101
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Martell JD, Yamagata M, Deerinck TJ, Phan S, Kwa CG, Ellisman MH, Sanes JR, Ting AY. A split horseradish peroxidase for the detection of intercellular protein-protein interactions and sensitive visualization of synapses. Nat Biotechnol 2016; 34:774-80. [PMID: 27240195 PMCID: PMC4942342 DOI: 10.1038/nbt.3563] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 04/07/2016] [Indexed: 12/26/2022]
Abstract
Intercellular protein-protein interactions (PPIs) enable communication between cells in diverse biological processes, including cell proliferation, immune responses, infection, and synaptic transmission, but they are challenging to visualize because existing techniques have insufficient sensitivity and/or specificity. Here we report a split horseradish peroxidase (sHRP) as a sensitive and specific tool for the detection of intercellular PPIs. The two sHRP fragments, engineered through screening of 17 cut sites in HRP followed by directed evolution, reconstitute into an active form when driven together by an intercellular PPI, producing bright fluorescence or contrast for electron microscopy. Fusing the sHRP fragments to the proteins neurexin (NRX) and neuroligin (NLG), which bind each other across the synaptic cleft, enabled sensitive visualization of synapses between specific sets of neurons, including two classes of synapses in the mouse visual system. sHRP should be widely applicable to studying mechanisms of communication between a variety of cell types.
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Affiliation(s)
- Jeffrey D Martell
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Masahito Yamagata
- Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, Cambridge, Massachusetts, USA
| | - Thomas J Deerinck
- National Center for Microscopy and Imaging Research, Center for Research on Biological Systems, University of California at San Diego, La Jolla, San Diego, California, USA
| | - Sébastien Phan
- National Center for Microscopy and Imaging Research, Center for Research on Biological Systems, University of California at San Diego, La Jolla, San Diego, California, USA
| | - Carolyn G Kwa
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Mark H Ellisman
- National Center for Microscopy and Imaging Research, Center for Research on Biological Systems, University of California at San Diego, La Jolla, San Diego, California, USA
- Department of Neurosciences, University of California at San Diego, La Jolla, San Diego, California, USA
- Salk Institute for Biological Studies, La Jolla, San Diego, California, USA
| | - Joshua R Sanes
- Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, Cambridge, Massachusetts, USA
| | - Alice Y Ting
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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102
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Bosmans RPG, Briels JM, Milroy LG, de Greef TFA, Merkx M, Brunsveld L. Supramolecular Control over Split-Luciferase Complementation. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201602807] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Ralph P. G. Bosmans
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems, Department of Biomedical Engineering; Eindhoven University of Technology; Den Dolech 2 5612 AZ Eindhoven The Netherlands
| | - Jeroen M. Briels
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems, Department of Biomedical Engineering; Eindhoven University of Technology; Den Dolech 2 5612 AZ Eindhoven The Netherlands
| | - Lech-Gustav Milroy
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems, Department of Biomedical Engineering; Eindhoven University of Technology; Den Dolech 2 5612 AZ Eindhoven The Netherlands
| | - Tom F. A. de Greef
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems, Department of Biomedical Engineering; Eindhoven University of Technology; Den Dolech 2 5612 AZ Eindhoven The Netherlands
| | - Maarten Merkx
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems, Department of Biomedical Engineering; Eindhoven University of Technology; Den Dolech 2 5612 AZ Eindhoven The Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems, Department of Biomedical Engineering; Eindhoven University of Technology; Den Dolech 2 5612 AZ Eindhoven The Netherlands
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103
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Corbi-Verge C, Kim PM. Motif mediated protein-protein interactions as drug targets. Cell Commun Signal 2016; 14:8. [PMID: 26936767 PMCID: PMC4776425 DOI: 10.1186/s12964-016-0131-4] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 02/25/2016] [Indexed: 12/17/2022] Open
Abstract
Protein-protein interactions (PPI) are involved in virtually every cellular process and thus represent an attractive target for therapeutic interventions. A significant number of protein interactions are frequently formed between globular domains and short linear peptide motifs (DMI). Targeting these DMIs has proven challenging and classical approaches to inhibiting such interactions with small molecules have had limited success. However, recent new approaches have led to the discovery of potent inhibitors, some of them, such as Obatoclax, ABT-199, AEG-40826 and SAH-p53-8 are likely to become approved drugs. These novel inhibitors belong to a wide range of different molecule classes, ranging from small molecules to peptidomimetics and biologicals. This article reviews the main reasons for limited success in targeting PPIs, discusses how successful approaches overcome these obstacles to discovery promising inhibitors for human protein double minute 2 (HDM2), B-cell lymphoma 2 (Bcl-2), X-linked inhibitor of apoptosis protein (XIAP), and provides a summary of the promising approaches currently in development that indicate the future potential of PPI inhibitors in drug discovery.
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Affiliation(s)
- Carles Corbi-Verge
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada.
| | - Philip M Kim
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 3E1, Canada.
- Department of Computer Science, University of Toronto, Toronto, ON, M5S 3E1, Canada.
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104
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105
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Offenborn JN, Waadt R, Kudla J. Visualization and translocation of ternary Calcineurin-A/Calcineurin-B/Calmodulin-2 protein complexes by dual-color trimolecular fluorescence complementation. THE NEW PHYTOLOGIST 2015; 208:269-79. [PMID: 25919910 DOI: 10.1111/nph.13439] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 03/31/2015] [Indexed: 06/04/2023]
Abstract
Fluorescence complementation (FC) techniques are expedient for analyzing bimolecular protein-protein interactions. Here we aimed to develop a method for visualization of ternary protein complexes using dual-color trimolecular fluorescence complementation (TriFC). Dual-color TriFC combines protein fragments of mCherry and mVenus, in which a scaffold protein is bilaterally fused to C-terminal fragments of both fluorescent proteins and combined with potential interacting proteins fused to an N-terminal fluorescent protein fragment. For efficient visual verification of ternary complex formation, TriFC was combined with a cytoplasm to plasma membrane translocation assay. Modular vector sets were designed which are fully compatible with previously reported bimolecular fluorescence complementation (BiFC) vectors. As a proof-of-principle, the ternary complex formation of the PP2B protein phosphatase Calcineurin-A/Calcineurin-B with Calmodulin-2 was investigated in transiently transformed Nicotiana benthamiana leaf epidermal cells. The results indicate a Calcineurin-B-induced interaction of Calmodulin-2 with Calcineurin-A. TriFC and the translocation of TriFC complexes provide a novel tool to investigate ternary complex formations with the simplicity of a BiFC approach. The robustness of FC applications and the opportunity to quantify fluorescence complementation render this assay suitable for a broad range of interaction analyses.
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Affiliation(s)
- Jan Niklas Offenborn
- Institut für Biologie und Biotechnologie der Pflanzen, Universität Münster, Schlossplatz 7, Münster, 48149, Germany
| | - Rainer Waadt
- Institut für Biologie und Biotechnologie der Pflanzen, Universität Münster, Schlossplatz 7, Münster, 48149, Germany
- Plant Developmental Biology, Centre for Organismal Studies, University of Heidelberg, Im Neuenheimer Feld 230, Heidelberg, 69120, Germany
| | - Jörg Kudla
- Institut für Biologie und Biotechnologie der Pflanzen, Universität Münster, Schlossplatz 7, Münster, 48149, Germany
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106
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Cesa LC, Mapp AK, Gestwicki JE. Direct and Propagated Effects of Small Molecules on Protein-Protein Interaction Networks. Front Bioeng Biotechnol 2015; 3:119. [PMID: 26380257 PMCID: PMC4547496 DOI: 10.3389/fbioe.2015.00119] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 08/05/2015] [Indexed: 12/15/2022] Open
Abstract
Networks of protein–protein interactions (PPIs) link all aspects of cellular biology. Dysfunction in the assembly or dynamics of PPI networks is a hallmark of human disease, and as such, there is growing interest in the discovery of small molecules that either promote or inhibit PPIs. PPIs were once considered undruggable because of their relatively large buried surface areas and difficult topologies. Despite these challenges, recent advances in chemical screening methodologies, combined with improvements in structural and computational biology have made some of these targets more tractable. In this review, we highlight developments that have opened the door to potent chemical modulators. We focus on how allostery is being used to produce surprisingly robust changes in PPIs, even for the most challenging targets. We also discuss how interfering with one PPI can propagate changes through the broader web of interactions. Through this analysis, it is becoming clear that a combination of direct and propagated effects on PPI networks is ultimately how small molecules re-shape biology.
