Affiliation(s)
- Julio Vera
- University of Rostock, Rostock, Germany.
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123
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Czlapinski JL, Schelle MW, Miller LW, Laughlin ST, Kohler JJ, Cornish VW, Bertozzi CR. Conditional glycosylation in eukaryotic cells using a biocompatible chemical inducer of dimerization. J Am Chem Soc 2008; 130:13186-7. [PMID: 18788807 PMCID: PMC2709988 DOI: 10.1021/ja8037728] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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Chemical inducers of dimerization (CIDs) are cell-permeable small molecules capable of dimerizing two protein targets. The most widely used CID, the natural product rapamycin and its relatives, is immunosuppressive due to interactions with endogenous targets and thus has limited utility in vivo. Here we report a new biocompatible CID, Tmp-SLF, which dimerizes E. coli DHFR and FKBP and has no endogenous mammalian targets that would lead to unwanted in vivo side effects. We employed Tmp-SLF to modulate gene expression in a yeast three-hybrid assay. Finally, we engineered the Golgi-resident glycosyltransferase FucT7 for tunable control by Tmp-SLF in mammalian cells.
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124
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Hamès C, Ptchelkine D, Grimm C, Thevenon E, Moyroud E, Gérard F, Martiel JL, Benlloch R, Parcy F, Müller CW. Structural basis for LEAFY floral switch function and similarity with helix-turn-helix proteins. EMBO J 2008; 27:2628-37. [PMID: 18784751 DOI: 10.1038/emboj.2008.184] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2008] [Accepted: 08/22/2008] [Indexed: 11/09/2022] Open
Abstract
The LEAFY (LFY) protein is a key regulator of flower development in angiosperms. Its gradually increased expression governs the sharp floral transition, and LFY subsequently controls the patterning of flower meristems by inducing the expression of floral homeotic genes. Despite a wealth of genetic data, how LFY functions at the molecular level is poorly understood. Here, we report crystal structures for the DNA-binding domain of Arabidopsis thaliana LFY bound to two target promoter elements. LFY adopts a novel seven-helix fold that binds DNA as a cooperative dimer, forming base-specific contacts in both the major and minor grooves. Cooperativity is mediated by two basic residues and plausibly accounts for LFY's effectiveness in triggering sharp developmental transitions. Our structure reveals an unexpected similarity between LFY and helix-turn-helix proteins, including homeodomain proteins known to regulate morphogenesis in higher eukaryotes. The appearance of flowering plants has been linked to the molecular evolution of LFY. Our study provides a unique framework to elucidate the molecular mechanisms underlying floral development and the evolutionary history of flowering plants.
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Affiliation(s)
- Cécile Hamès
- Laboratoire Physiologie Cellulaire Végétale, UMR5168, Centre National de la Recherche Scientifique, Commissariat à l'énergie atomique, Institut National de la Recherche Agronomique, Université Joseph Fourier, Grenoble, France
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125
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Yun J, Kim SG, Hong S, Park CM. Small interfering peptides as a novel way of transcriptional control. PLANT SIGNALING & BEHAVIOR 2008; 3:615-7. [PMID: 19513250 PMCID: PMC2634540 DOI: 10.4161/psb.3.9.6225] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2008] [Accepted: 05/02/2008] [Indexed: 05/04/2023]
Abstract
Transcription factors are key components of transcriptional regulatory networks governing virtually all aspects of plant growth and developmental processes. Their activities are regulated at various steps, including gene transcription, posttranscriptional mRNA metabolism, posttranslational modifications, nucleocytoplasmic transport, and controlled proteolytic cleavage of membrane-anchored, dormant forms. Dynamic protein dimerization also plays a critical role in this process. An exquisite regulatory scheme has recently been proposed to modulate the action of transcription factors. Small peptides possessing a protein dimerization motif but lacking the DNA-binding motif form nonfunctional heterodimers with a group of specific TFs, inhibiting their transcriptional activation activities. Extensive searches for small proteins that have a similar structural organization in the databases revealed that small peptide-mediated transcription control is not an exceptional case but would be a regulatory mechanism occurring widespread in the Arabidopsis genome.
