1
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Cuadrado AF, Van Damme D. Unlocking protein-protein interactions in plants: a comprehensive review of established and emerging techniques. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:5220-5236. [PMID: 38437582 DOI: 10.1093/jxb/erae088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 02/29/2024] [Indexed: 03/06/2024]
Abstract
Protein-protein interactions orchestrate plant development and serve as crucial elements for cellular and environmental communication. Understanding these interactions offers a gateway to unravel complex protein networks that will allow a better understanding of nature. Methods for the characterization of protein-protein interactions have been around over 30 years, yet the complexity of some of these interactions has fueled the development of new techniques that provide a better understanding of the underlying dynamics. In many cases, the application of these techniques is limited by the nature of the available sample. While some methods require an in vivo set-up, others solely depend on protein sequences to study protein-protein interactions via an in silico set-up. The vast number of techniques available to date calls for a way to select the appropriate tools for the study of specific interactions. Here, we classify widely spread tools and new emerging techniques for the characterization of protein-protein interactions based on sample requirements while providing insights into the information that they can potentially deliver. We provide a comprehensive overview of commonly used techniques and elaborate on the most recent developments, showcasing their implementation in plant research.
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Affiliation(s)
- Alvaro Furones Cuadrado
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Daniël Van Damme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
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2
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Swapna LS, Stevens GC, Sardinha-Silva A, Hu LZ, Brand V, Fusca DD, Wan C, Xiong X, Boyle JP, Grigg ME, Emili A, Parkinson J. ToxoNet: A high confidence map of protein-protein interactions in Toxoplasma gondii. PLoS Comput Biol 2024; 20:e1012208. [PMID: 38900844 PMCID: PMC11219001 DOI: 10.1371/journal.pcbi.1012208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 07/02/2024] [Accepted: 05/28/2024] [Indexed: 06/22/2024] Open
Abstract
The apicomplexan intracellular parasite Toxoplasma gondii is a major food borne pathogen that is highly prevalent in the global population. The majority of the T. gondii proteome remains uncharacterized and the organization of proteins into complexes is unclear. To overcome this knowledge gap, we used a biochemical fractionation strategy to predict interactions by correlation profiling. To overcome the deficit of high-quality training data in non-model organisms, we complemented a supervised machine learning strategy, with an unsupervised approach, based on similarity network fusion. The resulting combined high confidence network, ToxoNet, comprises 2,063 interactions connecting 652 proteins. Clustering identifies 93 protein complexes. We identified clusters enriched in mitochondrial machinery that include previously uncharacterized proteins that likely represent novel adaptations to oxidative phosphorylation. Furthermore, complexes enriched in proteins localized to secretory organelles and the inner membrane complex, predict additional novel components representing novel targets for detailed functional characterization. We present ToxoNet as a publicly available resource with the expectation that it will help drive future hypotheses within the research community.
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Affiliation(s)
| | - Grant C. Stevens
- Program in Molecular Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Aline Sardinha-Silva
- Molecular Parasitology Section, Laboratory of Parasitic Diseases, NIAID, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Lucas Zhongming Hu
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Verena Brand
- Program in Molecular Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Daniel D. Fusca
- Program in Molecular Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Cuihong Wan
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Xuejian Xiong
- Program in Molecular Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jon P. Boyle
- Department of Biological Sciences, Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Michael E. Grigg
- Molecular Parasitology Section, Laboratory of Parasitic Diseases, NIAID, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Andrew Emili
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Department of Biology and Biochemistry, Boston University, Boston, Massachusetts, United States of America
| | - John Parkinson
- Program in Molecular Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
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3
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Miotto M, Milanetti E, Mincigrucci R, Masciovecchio C, Ruocco G. High-Throughput Interactome Determination via Sulfur Anomalous Scattering. J Phys Chem Lett 2024; 15:3478-3485. [PMID: 38513124 PMCID: PMC11000237 DOI: 10.1021/acs.jpclett.3c03632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/16/2024] [Accepted: 02/22/2024] [Indexed: 03/23/2024]
Abstract
We propose a novel approach for detecting the binding between proteins making use of the anomalous diffraction of natively present heavy elements, e.g., sulfurs, inside molecular three-dimensional structures. In particular, we analytically and numerically show that the diffraction patterns produced by the anomalous scattering of the sulfur atoms in a given direction depend additively on the relative distances between all couples of sulfur atoms. Thus, the differences in the patterns produced by bound proteins with respect to their nonbonded states can be exploited to rapidly assess protein complex formation. On the basis of our results, we suggest a possible experimental procedure for detecting protein-protein binding. Overall, the completely label-free and rapid method we propose may be readily extended to probe interactions on a large scale, thus paving the way for the development of a novel field of research based on a synchrotron light source.
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Affiliation(s)
- Mattia Miotto
- Center
for Life Nano & Neuro Science, Istituto
Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
| | - Edoardo Milanetti
- Center
for Life Nano & Neuro Science, Istituto
Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
- Department
of Physics, Sapienza University, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Riccardo Mincigrucci
- Elettra-Sincrotrone
Trieste S.C.p.A. di interesse nazionale, Strada Statale 14 - km 163.5 in AREA Science Park,
Basovizza, 34149 Trieste, Italy
| | - Claudio Masciovecchio
- Elettra-Sincrotrone
Trieste S.C.p.A. di interesse nazionale, Strada Statale 14 - km 163.5 in AREA Science Park,
Basovizza, 34149 Trieste, Italy
| | - Giancarlo Ruocco
- Center
for Life Nano & Neuro Science, Istituto
Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
- Department
of Physics, Sapienza University, Piazzale Aldo Moro 5, 00185 Rome, Italy
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4
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Wang S, Uchida N, Ueno K, Matsubara T, Sato T, Aida T, Ishida Y. Effects of the Magnetic Orientation of M13 Bacteriophage on Phage Display Selection. Chemistry 2023; 29:e202302261. [PMID: 37638672 DOI: 10.1002/chem.202302261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/24/2023] [Accepted: 08/28/2023] [Indexed: 08/29/2023]
Abstract
Although phage display selection using a library of M13 bacteriophage has become a powerful tool for finding peptides that bind to target materials on demand, a remaining concern of this method is the interference by the M13 main body, which is a huge filament >103 times larger than the displayed peptide, and therefore would nonspecifically adhere to the target or sterically inhibit the binding of the displayed peptide. Meanwhile, filamentous phages are known to be orientable by an external magnetic field. If M13 filaments are magnetically oriented during the library selection, their angular arrangement relative to the target surface would be changed, being expected to control the interference by the M13 main body. This study reports that the magnetic orientation of M13 filaments vertical to the target surface significantly affects the selection. When the target surface was affinitive to the M13 main body, this orientation notably suppressed the nonspecific adhesion. Furthermore, when the target surface was less affinitive to the M13 main body and intrinsically free from the nonspecific adhesion, this orientation drastically changed the population of M13 clones obtained through library selection. The method of using no chemicals but only a physical stimulus is simple, clean, and expected to expand the scope of phage display selection.
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Affiliation(s)
- Shuxu Wang
- RIKEN Center for Emergent Matter Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Noriyuki Uchida
- RIKEN Center for Emergent Matter Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Kento Ueno
- RIKEN Center for Emergent Matter Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Teruhiko Matsubara
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kouhoku-ku, Yokohama, 223-8522, Japan
| | - Toshinori Sato
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kouhoku-ku, Yokohama, 223-8522, Japan
| | - Takuzo Aida
- RIKEN Center for Emergent Matter Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Yasuhiro Ishida
- RIKEN Center for Emergent Matter Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
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Saibu OA, Hammed SO, Oladipo OO, Odunitan TT, Ajayi TM, Adejuyigbe AJ, Apanisile BT, Oyeneyin OE, Oluwafemi AT, Ayoola T, Olaoba OT, Alausa AO, Omoboyowa DA. Protein-protein interaction and interference of carcinogenesis by supramolecular modifications. Bioorg Med Chem 2023; 81:117211. [PMID: 36809721 DOI: 10.1016/j.bmc.2023.117211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 02/18/2023]
Abstract
Protein-protein interactions (PPIs) are essential in normal biological processes, but they can become disrupted or imbalanced in cancer. Various technological advancements have led to an increase in the number of PPI inhibitors, which target hubs in cancer cell's protein networks. However, it remains difficult to develop PPI inhibitors with desired potency and specificity. Supramolecular chemistry has only lately become recognized as a promising method to modify protein activities. In this review, we highlight recent advances in the use of supramolecular modification approaches in cancer therapy. We make special note of efforts to apply supramolecular modifications, such as molecular tweezers, to targeting the nuclear export signal (NES), which can be used to attenuate signaling processes in carcinogenesis. Finally, we discuss the strengths and weaknesses of using supramolecular approaches to targeting PPIs.