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Affiliation(s)
- Laura C Cesa
- Program in Chemical Biology, Life Sciences Institute, University of Michigan , Ann Arbor, MI , USA
| | - Anna K Mapp
- Program in Chemical Biology, Life Sciences Institute, University of Michigan , Ann Arbor, MI , USA ; Department of Chemistry, University of Michigan , Ann Arbor, MI , USA
| | - Jason E Gestwicki
- Program in Chemical Biology, Life Sciences Institute, University of Michigan , Ann Arbor, MI , USA ; Department of Pharmaceutical Chemistry, Institute for Neurodegenerative Diseases, University of California San Francisco , San Francisco, CA , USA
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107
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Blikstad C, Ivarsson Y. High-throughput methods for identification of protein-protein interactions involving short linear motifs. Cell Commun Signal 2015; 13:38. [PMID: 26297553 PMCID: PMC4546347 DOI: 10.1186/s12964-015-0116-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 08/11/2015] [Indexed: 02/07/2023] Open
Abstract
Interactions between modular domains and short linear motifs (3–10 amino acids peptide stretches) are crucial for cell signaling. The motifs typically reside in the disordered regions of the proteome and the interactions are often transient, allowing for rapid changes in response to changing stimuli. The properties that make domain-motif interactions suitable for cell signaling also make them difficult to capture experimentally and they are therefore largely underrepresented in the known protein-protein interaction networks. Most of the knowledge on domain-motif interactions is derived from low-throughput studies, although there exist dedicated high-throughput methods for the identification of domain-motif interactions. The methods include arrays of peptides or proteins, display of peptides on phage or yeast, and yeast-two-hybrid experiments. We here provide a survey of scalable methods for domain-motif interaction profiling. These methods have frequently been applied to a limited number of ubiquitous domain families. It is now time to apply them to a broader set of peptide binding proteins, to provide a comprehensive picture of the linear motifs in the human proteome and to link them to their potential binding partners. Despite the plethora of methods, it is still a challenge for most approaches to identify interactions that rely on post-translational modification or context dependent or conditional interactions, suggesting directions for further method development.
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Affiliation(s)
- Cecilia Blikstad
- Department of Chemistry - BMC, Husargatan 3, 751 23, Uppsala, Sweden
| | - Ylva Ivarsson
- Department of Chemistry - BMC, Husargatan 3, 751 23, Uppsala, Sweden.
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108
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Lampel A, Bram Y, Ezer A, Shaltiel-Kario R, Saad JS, Bacharach E, Gazit E. Targeting the Early Step of Building Block Organization in Viral Capsid Assembly. ACS Chem Biol 2015; 10:1785-90. [PMID: 25997366 DOI: 10.1021/acschembio.5b00347] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Viral assembly, similar to other self-organizing protein systems, relies upon early building blocks, which associate into the late supramolecular structures. An initial and crucial event during HIV-1 core assembly is the dimerization of the capsid protein C-terminal domain, which stabilizes the viral capsid lattice. Thus, monitoring and manipulating this stage is desirable both from mechanistic as well as clinical perspectives. Here, we developed a fluorescent-based method for the detection and visualization of these early capsid interactions. We detected strong dimeric interactions, which were influenced by mutations in the capsid protein. We utilized this assay for potential assembly inhibitors screening, which resulted in the identification of a leading compound that hinders the assembly of capsid protein in vitro. Moreover, a derivative of the compound impaired virus production and infectivity in cell cultures. These findings demonstrate that the described assay efficiently detects the very first association events in HIV-1 capsid formation and emphasize the significance of targeting early intermolecular interactions.
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Affiliation(s)
- Ayala Lampel
- Department
of Molecular Microbiology and Biotechnology, George S. Wise Faculty
of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Yaron Bram
- Department
of Molecular Microbiology and Biotechnology, George S. Wise Faculty
of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Anat Ezer
- Department
of Molecular Microbiology and Biotechnology, George S. Wise Faculty
of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ronit Shaltiel-Kario
- Department
of Molecular Microbiology and Biotechnology, George S. Wise Faculty
of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Jamil S. Saad
- Department
of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294, United States
| | - Eran Bacharach
- Department
of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ehud Gazit
- Department
of Molecular Microbiology and Biotechnology, George S. Wise Faculty
of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
- Department
of Materials Science and Engineering, Iby and Aladar Fleischman Faculty
of Engineering, Tel Aviv University, Tel Aviv 69978, Israel
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109
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Janssen BMG, Engelen W, Merkx M. DNA-directed control of enzyme-inhibitor complex formation: a modular approach to reversibly switch enzyme activity. ACS Synth Biol 2015; 4:547-53. [PMID: 25216042 DOI: 10.1021/sb500278z] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
DNA-templated reversible assembly of an enzyme-inhibitor complex is presented as a new and highly modular approach to control enzyme activity. TEM1-β-lactamase and its inhibitor protein BLIP were conjugated to different oligonucleotides, resulting in enzyme inhibition in the presence of template strand. Formation of a rigid dsDNA linker upon addition of a complementary target strand disrupts the enzyme-inhibitor complex and results in the restoration of enzyme activity, enabling detection of as little as 2 fmol DNA. The noncovalent assembly of the complex allows easy tuning of target and template strands without changing the oligonucleotide-functionalized enzyme and inhibitor domains. Using a panel of eight different template sequences, restoration of enzyme activity was only observed in the presence of the target viral DNA sequence. The use of stable, well-characterized protein domains and the intrinsic modularity of our system should allow easy integration with DNA/RNA-based logic circuits for applications in biomedicine and molecular diagnostics.
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Affiliation(s)
- Brian M. G. Janssen
- Laboratory of Chemical Biology
and Institute for Complex Molecular Systems Eindhoven, University of Technology, Den Dolech 2, 5600
MB Eindhoven, The Netherlands
| | - Wouter Engelen
- Laboratory of Chemical Biology
and Institute for Complex Molecular Systems Eindhoven, University of Technology, Den Dolech 2, 5600
MB Eindhoven, The Netherlands
| | - Maarten Merkx
- Laboratory of Chemical Biology
and Institute for Complex Molecular Systems Eindhoven, University of Technology, Den Dolech 2, 5600
MB Eindhoven, The Netherlands
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110
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Mie M, Naoki T, Kobatake E. Tracking a protein following dissociation from a protein–protein complex using a split SNAP-tag system. Anal Biochem 2015; 477:53-5. [DOI: 10.1016/j.ab.2015.02.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Revised: 02/13/2015] [Accepted: 02/17/2015] [Indexed: 12/01/2022]
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111
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Campbell ST, Carlson KJ, Buchholz CJ, Helmers MR, Ghosh I. Mapping the BH3 Binding Interface of Bcl-xL, Bcl-2, and Mcl-1 Using Split-Luciferase Reassembly. Biochemistry 2015; 54:2632-43. [PMID: 25844633 DOI: 10.1021/bi501505y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The recognition of helical BH3 domains by Bcl-2 homology (BH) receptors plays a central role in apoptosis. The residues that determine specificity or promiscuity in this interactome are difficult to predict from structural and computational data. Using a cell free split-luciferase system, we have generated a 276 pairwise interaction map for 12 alanine mutations at the binding interface for three receptors, Bcl-xL, Bcl-2, and Mcl-1, and interrogated them against BH3 helices derived from Bad, Bak, Bid, Bik, Bim, Bmf, Hrk, and Puma. This panel, in conjunction with previous structural and functional studies, starts to provide a more comprehensive portrait of this interactome, explains promiscuity, and uncovers surprising details; for example, the Bcl-xL R139A mutation disrupts binding to all helices but the Bad-BH3 peptide, and Mcl-1 binding is particularly perturbed by only four mutations of the 12 tested (V220A, N260A, R263A, and F319A), while Bcl-xL and Bcl-2 have a more diverse set of important residues depending on the bound helix.
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Affiliation(s)
- Sean T Campbell
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, Arizona 85721, United States
| | - Kevin J Carlson
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, Arizona 85721, United States
| | - Carl J Buchholz
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, Arizona 85721, United States
| | - Mark R Helmers
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, Arizona 85721, United States
| | - Indraneel Ghosh
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, Arizona 85721, United States
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112
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Finkbeiner S, Frumkin M, Kassner PD. Cell-based screening: extracting meaning from complex data. Neuron 2015; 86:160-74. [PMID: 25856492 PMCID: PMC4457442 DOI: 10.1016/j.neuron.2015.02.023] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 09/23/2014] [Accepted: 01/22/2015] [Indexed: 01/23/2023]
Abstract
Unbiased discovery approaches have the potential to uncover neurobiological insights into CNS disease and lead to the development of therapies. Here, we review lessons learned from imaging-based screening approaches and recent advances in these areas, including powerful new computational tools to synthesize complex data into more useful knowledge that can reliably guide future research and development.