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Affiliation(s)
- Ju Yun
- Molecular Signaling Laboratory; Department of Chemistry; Seoul National University; Seoul, Korea
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126
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Ullah H, Scappini EL, Moon AF, Williams LV, Armstrong DL, Pedersen LC. Structure of a signal transduction regulator, RACK1, from Arabidopsis thaliana. Protein Sci 2008; 17:1771-80. [PMID: 18715992 DOI: 10.1110/ps.035121.108] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The receptor for activated C-kinase 1 (RACK1) is a highly conserved WD40 repeat scaffold protein found in a wide range of eukaryotic species from Chlamydymonas to plants and humans. In tissues of higher mammals, RACK1 is ubiquitously expressed and has been implicated in diverse signaling pathways involving neuropathology, cellular stress, protein translation, and developmental processes. RACK1 has established itself as a scaffold protein through physical interaction with a myriad of signaling proteins ranging from kinases, phosphatases, ion channels, membrane receptors, G proteins, IP3 receptor, and with widely conserved structural proteins associated with the ribosome. In the plant Arabidopsis thaliana, RACK1A is implicated in diverse developmental and environmental stress pathways. Despite the functional conservation of RACK1-mediated protein-protein interaction-regulated signaling modes, the structural basis of such interactions is largely unknown. Here we present the first crystal structure of a RACK1 protein, RACK1 isoform A from Arabidopsis thaliana, at 2.4 A resolution, as a C-terminal fusion of the maltose binding protein. The structure implicates highly conserved surface residues that could play critical roles in protein-protein interactions and reveals the surface location of proposed post-transcriptionally modified residues. The availability of this structure provides a structural basis for dissecting RACK1-mediated cellular signaling mechanisms in both plants and animals.
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Affiliation(s)
- Hemayet Ullah
- Department of Biology, Howard University, Washington, DC 20059, USA
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127
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Mack ET, Perez-Castillejos R, Suo Z, Whitesides GM. Exact analysis of ligand-induced dimerization of monomeric receptors. Anal Chem 2008; 80:5550-5. [PMID: 18543951 DOI: 10.1021/ac800578w] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This paper analyzes the equilibria involved in the dimerization of monomeric receptors with homo-bifunctional ligands. We provide analytical expressions that can be used to estimate the concentration of each species present in a mixture of homo-bifunctional ligand and monomeric proteins, given initial conditions defining the total concentration of bivalent ligand [L2]0, the total concentration of protein [P]0, one dissociation constant Kd, and a parameter to account for cooperativity alpha. We demonstrate that the fraction of protein present in a complex of two proteins and one bivalent ligand (P x L2 x P) is maximized at [L2]0 = Kd/2 + [P]0/2.
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Affiliation(s)
- Eric T Mack
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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128
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Abstract
Since the discovery of the physical interaction between phytochrome B and the basic helix-loop-helix (bHLH) transcription factor (TF) PIF3 a decade ago, plant phytochrome-signalling research has largely focused on understanding the mechanisms through which phytochromes and members of this bHLH family signal. This concerted effort has revealed how phytochrome and bHLH TF control gene expression and plant growth, and has assigned precise roles to a number of genes in the PIF3-like bHLH TF clade. This work has focused largely on cell autonomous signalling events; however, to synchronize plant growth and developmental events at the tissue and organ level, temporal and spatial signal integration is crucial. This review brings together current knowledge of phytochrome signalling through phytochrome-interacting factors (PIFs)/phytochrome-interacting factor-like (PILs), and it evaluates the current evidence for cross-tissue signal integration.
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Affiliation(s)
- Eve-Marie Josse
- Institute of Molecular Plant Sciences, Edinburgh University, Kings Buildings, Mayfield Road, Edinburgh, EH9 3 JR, UK
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129
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Amoutzias GD, Robertson DL, Van de Peer Y, Oliver SG. Choose your partners: dimerization in eukaryotic transcription factors. Trends Biochem Sci 2008; 33:220-9. [PMID: 18406148 DOI: 10.1016/j.tibs.2008.02.002] [Citation(s) in RCA: 186] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2007] [Revised: 02/12/2008] [Accepted: 02/15/2008] [Indexed: 11/16/2022]
Abstract
In many eukaryotic transcription factor gene families, proteins require a physical interaction with an identical molecule or with another molecule within the same family to form a functional dimer and bind DNA. Depending on the choice of partner and the cellular context, each dimer triggers a sequence of regulatory events that lead to a particular cellular fate, for example, proliferation or differentiation. Recent syntheses of genomic and functional data reveal that partner choice is not random; instead, dimerization specificities, which are strongly linked to the evolution of the protein family, apply. Our focus is on understanding these interaction specificities, their functional consequences and how they evolved. This knowledge is essential for understanding gene regulation and designing a new generation of drugs.