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Affiliation(s)
- Oluwatosin A Saibu
- Department of Environmental Toxicology, Universitat Duisburg-Essen, NorthRhine-Westphalia, Germany
| | - Sodiq O Hammed
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria; Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Oladapo O Oladipo
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria.
| | - Tope T Odunitan
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria; Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Temitope M Ajayi
- Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Aderonke J Adejuyigbe
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Boluwatife T Apanisile
- Department of Nutrition and Dietetics, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Oluwatoba E Oyeneyin
- Theoretical and Computational Chemistry Unit, Adekunle Ajasin University, Akungba-Akoko, Ondo State, Nigeria
| | - Adenrele T Oluwafemi
- Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Tolulope Ayoola
- Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Olamide T Olaoba
- Department of Molecular Pathogenesis and Therapeutics, University of Missouri-Columbia, Columbia, MO 65211, USA
| | - Abdullahi O Alausa
- Department of Molecular Biology and Biotechnology, ITMO University, St Petersburg, Russia
| | - Damilola A Omoboyowa
- Department of Biochemistry, Adekunle Ajasin University, Akungba-Akoko, Ondo State, Nigeria
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6
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Characterization of the Binding Behavior of Specific Cobalt and Nickel Ion-Binding Peptides Identified by Phage Surface Display. SEPARATIONS 2022. [DOI: 10.3390/separations9110354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
In recent years, the application focus of phage surface display (PSD) technology has been extended to the identification of metal ion-selective peptides. In previous studies, two phage clones—a nickel-binding one with the peptide motif CNAKHHPRCGGG and a cobalt-binding one with the peptide motif CTQMLGQLCGGG—were isolated, and their binding ability to metal-loaded NTA agarose beads was investigated. Here, the free cyclic peptides are characterized by UV/VIS spectroscopy with respect to their binding capacity for the respective target ion and in crossover experiments for the other ion by isothermal titration calorimetry (ITC) in different buffer systems. This revealed differences in selectivity and affinity. The cobalt-specific peptide is very sensitive to different buffers; it has a 20-fold higher affinity for cobalt and nickel under suitable conditions. The nickel-specific peptide binds more moderately and robustly in different buffers but only selectively to nickel.
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7
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Edwardson TGW, Levasseur MD, Tetter S, Steinauer A, Hori M, Hilvert D. Protein Cages: From Fundamentals to Advanced Applications. Chem Rev 2022; 122:9145-9197. [PMID: 35394752 DOI: 10.1021/acs.chemrev.1c00877] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Proteins that self-assemble into polyhedral shell-like structures are useful molecular containers both in nature and in the laboratory. Here we review efforts to repurpose diverse protein cages, including viral capsids, ferritins, bacterial microcompartments, and designed capsules, as vaccines, drug delivery vehicles, targeted imaging agents, nanoreactors, templates for controlled materials synthesis, building blocks for higher-order architectures, and more. A deep understanding of the principles underlying the construction, function, and evolution of natural systems has been key to tailoring selective cargo encapsulation and interactions with both biological systems and synthetic materials through protein engineering and directed evolution. The ability to adapt and design increasingly sophisticated capsid structures and functions stands to benefit the fields of catalysis, materials science, and medicine.
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Affiliation(s)
| | | | - Stephan Tetter
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Angela Steinauer
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Mao Hori
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
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8
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Elhabashy H, Merino F, Alva V, Kohlbacher O, Lupas AN. Exploring protein-protein interactions at the proteome level. Structure 2022; 30:462-475. [DOI: 10.1016/j.str.2022.02.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 10/26/2021] [Accepted: 02/02/2022] [Indexed: 02/08/2023]
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9
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Sun W, Zhang Y, Ju Z. Mimotopes for Mycotoxins Diagnosis Based on Random Peptides or Recombinant Antibodies from Phage Library. Molecules 2021; 26:7652. [PMID: 34946736 PMCID: PMC8707711 DOI: 10.3390/molecules26247652] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/12/2021] [Accepted: 12/14/2021] [Indexed: 11/23/2022] Open
Abstract
Mycotoxins, the small size secondary metabolites of fungi, have posed a threat to the safety of medicine, food and public health. Therefore, it is essential to create sensitive and effective determination of mycotoxins. Based on the special affinity between antibody and antigen, immunoassay has been proved to be a powerful technology for the detection of small analytes. However, the tedious preparation and instability of conventional antibodies restrict its application on easy and fast mycotoxins detection. By virtue of simplicity, ease of use, and lower cost, phage display library provides novel choices for antibodies or hapten conjugates, and lead random peptide or recombinant antibody to becoming the promising and environmental friendly immune-reagents in the next generation of immunoassays. This review briefly describes the latest developments on mycotoxins detection using M13 phage display, mainly focusing on the recent applications of phage display technology employed in mycotoxins detection, including the introduction of phage and phage display, the types of phage displayed peptide/recombinant antibody library, random peptides/recombinant antibodies-based immunoassays, as well as simultaneous determination of multiple mycotoxins.
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Affiliation(s)
- Wei Sun
- Key Laboratory of Plant Physiology and Development Regulation, School of Life Science, Guizhou Normal University, Guiyang 550001, China; (W.S.); (Y.Z.)
| | - Yan Zhang
- Key Laboratory of Plant Physiology and Development Regulation, School of Life Science, Guizhou Normal University, Guiyang 550001, China; (W.S.); (Y.Z.)
| | - Zhigang Ju
- Pharmacy School, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, China
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10
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Nubbemeyer B, Pepanian A, Paul George AA, Imhof D. Strategies towards Targeting Gαi/s Proteins: Scanning of Protein-Protein Interaction Sites To Overcome Inaccessibility. ChemMedChem 2021; 16:1696-1715. [PMID: 33615736 PMCID: PMC8252600 DOI: 10.1002/cmdc.202100039] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Indexed: 12/16/2022]
Abstract
Heterotrimeric G proteins are classified into four subfamilies and play a key role in signal transduction. They transmit extracellular signals to intracellular effectors subsequent to the activation of G protein-coupled receptors (GPCRs), which are targeted by over 30 % of FDA-approved drugs. However, addressing G proteins as drug targets represents a compelling alternative, for example, when G proteins act independently of the corresponding GPCRs, or in cases of complex multifunctional diseases, when a large number of different GPCRs are involved. In contrast to Gαq, efforts to target Gαi/s by suitable chemical compounds has not been successful so far. Here, a comprehensive analysis was conducted examining the most important interface regions of Gαi/s with its upstream and downstream interaction partners. By assigning the existing compounds and the performed approaches to the respective interfaces, the druggability of the individual interfaces was ranked to provide perspectives for selective targeting of Gαi/s in the future.
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Affiliation(s)
- Britta Nubbemeyer
- Pharmaceutical Biochemistry and BioanalyticsPharmaceutical InstituteUniversity of BonnAn der Immenburg 453121BonnGermany
| | - Anna Pepanian
- Pharmaceutical Biochemistry and BioanalyticsPharmaceutical InstituteUniversity of BonnAn der Immenburg 453121BonnGermany
| | | | - Diana Imhof
- Pharmaceutical Biochemistry and BioanalyticsPharmaceutical InstituteUniversity of BonnAn der Immenburg 453121BonnGermany
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11
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Choi MY, Vander Meer RK. GPCR-Based Bioactive Peptide Screening Using Phage-Displayed Peptides and an Insect Cell System for Insecticide Discovery. Biomolecules 2021; 11:biom11040583. [PMID: 33923387 PMCID: PMC8071521 DOI: 10.3390/biom11040583] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 04/12/2021] [Accepted: 04/13/2021] [Indexed: 01/12/2023] Open
Abstract
The discovery of new insecticides improves integrated pest management (IPM), but is usually a long high-risk process with a low probability of success. For over two decades, insect neuropeptides (NPs) and their G-protein coupled receptors (GPCRs) have been considered as biological targets for insect pest control, because they are involved in almost all physiological processes associated with insect life stages. A key roadblock to success has been the question of how large volume chemical libraries can be efficiently screened for active compounds. New genomic and proteomic tools have advanced and facilitated the development of new approaches to insecticide discovery. In this study, we report a novel GPCR-based screening technology that uses millions of short peptides randomly generated by bacteriophages, and a method using an insect Sf9 cell expression system. The fire ant is a good model system, since bioactive peptides have been identified for a specific GPCR. The novel small peptides could interfere with the target GPCR-ligand functions. Therefore, we refer to this new mechanism as “receptor interference” (RECEPTORi). The GPCR-based bioactive peptide screening method offers multiple advantages. Libraries of phage-displayed peptides (~109 peptides) are inexpensive. An insect cell-based screening system rapidly leads to target specific GPCR agonists or antagonists in weeks. Delivery of bioactive peptides to target pests can be flexible, such as topical, ingestion, and plant-incorporated protectants. A variety of GPCR targets are available, thus minimizing the development of potential insecticide resistance. This report provides the first proof-of-concept for the development of novel arthropod pest management strategies using neuropeptides, and GPCRs.