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Affiliation(s)
- Steven Finkbeiner
- Director of the Taube/Koret Center for Neurodegenerative Disease and the Hellman Family Foundation Program in Alzheimer's Disease Research, Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA; Departments of Neurology and Physiology, University of California, San Francisco, San Francisco, CA 94143, USA.
| | - Michael Frumkin
- Director of Engineering, Research, Google, Inc., 1600 Amphitheatre Parkway, Mountain View, CA 94043, USA
| | - Paul D Kassner
- Director of Research, Amgen, Inc., 1120 Veterans Boulevard South, San Francisco, CA 94080, USA
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113
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Wang CW, Yu WT, Lai HP, Lee BY, Gao RC, Tan KT. Steric-dependent label-free and washing-free enzyme amplified protein detection with dual-functional synthetic probes. Anal Chem 2015; 87:4231-6. [PMID: 25811916 DOI: 10.1021/ac504398g] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Enzyme-catalyzed signal amplification with an antibody-enzyme conjugate is commonly employed in many bioanalytical methods to increase assay sensitivity. However, covalent labeling of the enzyme to the antibody, laborious operating procedures, and extensive washing steps are necessary for protein recognition and signal amplification. Herein, we describe a novel label-free and washing-free enzyme-amplified protein detection method by using dual-functional synthetic molecules to impose steric effects upon protein binding. In our approach, protein recognition and signal amplification are modulated by a simple dual-functional synthetic probe which consists of a protein ligand and an inhibitor. In the absence of the target protein, the inhibitor from the dual-functional probe would inhibit the enzyme activity. In contrast, binding of the target protein to the ligand perturbs this enzyme-inhibitor affinity due to the generation of steric effects caused by the close proximity between the target protein and the enzyme, thereby activating the enzyme to initiate signal amplification. With this strategy, the fluorescence signal can be amplified to as high as 70-fold. The generality and versatility of this strategy are demonstrated by the rapid, selective, and sensitive detection of four different proteins, avidin, O6-methylguanine DNA methyltransferase (MGMT), SNAP-tag, and lactoferrin, with four different probes.
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Affiliation(s)
- Chia-Wen Wang
- †Department of Chemistry, National Tsing Hua University, 101 Sec. 2, Kuang Fu Rd., Hsinchu 30013, Taiwan (ROC)
| | - Wan-Ting Yu
- †Department of Chemistry, National Tsing Hua University, 101 Sec. 2, Kuang Fu Rd., Hsinchu 30013, Taiwan (ROC)
| | - Hsiu-Ping Lai
- †Department of Chemistry, National Tsing Hua University, 101 Sec. 2, Kuang Fu Rd., Hsinchu 30013, Taiwan (ROC)
| | - Bing-Yuan Lee
- †Department of Chemistry, National Tsing Hua University, 101 Sec. 2, Kuang Fu Rd., Hsinchu 30013, Taiwan (ROC)
| | - Ruo-Cing Gao
- †Department of Chemistry, National Tsing Hua University, 101 Sec. 2, Kuang Fu Rd., Hsinchu 30013, Taiwan (ROC)
| | - Kui-Thong Tan
- †Department of Chemistry, National Tsing Hua University, 101 Sec. 2, Kuang Fu Rd., Hsinchu 30013, Taiwan (ROC).,‡Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, 101 Sec. 2, Kuang Fu Rd., Hsinchu 30013, Taiwan (ROC)
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114
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Abstract
Cas9, an RNA-guided DNA endonuclease found in clustered regularly interspaced short palindromic repeats (CRISPR) bacterial immune systems, is a versatile tool for genome editing, transcriptional regulation, and cellular imaging applications. Structures of Streptococcus pyogenes Cas9 alone or bound to single-guide RNA (sgRNA) and target DNA revealed a bilobed protein architecture that undergoes major conformational changes upon guide RNA and DNA binding. To investigate the molecular determinants and relevance of the interlobe rearrangement for target recognition and cleavage, we designed a split-Cas9 enzyme in which the nuclease lobe and α-helical lobe are expressed as separate polypeptides. Although the lobes do not interact on their own, the sgRNA recruits them into a ternary complex that recapitulates the activity of full-length Cas9 and catalyzes site-specific DNA cleavage. The use of a modified sgRNA abrogates split-Cas9 activity by preventing dimerization, allowing for the development of an inducible dimerization system. We propose that split-Cas9 can act as a highly regulatable platform for genome-engineering applications.
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115
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Rogers TA, Andrews GE, Jaeger L, Grabow WW. Fluorescent monitoring of RNA assembly and processing using the split-spinach aptamer. ACS Synth Biol 2015; 4:162-6. [PMID: 24932527 DOI: 10.1021/sb5000725] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
As insights into RNA's many diverse cellular roles continue to be gained, interest and applications in RNA self-assembly and dynamics remain at the forefront of structural biology. The bifurcation of functional molecules into nonfunctional fragments provides a useful strategy for controlling and monitoring cellular RNA processes and functionalities. Herein we present the bifurcation of the preexisting Spinach aptamer and demonstrate its utility as a novel split aptamer system for monitoring RNA self-assembly as well as the processing of pre-short interfering substrates. We show for the first time that the Spinach aptamer can be divided into two nonfunctional halves that, once assembled, restore the original fluorescent signal characteristic of the unabridged aptamer. In this regard, the split-Spinach aptamer is represented as a potential tool for monitoring the self-assembly of artificial and/or natural RNAs.
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Affiliation(s)
- Tucker A. Rogers
- Department
of Chemistry and Biochemistry, Seattle Pacific University, 3307 Third
Avenue West, Seattle, Washington 98119, United States
| | - Grant E. Andrews
- Department
of Chemistry and Biochemistry, Seattle Pacific University, 3307 Third
Avenue West, Seattle, Washington 98119, United States
| | - Luc Jaeger
- Department
of Chemistry and Biochemistry, Bio-Molecular Science and Engineering
Program, University of California, Santa Barbara, California 93106-9510, United States
| | - Wade W. Grabow
- Department
of Chemistry and Biochemistry, Seattle Pacific University, 3307 Third
Avenue West, Seattle, Washington 98119, United States
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116
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Camacho-Soto K, Castillo-Montoya J, Tye B, Ogunleye LO, Ghosh I. Small molecule gated split-tyrosine phosphatases and orthogonal split-tyrosine kinases. J Am Chem Soc 2014; 136:17078-86. [PMID: 25409264 DOI: 10.1021/ja5080745] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Protein kinases phosphorylate client proteins, while protein phosphatases catalyze their dephosphorylation and thereby in concert exert reversible control over numerous signal transduction pathways. We have recently reported the design and validation of split-protein kinases that can be conditionally activated by an added small molecule chemical inducer of dimerization (CID), rapamycin. Herein, we provide the rational design and validation of three split-tyrosine phosphatases (PTPs) attached to FKBP and FRB, where catalytic activity can be modulated with rapamycin. We further demonstrate that the orthogonal CIDs, abscisic acid and gibberellic acid, can be used to impart control over the activity of split-tyrosine kinases (PTKs). Finally, we demonstrate that designed split-phosphatases and split-kinases can be activated by orthogonal CIDs in mammalian cells. In sum, we provide a methodology that allows for post-translational orthogonal small molecule control over the activity of user defined split-PTKs and split-PTPs. This methodology has the long-term potential for both interrogating and redesigning phosphorylation dependent signaling pathways.
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Affiliation(s)
- Karla Camacho-Soto
- Department of Chemistry and Biochemistry, University of Arizona , 1306 East University Boulevard, Tucson, Arizona 85721, United States
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117
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Hughes RM, Lawrence DS. Optogenetic engineering: light-directed cell motility. Angew Chem Int Ed Engl 2014; 53:10904-7. [PMID: 25156888 PMCID: PMC4196877 DOI: 10.1002/anie.201404198] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 07/25/2014] [Indexed: 11/10/2022]
Abstract
Genetically encoded, light-activatable proteins provide the means to probe biochemical pathways at specific subcellular locations with exquisite temporal control. However, engineering these systems in order to provide a dramatic jump in localized activity, while retaining a low dark-state background remains a significant challenge. When placed within the framework of a genetically encodable, light-activatable heterodimerizer system, the actin-remodelling protein cofilin induces dramatic changes in the F-actin network and consequent cell motility upon illumination. We demonstrate that the use of a partially impaired mutant of cofilin is critical for maintaining low background activity in the dark. We also show that light-directed recruitment of the reduced activity cofilin mutants to the cytoskeleton is sufficient to induce F-actin remodeling, formation of filopodia, and directed cell motility.