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Affiliation(s)
- Grigoris D Amoutzias
- Department of Plant Systems Biology, VIB, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium
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130
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Kim YS, Kim SG, Lee M, Lee I, Park HY, Seo PJ, Jung JH, Kwon EJ, Suh SW, Paek KH, Park CM. HD-ZIP III activity is modulated by competitive inhibitors via a feedback loop in Arabidopsis shoot apical meristem development. THE PLANT CELL 2008; 20:920-33. [PMID: 18408069 PMCID: PMC2390745 DOI: 10.1105/tpc.107.057448] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2007] [Revised: 03/23/2008] [Accepted: 03/28/2008] [Indexed: 05/19/2023]
Abstract
Shoot apical meristem (SAM) development is coordinately regulated by two interdependent signaling events: one maintaining stem cell identity and the other governing the initiation of lateral organs from the flanks of the SAM. The signaling networks involved in this process are interconnected and are regulated by multiple molecular mechanisms. Class III homeodomain-leucine zipper (HD-ZIP III) proteins are the most extensively studied transcription factors involved in this regulation. However, how different signals are integrated to maintain stem cell identity and to pattern lateral organ polarity remains unclear. Here, we demonstrated that a small ZIP protein, ZPR3, and its functionally redundant homolog, ZPR4, negatively regulate the HD-ZIP III activity in SAM development. ZPR3 directly interacts with PHABULOSA (PHB) and other HD-ZIP III proteins via the ZIP motifs and forms nonfunctional heterodimers. Accordingly, a double mutant, zpr3-2 zpr4-2, exhibits an altered SAM activity with abnormal stem cell maintenance. However, the mutant displays normal patterning of leaf polarity. In addition, we show that PHB positively regulates ZPR3 expression. We therefore propose that HD-ZIP III activity in regulating SAM development is modulated by, among other things, a feedback loop involving the competitive inhibitors ZPR3 and ZPR4.
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Affiliation(s)
- Youn-Sung Kim
- Department of Chemistry, Seoul National University, Seoul 151-742, Korea
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131
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Pazehoski KO, Collins TC, Boyle RJ, Jensen-Seaman MI, Dameron CT. Stalking metal-linked dimers. J Inorg Biochem 2008; 102:522-31. [DOI: 10.1016/j.jinorgbio.2007.10.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2007] [Revised: 10/02/2007] [Accepted: 10/18/2007] [Indexed: 10/22/2022]
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132
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Borrok MJ, Kolonko EM, Kiessling LL. Chemical probes of bacterial signal transduction reveal that repellents stabilize and attractants destabilize the chemoreceptor array. ACS Chem Biol 2008; 3:101-9. [PMID: 18278851 DOI: 10.1021/cb700211s] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The signal transduction cascade responsible for bacterial chemotaxis serves as a model for understanding how cells perceive and respond to their environments. Bacteria react to chemotactic signals by migrating toward attractants and away from repellents. Recent data suggest that the amplification of attractant stimuli depends on receptor collaboration: occupied and unoccupied chemoreceptors act together to relay attractant signals. Attractant signal transmission, therefore, depends on the organization of the chemoreceptors into a lattice of signaling proteins. The importance of this lattice for transducing repellent signals was unexplored. Here, we investigate the role of inter-receptor communication on repellent responses in Escherichia coli. Previously, we found that multivalent displays of attractants are more potent than their monovalent counterparts. To examine the importance of the chemoreceptor lattice in repellent signaling, we synthesized ligands displaying multiple copies of the repellent leucine. Monomeric leucine and low-valency leucine-displaying polymers were sensed as repellents. In contrast, multivalent displays of leucine capable of binding multiple chemoreceptors function not as potent repellents but as attractants. Intriguingly, chemical cross-linking studies indicate that these multivalent ligands, like monovalent attractants, disrupt the cellular chemoreceptor lattice. Thus, repellents stabilize the intrinsic chemoreceptor lattice, and attractants destabilize it. These results indicate that signals can be transmitted with high sensitivity via the disruption of protein-protein interactions. Moreover, our data demonstrate that repellents can be transformed into attractants merely by their multivalent display. These results have implications for designing agonists and antagonists for other signaling systems.
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Affiliation(s)
- M. Jack Borrok
- Department of Biochemistry
- Department of Chemistry
- University of Wisconsin, Madison, Wisconsin 53706
| | - Erin M. Kolonko
- Department of Biochemistry
- Department of Chemistry
- University of Wisconsin, Madison, Wisconsin 53706
| | - Laura L. Kiessling
- Department of Biochemistry
- Department of Chemistry
- University of Wisconsin, Madison, Wisconsin 53706
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133
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Abstract
Protein-protein interactions play a central role in biological processes and thus are an appealing target for innovative drug design a nd development. They can be targeted bysmall molecule inhibitors, peptides and peptidomimetics, which represent an alternative to protein therapeutics that carry many disadvantages. In this chapter, I describe specific protein-protein interactions suggested by a novel model of immune signaling, the Signaling Chain HOmoOLigomerization (SCHOOL) model, to be critical for cell activation mediated by multichain immune recognition receptors (MIRRs) expressed on different cells of the hematopoietic system. Unraveling a long-standing mystery of MIRR triggering and transmembrane signaling, the SCHOOL model reveals the intrareceptor transmembrane interactions and interreceptor cytoplasmic homointeractions as universal therapeutic targets for a diverse variety of disorders mediated by immune cells. Further, assuming that the general principles underlying MIRR-mediated transmembrane signaling mechanisms are similar, the SCHOOL model can be applied to any particular receptor of the MIRR family. Thus, an important application of the SCHOOL model is that global therapeutic strategies targeting key protein-protein interactions involved in MIRR triggering and transmembrane signal transduction may be used to treat a diverse set of immune-mediated diseases. This assumes that clinical knowledge and therapeutic strategies can be transferred between seemingly disparate disorders, such as T-cell-mediated skin diseases and platelet disorders, or combined to develop novel pharmacological approaches. Intriguingly, the SCHOOL model unravels the molecular mechanisms underlying ability of different human viruses such as human immunodeficiency virus, cytomegalovirus and severe acute respiratory syndrome coronavirus to modulate and/or escape the host immune response. It also demonstrates how the lessons learned from viral pathogenesis can be used practically for rational drug design. Application of this model to platelet collagen receptor signaling has already led to the development of a novel concept of platelet inhibition and the invention of new platelet inhibitors, thus proving the suggested hypothesis and highlighting the importance and broad perspectives of the SCHOOL model in the development of new targeting strategies.