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Affiliation(s)
- Man-Yeon Choi
- USDA-ARS, Horticultural Crops Research Laboratory, Corvallis, OR 97330, USA
- Correspondence:
| | - Robert K. Vander Meer
- USDA-ARS, Center for Medical, Agricultural, and Veterinary Entomology, Gainesville, FL 32608, USA;
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12
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Gong Y, Yi M, Zhang L, Feng S, Deng H. Characterization of the Fc-III-4C-based recombinant protein expression system by using carbonic anhydrase as the model protein. Protein Expr Purif 2020; 177:105761. [PMID: 32956801 DOI: 10.1016/j.pep.2020.105761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/10/2020] [Accepted: 09/12/2020] [Indexed: 11/25/2022]
Abstract
Development of new affinity tags is important for recombinant protein expression and purification. Based on our earlier work, we devised an affinity tag by addition of two cysteine residues onto the N- and C-termini of the Fc-III peptide and designated as the Fc-III-4C tag, in which four cysteine residues form two disulfide linkages. The binding affinity of Fc-III-4C tag to human IgG is measured as 2.28 nM (Kd) and is 100 times higher than that of the Fc-III tag to IgG. Fc-III-4C tagged carbonic anhydrase (CA) can be effectively purified with IgG-immobilized beads, and Fc-III-4C tag does not possess adverse effects on the structure and stability of CA. Furthermore, the Fc-III-4C tagged protein binds to multiple transition metal ions, which enhances activities of enzymes that use metal ions as co-factors. These results suggest that Fc-III-4C tag is a useful tool for expression and purification of recombinant proteins and enhances the activities of some fusion proteins that use Zn2+ or Cu2+ as cofactors.
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Affiliation(s)
- Yiyi Gong
- Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China; MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systematic Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Meiqi Yi
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systematic Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Lin Zhang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systematic Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China; Tsinghua University-Peking University Joint Center for Life Sciences, Beijing, 100084, China
| | - Shan Feng
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310024, China; Mass Spectrometry Core Facility, The Biomedical Research Core Facility, Center for Research Equipment and Facilities, Westlake University, Hangzhou, Zhejiang, 310024, China.
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systematic Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China; Tsinghua University-Peking University Joint Center for Life Sciences, Beijing, 100084, China.
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13
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Chen Z, Schmid SL. Evolving models for assembling and shaping clathrin-coated pits. J Cell Biol 2020; 219:e202005126. [PMID: 32770195 PMCID: PMC7480099 DOI: 10.1083/jcb.202005126] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/13/2020] [Accepted: 07/13/2020] [Indexed: 01/01/2023] Open
Abstract
Clathrin-mediated endocytosis occurs via the assembly of clathrin-coated pits (CCPs) that invaginate and pinch off to form clathrin-coated vesicles (CCVs). It is well known that adaptor protein 2 (AP2) complexes trigger clathrin assembly on the plasma membrane, and biochemical and structural studies have revealed the nature of these interactions. Numerous endocytic accessory proteins collaborate with clathrin and AP2 to drive CCV formation. However, many questions remain as to the molecular events involved in CCP initiation, stabilization, and curvature generation. Indeed, a plethora of recent evidence derived from cell perturbation, correlative light and EM tomography, live-cell imaging, modeling, and high-resolution structural analyses has revealed more complexity and promiscuity in the protein interactions driving CCP maturation than anticipated. After briefly reviewing the evidence supporting prevailing models, we integrate these new lines of evidence to develop a more dynamic and flexible model for how redundant, dynamic, and competing protein interactions can drive endocytic CCV formation and suggest new approaches to test emerging models.
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Affiliation(s)
| | - Sandra L. Schmid
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX
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14
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Dar KB, Bhat AH, Amin S, Anjum S, Reshi BA, Zargar MA, Masood A, Ganie SA. Exploring Proteomic Drug Targets, Therapeutic Strategies and Protein - Protein Interactions in Cancer: Mechanistic View. Curr Cancer Drug Targets 2020; 19:430-448. [PMID: 30073927 DOI: 10.2174/1568009618666180803104631] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Revised: 07/17/2018] [Accepted: 07/19/2018] [Indexed: 12/31/2022]
Abstract
Protein-Protein Interactions (PPIs) drive major signalling cascades and play critical role in cell proliferation, apoptosis, angiogenesis and trafficking. Deregulated PPIs are implicated in multiple malignancies and represent the critical targets for treating cancer. Herein, we discuss the key protein-protein interacting domains implicated in cancer notably PDZ, SH2, SH3, LIM, PTB, SAM and PH. These domains are present in numerous enzymes/kinases, growth factors, transcription factors, adaptor proteins, receptors and scaffolding proteins and thus represent essential sites for targeting cancer. This review explores the candidature of various proteins involved in cellular trafficking (small GTPases, molecular motors, matrix-degrading enzymes, integrin), transcription (p53, cMyc), signalling (membrane receptor proteins), angiogenesis (VEGFs) and apoptosis (BCL-2family), which could possibly serve as targets for developing effective anti-cancer regimen. Interactions between Ras/Raf; X-linked inhibitor of apoptosis protein (XIAP)/second mitochondria-derived activator of caspases (Smac/DIABLO); Frizzled (FRZ)/Dishevelled (DVL) protein; beta-catenin/T Cell Factor (TCF) have also been studied as prospective anticancer targets. Efficacy of diverse molecules/ drugs targeting such PPIs although evaluated in various animal models/cell lines, there is an essential need for human-based clinical trials. Therapeutic strategies like the use of biologicals, high throughput screening (HTS) and fragment-based technology could play an imperative role in designing cancer therapeutics. Moreover, bioinformatic/computational strategies based on genome sequence, protein sequence/structure and domain data could serve as competent tools for predicting PPIs. Exploring hot spots in proteomic networks represents another approach for developing targetspecific therapeutics. Overall, this review lays emphasis on a productive amalgamation of proteomics, genomics, biochemistry, and molecular dynamics for successful treatment of cancer.
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Affiliation(s)
- Khalid Bashir Dar
- Department of Clinical Biochemistry, School of Biological Sciences, University of Kashmir, Srinagar, India.,Department of Biochemistry, School of Biological Sciences, University of Kashmir, Srinagar, India
| | - Aashiq Hussain Bhat
- Department of Clinical Biochemistry, School of Biological Sciences, University of Kashmir, Srinagar, India.,Department of Biochemistry, School of Biological Sciences, University of Kashmir, Srinagar, India
| | - Shajrul Amin
- Department of Biochemistry, School of Biological Sciences, University of Kashmir, Srinagar, India
| | - Syed Anjum
- Amity Institute of Biotechnology, Amity University, Rajasthan, India
| | - Bilal Ahmad Reshi
- Department of Biotechnology, School of Biological Sciences, University of Kashmir, Srinagar, India
| | - Mohammad Afzal Zargar
- Department of Clinical Biochemistry, School of Biological Sciences, University of Kashmir, Srinagar, India
| | - Akbar Masood
- Department of Clinical Biochemistry, School of Biological Sciences, University of Kashmir, Srinagar, India
| | - Showkat Ahmad Ganie
- Department of Clinical Biochemistry, School of Biological Sciences, University of Kashmir, Srinagar, India
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15
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Ramanayake Mudiyanselage TM, Michigami M, Ye Z, Uyeda A, Inoue N, Sugiura K, Fujii I, Fujiwara D. An Immune-Stimulatory Helix-Loop-Helix Peptide: Selective Inhibition of CTLA-4-B7 Interaction. ACS Chem Biol 2020; 15:360-368. [PMID: 31841301 DOI: 10.1021/acschembio.9b00743] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Molecular-targeting peptides and mini-proteins are promising alternatives to antibodies in a wide range of applications in bioscience and medicine. We have developed a helix-loop-helix (HLH) peptide as an alternative to antibodies to inhibit specific protein interactions. Cytotoxic T lymphocyte antigen-4 (CTLA-4) downregulates immune responses of cytotoxic T-cells by interaction with B7-1, a co-stimulatory molecule expressed on antigen presenting cells (APCs). To induce immune stimulatory activity, we used directed evolution methods to generate a HLH peptide that binds to CTLA-4, inhibiting the CTLA-4-B7-1 interaction and inducing immune stimulatory activity. Yeast-displayed libraries of HLH peptides were constructed and screened against CTLA-4 and identified the binding peptide Y-2, which exhibits a moderate affinity. The affinity of Y-2 was improved by in vitro affinity maturation to afford a stronger binder, ERY2-4. Peptide ERY2-4 specifically bound to CTLA-4 with a KD of 196.8 ± 2.3 nM, comparable to the affinity of the CTLA-4-B7-1 interaction. Furthermore, ERY2-4 inhibited the CTLA-4-B7-1 interaction with an IC50 of 1.1 ± 0.03 μM and blocked the interaction between CTLA-4 and dendritic cells (DCs) presenting B7 on their surface. Importantly, ERY2-4 showed no cross-reactivity against CD28, suggesting it does not suppress T-cell activation. Finally, in a mixed lymphocyte reaction assay with DCs and T cells, ERY2-4 enhanced an allogeneic lymphocyte response. Since CTLA-4 is a critical immune checkpoint for restricting the cancer immune response, this inhibitory HLH peptide represents a new class of drug candidates for immunotherapy.