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Affiliation(s)
- Robert M. Hughes
- Department of Chemistry, Division of Chemical Biology and Medicinal Chemistry, and Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599 (USA)
| | - David S. Lawrence
- Department of Chemistry, Division of Chemical Biology and Medicinal Chemistry, and Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599 (USA)
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118
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Zhou Y, Asahara H, Schneider N, Dranchak P, Inglese J, Chong S. Engineering bacterial transcription regulation to create a synthetic in vitro two-hybrid system for protein interaction assays. J Am Chem Soc 2014; 136:14031-8. [PMID: 25188838 PMCID: PMC4195380 DOI: 10.1021/ja502512g] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Transcriptional activation of σ(54)-RNA polymerase holoenzyme (σ(54)-RNAP) in bacteria is dependent on a cis-acting DNA element (bacterial enhancer), which recruits the bacterial enhancer-binding protein to contact the holoenzyme via DNA looping. Using a constructive synthetic biology approach, we recapitulated such process of transcriptional activation by recruitment in a reconstituted cell-free system, assembled entirely from a defined number of purified components. We further engineered the bacterial enhancer-binding protein PspF to create an in vitro two-hybrid system (IVT2H), capable of carrying out gene regulation in response to expressed protein interactions. Compared with genetic systems and other in vitro methods, IVT2H not only allows detection of different types of protein interactions in just a few hours without involving cells but also provides a general correlation of the relative binding strength of the protein interaction with the IVT2H signal. Due to its reconstituted nature, IVT2H provides a biochemical assay platform with a clean and defined background. We demonstrated the proof-of-concept of using IVT2H as an alternative assay for high throughput screening of small-molecule inhibitors of protein-protein interaction.
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Affiliation(s)
- Ying Zhou
- New England Biolabs, Inc. 240 County Road, Ipswich, Massachusetts 01938, United States
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119
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Ma Y, Nagamune T, Kawahara M. Split focal adhesion kinase for probing protein–protein interactions. Biochem Eng J 2014. [DOI: 10.1016/j.bej.2014.06.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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120
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Veggiani G, Zakeri B, Howarth M. Superglue from bacteria: unbreakable bridges for protein nanotechnology. Trends Biotechnol 2014; 32:506-12. [PMID: 25168413 DOI: 10.1016/j.tibtech.2014.08.001] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 07/13/2014] [Accepted: 08/04/2014] [Indexed: 11/28/2022]
Abstract
Biotechnology is often limited by weak interactions. We suggest that an ideal interaction between proteins would be covalent, specific, require addition of only a peptide tag to the protein of interest, and form under a wide range of conditions. Here we summarize peptide tags that are able to form spontaneous amide bonds, based on harnessing reactions of adhesion proteins from the bacterium Streptococcus pyogenes. These include the irreversible peptide-protein interaction of SpyTag with SpyCatcher, as well as irreversible peptide-peptide interactions via SpyLigase. We describe existing applications, including polymerization to enhance cancer cell capture, assembly of living biomaterial, access to diverse protein shapes, and improved enzyme resilience. We also indicate future opportunities for resisting biological force and extending the scope of protein nanotechnology.
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Affiliation(s)
- Gianluca Veggiani
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Bijan Zakeri
- MIT Synthetic Biology Center, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Mark Howarth
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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121
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Hughes RM, Lawrence DS. Optogenetic Engineering: Light-Directed Cell Motility. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201404198] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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122
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Detecting protein-protein interactions based on kinase-mediated growth induction of mammalian cells. Sci Rep 2014; 4:6127. [PMID: 25135216 PMCID: PMC4137342 DOI: 10.1038/srep06127] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 08/01/2014] [Indexed: 01/04/2023] Open
Abstract
Detection of protein–protein interactions (PPIs) is important for understanding numerous processes in mammalian cells; however, existing PPI detection methods often give significant background signals. Here, we propose a novel PPI-detection method based on kinase-mediated growth induction of mammalian cells. In this method, target proteins are fused to the intracellular domain of c-kit (c-kit ICD) and expressed in interleukin-3-dependent mammalian cells. The PPI induces dimerization and activation of c-kit ICDs, which leads to cell growth in the absence of interleukin-3. Using this system, we successfully detected the ligand-dependent homo-interaction of FKBPF36V and hetero-interaction of FKBP and FRBT2098L, as well as the constitutive interaction between MDM2 and a known peptide inhibitor. Intriguingly, cells expressing high-affinity peptide chimeras are selected from the mixture of the cell populations dominantly expressing low-affinity peptide chimeras. These results indicate that this method can detect PPIs with low background levels and is suitable for peptide inhibitor screening.
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123
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Newman RH, Zhang J, Zhu H. Toward a systems-level view of dynamic phosphorylation networks. Front Genet 2014; 5:263. [PMID: 25177341 PMCID: PMC4133750 DOI: 10.3389/fgene.2014.00263] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 07/16/2014] [Indexed: 11/13/2022] Open
Abstract
To better understand how cells sense and respond to their environment, it is important to understand the organization and regulation of the phosphorylation networks that underlie most cellular signal transduction pathways. These networks, which are composed of protein kinases, protein phosphatases and their respective cellular targets, are highly dynamic. Importantly, to achieve signaling specificity, phosphorylation networks must be regulated at several levels, including at the level of protein expression, substrate recognition, and spatiotemporal modulation of enzymatic activity. Here, we briefly summarize some of the traditional methods used to study the phosphorylation status of cellular proteins before focusing our attention on several recent technological advances, such as protein microarrays, quantitative mass spectrometry, and genetically-targetable fluorescent biosensors, that are offering new insights into the organization and regulation of cellular phosphorylation networks. Together, these approaches promise to lead to a systems-level view of dynamic phosphorylation networks.
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Affiliation(s)
- Robert H Newman
- Department of Biology, North Carolina Agricultural and Technical State University Greensboro, NC, USA
| | - Jin Zhang
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine Baltimore, MD, USA ; The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine Baltimore, MD, USA ; Department of Oncology, Johns Hopkins University School of Medicine Baltimore, MD, USA ; Department of Chemical and Biomolecular Engineering, Johns Hopkins University School of Medicine Baltimore, MD, USA
| | - Heng Zhu
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine Baltimore, MD, USA ; High-Throughput Biology Center, Institute for Basic Biomedical Sciences, Johns Hopkins University Baltimore, MD, USA
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124
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Swanson CJ, Sivaramakrishnan S. Harnessing the unique structural properties of isolated α-helices. J Biol Chem 2014; 289:25460-7. [PMID: 25059657 DOI: 10.1074/jbc.r114.583906] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The α-helix is a ubiquitous secondary structural element that is almost exclusively observed in proteins when stabilized by tertiary or quaternary interactions. However, beginning with the unexpected observations of α-helix formation in the isolated C-peptide in ribonuclease A, there is growing evidence that a significant percentage (0.2%) of all proteins contain isolated stable single α-helical domains (SAH). These SAH domains provide unique structural features essential for normal protein function. A subset of SAH domains contain a characteristic ER/K motif, composed of a repeating sequence of ∼4 consecutive glutamic acids followed by ∼4 consecutive basic arginine or lysine (R/K) residues. The ER/K α-helix, also termed the ER/K linker, has been extensively characterized in the context of the myosin family of molecular motors and is emerging as a versatile structural element for protein and cellular engineering applications. Here, we review the structure and function of SAH domains, as well as the tools to identify them in natural proteins. We conclude with a discussion of recent studies that have successfully used the modular ER/K linker for engineering chimeric myosin proteins with altered mechanical properties, as well as synthetic polypeptides that can be used to monitor and systematically modulate protein interactions within cells.
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Affiliation(s)
| | - Sivaraj Sivaramakrishnan
- From the Departments of Biophysics, Cell and Developmental Biology, and Biomedical Engineering, University of Michigan, Ann Arbor, Michigan 48109
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125
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Yoshimura H, Ozawa T. Methods of Split Reporter Reconstitution for the Analysis of Biomolecules. CHEM REC 2014; 14:492-501. [DOI: 10.1002/tcr.201402001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Indexed: 12/31/2022]
Affiliation(s)
- Hideaki Yoshimura
- Department of Chemistry; Graduate School of Science; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Takeaki Ozawa
- Department of Chemistry; Graduate School of Science; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
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126
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Spontaneous self-assembly of engineered armadillo repeat protein fragments into a folded structure. Structure 2014; 22:985-95. [PMID: 24931467 DOI: 10.1016/j.str.2014.05.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 04/30/2014] [Accepted: 05/02/2014] [Indexed: 11/21/2022]
Abstract
Repeat proteins are built of modules, each of which constitutes a structural motif. We have investigated whether fragments of a designed consensus armadillo repeat protein (ArmRP) recognize each other. We examined a split ArmRP consisting of an N-capping repeat (denoted Y), three internal repeats (M), and a C-capping repeat (A). We demonstrate that the C-terminal MA fragment adopts a fold similar to the corresponding part of the entire protein. In contrast, the N-terminal YM2 fragment constitutes a molten globule. The two fragments form a 1:1 YM2:MA complex with a nanomolar dissociation constant essentially identical to the crystal structure of the continuous YM3A protein. Molecular dynamics simulations show that the complex is structurally stable over a 1 μs timescale and reveal the importance of hydrophobic contacts across the interface. We propose that the existence of a stable complex recapitulates possible intermediates in the early evolution of these repeat proteins.