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134
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Angell Y, Chen D, Brahimi F, Saragovi HU, Burgess K. A combinatorial method for solution-phase synthesis of labeled bivalent beta-turn mimics. J Am Chem Soc 2007; 130:556-65. [PMID: 18088119 DOI: 10.1021/ja074717z] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Piperidine-functionalized, 1,4-disubstituted-1,2,3-triazoles of generic structure 1 were conceived as "minimalist" mimics of peptidic beta-turn structures. Key features of these molecules include (i) the possibility of incorporating amino acid side chains corresponding to many of the protein amino acids; (ii) a close correspondence of separations of these side chains to i + 1 to i + 2 residues in turns; (iii) facile adjustment of the side-chain vectors on docking while only influencing two critical degrees of freedom; and (iv) some electrostatic polarity. Fifteen monomers of this type were made via copper-mediated cycloaddition reactions. Solution-phase methodologies were devised to assemble these monomers into bivalent compounds in high purity states (typically >85%) so that they could be used in first-pass biological assays without further purification. The skeleton for forming these bivalent compounds is triazine-based. There is a third site which allowed for introduction of a fluorescent label (library of compounds 2) or an alkyne-functionalized triethylene glycol chain (library of compounds 3) included to promote water-solubility and to allow incorporation of probes via copper-mediated cycloaddition reactions. In the event, two 135-membered libraries were prepared, one consisting of compounds 2 and the other of 3. No protecting groups or coupling agents were required; these attributes of the method were important to allow most of the products to be obtained in over 85% purities. The fluorescein-tagged library of compounds 2 was screened in a fluorescence-activated cell sorting (FACS) assay using cells transfected to overexpress one of the following neurotrophin receptors: TrkA, TrkC, and p75. Preliminary findings indicate four compounds 2gm, 2gn, 2gi, and 2gj bound the TrkA receptor selectively; all of these contain a threonine-lysine turn mimic. Thus, a pharmacological probe for the TrkA receptor has been developed.
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Affiliation(s)
- Yu Angell
- Department of Chemistry, Texas A & M University, Box 30012, College Station, Texas 77841, USA
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135
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Vincent F, Cook SP, Johnson EO, Emmert D, Shah K. Engineering unnatural nucleotide specificity to probe G protein signaling. ACTA ACUST UNITED AC 2007; 14:1007-18. [PMID: 17884633 DOI: 10.1016/j.chembiol.2007.08.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2007] [Revised: 07/23/2007] [Accepted: 08/01/2007] [Indexed: 11/26/2022]
Abstract
G proteins comprise approximately 0.5% of proteins encoded by mammalian genomes. To date, there exists a lack of small-molecule modulators that could contribute to their functional study. In this report, we present the use of H-Ras to develop a system that answers this need. Small molecules that allow for the highly specific inhibition or activation of the engineered G protein were developed. The rational design preserved binding of the natural substrates to the G protein, and the mutations were functionally innocuous in a cellular context. This tool can be used for isolating specific G protein effectors, as we demonstrate with the identification of Nol1 as a putative effector of H-Ras. Finally, the generalization of this system was confirmed by applying it to Rap1B, suggesting that this method will be applicable to other G proteins.
