1
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Huszenicza Z, Gilmour BC, Koll L, Kjelstrup H, Chan H, Sundvold V, Granum S, Spurkland A. Interaction of T-cell-specific adapter protein with Src- and Tec-family kinases. Scand J Immunol 2024; 99:e13358. [PMID: 38605535 DOI: 10.1111/sji.13358] [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: 10/25/2023] [Revised: 01/05/2024] [Accepted: 01/08/2024] [Indexed: 04/13/2024]
Abstract
Adapter proteins are flexible and dynamic modulators of cellular signalling that are important for immune cell function. One of these, the T-cell-specific adapter protein (TSAd), interacts with the non-receptor tyrosine kinases Src and Lck of the Src family kinases (SFKs) and Itk of the Tec family kinases (TFKs). Three tyrosine residues in the TSAd C-terminus are phosphorylated by Lck and serve as docking sites for the Src homology 2 (SH2) domains of Src and Lck. The TSAd proline-rich region (PRR) binds to the Src homology 3 (SH3) domains found in Lck, Src and Itk. Despite known interactors, the role TSAd plays in cellular signalling remains largely unknown. TSAd's ability to bind both SFKs and TFKs may point to its function as a general scaffold for both kinase families. Using GST-pulldown as well as peptide array experiments, we found that both the SH2 and SH3 domains of the SFKs Fyn and Hck, as well as the TFKs Tec and Txk, interact with TSAd. This contrasts with Itk, which interacts with TSAd only through its SH3 domain. Although our analysis showed that TSAd is both co-expressed and may interact with Fyn, we were unable to co-precipitate Fyn with TSAd from Jurkat cells, as detected by Western blotting and affinity purification mass spectrometry. This may suggest that TSAd-Fyn interaction in intact cells may be limited by other factors, such as the subcellular localization of the two molecules or the co-expression of competing binding partners.
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Affiliation(s)
- Zsuzsa Huszenicza
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Brian C Gilmour
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Lise Koll
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Hanna Kjelstrup
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Hanna Chan
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Vibeke Sundvold
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Stine Granum
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Anne Spurkland
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
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2
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Hilpert K, Munshi T, López-Pérez PM, Sequeira-Garcia J, Bull TJ. Redefining Peptide 14D: Substitutional Analysis for Accelerated TB Diagnosis and Enhanced Activity against Mycobacterium tuberculosis. Microorganisms 2024; 12:177. [PMID: 38258003 PMCID: PMC10819809 DOI: 10.3390/microorganisms12010177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/08/2024] [Accepted: 01/12/2024] [Indexed: 01/24/2024] Open
Abstract
Tuberculosis (TB) caused by Mycobacterium tuberculosis remains a predominant cause of mortality, especially in low- and middle-income nations. Recently, antimicrobial peptides have been discovered that at low concentrations could stimulate the growth of M. tuberculosis (hormetic response). In this study, such a peptide was used to investigate the effects on the time to positivity (TTP). A systematic substitution analysis of peptide 14D was synthesized using Spot synthesis technology, resulting in 171 novel peptides. Our findings revealed a spectrum of interactions, with some peptides accelerating M. tuberculosis growth, potentially aiding in faster diagnostics, while others exhibited inhibitory effects. Notably, peptide NH2-wkivfiwrr-CONH2 significantly reduced the TTP by 25 h compared to the wild-type peptide 14D, highlighting its potential in improving TB diagnostics by culture. Several peptides demonstrated potent antimycobacterial activity, with a minimum inhibitory concentration (MIC) of 20 µg/mL against H37Rv and a multidrug-resistant M. tuberculosis strain. Additionally, for two peptides, a strongly diminished formation of cord-like structures was observed, which is indicative of reduced virulence and transmission potential. This study underscores the multifaceted roles of antimicrobial peptides in TB management, from enhancing diagnostic efficiency to offering therapeutic avenues against M. tuberculosis.