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Affiliation(s)
- Tharanga M.R. Ramanayake Mudiyanselage
- Department of Veterinary Science, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-58 Rinku-oraikita, Izumisano, Osaka 598-8531, Japan
| | - Masataka Michigami
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Zhengmao Ye
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Atsuko Uyeda
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Norimitsu Inoue
- Department of Tumor Immunology, Osaka International Cancer Institute, 3-1-69 Otemae, Chuo-ku, Osaka-shi, Osaka 541-8567, Japan
| | - Kikuya Sugiura
- Department of Veterinary Science, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-58 Rinku-oraikita, Izumisano, Osaka 598-8531, Japan
| | - Ikuo Fujii
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Daisuke Fujiwara
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
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16
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Nahar S, Sokullu E, Gauthier MA. The phage display of Bacillus subtilis Lipase A significantly enhances catalytic activity due to altered nanoscale distribution in colloidal solution. Biotechnol Bioeng 2019; 117:868-872. [PMID: 31758554 DOI: 10.1002/bit.27229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/08/2019] [Accepted: 11/17/2019] [Indexed: 11/10/2022]
Abstract
Screening libraries of mutant proteins by phage display is now relatively common. However, one unknown factor is how the bacteriophage scaffold itself influences the properties of the displayed protein. This communication evaluates the effect of solution parameters on the catalytic activity of phage displayed Bacillus subtilis Lipase A (BSLA), compared to the free enzyme in solution. While the pH- and temperature-activity profiles of BSLA were not intrinsically affected by phage display, the nanoscale distribution of BSLA within the micellar assay buffer was. This lead to a pronounced increase of activity of phage-BSLA relative to the free enzyme, owing to the accumulation of phage-BSLA at the substrate-rich micelles. Considering this result obtained for BSLA, caution is warranted and similar effects should be considered when selecting other enzymes/proteins by phage display, as the activity of the displayed protein may differ from that of the free protein.
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Affiliation(s)
- Sharifun Nahar
- Institut National de la Recherche Scientifique (INRS), EMT Research Center, Varennes, Quebec, Canada
| | - Esen Sokullu
- Institut National de la Recherche Scientifique (INRS), EMT Research Center, Varennes, Quebec, Canada
| | - Marc A Gauthier
- Institut National de la Recherche Scientifique (INRS), EMT Research Center, Varennes, Quebec, Canada
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17
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Hirose H, Hideshima T, Katoh T, Suga H. A Case Study on the Keap1 Interaction with Peptide Sequence Epitopes Selected by the Peptidomic mRNA Display. Chembiochem 2019; 20:2089-2100. [PMID: 31169361 DOI: 10.1002/cbic.201900039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 03/12/2019] [Indexed: 11/08/2022]
Abstract
Many protein-protein and peptide-protein interactions (PPIs) play key roles in the regulation of biological functions, and therefore, the modulation of PPIs has become an attractive target of new drug development. Although a number of PPIs have already been identified, over 100 000 unknown PPIs are predicted to exist. To uncover such unknown PPIs, it is important to devise a conceptually distinct method from that of currently available methods. Herein, an mRNA display by using a total RNA library derived from various human tissues, which serves as a unique method to physically isolate peptide epitopes that potentially bind to a target protein of interest, is reported. In this study, selection was performed against Kelch-like ECH-associated protein (Keap1) as a model target protein, leading to a peptide epitope originating from astrotactin-1 (ASTN1). It turned out that this ASTN1 peptide was able to interact with Keap1 more strongly than that with a known peptide derived from Nrf2; a well-known, naturally occurring Keap1 binder. This case study demonstrates the applicability of peptidomic mRNA display for the rapid exploration of consensus binding peptide motifs and the potential for the discovery of unknown PPIs with other proteins of interest.
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Affiliation(s)
- Hisaaki Hirose
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Tomoki Hideshima
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Takayuki Katoh
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Hiroaki Suga
- 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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18
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Zhao Y, Xiao K. Proteomic Analysis of the β-Arrestin Interactomes. Methods Mol Biol 2019; 1957:217-232. [PMID: 30919357 DOI: 10.1007/978-1-4939-9158-7_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Protein-protein interaction is crucial to protein function and cellular signaling. A number of approaches were developed and applied to characterize protein-protein interactions in the past decades. In recent years, mass spectrometry (MS)-based proteomic methods have emerged as powerful tools to identify protein binding partners in a global and high-throughput manner. In this chapter, we describe the proteomic methods used to characterize the whole sets of proteins associated with β-arrestins (β-arrestin interactomes). The method starts with co-immunoprecipitation (co-IP) of β-arrestin signaling complexes from cells followed by protease digestion and LC/MS/MS analysis (liquid chromatography/tandem mass spectrometry) of proteins in the β-arrestin signaling complexes. To investigate changes in the amounts of binding partners under different conditions, we also describe a SILAC (stable isotope labeling by amino acids in cell culture) method to obtain quantitative information for β-arrestin interactomes.
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Affiliation(s)
- Yang Zhao
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kunhong Xiao
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA. .,Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, USA. .,Biomedical Mass Spectrometry Center, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
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19
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Van Blarcom T, Rossi A, Foletti D, Sundar P, Pitts S, Melton Z, Telman D, Zhao L, Cheung WL, Berka J, Zhai W, Strop P, Pons J, Rajpal A, Chaparro-Riggers J. Epitope Mapping Using Yeast Display and Next Generation Sequencing. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2019; 1785:89-118. [PMID: 29714014 DOI: 10.1007/978-1-4939-7841-0_7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Monoclonal antibodies are the largest class of therapeutic proteins due in part to their ability to bind an antigen with a high degree of affinity and specificity. A precise determination of their epitope is important for gaining insights into their therapeutic mechanism of action and to help differentiate antibodies that bind the same antigen. Here, we describe a method to precisely and efficiently map the epitopes of multiple antibodies in parallel over the course of just several weeks. This approach is based on a combination of rational library design, yeast surface display, and next generation DNA sequencing and provides quantitative insights into the epitope residues most critical for the antibody-antigen interaction. As an example, we will use this method to map the epitopes of several antibodies that neutralize alpha toxin from Staphylococcus aureus.
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Affiliation(s)
| | - Andrea Rossi
- Rinat, Pfizer Inc., South San Francisco, CA, USA
| | - Davide Foletti
- Rinat, Pfizer Inc., South San Francisco, CA, USA.,23andMe Inc., South San Francisco, CA, USA
| | | | - Steven Pitts
- Rinat, Pfizer Inc., South San Francisco, CA, USA.,23andMe Inc., South San Francisco, CA, USA
| | - Zea Melton
- Rinat, Pfizer Inc., South San Francisco, CA, USA
| | | | - Lora Zhao
- Rinat, Pfizer Inc., South San Francisco, CA, USA
| | - Wai Ling Cheung
- Rinat, Pfizer Inc., South San Francisco, CA, USA.,Princeton University, Princeton, NJ, USA
| | - Jan Berka
- Rinat, Pfizer Inc., South San Francisco, CA, USA.,Roche Sequencing Solutions, Pleasanton, CA, USA
| | - Wenwu Zhai
- Rinat, Pfizer Inc., South San Francisco, CA, USA.,NGM Biopharmaceuticals Inc., South San Francisco, CA, USA
| | - Pavel Strop
- Rinat, Pfizer Inc., South San Francisco, CA, USA.,Bristol-Myers Squibb Inc., Redwood City, CA, USA
| | - Jaume Pons
- Rinat, Pfizer Inc., South San Francisco, CA, USA.,Alexo Therapeutics Inc., South San Francisco, CA, USA
| | - Arvind Rajpal
- Rinat, Pfizer Inc., South San Francisco, CA, USA.,Bristol-Myers Squibb Inc., Redwood City, CA, USA
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20
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21
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22
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Ryvkin A, Ashkenazy H, Weiss-Ottolenghi Y, Piller C, Pupko T, Gershoni JM. Phage display peptide libraries: deviations from randomness and correctives. Nucleic Acids Res 2018; 46:e52. [PMID: 29420788 PMCID: PMC5961013 DOI: 10.1093/nar/gky077] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 12/25/2017] [Accepted: 01/31/2018] [Indexed: 12/14/2022] Open
Abstract
Peptide-expressing phage display libraries are widely used for the interrogation of antibodies. Affinity selected peptides are then analyzed to discover epitope mimetics, or are subjected to computational algorithms for epitope prediction. A critical assumption for these applications is the random representation of amino acids in the initial naïve peptide library. In a previous study, we implemented next generation sequencing to evaluate a naïve library and discovered severe deviations from randomness in UAG codon over-representation as well as in high G phosphoramidite abundance causing amino acid distribution biases. In this study, we demonstrate that the UAG over-representation can be attributed to the burden imposed on the phage upon the assembly of the recombinant Protein 8 subunits. This was corrected by constructing the libraries using supE44-containing bacteria which suppress the UAG driven abortive termination. We also demonstrate that the overabundance of G stems from variant synthesis-efficiency and can be corrected using compensating oligonucleotide-mixtures calibrated by mass spectroscopy. Construction of libraries implementing these correctives results in markedly improved libraries that display random distribution of amino acids, thus ensuring that enriched peptides obtained in biopanning represent a genuine selection event, a fundamental assumption for phage display applications.