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Affiliation(s)
- Fabien Vincent
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907, USA
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136
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Vázquez O, Vázquez ME, Blanco JB, Castedo L, Mascareñas JL. Specific DNA recognition by a synthetic, monomeric Cys2His2 zinc-finger peptide conjugated to a minor-groove binder. Angew Chem Int Ed Engl 2007; 46:6886-90. [PMID: 17674388 DOI: 10.1002/anie.200702345] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Olalla Vázquez
- Department de Química Orgánica y Unidad Asociada al CSIC, Universidade de Santiago de Compostela, Facultade de Química, 15782 Santiago de Compostela, Spain
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137
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Abstract
A protein-DNA dimerizer constructed from a DNA-binding pyrrole-imidazole polyamide and the peptide FYPWMK facilitates binding of the natural transcription factor Exd to an adjacent DNA site. Previous dimerizers have been constructed with the peptide attached to an internal pyrrole monomer in an overall branched oligomer. Linear oligomers constructed by attaching the peptide to the polyamide C-terminus expand the range of protein-DNA dimerization to six additional DNA sites. Replacing the FYPWMK hexapeptide with a WM dipeptide, which was previously functional in branched compounds, does not lead to a functional linear dimerizer. Instead, inserting an additional lysine generates a minimal, linear WMK tripeptide conjugate that maintains the activity of the larger FYPWMK dimerizers in a single DNA-binding site orientation. These studies provide insight into the importance of linker length and composition, binding site spacing and orientation, and the protein-binding domain content that are important for the optimization of protein-DNA dimerizers suitable for biological experiments.
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Affiliation(s)
- Ryan L Stafford
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, USA
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138
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Trouche N, Wieckowski S, Sun W, Chaloin O, Hoebeke J, Fournel S, Guichard G. Small Multivalent Architectures Mimicking Homotrimers of the TNF Superfamily Member CD40L: Delineating the Relationship between Structure and Effector Function. J Am Chem Soc 2007; 129:13480-92. [DOI: 10.1021/ja073169m] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Nathalie Trouche
- Contribution from the CNRS, Institut de Biologie Moléculaire et Cellulaire, laboratoire d'Immunologie et Chimie Thérapeutiques, 15 rue René Descartes, 67084 Strasbourg, France
| | - Sébastien Wieckowski
- Contribution from the CNRS, Institut de Biologie Moléculaire et Cellulaire, laboratoire d'Immunologie et Chimie Thérapeutiques, 15 rue René Descartes, 67084 Strasbourg, France
| | - Weimin Sun
- Contribution from the CNRS, Institut de Biologie Moléculaire et Cellulaire, laboratoire d'Immunologie et Chimie Thérapeutiques, 15 rue René Descartes, 67084 Strasbourg, France
| | - Olivier Chaloin
- Contribution from the CNRS, Institut de Biologie Moléculaire et Cellulaire, laboratoire d'Immunologie et Chimie Thérapeutiques, 15 rue René Descartes, 67084 Strasbourg, France
| | - Johan Hoebeke
- Contribution from the CNRS, Institut de Biologie Moléculaire et Cellulaire, laboratoire d'Immunologie et Chimie Thérapeutiques, 15 rue René Descartes, 67084 Strasbourg, France
| | - Sylvie Fournel
- Contribution from the CNRS, Institut de Biologie Moléculaire et Cellulaire, laboratoire d'Immunologie et Chimie Thérapeutiques, 15 rue René Descartes, 67084 Strasbourg, France
| | - Gilles Guichard
- Contribution from the CNRS, Institut de Biologie Moléculaire et Cellulaire, laboratoire d'Immunologie et Chimie Thérapeutiques, 15 rue René Descartes, 67084 Strasbourg, France
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139
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Vázquez O, Vázquez M, Blanco J, Castedo L, Mascareñas J. Specific DNA Recognition by a Synthetic, Monomeric Cys2His2 Zinc-Finger Peptide Conjugated to a Minor-Groove Binder. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200702345] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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140
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Lemercier G, Gendreizig S, Kindermann M, Johnsson K. Inducing and sensing protein--protein interactions in living cells by selective cross-linking. Angew Chem Int Ed Engl 2007; 46:4281-4. [PMID: 17465435 DOI: 10.1002/anie.200700408] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Guillaume Lemercier
- ISIC-Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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141
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Amoutzias GD, Pichler EE, Mian N, De Graaf D, Imsiridou A, Robinson-Rechavi M, Bornberg-Bauer E, Robertson DL, Oliver SG. A protein interaction atlas for the nuclear receptors: properties and quality of a hub-based dimerisation network. BMC SYSTEMS BIOLOGY 2007; 1:34. [PMID: 17672894 PMCID: PMC1971058 DOI: 10.1186/1752-0509-1-34] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2007] [Accepted: 07/31/2007] [Indexed: 12/16/2022]
Abstract
BACKGROUND The nuclear receptors are a large family of eukaryotic transcription factors that constitute major pharmacological targets. They exert their combinatorial control through homotypic heterodimerisation. Elucidation of this dimerisation network is vital in order to understand the complex dynamics and potential cross-talk involved. RESULTS Phylogeny, protein-protein interactions, protein-DNA interactions and gene expression data have been integrated to provide a comprehensive and up-to-date description of the topology and properties of the nuclear receptor interaction network in humans. We discriminate between DNA-binding and non-DNA-binding dimers, and provide a comprehensive interaction map, that identifies potential cross-talk between the various pathways of nuclear receptors. CONCLUSION We infer that the topology of this network is hub-based, and much more connected than previously thought. The hub-based topology of the network and the wide tissue expression pattern of NRs create a highly competitive environment for the common heterodimerising partners. Furthermore, a significant number of negative feedback loops is present, with the hub protein SHP [NR0B2] playing a major role. We also compare the evolution, topology and properties of the nuclear receptor network with the hub-based dimerisation network of the bHLH transcription factors in order to identify both unique themes and ubiquitous properties in gene regulation. In terms of methodology, we conclude that such a comprehensive picture can only be assembled by semi-automated text-mining, manual curation and integration of data from various sources.