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Affiliation(s)
- Kai Hilpert
- Institute of Infection and Immunity, St George’s, University of London, Cranmer Terrace, London SW17 0RE, UK
| | - Tulika Munshi
- Institute of Infection and Immunity, St George’s, University of London, Cranmer Terrace, London SW17 0RE, UK
| | | | | | - Tim J. Bull
- Institute of Infection and Immunity, St George’s, University of London, Cranmer Terrace, London SW17 0RE, UK
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3
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Lin W, Gandhi S, Oviedo Lara AR, Thomas AK, Helbig R, Zhang Y. Controlling Surface Wettability for Automated In Situ Array Synthesis and Direct Bioscreening. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2102349. [PMID: 34309086 DOI: 10.1002/adma.202102349] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/30/2021] [Indexed: 06/13/2023]
Abstract
The in situ synthesis of biomolecules on glass surfaces for direct bioscreening can be a powerful tool in the fields of pharmaceutical sciences, biomaterials, and chemical biology. However, it is still challenging to 1) achieve this conventional multistep combinatorial synthesis on glass surfaces with small feature sizes and high yields and 2) develop a surface which is compatible with solid-phase syntheses, as well as the subsequent bioscreening. This work reports an amphiphilic coating of a glass surface on which small droplets of polar aprotic organic solvents can be deposited with an enhanced contact angle and inhibited motion to permit fully automated multiple rounds of the combinatorial synthesis of small-molecule compounds and peptides. This amphiphilic coating can be switched into a hydrophilic network for protein- and cell-based screening. Employing this in situ synthesis method, chemical space can be probed via array technology with unprecedented speed for various applications, such as lead discovery/optimization in medicinal chemistry and biomaterial development.
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Affiliation(s)
- Weilin Lin
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Tatzberg 41, 01307, Dresden, Germany
| | - Shanil Gandhi
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Tatzberg 41, 01307, Dresden, Germany
| | - Alan Rodrigo Oviedo Lara
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Tatzberg 41, 01307, Dresden, Germany
| | - Alvin K Thomas
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Tatzberg 41, 01307, Dresden, Germany
| | - Ralf Helbig
- Leibniz Institute of Polymer Research Dresden, Max Bergmann Center of Biomaterials Dresden, Hohe Strasse 6, 01069, Dresden, Germany
| | - Yixin Zhang
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Tatzberg 41, 01307, Dresden, Germany
- Cluster of Excellence "Physics of Life", Technische Universität Dresden, 01062, Dresden, Germany
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4
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Mao X, Sokpor G, Staiger J, Nguyen HP, Tuoc T. Mapping of domain-mediated protein-protein interaction by SPOT peptide assay. STAR Protoc 2021; 2:100503. [PMID: 33997817 PMCID: PMC8100624 DOI: 10.1016/j.xpro.2021.100503] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Identification of peptides mediating protein-protein interaction (PPI) is crucial for understanding the function of interlinked proteins in cellular processes and amino acid-associated diseases. Traditional PPI assays are laborious, involving the generation of many truncated proteins. SPOT peptide assay allows high-throughput detection of domains essential for PPI by synthesizing several hundred peptides on a cellulose membrane. Here, we present a rapid SPOT peptide protocol for identifying the binding motifs, which mediate interaction between the chromatin remodeling factors BAF155/BAF170 and the epigenetic factor Kdm6b. For complete details on the use and execution of this protocol, please refer to Narayanan et al. (2015).
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Affiliation(s)
- Xiaoyi Mao
- University Medical Center Goettingen, 37077 Goettingen, Germany
| | | | - Jochen Staiger
- University Medical Center Goettingen, 37077 Goettingen, Germany
| | | | - Tran Tuoc
- Ruhr University of Bochum, 44791 Bochum, Germany
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5
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Pepscan Approach for the Identification of Protein-Protein Interfaces: Lessons from Experiment. Biomolecules 2021; 11:biom11060772. [PMID: 34063976 PMCID: PMC8224071 DOI: 10.3390/biom11060772] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/11/2021] [Accepted: 05/18/2021] [Indexed: 12/12/2022] Open
Abstract
PEPscan is an old approach that has recently gained renewed interest for the identification of interfering peptides (IPs), i.e., peptides able to interfere with protein-protein interactions (PPIs). Its principle is to slice a protein sequence as a series of short overlapping peptides that are synthesized on a peptide array and tested for their ability to bind a partner, with positive spots corresponding to candidate IPs. PEPscan has been applied with a rather large success in various contexts, but the structural determinants underlying this success remain obscure. Here, we analyze the results of 14 PEPscan experiments, and confront the in vitro results with the available structural information. PEPscan identifies candidate IPs in limited numbers that in all cases correspond to solvent-accessible regions of the structures, their location at the protein-protein interface remaining to be further demonstrated. A strong point of PEPscan seems to be its ability to identify specific IPs. IPs identified from the same protein differ depending on the target PPI, and correspond to patches not frequently involved in the interactions seen in the 3D structures available. Overall, PEPscan seems to provide a cheap and rapid manner to identify candidate IPs, that also comes with room for improvement.