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127
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Mayer C, Müller MM, Gellman SH, Hilvert D. Building Proficient Enzymes with Foldamer Prostheses. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201400945] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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128
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Mayer C, Müller MM, Gellman SH, Hilvert D. Building proficient enzymes with foldamer prostheses. Angew Chem Int Ed Engl 2014; 53:6978-81. [PMID: 24828837 DOI: 10.1002/anie.201400945] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Indexed: 01/28/2023]
Abstract
Foldamers are non-natural oligomers that adopt stable conformations reminiscent of those found in proteins. To evaluate the potential of foldameric subunits for catalysis, semisynthetic enzymes containing foldamer fragments constructed from α- and β-amino acid residues were designed and characterized. Systematic variation of the α→β substitution pattern and types of β-residue afforded highly proficient hybrid catalysts, thus demonstrating the feasibility of expanding the enzyme-engineering toolkit with non-natural backbones.
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Affiliation(s)
- Clemens Mayer
- Laboratory of Organic Chemistry, ETH Zürich, Hönggerberg HCI F339, 8093 Zürich (Switzerland)
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129
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Bale SS, Vernetti L, Senutovitch N, Jindal R, Hegde M, Gough A, McCarty WJ, Bakan A, Bhushan A, Shun TY, Golberg I, DeBiasio R, Usta BO, Taylor DL, Yarmush ML. In vitro platforms for evaluating liver toxicity. Exp Biol Med (Maywood) 2014; 239:1180-1191. [PMID: 24764241 DOI: 10.1177/1535370214531872] [Citation(s) in RCA: 125] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The liver is a heterogeneous organ with many vital functions, including metabolism of pharmaceutical drugs and is highly susceptible to injury from these substances. The etiology of drug-induced liver disease is still debated although generally regarded as a continuum between an activated immune response and hepatocyte metabolic dysfunction, most often resulting from an intermediate reactive metabolite. This debate stems from the fact that current animal and in vitro models provide limited physiologically relevant information, and their shortcomings have resulted in "silent" hepatotoxic drugs being introduced into clinical trials, garnering huge financial losses for drug companies through withdrawals and late stage clinical failures. As we advance our understanding into the molecular processes leading to liver injury, it is increasingly clear that (a) the pathologic lesion is not only due to liver parenchyma but is also due to the interactions between the hepatocytes and the resident liver immune cells, stellate cells, and endothelial cells; and (b) animal models do not reflect the human cell interactions. Therefore, a predictive human, in vitro model must address the interactions between the major human liver cell types and measure key determinants of injury such as the dosage and metabolism of the drug, the stress response, cholestatic effect, and the immune and fibrotic response. In this mini-review, we first discuss the current state of macro-scale in vitro liver culture systems with examples that have been commercialized. We then introduce the paradigm of microfluidic culture systems that aim to mimic the liver with physiologically relevant dimensions, cellular structure, perfusion, and mass transport by taking advantage of micro and nanofabrication technologies. We review the most prominent liver-on-a-chip platforms in terms of their physiological relevance and drug response. We conclude with a commentary on other critical advances such as the deployment of fluorescence-based biosensors to identify relevant toxicity pathways, as well as computational models to create a predictive tool.
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Affiliation(s)
- Shyam Sundhar Bale
- Center for Engineering in Medicine (CEM) at Massachusetts General Hospital, Harvard Medical School, Shriners Hospital for Children, Boston MA 02114
| | - Lawrence Vernetti
- University of Pittsburgh Drug Discovery Institute, Pittsburgh PA 15260.,University of Pittsburgh Department of Computational and Systems Biology, Pittsburgh PA 15260
| | - Nina Senutovitch
- University of Pittsburgh Drug Discovery Institute, Pittsburgh PA 15260.,University of Pittsburgh Department of Computational and Systems Biology, Pittsburgh PA 15260
| | - Rohit Jindal
- Center for Engineering in Medicine (CEM) at Massachusetts General Hospital, Harvard Medical School, Shriners Hospital for Children, Boston MA 02114
| | - Manjunath Hegde
- Center for Engineering in Medicine (CEM) at Massachusetts General Hospital, Harvard Medical School, Shriners Hospital for Children, Boston MA 02114
| | - Albert Gough
- University of Pittsburgh Drug Discovery Institute, Pittsburgh PA 15260.,University of Pittsburgh Department of Computational and Systems Biology, Pittsburgh PA 15260
| | - William J McCarty
- Center for Engineering in Medicine (CEM) at Massachusetts General Hospital, Harvard Medical School, Shriners Hospital for Children, Boston MA 02114
| | - Ahmet Bakan
- University of Pittsburgh Department of Computational and Systems Biology, Pittsburgh PA 15260
| | - Abhinav Bhushan
- Center for Engineering in Medicine (CEM) at Massachusetts General Hospital, Harvard Medical School, Shriners Hospital for Children, Boston MA 02114
| | - Tong Ying Shun
- University of Pittsburgh Drug Discovery Institute, Pittsburgh PA 15260
| | - Inna Golberg
- Center for Engineering in Medicine (CEM) at Massachusetts General Hospital, Harvard Medical School, Shriners Hospital for Children, Boston MA 02114
| | - Richard DeBiasio
- University of Pittsburgh Drug Discovery Institute, Pittsburgh PA 15260
| | - Berk Osman Usta
- Center for Engineering in Medicine (CEM) at Massachusetts General Hospital, Harvard Medical School, Shriners Hospital for Children, Boston MA 02114
| | - D Lansing Taylor
- University of Pittsburgh Drug Discovery Institute, Pittsburgh PA 15260.,University of Pittsburgh Department of Computational and Systems Biology, Pittsburgh PA 15260
| | - Martin L Yarmush
- Center for Engineering in Medicine (CEM) at Massachusetts General Hospital, Harvard Medical School, Shriners Hospital for Children, Boston MA 02114
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130
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Paley MA, Prescher JA. Bioluminescence: a versatile technique for imaging cellular and molecular features. MEDCHEMCOMM 2014; 5:255-267. [PMID: 27594981 PMCID: PMC5006753 DOI: 10.1039/c3md00288h] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Bioluminescence is a ubiquitous imaging modality for visualizing biological processes in vivo. This technique employs visible light and interfaces readily with most cell and tissue types, making it a versatile technology for preclinical studies. Here we review basic bioluminescence imaging principles, along with applications of the technology that are relevant to the medicinal chemistry community. These include noninvasive cell tracking experiments, analyses of protein function, and methods to visualize small molecule metabolites. In each section, we also discuss how bioluminescent tools have revealed insights into experimental therapies and aided drug discovery. Last, we highlight the development of new bioluminescent tools that will enable more sensitive and multi-component imaging experiments and, thus, expand our broader understanding of living systems.
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Affiliation(s)
- Miranda A. Paley
- Department of Chemistry, University of California, Irvine, CA, USA
| | - Jennifer A. Prescher
- Department of Chemistry, University of California, Irvine, CA, USA
- Department of Molecular Biology & Biochemistry, University of California, Irvine, CA, USA
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, USA
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131
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Camacho-Soto K, Castillo-Montoya J, Tye B, Ghosh I. Ligand-Gated Split-Kinases. J Am Chem Soc 2014; 136:3995-4002. [DOI: 10.1021/ja4130803] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Karla Camacho-Soto
- Department of Chemistry and
Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, Arizona 85721, United States
| | - Javier Castillo-Montoya
- Department of Chemistry and
Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, Arizona 85721, United States
| | - Blake Tye
- Department of Chemistry and
Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, Arizona 85721, United States
| | - Indraneel Ghosh
- Department of Chemistry and
Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, Arizona 85721, United States
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132
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Abstract
The use of fluorescent proteins (FPs) in modern cell biology and microscopy has had an extraordinary impact on our ability to investigate dynamic processes in living cells. FPs are unique in that fluorescence is encoded solely by the primary amino acid sequence of the FP and does not require enzymatic modification or cofactors. This genetically encoded fluorescence enables the expression of FPs in diverse cells and organisms and the detection of that fluorescence in living systems. This chapter focuses on microscopy-based applications of FP detection to monitor protein localization, dynamics, interaction, and the cellular environment.