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Affiliation(s)
- Gregory D Amoutzias
- Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK
- Department of Ecology and Evolution, University of Lausanne & Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
- Discovery Information, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, USA
- Bioinformatics & Evolutionary Genomics, Department of Plant Systems Biology, VIB/Ghent University, Technologiepark 927, B-9052 Ghent, Belgium
| | - Elgar E Pichler
- Discovery Information, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, USA
| | | | - David De Graaf
- Discovery Information, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, USA
- Pfizer RTC Cambridge, Cambridge, MA, USA
| | - Anastasia Imsiridou
- Higher Technological Educational Institute of Thessaloniki, 63200 Nea Moudania, Halkidiki, Greece
| | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, University of Lausanne & Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Erich Bornberg-Bauer
- Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK
- Bioinformatics Division, Institute for Evolution and Biodiversity, School of Biological Sciences, University of Muenster, Schlossplatz 4, D48149, Muenster, Germany
| | - David L Robertson
- Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK
| | - Stephen G Oliver
- Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK
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142
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Sun JP, Luo Y, Yu X, Wang WQ, Zhou B, Liang F, Zhang ZY. Phosphatase activity, trimerization, and the C-terminal polybasic region are all required for PRL1-mediated cell growth and migration. J Biol Chem 2007; 282:29043-29051. [PMID: 17656357 DOI: 10.1074/jbc.m703537200] [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] [Indexed: 11/06/2022] Open
Abstract
The phosphatase of regenerating liver (PRL) phosphatases are implicated in a number of tumorigenesis and metastasis processes. The PRLs are unique among protein-tyrosine phosphatases in that they have extremely low phosphatase activity, a high propensity for trimer formation, and a polybasic region that precedes the C-terminal prenylation motif. To investigate the functional significance of these distinctive biochemical and structural features, we established a cell-based system in which ectopic PRL1 expression increased cell proliferation and migration, whereas knockdown of endogenous PRL1 abrogated these cellular activities. We showed that the intrinsic PRL1 phosphatase activity is obligatory for its biological function. We provided evidence that trimerization may be a general property for all PRL enzymes, and that PRL1 trimer formation is essential for the PRL1-mediated cell growth and migration. This finding indicates a novel mechanism for phosphatase regulation. We further demonstrated that the conserved C-terminal polybasic region is important for specific phosphoinositide recognition by PRL1. Both the polybasic residues and the adjacent prenylation motif are required for proper PRL1 subcellular localization and full biological activity.
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Affiliation(s)
- Jin-Peng Sun
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202
| | - Yong Luo
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202
| | - Xiao Yu
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202
| | - Wei-Qing Wang
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202
| | - Bo Zhou
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202
| | - Fubo Liang
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202
| | - Zhong-Yin Zhang
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202.
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143
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Affiliation(s)
- Daniel P Walsh
- Department of Chemistry, New York University, New York, New York 10003, USA
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144
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Lemercier G, Gendreizig S, Kindermann M, Johnsson K. Inducing and Sensing Protein–Protein Interactions in Living Cells by Selective Cross-linking. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200700408] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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145
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Fuentes M, Mateo C, Pessela BCC, Batalla P, Fernandez-Lafuente R, Guisán JM. Solid phase proteomics: Dramatic reinforcement of very weak protein–protein interactions. J Chromatogr B Analyt Technol Biomed Life Sci 2007; 849:243-50. [PMID: 17035103 DOI: 10.1016/j.jchromb.2006.09.024] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2006] [Revised: 09/14/2006] [Accepted: 09/18/2006] [Indexed: 11/19/2022]
Abstract
Very weak protein-protein interactions may play a critical role in cell physiology but they are not easily detectable in "in vitro" experiments. To detect these weak interactions, we have developed a strategy that included: (a) design of a rapid and very effective crosslinking of protein-protein complexes with poly-functional reagents; (b) selective adsorption of very large proteins on lowly activated ionic exchangers, based on the need of a multipoint physical adsorption to incorporate the proteins into the matrix; (c) purification by selective adsorption of protein-protein complexes formed by strong protein-protein interactions, via selective adsorption of the complexes on lowly activated ionic exchangers via multi-protein physical adsorption and leaving the non-associated proteins in the solution; (d) reinforcement of very weak protein-protein interactions by selective adsorption of the complex on lowly activated ionic exchange supports via a synergetic cooperation of the weak protein-protein interaction plus the interactions of both proteins with the support enabling the almost full shifting of the equilibrium towards the association position; (e) control of the aggregation state of proteins like BSA, formed by weak protein-protein interactions. In this last case, it seems that the interaction of the protein molecules placed on the borders of the aggregate with the groups on the support partially stabilizes the whole aggregate, although, some molecules of the aggregate cannot interact with the support. The size of the aggregates may be defined by controlling the concentration of ionised groups on the support: the less activated the supports are, the bigger the complexes. In this way, solid-phase proteomics could be a very interesting tool to detect weak protein-protein interactions.