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6
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Brehm M, Heissler S, Afonin S, Levkin PA. Nanomolar Synthesis in Droplet Microarrays with UV-Triggered On-Chip Cell Screening. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e1905971. [PMID: 31985878 DOI: 10.1002/smll.201905971] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 12/04/2019] [Indexed: 06/10/2023]
Abstract
Miniaturization and parallelization of combinatorial organic synthesis is important to accelerate the process of drug discovery while reducing the consumption of reagents and solvents. This work presents a miniaturized platform for on-chip solid-phase combinatorial library synthesis with UV-triggered on-chip cell screening. The platform is based on a nanoporous polymer coating on a glass slide, which is modified via photolithography to yield arrays of hydrophilic (HL) spots surrounded by superhydrophobic (SH) surface. The combination of HL spots and SH background enables confinement of nanoliter droplets, functioning as miniaturized reactors for the solid-phase synthesis. The polymer serves as support for nanomolar solid-phase synthesis, while a photocleavable linker enables the release of the synthesized compounds into the droplets containing live cells. A 588 compound library of bisamides is synthesized via a four-component Ugi reaction on the chip and products are detected via stamping of the droplet array onto a conductive substrate and subsequent matrix-assisted laser desorption ionization mass spectrometry. The light-induced cleavage shows high flexibility in screening conditions by spatial, temporal, and quantitative control.
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Affiliation(s)
- Marius Brehm
- Karlsruhe Institute of Technology (KIT), Institute of Toxicology and Genetics, Hermann-von Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Stefan Heissler
- Karlsruhe Institute of Technology (KIT), Institute of Functional Interfaces, Hermann-von Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Sergii Afonin
- Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), POB 3640, 76021, Karlsruhe, Germany
| | - Pavel A Levkin
- Karlsruhe Institute of Technology (KIT), Institute of Toxicology and Genetics, Hermann-von Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
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7
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Sereikaite V, Fritzius T, Kasaragod VB, Bader N, Maric HM, Schindelin H, Bettler B, Strømgaard K. Targeting the γ-Aminobutyric Acid Type B (GABA B) Receptor Complex: Development of Inhibitors Targeting the K + Channel Tetramerization Domain (KCTD) Containing Proteins/GABA B Receptor Protein-Protein Interaction. J Med Chem 2019; 62:8819-8830. [PMID: 31509708 DOI: 10.1021/acs.jmedchem.9b01087] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Targeting multiprotein receptor complexes, rather than receptors directly, is a promising concept in drug discovery. This is particularly relevant to the GABAB receptor complex, which plays a prominent role in many brain functions and diseases. Here, we provide the first studies targeting a key protein-protein interaction of the GABAB receptor complex-the interaction with KCTD proteins. By employing the μSPOT technology, we first defined the GABAB receptor-binding epitope mediating the KCTD interaction. Subsequently, we developed a highly potent peptide-based inhibitor that interferes with the KCTD/GABAB receptor complex and efficiently isolates endogenous KCTD proteins from mouse brain lysates. X-ray crystallography and SEC-MALS revealed inhibitor induced oligomerization of KCTD16 into a distinct hexameric structure. Thus, we provide a template for modulating the GABAB receptor complex, revealing a fundamentally novel approach for targeting GABAB receptor-associated neuropsychiatric disorders.