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133
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Large-scale interaction profiling of PDZ domains through proteomic peptide-phage display using human and viral phage peptidomes. Proc Natl Acad Sci U S A 2014; 111:2542-7. [PMID: 24550280 DOI: 10.1073/pnas.1312296111] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The human proteome contains a plethora of short linear motifs (SLiMs) that serve as binding interfaces for modular protein domains. Such interactions are crucial for signaling and other cellular processes, but are difficult to detect because of their low to moderate affinities. Here we developed a dedicated approach, proteomic peptide-phage display (ProP-PD), to identify domain-SLiM interactions. Specifically, we generated phage libraries containing all human and viral C-terminal peptides using custom oligonucleotide microarrays. With these libraries we screened the nine PSD-95/Dlg/ZO-1 (PDZ) domains of human Densin-180, Erbin, Scribble, and Disks large homolog 1 for peptide ligands. We identified several known and putative interactions potentially relevant to cellular signaling pathways and confirmed interactions between full-length Scribble and the target proteins β-PIX, plakophilin-4, and guanylate cyclase soluble subunit α-2 using colocalization and coimmunoprecipitation experiments. The affinities of recombinant Scribble PDZ domains and the synthetic peptides representing the C termini of these proteins were in the 1- to 40-μM range. Furthermore, we identified several well-established host-virus protein-protein interactions, and confirmed that PDZ domains of Scribble interact with the C terminus of Tax-1 of human T-cell leukemia virus with micromolar affinity. Previously unknown putative viral protein ligands for the PDZ domains of Scribble and Erbin were also identified. Thus, we demonstrate that our ProP-PD libraries are useful tools for probing PDZ domain interactions. The method can be extended to interrogate all potential eukaryotic, bacterial, and viral SLiMs and we suggest it will be a highly valuable approach for studying cellular and pathogen-host protein-protein interactions.
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134
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Kilcher S, Mercer J. Next generation approaches to study virus entry and infection. Curr Opin Virol 2014; 4:8-14. [DOI: 10.1016/j.coviro.2013.10.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 10/14/2013] [Accepted: 10/16/2013] [Indexed: 12/11/2022]
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135
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Afonin KA, Desai R, Viard M, Kireeva ML, Bindewald E, Case CL, Maciag AE, Kasprzak WK, Kim T, Sappe A, Stepler M, KewalRamani VN, Kashlev M, Blumenthal R, Shapiro BA. Co-transcriptional production of RNA-DNA hybrids for simultaneous release of multiple split functionalities. Nucleic Acids Res 2014; 42:2085-97. [PMID: 24194608 PMCID: PMC3919563 DOI: 10.1093/nar/gkt1001] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 09/30/2013] [Accepted: 10/04/2013] [Indexed: 12/12/2022] Open
Abstract
Control over the simultaneous delivery of different functionalities and their synchronized intracellular activation can greatly benefit the fields of RNA and DNA biomedical nanotechnologies and allow for the production of nanoparticles and various switching devices with controllable functions. We present a system of multiple split functionalities embedded in the cognate pairs of RNA-DNA hybrids which are programmed to recognize each other, re-associate and form a DNA duplex while also releasing the split RNA fragments which upon association regain their original functions. Simultaneous activation of three different functionalities (RNAi, Förster resonance energy transfer and RNA aptamer) confirmed by multiple in vitro and cell culture experiments prove the concept. To automate the design process, a novel computational tool that differentiates between the thermodynamic stabilities of RNA-RNA, RNA-DNA and DNA-DNA duplexes was developed. Moreover, here we demonstrate that besides being easily produced by annealing synthetic RNAs and DNAs, the individual hybrids carrying longer RNAs can be produced by RNA polymerase II-dependent transcription of single-stranded DNA templates.
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Affiliation(s)
- Kirill A. Afonin
- Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702, USA, Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, HIV Drug Resistance Program, NCI-Frederick, Frederick, MD 21702, USA and Chemical Biology Laboratory, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Ravi Desai
- Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702, USA, Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, HIV Drug Resistance Program, NCI-Frederick, Frederick, MD 21702, USA and Chemical Biology Laboratory, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Mathias Viard
- Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702, USA, Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, HIV Drug Resistance Program, NCI-Frederick, Frederick, MD 21702, USA and Chemical Biology Laboratory, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Maria L. Kireeva
- Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702, USA, Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, HIV Drug Resistance Program, NCI-Frederick, Frederick, MD 21702, USA and Chemical Biology Laboratory, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Eckart Bindewald
- Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702, USA, Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, HIV Drug Resistance Program, NCI-Frederick, Frederick, MD 21702, USA and Chemical Biology Laboratory, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Christopher L. Case
- Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702, USA, Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, HIV Drug Resistance Program, NCI-Frederick, Frederick, MD 21702, USA and Chemical Biology Laboratory, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Anna E. Maciag
- Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702, USA, Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, HIV Drug Resistance Program, NCI-Frederick, Frederick, MD 21702, USA and Chemical Biology Laboratory, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Wojciech K. Kasprzak
- Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702, USA, Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, HIV Drug Resistance Program, NCI-Frederick, Frederick, MD 21702, USA and Chemical Biology Laboratory, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Taejin Kim
- Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702, USA, Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, HIV Drug Resistance Program, NCI-Frederick, Frederick, MD 21702, USA and Chemical Biology Laboratory, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Alison Sappe
- Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702, USA, Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, HIV Drug Resistance Program, NCI-Frederick, Frederick, MD 21702, USA and Chemical Biology Laboratory, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Marissa Stepler
- Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702, USA, Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, HIV Drug Resistance Program, NCI-Frederick, Frederick, MD 21702, USA and Chemical Biology Laboratory, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Vineet N. KewalRamani
- Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702, USA, Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, HIV Drug Resistance Program, NCI-Frederick, Frederick, MD 21702, USA and Chemical Biology Laboratory, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Mikhail Kashlev
- Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702, USA, Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, HIV Drug Resistance Program, NCI-Frederick, Frederick, MD 21702, USA and Chemical Biology Laboratory, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Robert Blumenthal
- Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702, USA, Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, HIV Drug Resistance Program, NCI-Frederick, Frederick, MD 21702, USA and Chemical Biology Laboratory, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Bruce A. Shapiro
- Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702, USA, Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, HIV Drug Resistance Program, NCI-Frederick, Frederick, MD 21702, USA and Chemical Biology Laboratory, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
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136
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Li L, Fierer JO, Rapoport TA, Howarth M. Structural analysis and optimization of the covalent association between SpyCatcher and a peptide Tag. J Mol Biol 2014; 426:309-17. [PMID: 24161952 PMCID: PMC3959856 DOI: 10.1016/j.jmb.2013.10.021] [Citation(s) in RCA: 200] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 10/15/2013] [Accepted: 10/16/2013] [Indexed: 01/07/2023]
Abstract
Peptide tagging is a key strategy for observing and isolating proteins. However, the interactions of proteins with peptides are nearly all rapidly reversible. Proteins tagged with the peptide SpyTag form an irreversible covalent bond to the SpyCatcher protein via a spontaneous isopeptide linkage, thereby offering a genetically encoded way to create peptide interactions that resist force and harsh conditions. Here, we determined the crystal structure of the reconstituted covalent complex of SpyTag and SpyCatcher at 2.1Å resolution. The structure showed the expected reformation of the β-sandwich domain seen in the parental streptococcal adhesin, but flanking sequences at both N- and C-termini of SpyCatcher were disordered. In addition, only 10 out of 13 amino acids of the SpyTag peptide were observed to interact with SpyCatcher, pointing to specific contacts important for rapid split protein reconstitution. Based on these structural insights, we expressed a range of SpyCatcher variants and identified a minimized SpyCatcher, 32 residues shorter, that maintained rapid reaction with SpyTag. Together, these results give insight into split protein β-strand complementation and enhance a distinct approach to ultrastable molecular interaction.