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Affiliation(s)
- Manuel Fuentes
- Departamento de Biocatálisis, Instituto de Catálisis y Petroleoquímica-CSIC, Campus UAM, Cantoblanco, 28049 Madrid, Spain
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146
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West J, Perkins J, Hok S, Balhorn R, Lightstone FC, Cosman M, DeNardo SJ, DeNardo GL. Direct antilymphoma activity of novel, first-generation "antibody mimics" that bind HLA-DR10-positive non-Hodgkin's lymphoma cells. Cancer Biother Radiopharm 2007; 21:645-54. [PMID: 17257080 DOI: 10.1089/cbr.2006.21.645] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A first-generation series of novel small molecules, collectively known as selective high-affinity ligands (SHALs), were designed and synthesized to mimic the binding of Lym-1, a monoclonal antibody (mAb) shown to be an effective cytotoxic and radionuclide carrier molecule for targeting non-Hodgkin's lymphoma (NHL). Created as radionuclide targeting molecules, these SHALs were intended to have the human leukocyte antigen-DR (HLA-DR) selectivity of Lym-1 mAb and the pharmacokinetics of a small molecule. Because of the remarkable bioactivity of Lym-1 in vitro, the direct antilymphoma activity of three of these SHALs was tested. Two of these SHALs were bidentate and consisted of two ligands connected to the carboxyl and amino groups of lysine and polyethylene glycol (PEG); the third SHAL was a dimeric version of one of the former two SHALs linked with PEG. The three SHALs tested were: LeLPLDB, that contained one deoxycholate and one 5-leu-enkephalin as ligands; (LeacPLD)2LPB, a bis version of LeLPLDB intended to improve "functional affinity"; and ItPLDB, that contained the ligands, deoxycholate and triiodothyronine. Micromolar concentrations of all three SHALs showed binding to Raji, an HLA-DR10-positive human malignant B-cell line but no binding to CEM or Jurkat's, HLA-DR10-negative malignant T-cell lines. Additionally, the Raji cell membrane distributions of all three SHALs and of Lym-1 were remarkably similar. Unlike Lym-1, which causes substantial growth inhibition and cell death in NHL cell lines, these SHALs had no direct antilymphoma activity. In summary, three first-generation SHALs lacked direct antilymphoma activity, although they had selective NHL B-cell binding like Lym-1 mAb. Because of their small size, these SHALs have potential as radionuclide carrier substitutes for Lym-1 mAb to target the HLA-DR10 NHL-related cell-surface protein.
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Affiliation(s)
- Jeremy West
- Department of Internal Medicine and Radiology, University of California, Davis, Sacramento, CA 95816, USA
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147
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Stafford RL, Arndt HD, Brezinski ML, Ansari AZ, Dervan PB. Minimization of a protein-DNA dimerizer. J Am Chem Soc 2007; 129:2660-8. [PMID: 17290996 PMCID: PMC3064071 DOI: 10.1021/ja067971k] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A protein-DNA dimerizer constructed from a DNA-binding polyamide and the peptide FYPWMKG facilitates the binding of a natural transcription factor Exd to an adjacent DNA site. The Exd binding domain can be reduced to a dipeptide WM attached to the polyamide through an epsilon-aminohexanoic acid linker with retention of protein-DNA dimerizer activity. Screening a library of analogues indicated that the tryptophan indole moiety is more important than methionine's side chain or the N-terminal acetamide. Remarkably, switching the stereochemistry of the tryptophan residue (l to d) stabilizes the dimerizer*Exd*DNA ternary complex at 37 degrees C. These observations provide design principles for artificial transcription factors that may function in concert with the cellular regulatory circuitry.