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Affiliation(s)
- Vita Sereikaite
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology , University of Copenhagen , 2100 Copenhagen , Denmark
| | - Thorsten Fritzius
- Department of Biomedicine , University of Basel , CH-4056 Basel , Switzerland
| | - Vikram B Kasaragod
- Rudolf Virchow Center for Experimental Biomedicine , University of Würzburg , 97080 Würzburg , Germany
| | - Nicole Bader
- Rudolf Virchow Center for Experimental Biomedicine , University of Würzburg , 97080 Würzburg , Germany
| | - Hans M Maric
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology , University of Copenhagen , 2100 Copenhagen , Denmark
| | - Hermann Schindelin
- Rudolf Virchow Center for Experimental Biomedicine , University of Würzburg , 97080 Würzburg , Germany
| | - Bernhard Bettler
- Department of Biomedicine , University of Basel , CH-4056 Basel , Switzerland
| | - Kristian Strømgaard
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology , University of Copenhagen , 2100 Copenhagen , Denmark
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8
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Petell CJ, Pham AT, Skela J, Strahl BD. Improved methods for the detection of histone interactions with peptide microarrays. Sci Rep 2019; 9:6265. [PMID: 31000785 PMCID: PMC6472351 DOI: 10.1038/s41598-019-42711-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 04/05/2019] [Indexed: 02/07/2023] Open
Abstract
Histone post-translational modifications contribute to chromatin function largely through the recruitment of effector proteins that contain specialized "reader" domains. While a significant number of reader domains have been characterized for their histone binding specificities, many of these domains remain poorly characterized. Peptide microarrays have been widely employed for the characterization of histone readers, as well as modifying enzymes and histone antibodies. While powerful, this platform has limitations in terms of its sensitivity and they frequently miss low affinity reader domain interactions. Here, we provide several technical changes that improve reader domain detection of low-affinity interactions. We show that 1% non-fat milk in 1X PBST as the blocking reagent during incubation improved reader-domain interaction results. Further, coupling this with post-binding high-salt washes and a brief, low-percentage formaldehyde cross-linking step prior to the high-salt washes provided the optimal balance between resolving specific low-affinity interactions and minimizing background or spurious signals. We expect this improved methodology will lead to the elucidation of previously unreported reader-histone interactions that will be important for chromatin function.
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Affiliation(s)
- Christopher J Petell
- Department of Biochemistry and Biophysics, 120 Mason Farm Rd, University of North Carolina at Chapel Hill, NC, Chapel Hill, 27599, USA
- UNC Lineberger Comprehensive Cancer Center, 450 West Drive, University of North Carolina at Chapel Hill, NC, Chapel Hill, 27599, USA
| | - Andrea T Pham
- Department of Biochemistry and Biophysics, 120 Mason Farm Rd, University of North Carolina at Chapel Hill, NC, Chapel Hill, 27599, USA
| | - Jessica Skela
- Department of Biochemistry and Biophysics, 120 Mason Farm Rd, University of North Carolina at Chapel Hill, NC, Chapel Hill, 27599, USA
| | - Brian D Strahl
- Department of Biochemistry and Biophysics, 120 Mason Farm Rd, University of North Carolina at Chapel Hill, NC, Chapel Hill, 27599, USA.
- UNC Lineberger Comprehensive Cancer Center, 450 West Drive, University of North Carolina at Chapel Hill, NC, Chapel Hill, 27599, USA.