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Affiliation(s)
- Arie Ryvkin
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Haim Ashkenazy
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Yael Weiss-Ottolenghi
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Chen Piller
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Tal Pupko
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Jonathan M Gershoni
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
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23
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Highly multiplexed and quantitative cell-surface protein profiling using genetically barcoded antibodies. Proc Natl Acad Sci U S A 2018; 115:2836-2841. [PMID: 29476010 PMCID: PMC5856557 DOI: 10.1073/pnas.1721899115] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Next-generation sequencing (NGS) has allowed the comprehensive study of the genome and transcriptome. However, a similarly broad, highly multiplexed, and inexpensive method for proteomics using NGS remains elusive. Here, we describe a phage display-based method using preselected antibodies that are genetically encoded and capable of simultaneous profiling of hundreds of cell-surface targets on cells in culture or singly at low cost and without the need for chemical conjugation to purified antibodies. We use the method to identify cell-surface proteins that change in cancer cells, some of which are coordinately regulated and could lead to new biomarkers and cancer targets. Human cells express thousands of different surface proteins that can be used for cell classification, or to distinguish healthy and disease conditions. A method capable of profiling a substantial fraction of the surface proteome simultaneously and inexpensively would enable more accurate and complete classification of cell states. We present a highly multiplexed and quantitative surface proteomic method using genetically barcoded antibodies called phage-antibody next-generation sequencing (PhaNGS). Using 144 preselected antibodies displayed on filamentous phage (Fab-phage) against 44 receptor targets, we assess changes in B cell surface proteins after the development of drug resistance in a patient with acute lymphoblastic leukemia (ALL) and in adaptation to oncogene expression in a Myc-inducible Burkitt lymphoma model. We further show PhaNGS can be applied at the single-cell level. Our results reveal that a common set of proteins including FLT3, NCR3LG1, and ROR1 dominate the response to similar oncogenic perturbations in B cells. Linking high-affinity, selective, genetically encoded binders to NGS enables direct and highly multiplexed protein detection, comparable to RNA-sequencing for mRNA. PhaNGS has the potential to profile a substantial fraction of the surface proteome simultaneously and inexpensively to enable more accurate and complete classification of cell states.
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24
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Li X, Yuan S, Huang M, Gao J, Wu Z, Tong P, Yang A, Chen H. Identification of IgE and IgG epitopes on native Bos d 4 allergen specific to allergic children. Food Funct 2018; 7:2996-3005. [PMID: 27273451 DOI: 10.1039/c6fo00416d] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Alpha-lactalbumin (ALA) is one of the major allergens in cow's milk. However, research on its conformational epitopes has been relatively limited. In our study, specific antibodies against cow's milk ALA were purified from eight children by two-step affinity chromatography. Subsequently, mimotopes against IgG and IgE were biopanned from Ph.D.-12 and Ph.D.-C7C, respectively. Based on the mimotopes, linear epitopes were defined with the UniProt alignment tool. Conformational epitopes were computed using the Pepitope Server. Six IgE and seven IgG linear epitopes were identified. Meanwhile, five IgE and three IgG conformational epitopes were revealed with PyMOL. The results showed that common residues were identified in both IgE and IgG epitopes and some residues of the conformational epitopes were composed of linear epitopes on bovine α-lactalbumin. The results indicated that the data could be used for developing hypoallergenic dairy products on the basis of epitopes and providing a diagnostic tool for the assessment of patients who are allergic to cow's milk.
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Affiliation(s)
- Xin Li
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, P.R.China and School of Food Science & Technology, Nanchang University, Nanchang 330047, P.R.China
| | - Shuilin Yuan
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, P.R.China and School of Food Science & Technology, Nanchang University, Nanchang 330047, P.R.China
| | - Meijia Huang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, P.R.China and School of Food Science & Technology, Nanchang University, Nanchang 330047, P.R.China
| | - Jinyan Gao
- School of Food Science & Technology, Nanchang University, Nanchang 330047, P.R.China
| | - Zhihua Wu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, P.R.China and Jiangxi-OAI Joint Research Institute, Nanchang University, Nanchang 330047, P.R.China.
| | - Ping Tong
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, P.R.China and School of Food Science & Technology, Nanchang University, Nanchang 330047, P.R.China
| | - Anshu Yang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, P.R.China and Jiangxi-OAI Joint Research Institute, Nanchang University, Nanchang 330047, P.R.China.
| | - Hongbing Chen
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, P.R.China and Jiangxi-OAI Joint Research Institute, Nanchang University, Nanchang 330047, P.R.China.
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25
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Chen L, Fu W, Zheng L, Wang Y, Liang G. Recent progress in the discovery of myeloid differentiation 2 (MD2) modulators for inflammatory diseases. Drug Discov Today 2018; 23:1187-1202. [PMID: 29330126 DOI: 10.1016/j.drudis.2018.01.015] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 10/09/2017] [Accepted: 01/04/2018] [Indexed: 02/07/2023]
Abstract
Myeloid differentiation protein 2 (MD2), together with Toll-like receptor 4 (TLR4), binds lipopolysaccharide (LPS) with high affinity, inducing the formation of the activated homodimer LPS-MD2-TLR4. MD2 directly recognizes the Lipid A domain of LPS, leading to the activation of downstream signaling of cytokine and chemokine production, and initiation of inflammatory and immune responses. However, excessive activation and potent host responses generate severe inflammatory syndromes such as acute sepsis and septic shock. MD2 is increasingly being considered as an attractive pharmacological target for the development of potent anti-inflammatory agents. In this Keynote review, we provide a comprehensive overview of the recent advances in the structure and biology of MD2, and present MD2 modulators as promising agents for anti-inflammatory intervention.
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Affiliation(s)
- Lingfeng Chen
- Chemical Biology Research Center at School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China; School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing, Jiangsu 210094, China
| | - Weitao Fu
- Chemical Biology Research Center at School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Lulu Zheng
- Chemical Biology Research Center at School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Yi Wang
- Chemical Biology Research Center at School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China.
| | - Guang Liang
- Chemical Biology Research Center at School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China; School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing, Jiangsu 210094, China.
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26
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Feng J, Xu R, Zhang X, Han Y, He C, Lu C, Hong Y, Lu K, Li H, Jin Y, Lin J, Liu J. A candidate recombinant antigen for diagnosis of schistosomiasis japonica in domestic animals. Vet Parasitol 2017; 243:242-247. [PMID: 28807301 DOI: 10.1016/j.vetpar.2017.06.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 06/01/2017] [Accepted: 06/17/2017] [Indexed: 01/24/2023]
Abstract
Domestic animals infected with Schistosoma japonicum are a major source of infection and play an important role in transmission to humans. A key strategy for the elimination of schistosomiasis is to control the sources of infection. In the present study, we identified a candidate diagnostic antigen-encoding gene, SjMRP1, the putative multidrug resistance protein 1 gene, by screening a cDNA phage display library from 44-day-old S. japonicum worms using IgGs from goat, cattle, and buffalo infected with S. japonicum. We cloned and expressed the fragment of SjMRP1 and subsequently evaluated the diagnostic potential of the recombinant protein rSjMRP1. In the enzyme-linked immunosorbent assay of rSjMRP1 (rSjMRP1-ELISA), the sensitivity in goat, cattle, and buffalo was 95.6% (86/90), 100% (22/22), and 90% (81/90), respectively, and the specificity was 100% (30/30) in goat and cattle and 96.67% (29/30) in buffalo. These results were not significantly different from soluble egg antigen (SEA)-ELISA results. Notably, rSjMRP1-ELISA has no cross reaction with Haemonchus contortus, a most common nematode seen in goat and bovine in China, in 13 infected goats, and with Orientobilhazia turkestanica, which is genetically under Schistosoma, in 36 infected goats; whereas SEA-ELISA showed false positive rate of 15.38% and 83.33% in the two respective animal groups. The results obtained here suggest that rSjMRP1 may be used for diagnosis of S. japonicum infection of domestic animals.
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Affiliation(s)
- Jintao Feng
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture, Shanghai 200241, PR China
| | - Rui Xu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture, Shanghai 200241, PR China
| | - Xin Zhang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture, Shanghai 200241, PR China
| | - Yu Han
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture, Shanghai 200241, PR China
| | - Chuanchuan He
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture, Shanghai 200241, PR China
| | - Chao Lu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture, Shanghai 200241, PR China
| | - Yang Hong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture, Shanghai 200241, PR China
| | - Ke Lu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture, Shanghai 200241, PR China
| | - Hao Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture, Shanghai 200241, PR China
| | - Yamei Jin
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture, Shanghai 200241, PR China
| | - Jiaojiao Lin
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture, Shanghai 200241, PR China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious and Zoonosea, Yangzhou, Jiangsu Province 225009, PR China
| | - Jinming Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture, Shanghai 200241, PR China.
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Jiang ZY, Lu MC, You QD. Discovery and Development of Kelch-like ECH-Associated Protein 1. Nuclear Factor Erythroid 2-Related Factor 2 (KEAP1:NRF2) Protein-Protein Interaction Inhibitors: Achievements, Challenges, and Future Directions. J Med Chem 2016; 59:10837-10858. [PMID: 27690435 DOI: 10.1021/acs.jmedchem.6b00586] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The transcription factor Nrf2 is the primary regulator of the cellular defense system, and enhancing Nrf2 activity has potential usages in various diseases, especially chronic age-related and inflammatory diseases. Recently, directly targeting Keap1-Nrf2 protein-protein interaction (PPI) has been an emerging strategy to selectively and effectively activate Nrf2. This Perspective summarizes the progress in the discovery and development of Keap1-Nrf2 PPI inhibitors, including the Keap1-Nrf2 regulatory mechanisms, biochemical techniques for inhibitor identification, and approaches for identifying peptide and small-molecule inhibitors, as well as discusses privileged structures and future directions for further development of Keap1-Nrf2 PPI inhibitors.