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Affiliation(s)
- Long Li
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, US
| | - Jacob O. Fierer
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Tom A. Rapoport
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, US
| | - Mark Howarth
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
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137
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Syafrizayanti, Betzen C, Hoheisel JD, Kastelic D. Methods for analyzing and quantifying protein–protein interaction. Expert Rev Proteomics 2014; 11:107-20. [DOI: 10.1586/14789450.2014.875857] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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138
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Guo Z, Zhong X, Lin L, Wu S, Wang T, Chen Y, Zhai X, Wang Y, Wu H, Tong L, Han Y, Pan B, Peng Y, Si X, Zhang F, Zhao W, Zhong Z. A 3C(pro)-dependent bioluminescence imaging assay for in vivo evaluation of anti-enterovirus 71 agents. Antiviral Res 2014; 101:82-92. [PMID: 24263113 DOI: 10.1016/j.antiviral.2013.11.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 11/01/2013] [Accepted: 11/06/2013] [Indexed: 11/29/2022]
Abstract
Enterovirus 71 (EV71), a member of Picornaviridae, is one of the major pathogens of human hand, foot and mouth disease. EV71 mainly infects children and causes severe neurological complications and even death. The pathogenesis of EV71 infection is largely unknown, and no clinically approved vaccine or effective treatment is available to date. Here we described a novel bioluminescence imaging approach for EV71 detection. In this approach, a plasmid-based reporter was constructed to express the fusion protein AmN(Q/G)BC, a split firefly luciferase mutant, which can be specifically cleaved by EV71 protease 3C(pro). Upon cleavage, the splitting fusion protein restores luciferase activity. Our test confirmed that AmN(Q/G)BC was specifically cleaved by 3C(pro) and EV71 and restored the luciferase activity to a degree that corresponds to the 3C(pro) and virus doses in cells and mice. The anti-EV71 effect of GW5074 and U0126, two mitogen-activated protein kinase (MAPK) inhibitors, was evaluated using this approach to validate its application of screening anti-EV71 agents. We found that the AmN(Q/G)BC reporter efficiently monitored the inhibitory effect of GW5074 and U0126 on EV71 infection under in vitro and in vivo conditions. The data from AmN(Q/G)BC reporter were consistent with Western blotting and histopathology examination. Taken together, this real-time imaging approach can quantitatively monitor the efficacy of anti-EV71 agents and is valuable for anti-EV71 drug screening and evaluation, especially, under in vivo conditions.
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Affiliation(s)
- Zhiwei Guo
- Department of Microbiology, Harbin Medical University, Harbin 150081, China
| | - Xiaoyan Zhong
- Department of Microbiology, Harbin Medical University, Harbin 150081, China
| | - Lexun Lin
- Department of Microbiology, Harbin Medical University, Harbin 150081, China
| | - Shuo Wu
- Department of Microbiology, Harbin Medical University, Harbin 150081, China
| | - Tianying Wang
- Department of Microbiology, Harbin Medical University, Harbin 150081, China
| | - Yang Chen
- Department of Microbiology, Harbin Medical University, Harbin 150081, China
| | - Xia Zhai
- Department of Microbiology, Harbin Medical University, Harbin 150081, China
| | - Yan Wang
- Department of Microbiology, Harbin Medical University, Harbin 150081, China
| | - Heng Wu
- Department of Microbiology, Harbin Medical University, Harbin 150081, China
| | - Lei Tong
- Department of Microbiology, Harbin Medical University, Harbin 150081, China
| | - Yelu Han
- Department of Microbiology, Harbin Medical University, Harbin 150081, China
| | - Bo Pan
- Department of Microbiology, Harbin Medical University, Harbin 150081, China
| | - Yihong Peng
- Department of Microbiology, Peking University Health Science Center, Beijing 100191, China
| | - Xiaoning Si
- Department of Microbiology, Harbin Medical University, Harbin 150081, China
| | - Fengmin Zhang
- Department of Microbiology, Harbin Medical University, Harbin 150081, China
| | - Wenran Zhao
- Department of Cell Biology, Harbin Medical University, Harbin 150081, China.
| | - Zhaohua Zhong
- Department of Microbiology, Harbin Medical University, Harbin 150081, China.
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139
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Application of enzyme bioluminescence for medical diagnostics. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2014; 144:175-97. [PMID: 25084998 DOI: 10.1007/978-3-662-43385-0_6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Nowadays luciferases are effectively used as analytical instruments in a great variety of research fields. Of special interest are the studies dealing with elaboration of novel analytical systems for the purposes of medical diagnostics. The ever-expanding spectrum of clinically important analytes accounts for the increasing demand for new techniques for their detection. In this chapter we have made an attempt to summarize the results on applications of luciferases as reporters in binding assays including immunoassay, nucleic acid hybridization assay, and so on. The data over the last 15 years have been analyzed and clearly show that luciferase-based assays, due to extremely high sensitivity, low cost, and the lack of need for skilled personnel, hold much promise for clinical diagnostics.
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140
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Stoilova-McPhie S, Ali S, Laezza F. Protein-Protein Interactions as New Targets for Ion Channel Drug Discovery. AUSTIN JOURNAL OF PHARMACOLOGY AND THERAPEUTICS 2013; 1:5. [PMID: 25485305 PMCID: PMC4255474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Protein-protein interactions (PPI) are key molecular elements that provide the basis of signaling in virtually all cellular processes. The precision and specificity of these molecular interactions have ignited a strong interest in pursuing PPI surfaces as new targets for drug discovery, especially against ion channels in the central nervous system (CNS) where selectivity and specificity are vital for developing drugs with limited side effects. Ion channels are large transmembrane domain proteins assembled with multiple regulatory proteins binding to the intracellular portion of channels. These macromolecular complexes are difficult to isolate, purify and reconstitute, posing a significant barrier in targeting these PPI for drug discovery purposes. Here, we will provide a short overview of salient features of PPI and discuss successful studies focusing on protein-channel interactions that could inspire new drug discovery campaigns targeting ion channel complexes.
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Affiliation(s)
- Svetla Stoilova-McPhie
- Department of Neuroscience and Cell Biology, The University of Texas Medical Branch, Galveston, TX 77555, USA
- Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Syed Ali
- Department Pharmacology & Toxicology, The University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Fernanda Laezza
- Department Pharmacology & Toxicology, The University of Texas Medical Branch, Galveston, TX 77555, USA
- Center for Neurodegenerative Diseases, The University of Texas Medical Branch, Galveston, TX 77555, USA
- Center for Addiction Research, The University of Texas Medical Branch, Galveston, TX 77555, USA
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141
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Blackstock D, Park M, Sun Q, Tsai SL, Chen W. Engineering protein modules for diagnostic applications. Curr Opin Chem Eng 2013. [DOI: 10.1016/j.coche.2013.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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142
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Cabantous S, Nguyen HB, Pedelacq JD, Koraïchi F, Chaudhary A, Ganguly K, Lockard MA, Favre G, Terwilliger TC, Waldo GS. A new protein-protein interaction sensor based on tripartite split-GFP association. Sci Rep 2013; 3:2854. [PMID: 24092409 PMCID: PMC3790201 DOI: 10.1038/srep02854] [Citation(s) in RCA: 167] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 09/16/2013] [Indexed: 11/12/2022] Open
Abstract
Monitoring protein-protein interactions in living cells is key to unraveling their roles in numerous cellular processes and various diseases. Previously described split-GFP based sensors suffer from poor folding and/or self-assembly background fluorescence. Here, we have engineered a micro-tagging system to monitor protein-protein interactions in vivo and in vitro. The assay is based on tripartite association between two twenty amino-acids long GFP tags, GFP10 and GFP11, fused to interacting protein partners, and the complementary GFP1-9 detector. When proteins interact, GFP10 and GFP11 self-associate with GFP1-9 to reconstitute a functional GFP. Using coiled-coils and FRB/FKBP12 model systems we characterize the sensor in vitro and in Escherichia coli. We extend the studies to mammalian cells and examine the FK-506 inhibition of the rapamycin-induced association of FRB/FKBP12. The small size of these tags and their minimal effect on fusion protein behavior and solubility should enable new experiments for monitoring protein-protein association by fluorescence.
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Affiliation(s)
- Stéphanie Cabantous
- INSERM UMR1037, Cancer Research Center of Toulouse, Université de Toulouse, Institut Claudius Regaud, F-31052 Toulouse, France
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143
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Wang L, Carnegie GK. Flow cytometric analysis of bimolecular fluorescence complementation: a high throughput quantitative method to study protein-protein interaction. J Vis Exp 2013. [PMID: 23979513 DOI: 10.3791/50529] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Among methods to study protein-protein interaction inside cells, Bimolecular Fluorescence Complementation (BiFC) is relatively simple and sensitive. BiFC is based on the production of fluorescence using two non-fluorescent fragments of a fluorescent protein (Venus, a Yellow Fluorescent Protein variant, is used here). Non-fluorescent Venus fragments (VN and VC) are fused to two interacting proteins (in this case, AKAP-Lbc and PDE4D3), yielding fluorescence due to VN-AKAP-Lbc-VC-PDE4D3 interaction and the formation of a functional fluorescent protein inside cells. BiFC provides information on the subcellular localization of protein complexes and the strength of protein interactions based on fluorescence intensity. However, BiFC analysis using microscopy to quantify the strength of protein-protein interaction is time-consuming and somewhat subjective due to heterogeneity in protein expression and interaction. By coupling flow cytometric analysis with BiFC methodology, the fluorescent BiFC protein-protein interaction signal can be accurately measured for a large quantity of cells in a short time. Here, we demonstrate an application of this methodology to map regions in PDE4D3 that are required for the interaction with AKAP-Lbc. This high throughput methodology can be applied to screening factors that regulate protein-protein interaction.