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9
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ten Brummelhuis N, Wilke P, Börner HG. Identification of Functional Peptide Sequences to Lead the Design of Precision Polymers. Macromol Rapid Commun 2017; 38. [DOI: 10.1002/marc.201700632] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 09/26/2017] [Indexed: 12/16/2022]
Affiliation(s)
- Niels ten Brummelhuis
- Laboratory for Organic Synthesis of Functional Systems; Department of Chemistry; Humboldt-Universität zu Berlin; Brook-Taylor-Str. 2 D-12489 Berlin Germany
| | - Patrick Wilke
- Laboratory for Organic Synthesis of Functional Systems; Department of Chemistry; Humboldt-Universität zu Berlin; Brook-Taylor-Str. 2 D-12489 Berlin Germany
| | - Hans G. Börner
- Laboratory for Organic Synthesis of Functional Systems; Department of Chemistry; Humboldt-Universität zu Berlin; Brook-Taylor-Str. 2 D-12489 Berlin Germany
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10
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Deschamps T, Bazot Q, Leske DM, MacLeod R, Mompelat D, Tafforeau L, Lotteau V, Maréchal V, Baillie GS, Gruffat H, Wilson JB, Manet E. Epstein-Barr virus nuclear antigen 1 interacts with regulator of chromosome condensation 1 dynamically throughout the cell cycle. J Gen Virol 2017; 98:251-265. [PMID: 28284242 DOI: 10.1099/jgv.0.000681] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The Epstein-Barr virus (EBV) nuclear antigen 1 (EBNA1) is a sequence-specific DNA-binding protein that plays an essential role in viral episome replication and segregation, by recruiting the cellular complex of DNA replication onto the origin (oriP) and by tethering the viral DNA onto the mitotic chromosomes. Whereas the mechanisms of viral DNA replication are well documented, those involved in tethering EBNA1 to the cellular chromatin are far from being understood. Here, we have identified regulator of chromosome condensation 1 (RCC1) as a novel cellular partner for EBNA1. RCC1 is the major nuclear guanine nucleotide exchange factor for the small GTPase Ran enzyme. RCC1, associated with chromatin, is involved in the formation of RanGTP gradients critical for nucleo-cytoplasmic transport, mitotic spindle formation and nuclear envelope reassembly following mitosis. Using several approaches, we have demonstrated a direct interaction between these two proteins and found that the EBNA1 domains responsible for EBNA1 tethering to the mitotic chromosomes are also involved in the interaction with RCC1. The use of an EBNA1 peptide array confirmed the interaction of RCC1 with these regions and also the importance of the N-terminal region of RCC1 in this interaction. Finally, using confocal microscopy and Förster resonance energy transfer analysis to follow the dynamics of interaction between the two proteins throughout the cell cycle, we have demonstrated that EBNA1 and RCC1 closely associate on the chromosomes during metaphase, suggesting an essential role for the interaction during this phase, perhaps in tethering EBNA1 to mitotic chromosomes.
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Affiliation(s)
- Thibaut Deschamps
- Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon 69364, France.,CNRS, UMR5308, Lyon 69364, France.,CIRI, International Center for Infectiology Research, Oncogenic Herpesviruses Team, Université de Lyon, Lyon 69364, France.,Ecole Normale Supérieure de Lyon, Lyon 69364, France.,INSERM, U1111, Lyon 69364, France
| | - Quentin Bazot
- Ecole Normale Supérieure de Lyon, Lyon 69364, France.,CNRS, UMR5308, Lyon 69364, France.,Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon 69364, France.,Present address: Section of Virology, Department of Medicine, Imperial College London, St Mary's Campus, London, UK.,CIRI, International Center for Infectiology Research, Oncogenic Herpesviruses Team, Université de Lyon, Lyon 69364, France.,INSERM, U1111, Lyon 69364, France
| | - Derek M Leske
- Present address: University of Oxford, Ludwig Institute for Cancer Research, Oxford, UK.,College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Ruth MacLeod
- College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Dimitri Mompelat
- Present address: University Joseph Fourier, Pathogenesis and Lentiviral Vaccination Laboratory, Grenoble, France.,INSERM, U1111, Lyon 69364, France.,Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon 69364, France.,Ecole Normale Supérieure de Lyon, Lyon 69364, France.,CIRI, International Center for Infectiology Research, Oncogenic Herpesviruses Team, Université de Lyon, Lyon 69364, France.,CNRS, UMR5308, Lyon 69364, France
| | - Lionel Tafforeau
- CIRI, International Center for Infectiology Research, Cell Biology of Viral Infections Team, Université de Lyon, Lyon 69364, France.,INSERM, U1111, Lyon 69364, France.,Present address: Cell Biology Lab, University of Mons, Mons, Belgium.,Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon 69364, France