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Affiliation(s)
- Zheng-Yu Jiang
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University , Nanjing 210009, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University , 24 Tongjiaxiang, Nanjing 210009, China
| | - Meng-Chen Lu
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University , Nanjing 210009, China
| | - Qi-Dong You
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University , Nanjing 210009, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University , 24 Tongjiaxiang, Nanjing 210009, China
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Park D, Park CW, Choi Y, Lin J, Seo DH, Kim HS, Lee SY, Kang IC. A novel small-molecule PPI inhibitor targeting integrin αvβ3-osteopontin interface blocks bone resorption in vitro and prevents bone loss in mice. Biomaterials 2016; 98:131-42. [DOI: 10.1016/j.biomaterials.2016.05.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 05/02/2016] [Indexed: 01/11/2023]
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Gong Y, Zhang L, Li J, Feng S, Deng H. Development of the Double Cyclic Peptide Ligand for Antibody Purification and Protein Detection. Bioconjug Chem 2016; 27:1569-73. [DOI: 10.1021/acs.bioconjchem.6b00170] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yiyi Gong
- MOE Key Laboratory of Bioinformatics, School of Life Sciences and ‡Tsinghua University-Peking
University Joint Center for Life Sciences, Tsinghua University, Beijing, China, 100084
| | - Lin Zhang
- MOE Key Laboratory of Bioinformatics, School of Life Sciences and ‡Tsinghua University-Peking
University Joint Center for Life Sciences, Tsinghua University, Beijing, China, 100084
| | - Jin Li
- MOE Key Laboratory of Bioinformatics, School of Life Sciences and ‡Tsinghua University-Peking
University Joint Center for Life Sciences, Tsinghua University, Beijing, China, 100084
| | - Shan Feng
- MOE Key Laboratory of Bioinformatics, School of Life Sciences and ‡Tsinghua University-Peking
University Joint Center for Life Sciences, Tsinghua University, Beijing, China, 100084
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics, School of Life Sciences and ‡Tsinghua University-Peking
University Joint Center for Life Sciences, Tsinghua University, Beijing, China, 100084
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30
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Piggott AM, Karuso P. Identifying the cellular targets of natural products using T7 phage display. Nat Prod Rep 2016; 33:626-36. [DOI: 10.1039/c5np00128e] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A description of the T7 phage biopanning procedure is provided with tips and advice suitable for setup in a chemistry laboratory.
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Affiliation(s)
- Andrew M. Piggott
- Department of Chemistry and Biomolecular Sciences
- Macquarie University
- Sydney
- Australia
| | - Peter Karuso
- Department of Chemistry and Biomolecular Sciences
- Macquarie University
- Sydney
- Australia
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31
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Precise and Efficient Antibody Epitope Determination through Library Design, Yeast Display and Next-Generation Sequencing. J Mol Biol 2015; 427:1513-1534. [DOI: 10.1016/j.jmb.2014.09.020] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 09/17/2014] [Accepted: 09/26/2014] [Indexed: 01/18/2023]
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32
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Addepalli B, Rao S, Hunt AG. Phage display library screening for identification of interacting protein partners. Methods Mol Biol 2015; 1255:147-158. [PMID: 25487211 DOI: 10.1007/978-1-4939-2175-1_13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Phage display is a versatile high-throughput screening method employed to understand and improve the chemical biology, be it production of human monoclonal antibodies or identification of interacting protein partners. A majority of cell proteins operate in a concerted fashion either by stable or transient interactions. Such interactions can be mediated by recognition of small amino acid sequence motifs on the protein surface. Phage display can play a crucial role in identification of such motifs. This report describes the use of phage display for the identification of high affinity sequence motifs that could be responsible for interactions with a target (bait) protein.
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Affiliation(s)
- Balasubrahmanyam Addepalli
- Rieveschl laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, 312 College Dr, Cincinnati, OH, 45221, USA,
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Hodyra K, Dąbrowska K. Molecular and chemical engineering of bacteriophages for potential medical applications. Arch Immunol Ther Exp (Warsz) 2014; 63:117-27. [PMID: 25048831 PMCID: PMC4359349 DOI: 10.1007/s00005-014-0305-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 05/20/2014] [Indexed: 12/19/2022]
Abstract
Recent progress in molecular engineering has contributed to the great progress of medicine. However, there are still difficult problems constituting a challenge for molecular biology and biotechnology, e.g. new generation of anticancer agents, alternative biosensors or vaccines. As a biotechnological tool, bacteriophages (phages) offer a promising alternative to traditional approaches. They can be applied as anticancer agents, novel platforms in vaccine design, or as target carriers in drug discovery. Phages also offer solutions for modern cell imaging, biosensor construction or food pathogen detection. Here we present a review of bacteriophage research as a dynamically developing field with promising prospects for further development of medicine and biotechnology.
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Affiliation(s)
- Katarzyna Hodyra
- Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, R. Weigla 12, 53-114, Wrocław, Poland
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Sangith N, Srinivasaraghavan K, Sahu I, Desai A, Medipally S, Somavarappu AK, Verma C, Venkatraman P. Discovery of novel interacting partners of PSMD9, a proteasomal chaperone: Role of an Atypical and versatile PDZ-domain motif interaction and identification of putative functional modules. FEBS Open Bio 2014; 4:571-83. [PMID: 25009770 PMCID: PMC4087146 DOI: 10.1016/j.fob.2014.05.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 05/20/2014] [Accepted: 05/24/2014] [Indexed: 12/21/2022] Open
Abstract
The structure and functions of PSMD9, a proteasomal chaperone, are uncharacterized. PDZ-like domain of PSMD9 may recognize C-terminal residues in proteins. Using conserved C-terminal motifs in human proteome, we identify novel binding partners. hnRNPA1, GH, IL6-receptor, S14 and E12 interact with PSMD9 via a specific C-terminal motif. We predict and confirm residues in the PDZ domain that are involved in this interaction.
PSMD9 (Proteasome Macropain non-ATPase subunit 9), a proteasomal assembly chaperone, harbors an uncharacterized PDZ-like domain. Here we report the identification of five novel interacting partners of PSMD9 and provide the first glimpse at the structure of the PDZ-domain, including the molecular details of the interaction. We based our strategy on two propositions: (a) proteins with conserved C-termini may share common functions and (b) PDZ domains interact with C-terminal residues of proteins. Screening of C-terminal peptides followed by interactions using full-length recombinant proteins, we discovered hnRNPA1 (an RNA binding protein), S14 (a ribosomal protein), CSH1 (a growth hormone), E12 (a transcription factor) and IL6 receptor as novel PSMD9-interacting partners. Through multiple techniques and structural insights, we clearly demonstrate for the first time that human PDZ domain interacts with the predicted Short Linear Sequence Motif (SLIM) at the C-termini of the client proteins. These interactions are also recapitulated in mammalian cells. Together, these results are suggestive of the role of PSMD9 in transcriptional regulation, mRNA processing and editing, hormone and receptor activity and protein translation. Our proof-of-principle experiments endorse a novel and quick method for the identification of putative interacting partners of similar PDZ-domain proteins from the proteome and for discovering novel functions.
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Affiliation(s)
- Nikhil Sangith
- Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre (TMC), Kharghar, Navi Mumbai 410210, India
| | - Kannan Srinivasaraghavan
- Bioinformatics Institute ASTAR, 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore ; Experimental Therapeutics Centre (A*STAR), 31 Biopolis Street, #03-01 Helios, Singapore 138669, Singapore
| | - Indrajit Sahu
- Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre (TMC), Kharghar, Navi Mumbai 410210, India
| | - Ankita Desai
- Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre (TMC), Kharghar, Navi Mumbai 410210, India
| | - Spandana Medipally
- Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre (TMC), Kharghar, Navi Mumbai 410210, India
| | - Arun Kumar Somavarappu
- Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre (TMC), Kharghar, Navi Mumbai 410210, India
| | - Chandra Verma
- Bioinformatics Institute ASTAR, 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore ; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore ; Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
| | - Prasanna Venkatraman
- Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre (TMC), Kharghar, Navi Mumbai 410210, India
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London N, Raveh B, Schueler-Furman O. Druggable protein-protein interactions--from hot spots to hot segments. Curr Opin Chem Biol 2013; 17:952-9. [PMID: 24183815 DOI: 10.1016/j.cbpa.2013.10.011] [Citation(s) in RCA: 151] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 10/05/2013] [Accepted: 10/07/2013] [Indexed: 11/24/2022]
Abstract
Protein-Protein Interactions (PPIs) mediate numerous biological functions. As such, the inhibition of specific PPIs has tremendous therapeutic value. The notion that these interactions are 'undruggable' has petered out with the emergence of more and more successful examples of PPI inhibitors, expanding considerably the scope of potential drug targets. The accumulated data on successes in the inhibition of PPIs allow us to analyze the features that are required for such inhibition. Whereas it has been suggested and shown that targeting hot spots at PPI interfaces is a good strategy to achieve inhibition, in this review we focus on the notion that the most amenable interactions for inhibition are those that are mediated by a 'hot segment', a continuous epitope that contributes the majority of the binding energy. This criterion is both useful in guiding future target selection efforts, and in suggesting immediate inhibitory candidates--the dominant peptidic segment that mediates the targeted interaction.