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148
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Hirst-Jensen BJ, Sahoo P, Kieken F, Delmar M, Sorgen PL. Characterization of the pH-dependent interaction between the gap junction protein connexin43 carboxyl terminus and cytoplasmic loop domains. J Biol Chem 2006; 282:5801-13. [PMID: 17178730 DOI: 10.1074/jbc.m605233200] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A prevailing view regarding the regulation of connexin43 (Cx43) gap junction channels is that, upon intracellular acidification, the carboxyl-terminal domain (Cx43CT) moves toward the channel opening to interact with specific residues acting as a receptor site. Previous studies have demonstrated a direct, pH-dependent interaction between the Cx43CT and a Cx43 cytoplasmic loop (Cx43CL) peptide. This interaction was dependent on alpha-helical formation for the peptide in response to acidification; more recent studies have shown that acidification also induces Cx43CT dimerization. Whether Cx43CT dimerization is an important structural component in Cx43 regulation remains to be determined. Here we used an assortment of complimentary biophysical techniques to characterize the binding of Cx43CT or its mutants to itself and/or to a more native-like Cx43CL construct (Cx43CL(100-155), residues 100-155). Our studies expand the observation that specific Cx43CT domains are important for dimerization. We further show that properties of the Cx43CL(100-155) are different from those of the Cx43CL peptide; solvent acidification leads to Cx43CL(100-155) oligomerization and a change in the stoichiometry and binding affinity for the Cx43CT. Homo-Cx43CT and Cx43CL(100-155) oligomerization as well as the Cx43CT/Cx43CL(100-155) interaction can occur under in vivo conditions; moreover, we show that Cx43CL(100-155) strongly affects resonance peaks corresponding to Cx43CT residues Arg-376-Asp-379 and Asn-343-Lys-346. Overall, our data indicate that many of the sites involved in Cx43CT dimerization are also involved in the Cx43CT/Cx43CL interaction; we further propose that chemically induced Cx43CT and Cx43CL oligomerization is important for the interaction between these cytoplasmic domains, which leads to chemically induced gating of Cx43 channels.
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Affiliation(s)
- Bethany J Hirst-Jensen
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska 68198, USA
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149
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Cairo CW, Mirchev R, Golan DE. Cytoskeletal regulation couples LFA-1 conformational changes to receptor lateral mobility and clustering. Immunity 2006; 25:297-308. [PMID: 16901728 DOI: 10.1016/j.immuni.2006.06.012] [Citation(s) in RCA: 112] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2005] [Revised: 05/19/2006] [Accepted: 06/06/2006] [Indexed: 11/21/2022]
Abstract
The alpha(L)beta(2) integrin (leukocyte function-associated antigen-1 [LFA-1]) is regulated to engage and maintain T cell adhesion. Conformational changes in the receptor are associated with changes in receptor-ligand affinity and are necessary for firm adhesion. Less well understood is the relationship between receptor conformation and the regulation of its lateral mobility. We have used fluorescence photobleaching recovery and single-particle tracking to measure the lateral mobility of specific conformations of LFA-1. These measurements show that different receptor conformations have distinct diffusion profiles and that these profiles vary according to the activation state of the cell. Notably, a high-affinity conformation of LFA-1 is mobile on resting cells but immobile on phorbol-12-myristate-13-acetate-activated cells. This activation-induced immobilization is prevented by a calpain inhibitor and by an allosteric LFA-1 inhibitor. Our results suggest that current models of LFA-1 regulation are incomplete and that LFA-1 confinement by cytoskeletal attachment regulates cell adhesion both negatively and positively.
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Affiliation(s)
- Christopher W Cairo
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
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150
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Bernad R, Engelsma D, Sanderson H, Pickersgill H, Fornerod M. Nup214-Nup88 nucleoporin subcomplex is required for CRM1-mediated 60 S preribosomal nuclear export. J Biol Chem 2006; 281:19378-86. [PMID: 16675447 DOI: 10.1074/jbc.m512585200] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The nuclear pore complex (NPC) conducts macromolecular transport to and from the nucleus and provides a kinetic/hydrophobic barrier composed of phenylalanine-glycine (FG) repeats. Nuclear transport is achieved through permeation of this barrier by transport receptors. The transport receptor CRM1 facilitates export of a large variety of cargoes. Export of the preribosomal 60 S subunit follows this pathway through the adaptor protein NMD3. Using RNA interference, we depleted two FG-containing cytoplasmically oriented NPC complexes, Nup214-Nup88 and Nup358, and investigated CRM1-mediated export. A dramatic defect in NMD3-mediated export of preribosomes was found in Nup214-Nup88-depleted cells, whereas only minor export defects were evident in other CRM1 cargoes or upon depletion of Nup358. We show that the large C-terminal FG domain of Nup214 is not accessible to freely diffusing molecules from the nucleus, indicating that it does not conduct 60 S preribosomes through the NPC. Consistently, derivatives of Nup214 lacking the FG-repeat domain rescued the 60 S export defect. We show that the coiled-coil region of Nup214 is sufficient for 60 S nuclear export, coinciding with recruitment of Nup88 to the NPC. Our data indicate that Nup214 plays independent roles in NPC function by participating in the kinetic/hydrophobic barrier through its FG-rich domain and by enabling NPC gating through association with Nup88.
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Affiliation(s)
- Rafael Bernad
- Department of Tumor Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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