| | - Vincent Lotteau
- Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon 69364, France.,Ecole Normale Supérieure de Lyon, Lyon 69364, France.,CNRS, UMR5308, Lyon 69364, France.,INSERM, U1111, Lyon 69364, France.,CIRI, International Center for Infectiology Research, Cell Biology of Viral Infections Team, Université de Lyon, Lyon 69364, France
| | - Vincent Maréchal
- UPMC Université Paris 6, Inserm, Centre d'Immunologie et des Maladies Infectieuses (Cimi-Paris), UMR 1135, ERL CNRS 8255, F-75013 Paris, France
| | - George S Baillie
- College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Henri Gruffat
- CNRS, UMR5308, Lyon 69364, France.,INSERM, U1111, Lyon 69364, France.,Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon 69364, France.,CIRI, International Center for Infectiology Research, Oncogenic Herpesviruses Team, Université de Lyon, Lyon 69364, France.,Ecole Normale Supérieure de Lyon, Lyon 69364, France
| | - Joanna B Wilson
- College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Evelyne Manet
- INSERM, U1111, Lyon 69364, France.,Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon 69364, France.,CIRI, International Center for Infectiology Research, Oncogenic Herpesviruses Team, Université de Lyon, Lyon 69364, France.,Ecole Normale Supérieure de Lyon, Lyon 69364, France.,CNRS, UMR5308, Lyon 69364, France
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11
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Engelmann BW. High-Throughput Quantification of SH2 Domain-Phosphopeptide Interactions with Cellulose-Peptide Conjugate Microarrays. Methods Mol Biol 2017; 1555:375-394. [PMID: 28092044 DOI: 10.1007/978-1-4939-6762-9_21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The Src Homology 2 (SH2) domain family primarily recognizes phosphorylated tyrosine (pY) containing peptide motifs. The relative affinity preferences among competing SH2 domains for phosphopeptide ligands define "specificity space," and underpins many functional pY mediated interactions within signaling networks. The degree of promiscuity exhibited and the dynamic range of affinities supported by individual domains or phosphopeptides is best resolved by a carefully executed and controlled quantitative high-throughput experiment. Here, I describe the fabrication and application of a cellulose-peptide conjugate microarray (CPCMA) platform to the quantitative analysis of SH2 domain specificity space. Included herein are instructions for optimal experimental design with special attention paid to common sources of systematic error, phosphopeptide SPOT synthesis, microarray fabrication, analyte titrations, data capture, and analysis.
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Affiliation(s)
- Brett W Engelmann
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA.
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12
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Gilliam AJH, Smith JN, Flather D, Johnston KM, Gansmiller AM, Fishman DA, Edgar JM, Balk M, Majumdar S, Weiss GA. Affinity-Guided Design of Caveolin-1 Ligands for Deoligomerization. J Med Chem 2016; 59:4019-25. [PMID: 27010220 DOI: 10.1021/acs.jmedchem.5b01536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Caveolin-1 is a target for academic and pharmaceutical research due to its many cellular roles and associated diseases. We report peptide WL47 (1), a small, high-affinity, selective disrupter of caveolin-1 oligomers. Developed and optimized through screening and analysis of synthetic peptide libraries, ligand 1 has 7500-fold improved affinity compared to its T20 parent ligand and an 80% decrease in sequence length. Ligand 1 will permit targeted study of caveolin-1 function.
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Affiliation(s)
- Amanda J H Gilliam
- Department of Chemistry, and ‡Department of Molecular Biology and Biochemistry, University of California , Irvine, California 92697-2025, United States
| | - Joshua N Smith
- Department of Chemistry, and ‡Department of Molecular Biology and Biochemistry, University of California , Irvine, California 92697-2025, United States
| | - Dylan Flather
- Department of Chemistry, and ‡Department of Molecular Biology and Biochemistry, University of California , Irvine, California 92697-2025, United States
| | - Kevin M Johnston
- Department of Chemistry, and ‡Department of Molecular Biology and Biochemistry, University of California , Irvine, California 92697-2025, United States
| | - Andrew M Gansmiller
- Department of Chemistry, and ‡Department of Molecular Biology and Biochemistry, University of California , Irvine, California 92697-2025, United States
| | - Dmitry A Fishman
- Department of Chemistry, and ‡Department of Molecular Biology and Biochemistry, University of California , Irvine, California 92697-2025, United States
| | - Joshua M Edgar