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Affiliation(s)
- Nir London
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
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36
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Góngora-Benítez M, Tulla-Puche J, Albericio F. Multifaceted Roles of Disulfide Bonds. Peptides as Therapeutics. Chem Rev 2013; 114:901-26. [DOI: 10.1021/cr400031z] [Citation(s) in RCA: 388] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Miriam Góngora-Benítez
- Institute
for Research in Biomedicine (IRB Barcelona), Barcelona, 08028 Spain
- CIBER-BBN, Barcelona Science
Park, Barcelona, 08028 Spain
| | - Judit Tulla-Puche
- Institute
for Research in Biomedicine (IRB Barcelona), Barcelona, 08028 Spain
- CIBER-BBN, Barcelona Science
Park, Barcelona, 08028 Spain
| | - Fernando Albericio
- Institute
for Research in Biomedicine (IRB Barcelona), Barcelona, 08028 Spain
- CIBER-BBN, Barcelona Science
Park, Barcelona, 08028 Spain
- Department
of Organic Chemistry, University of Barcelona, Barcelona, 08028 Spain
- School of Chemistry & Physics, University of KwaZulu-Natal, 4001 Durban, South Africa
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Knez K, Noppe W, Geukens N, Janssen KPF, Spasic D, Heyligen J, Vriens K, Thevissen K, Cammue BPA, Petrenko V, Ulens C, Deckmyn H, Lammertyn J. Affinity Comparison of p3 and p8 Peptide Displaying Bacteriophages Using Surface Plasmon Resonance. Anal Chem 2013; 85:10075-82. [DOI: 10.1021/ac402192k] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Karel Knez
- BIOSYST-MeBioS, KU Leuven, Willem De Croylaan 42, P.O. Box 2428, B-3001 Leuven, Belgium
| | - Wim Noppe
- IRF
Life Siences, KU Leuven Kulak, E. Sabbelaan 53, B-8500 Kortrijk, Belgium
| | - Nick Geukens
- PharmAbs, The KU Leuven Antibody Center, O&N II, Herestraat 49, P.O. Box 824, B-3000 Leuven, Belgium
| | - Kris P. F. Janssen
- BIOSYST-MeBioS, KU Leuven, Willem De Croylaan 42, P.O. Box 2428, B-3001 Leuven, Belgium
| | - Dragana Spasic
- BIOSYST-MeBioS, KU Leuven, Willem De Croylaan 42, P.O. Box 2428, B-3001 Leuven, Belgium
| | - Jeroen Heyligen
- BIOSYST-MeBioS, KU Leuven, Willem De Croylaan 42, P.O. Box 2428, B-3001 Leuven, Belgium
| | - Kim Vriens
- Centre
for Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, P.O. 2460, B-3001 Heverlee, Belgium
| | - Karin Thevissen
- Centre
for Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, P.O. 2460, B-3001 Heverlee, Belgium
| | - Bruno P. A. Cammue
- Centre
for Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, P.O. 2460, B-3001 Heverlee, Belgium
| | - Valery Petrenko
- Auburn University, College of Veterinary Medicine,
Department of Pathobiology, 269 Greene Hall, Auburn, Alabama 36849-5519, United States
| | - Chris Ulens
- Laboratory for Structural Neurobiology, KU Leuven, O&N I, Herestraat 49, P.O. Box 601, B-3000 Leuven, Belgium
| | - Hans Deckmyn
- IRF
Life Siences, KU Leuven Kulak, E. Sabbelaan 53, B-8500 Kortrijk, Belgium
- PharmAbs, The KU Leuven Antibody Center, O&N II, Herestraat 49, P.O. Box 824, B-3000 Leuven, Belgium
| | - Jeroen Lammertyn
- BIOSYST-MeBioS, KU Leuven, Willem De Croylaan 42, P.O. Box 2428, B-3001 Leuven, Belgium
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38
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Lawson KV, Rose TE, Harran PG. Template-induced macrocycle diversity through large ring-forming alkylations of tryptophan. Tetrahedron 2013; 69:7683-7691. [PMID: 23976797 DOI: 10.1016/j.tet.2013.05.060] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Macrocyclic peptidomimetics are valuable in research and serve as lead compounds in drug discovery efforts. New methods to prepare such structures are of considerable interest. In this pilot study, we show that an organic template harboring a latent cinnamyl cation participates in novel Friedel-Crafts macrocyclization reactions with tryptophan. Upon joining the template to Trp-Trp-Tyr, a single operation efficiently generates eight unique macrocycles. Each has been isolated and thoroughly characterized. Product distribution as a function of Brønsted and/or Lewis acidic conditions was explored, and outcomes were compared to rearrangements induced within a corresponding tyrosine-linked cyclic ether. The solution structure of a new macrocyclic pyrroloindoline was solved using a combination of two-dimensional NMR methods and molecular mechanics simulations. Template-induced structural diversification of peptide sequences harboring aromatic residues has potential to create myriad macrocycles that target surfaces involved in protein-protein interactions.
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Affiliation(s)
- Kenneth V Lawson
- Department of Chemistry and Biochemistry, University of California Los Angeles, 607 Charles E. Young Drive East, Los Angeles, CA 90095-1569 (USA)
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Frascione N, Codina-Barrios A, Bassindale AR, Taylor PG. Enhancing in vitro selection techniques to assist the discovery, understanding and use of inorganic binding peptides. Dalton Trans 2013; 42:10337-46. [PMID: 23740479 DOI: 10.1039/c3dt50541c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Reflecting the increasing interest in combinatorial approaches, peptide phage display has seen an unprecedented expansion in a wide range of research areas. Its application to the discovery and analysis of metal binding peptides has opened up new research directions and largely contributed to the nanotechnology field. The rationale behind the need to identify such peptides varies depending on the final aim of the research and its application. Therefore, the possibility to modify the selection technique according to the different requirements would allow for a more systematic approach to be adopted and would ultimately provide substantial benefits. Although the standard panning method can be virtually applied to any target, its use for the identification of metal binding peptides does not provide the characteristics and the flexibility required for an efficient and tailored selection. Here we report on the development of a new panning method that can contribute to a faster, versatile and more informative analysis. Through the use of rolling-circle amplification, polymerase reaction and wild type phage, we have converted the standard selection technique into a more dynamic process in which adjustments can be evaluated and made consistently with the need of the experiment. The successfulness of the improved method is demonstrated in a number of panning experiments with different inorganic targets. The modifications applied to each selection are described and comparisons between the results obtained are made in order to extensively assess and evaluate the impact of the new process. The importance of tailoring the screening method to the specific objectives of a study is also considered. New binder sequences for the materials included in the investigation are identified; their sequences and distinctive characteristics are reported and their ability to act as templates for the nucleation of inorganic material is demonstrated and discussed.
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Affiliation(s)
- Nunzianda Frascione
- Department of Life, Health and Chemical Sciences, Open University, Venables Building, Walton Hall, Milton Keynes, UK.
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40
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Meyer MR, Shah S, Rao AG. Insights into molecular interactions between the juxtamembrane and kinase subdomains of the Arabidopsis Crinkly-4 receptor-like kinase. Arch Biochem Biophys 2013; 535:101-10. [DOI: 10.1016/j.abb.2013.03.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 03/25/2013] [Accepted: 03/26/2013] [Indexed: 01/10/2023]
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41
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Shah S, Butler NM, Hannapel DJ, Rao AG. Mapping and characterization of the interaction interface between two polypyrimidine-tract binding proteins and a nova-type protein of Solanum tuberosum. PLoS One 2013; 8:e64783. [PMID: 23717658 PMCID: PMC3663837 DOI: 10.1371/journal.pone.0064783] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 04/18/2013] [Indexed: 11/21/2022] Open
Abstract
Polypyrimidine tract-binding (PTB) proteins are RNA-binding proteins that generally contain four RNA recognition motifs (RRMs). In potato, six cDNAs encoding full-length PTB proteins have been identified. In the present study Nova1-like protein, designated StNova1, was identified as a potential interacting partner of the StPTB proteins via yeast two-hybrid screening. Nova protein is a RNA-binding protein that contains three K-homology (KH) domains. In humans, these proteins are involved in regulation of neuronal RNA metabolism but the role of Nova-like proteins in plants is poorly understood. We have validated this interaction and mapped the protein binding region on StNova1 and StPTB1 and −6 using a novel domain interaction phage display (DIPP) technique. The interaction between the two RNA-binding proteins StPTB1/6 and StNova1 is mediated through linker regions that are distinctly separated from the RRMs. Furthermore, using a random 21-mer phage-peptide library, we have identified a number of peptides with the consensus sequence motif [S/G][V/I][L/V]G that recognize the StPTB proteins. One over-represented peptide that recognizes StPTB6 contains the GVLGPWP sequence that is similar to the GIGGRYP sequence in the glycine-rich linker region between the KH2 and KH3 domains of StNova1. We show, through site-specific mutations, the importance of glycine and proline residues in StNova1-StPTB interactions.