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Affiliation(s)
- Li Wang
- Department of Pharmacology, University of Illinois at Chicago, USA
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144
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Meister GE, Joshi NS. An Engineered Calmodulin-Based Allosteric Switch for Peptide Biosensing. Chembiochem 2013; 14:1460-7. [DOI: 10.1002/cbic.201300168] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Indexed: 11/07/2022]
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145
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Afonin KA, Viard M, Martins AN, Lockett SJ, Maciag AE, Freed EO, Heldman E, Jaeger L, Blumenthal R, Shapiro BA. Activation of different split functionalities on re-association of RNA-DNA hybrids. NATURE NANOTECHNOLOGY 2013; 8:296-304. [PMID: 23542902 PMCID: PMC3618561 DOI: 10.1038/nnano.2013.44] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Accepted: 02/26/2013] [Indexed: 05/12/2023]
Abstract
Split-protein systems, an approach that relies on fragmentation of proteins with their further conditional re-association to form functional complexes, are increasingly used for various biomedical applications. This approach offers tight control of protein functions and improved detection sensitivity. Here we report a similar technique based on a pair of RNA-DNA hybrids that can be used generally for triggering different split functionalities. Individually, each hybrid is inactive but when two cognate hybrids re-associate, different functionalities are triggered inside mammalian cells. As a proof of concept, this work mainly focuses on the activation of RNA interference. However, the release of other functionalities (such as resonance energy transfer and RNA aptamer) is also shown. Furthermore, in vivo studies demonstrate a significant uptake of the hybrids by tumours together with specific gene silencing. This split-functionality approach presents a new route in the development of 'smart' nucleic acid-based nanoparticles and switches for various biomedical applications.
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Affiliation(s)
- Kirill A. Afonin
- Center for Cancer Research Nanobiology Program, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Mathias Viard
- Center for Cancer Research Nanobiology Program, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
- Basic Science Program, SAIC-Frederick, Inc., NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Angelica N. Martins
- HIV Drug Resistance Program, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Stephen J. Lockett
- Advanced Technology Program, SAIC-Frederick, Inc., NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Anna E. Maciag
- Basic Science Program, SAIC-Frederick, Inc., NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
- Chemical Biology Laboratory, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Eric O. Freed
- HIV Drug Resistance Program, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Eliahu Heldman
- Basic Science Program, SAIC-Frederick, Inc., NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Luc Jaeger
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106-9510, USA
| | - Robert Blumenthal
- Center for Cancer Research Nanobiology Program, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Bruce A. Shapiro
- Center for Cancer Research Nanobiology Program, NCI, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
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146
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Ohmuro-Matsuyama Y, Chung CI, Ueda H. Demonstration of protein-fragment complementation assay using purified firefly luciferase fragments. BMC Biotechnol 2013; 13:31. [PMID: 23536995 PMCID: PMC3626928 DOI: 10.1186/1472-6750-13-31] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Accepted: 03/15/2013] [Indexed: 12/25/2022] Open
Abstract
Background Human interactome is predicted to contain 150,000 to 300,000 protein-protein interactions, (PPIs). Protein-fragment complementation assay (PCA) is one of the most widely used methods to detect PPI, as well as Förster resonance energy transfer (FRET). To date, successful applications of firefly luciferase (Fluc)-based PCA have been reported in vivo, in cultured cells and in cell-free lysate, owing to its high sensitivity, high signal-to-background (S/B) ratio, and reversible response. Here we show the assay also works with purified proteins with unexpectedly rapid kinetics. Results Split Fluc fragments both fused with a rapamycin-dependently interacting protein pair were made and expressed in E. coli system, and purified to homogeneity. When the proteins were used for PCA to detect rapamycin-dependent PPI, they enabled a rapid detection (~1 s) of PPI with high S/B ratio. When Fn7-8 domains (7 nm in length) that was shown to abrogate GFP mutant-based FRET was inserted between split Fluc and FKBP12 as a rigid linker, it still showed some response, suggesting less limitation in interacting partner’s size. Finally, the stability of the probe was investigated. Preincubation of the probes at 37 degreeC up to 1 h showed marked decrease of the luminescent signal to 1.5%, showing the limited stability of this system. Conclusion Fluc PCA using purified components will enable a rapid and handy detection of PPIs with high S/B ratio, avoiding the effects of concomitant components. Although the system might not be suitable for large-scale screening due to its limited stability, it can detect an interaction over larger distance than by FRET. This would be the first demonstration of Fluc PCA in vitro, which has a distinct advantage over other PPI assays. Our system enables detection of direct PPIs without risk of perturbation by PPI mediators in the complex cellular milieu.
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Affiliation(s)
- Yuki Ohmuro-Matsuyama
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
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147
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Braun P, Aubourg S, Van Leene J, De Jaeger G, Lurin C. Plant protein interactomes. ANNUAL REVIEW OF PLANT BIOLOGY 2013; 64:161-87. [PMID: 23330791 DOI: 10.1146/annurev-arplant-050312-120140] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Protein-protein interactions are a critical element of biological systems, and the analysis of interaction partners can provide valuable hints about unknown functions of a protein. In recent years, several large-scale protein interaction studies have begun to unravel the complex networks through which plant proteins exert their functions. Two major classes of experimental approaches are used for protein interaction mapping: analysis of direct interactions using binary methods such as yeast two-hybrid or split ubiquitin, and analysis of protein complexes through affinity purification followed by mass spectrometry. In addition, bioinformatics predictions can suggest interactions that have evaded detection by other methods or those of proteins that have not been investigated. Here we review the major approaches to construct, analyze, use, and carry out quality control on plant protein interactome networks. We present experimental and computational approaches for large-scale mapping, methods for validation or smaller-scale functional studies, important bioinformatics resources, and findings from recently published large-scale plant interactome network maps.
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Affiliation(s)
- Pascal Braun
- Department of Plant Systems Biology, Center for Life and Food Sciences Weihenstephan, Technische Universität München (TUM), 85354 Freising-Weihenstephan, Germany.
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148
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Chumakov SP, Kravchenko YE, Chumakov PM. Protein complementation as tool for studying protein-protein interactions in living cells. Mol Biol 2012. [DOI: 10.1134/s0026893312050020] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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149
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Ishikawa H, Meng F, Kondo N, Iwamoto A, Matsuda Z. Generation of a dual-functional split-reporter protein for monitoring membrane fusion using self-associating split GFP. Protein Eng Des Sel 2012; 25:813-20. [PMID: 22942393 DOI: 10.1093/protein/gzs051] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Split reporter proteins capable of self-association and reactivation have applications in biomedical research, but designing these proteins, especially the selection of appropriate split points, has been somewhat arbitrary. We describe a new methodology to facilitate generating split proteins using split GFP as a self-association module. We first inserted the entire GFP module at one of several candidate split points in the protein of interest, and chose clones that retained the GFP signal and high activity relative to the original protein. Once such chimeric clones were identified, a final pair of split proteins was generated by splitting the GFP-inserted chimera within the GFP domain. Applying this strategy to Renilla reniformis luciferase, we identified a new split point that gave 10 times more activity than the previous split point. The process of membrane fusion was monitored with high sensitivity using a new pair of split reporter proteins. We also successfully identified new split points for HaloTag protein and firefly luciferase, generating pairs of self-associating split proteins that recovered the functions of both GFP and the original protein. This simple method of screening will facilitate the designing of split proteins that are capable of self-association through the split GFP domains.
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Affiliation(s)
- Hirohito Ishikawa
- Research Center for Asian Infectious Diseases, Institute of Medical Science, University of Tokyo, Shirokanedai, Minato-ku, Tokyo, Japan
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150
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Yeast “N”-hybrid systems for protein–protein and drug–protein interaction discovery. Methods 2012; 57:423-9. [DOI: 10.1016/j.ymeth.2012.06.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Revised: 06/01/2012] [Accepted: 06/08/2012] [Indexed: 01/05/2023] Open
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