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Affiliation(s)
- Shweta Shah
- Roy J. Carver Department of Biochemistry Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, United States of America
| | - Nathaniel M. Butler
- Plant Biology Major, Iowa State University, Ames, Iowa, United States of America
| | - David J. Hannapel
- Plant Biology Major, Iowa State University, Ames, Iowa, United States of America
| | - A. Gururaj Rao
- Roy J. Carver Department of Biochemistry Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, United States of America
- * E-mail:
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42
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Identification and characterization of a peptide affinity reagent for detection of noroviruses in clinical samples. J Clin Microbiol 2013; 51:1803-8. [PMID: 23554202 DOI: 10.1128/jcm.00295-13] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Norovirus (NoV) is the most common agent of nonbacterial epidemic gastroenteritis and is estimated to cause 21 million cases of the disease in the United States annually. The antigen enzyme-linked immunosorbent assays (ELISAs) currently available for NoV diagnosis detect only certain strains and are approved for use in the United States only in epidemics where NoV is suspected. There is a clear need for simpler, more rapid, and more reliable diagnostic tools for the detection of NoV. In this study, phage display technology was used to screen a library of phage displaying random 12-mer peptides for those that bind to Norwalk virus virus-like particles (NV VLPs). Three phage clones displaying unique peptides were identified, and both the peptide-displaying phages and the peptides were confirmed to bind specifically to NV VLPs. The peptide displayed on phage clone NV-N-R5-1 was determined to bind to the protruding domain of the VP1 capsid protein. This phage also bound to NV VLPs seeded into NoV-negative stool with a limit of detection of 1.56 ng NV VLP. This value was comparable to monoclonal antibody (MAb) 3912, which is currently used in commercially available assays. Furthermore, the NV-N-R5-1 phage exhibited high specificity by detecting NV only in previously characterized NV-positive stool samples in contrast to no detection in NV-negative stool samples. These data demonstrate that the further development of NV-N-R5-1 phage as a diagnostic reagent is possible and might offer several distinct advantages over antibodies, such as decreases in the time and cost of production and ease of isolating phage against other epidemic strains currently circulating as well as those that are emerging.
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Gagic D, Wen W, Collett MA, Rakonjac J. Unique secreted-surface protein complex of Lactobacillus rhamnosus, identified by phage display. Microbiologyopen 2012; 2:1-17. [PMID: 23233310 PMCID: PMC3584209 DOI: 10.1002/mbo3.53] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Accepted: 10/25/2012] [Indexed: 12/19/2022] Open
Abstract
Proteins are the most diverse structures on bacterial surfaces; hence, they are candidates for species- and strain-specific interactions of bacteria with the host, environment, and other microorganisms. Genomics has decoded thousands of bacterial surface and secreted proteins, yet the function of most cannot be predicted because of the enormous variability and a lack of experimental data that would allow deduction of function through homology. Here, we used phage display to identify a pair of interacting extracellular proteins in the probiotic bacterium Lactobacillus rhamnosus HN001. A secreted protein, SpcA, containing two bacterial immunoglobulin-like domains type 3 (Big-3) and a domain distantly related to plant pathogen response domain 1 (PR-1-like) was identified by screening of an L. rhamnosus HN001 library using HN001 cells as bait. The SpcA-"docking" protein, SpcB, was in turn detected by another phage display library screening, using purified SpcA as bait. SpcB is a 3275-residue cell-surface protein that contains general features of large glycosylated Serine-rich adhesins/fibrils from gram-positive bacteria, including the hallmark signal sequence motif KxYKxGKxW. Both proteins are encoded by genes within a L. rhamnosus-unique gene cluster that distinguishes this species from other lactobacilli. To our knowledge, this is the first example of a secreted-docking protein pair identified in lactobacilli.
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Affiliation(s)
- Dragana Gagic
- Institute of Molecular BioSciences, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
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44
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Abstract
Modular protein interaction domains (PIDs) that recognize linear peptide motifs are found in hundreds of proteins within the human genome. Some PIDs such as SH2, 14-3-3, Chromo, and Bromo domains serve to recognize posttranslational modification (PTM) of amino acids (such as phosphorylation, acetylation, methylation, etc.) and translate these into discrete cellular responses. Other modules such as SH3 and PSD-95/Discs-large/ZO-1 (PDZ) domains recognize linear peptide epitopes and serve to organize protein complexes based on localization and regions of elevated concentration. In both cases, the ability to nucleate-specific signaling complexes is in large part dependent on the selectivity of a given protein module for its cognate peptide ligand. High-throughput (HTP) analysis of peptide-binding domains by peptide or protein arrays, phage display, mass spectrometry, or other HTP techniques provides new insight into the potential protein-protein interactions prescribed by individual or even whole families of modules. Systems level analyses have also promoted a deeper understanding of the underlying principles that govern selective protein-protein interactions and how selectivity evolves. Lastly, there is a growing appreciation for the limitations and potential pitfalls associated with HTP analysis of protein-peptide interactomes. This review will examine some of the common approaches utilized for large-scale studies of PIDs and suggest a set of standards for the analysis and validation of datasets from large-scale studies of peptide-binding modules. We will also highlight how data from large-scale studies of modular interaction domain families can provide insight into systems level properties such as the linguistics of selective interactions.
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Affiliation(s)
- Bernard A Liu
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
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45
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Jenkins RJ, Dotson GD. Dual targeting antibacterial peptide inhibitor of early lipid A biosynthesis. ACS Chem Biol 2012; 7:1170-7. [PMID: 22530734 DOI: 10.1021/cb300094a] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
UDP-3-O-(R-3-hydroxyacyl)GlcN N-acyltransferase (LpxD) has been shown to be essential to survival of lipid A producing Gram-negative bacteria. In this study, LpxD-binding peptides 12 amino acids in length were identified from a phage-bound random peptide library screen. Three peptides displayed antibacterial activity when expressed intracellularly, one of which (RJPXD33) represented 15% of the total hits. RJPXD33 binds to E. coli LpxD with a K(d) of 6 μM and is competitive with R-3-hydroxymyristoyl-ACP binding. RJPXD33 can be C-terminally fused in vivo with thioredoxin or N-terminally modified in vitro with β-alanyl-fluorescein and maintain LpxD binding. The latter was used to develop an LpxD fluorescent binding assay used to evaluate unlabeled ligands and is amenable to small molecule library screening. Furthermore, RJPXD33 also binds to and inhibits E. coli UDP-N-acetylglucosamine acyltransferase (LpxA) with a K(d) of 20 μM, unearthing the possibility for the development of small molecule, dual-binding LpxA/LpxD inhibitors as novel antimicrobials.
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Affiliation(s)
- Ronald J. Jenkins
- Department of Medicinal Chemistry,
College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Garry D. Dotson
- Department of Medicinal Chemistry,
College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
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Grimme D, González-ruiz D, Gohlke* H. Computational Strategies and Challenges for Targeting Protein–Protein Interactions with Small Molecules. PHYSICO-CHEMICAL AND COMPUTATIONAL APPROACHES TO DRUG DISCOVERY 2012. [DOI: 10.1039/9781849735377-00319] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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Abstract
Synthetic antibody libraries are constructed from scratch using designed synthetic DNA. Precise control over design enables the use of highly optimized human frameworks and the introduction of defined chemical diversity at positions that are most likely to contribute to antigen recognition. We describe complete methods for the design, construction, and application of simplified synthetic antibody libraries built on a single human framework with diversity restricted to four complementarity-determining regions and two amino acids (tyrosine and serine). Despite the extreme simplicity of design, these libraries are capable of generating specific antibodies against diverse protein antigens. Moreover, the same methods can be used to build more complex libraries that can produce synthetic antibodies with affinities and specificities beyond the scope of natural antibodies. Most importantly, these simplified methods rely on standard supplies, equipment, and methods that are accessible to any molecular biology laboratory.
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Affiliation(s)
- Saravanan Rajan
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
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49
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Dudak FC, Kılıç N, Demir K, Yaşar F, Boyacı İH. Enhancing the affinity of SEB-binding peptides by repeating their sequence. Biopolymers 2011; 98:145-54. [DOI: 10.1002/bip.22012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2011] [Revised: 09/29/2011] [Accepted: 11/04/2011] [Indexed: 11/08/2022]
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50
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Fedorova A, Zobel K, Gill HS, Ogasawara A, Flores JE, Tinianow JN, Vanderbilt AN, Wu P, Meng YG, Williams SP, Wiesmann C, Murray J, Marik J, Deshayes K. The development of peptide-based tools for the analysis of angiogenesis. ACTA ACUST UNITED AC 2011; 18:839-45. [PMID: 21802005 DOI: 10.1016/j.chembiol.2011.05.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Revised: 04/26/2011] [Accepted: 05/02/2011] [Indexed: 01/28/2023]
Abstract
Limitations to the application of molecularly targeted cancer therapies are the inability to accurately match patient with effective treatment and the absence of a prompt readout of posttreatment response. Noninvasive agents that rapidly report vascular endothelial growth factor (VEGF) levels using positron emission tomography (PET) have the potential to enhance anti-angiogenesis therapies. Using phage display, two distinct classes of peptides were identified that bind to VEGF with nanomolar affinity and high selectivity. Co-crystal structures of these different peptide classes demonstrate that both bind to the receptor-binding region of VEGF. (18)F-radiolabelling of these peptides facilitated the acquisition of PET images of tumor VEGF levels in a HM7 xenograph model. The images obtained from one 59-residue probe, (18)F-Z-3B, 2 hr postinjection are comparable to those obtained with anti-VEGF antibody B20 72 hr postinjection. Furthermore, VEGF levels in growing SKOV3 tumors were followed using (18)F-Z-3B as a PET probe with VEGF levels increasing with tumor size.
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Affiliation(s)
- Anna Fedorova
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, CA 94080, USA
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