- Department of Chemistry, and ‡Department of Molecular Biology and Biochemistry, University of California , Irvine, California 92697-2025, United States
| | - Mark Balk
- Department of Chemistry, and ‡Department of Molecular Biology and Biochemistry, University of California , Irvine, California 92697-2025, United States
| | - Sudipta Majumdar
- Department of Chemistry, and ‡Department of Molecular Biology and Biochemistry, University of California , Irvine, California 92697-2025, United States
| | - Gregory A Weiss
- Department of Chemistry, and ‡Department of Molecular Biology and Biochemistry, University of California , Irvine, California 92697-2025, United States
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13
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Lai S, Winkler DFH, Zhang H, Pelech S. Determination of the Substrate Specificity of Protein Kinases with Peptide Micro- and Macroarrays. Methods Mol Biol 2016; 1360:183-202. [PMID: 26501911 DOI: 10.1007/978-1-4939-3073-9_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Elucidation of the key determinants for the phosphorylation site specificities of protein kinases facilitates identification of their physiological substrates, and serves to better define their critical roles in the signaling networks that underlie a multitude of cellular activities. Albeit with some apparent limitations, such as the lack of contextual information for secondary substrate-binding sites, the synthetic peptide-based approach has been adopted widely for the kinase specificity profiling studies, especially when they are used in an array format, which permits the screening of large numbers of potential peptide substrates in parallel. In this chapter, we present detailed protocols for determining protein kinase substrate specificity using an approach that involves both peptide microarrays and macroarrays. In particular, SPOT synthesis on macroarrays can be used to follow up on in silico predictions of protein kinase substrate specificity with predictive algorithms.
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Affiliation(s)
- Shenshen Lai
- Kinexus Bioinformatics Corporation, Suite 1, 8755 Ash Street, Vancouver, British Columbia, Canada, V6P 6T3
| | - Dirk F H Winkler
- Kinexus Bioinformatics Corporation, Suite 1, 8755 Ash Street, Vancouver, British Columbia, Canada, V6P 6T3
| | - Hong Zhang
- Kinexus Bioinformatics Corporation, Suite 1, 8755 Ash Street, Vancouver, British Columbia, Canada, V6P 6T3
| | - Steven Pelech
- Kinexus Bioinformatics Corporation, Suite 1, 8755 Ash Street, Vancouver, British Columbia, Canada, V6P 6T3.
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.
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De-Simone SG, Napoleão-Pêgo P, De-Simone TS. Spot Synthesis: An Optimized Microarray to Detect IgE Epitopes. Methods Mol Biol 2016; 1352:263-77. [PMID: 26490482 DOI: 10.1007/978-1-4939-3037-1_20] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Peptide microarrays have become increasingly more affordable in recent years with the SPOT technique being one of the most frequently used methods for synthesis and screening of peptides in arrays. Here, a protocol is presented for the identification of the amino acid sites involved in the conversion of human IgG to IgE response during the passive administration of therapeutic, anti-snake venom sera. Similarly, the minimal region of both the IgG and IgE binding epitopes, important for its interaction with ligand, were identified. As the ratio of concentrations for IgG to IgE in human serum is 1:10,000, also presented is a reproductive protocol of chemiluminescence-scanning for the detection of both immunoglobulins.
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Affiliation(s)
- Salvatore G De-Simone
- FIOCRUZ, Center of Technological Development in Health (CDTS) / National Institute of Science and Technology for Innovation on Neglected Diseases (INCT-IDN), FIOCRUZ, Rio de Janeiro, Brazil.
| | - Paloma Napoleão-Pêgo
- Department of Cellular andMolecularBiology, Federal FluminenseUniversity,Biology Institute, Niterói, Rio de Janeiro, Brazil
| | - Thatiane S De-Simone
- IOCRUZ, Center of Technological Development in Health (CDTS) / National Institute of Science and Technology for Innovation on Neglected Diseases (INCT-IDN) FIOCRUZ, Rio de Janeiro, Brazil
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15
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Gauna A, Losada S, Lorenzo M, Bermúdez H, Toledo M, Pérez H, Chacón E, Noya O. Synthetic peptides for the immunodiagnosis of hepatitis A virus infection. J Immunol Methods 2015; 427:1-5. [PMID: 26321053 DOI: 10.1016/j.jim.2015.08.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 08/21/2015] [Accepted: 08/25/2015] [Indexed: 11/17/2022]
Abstract
VP1, VP2 and VP3 molecules of hepatitis A virus are exposed capsid proteins that have shown to be antigenic and are used for diagnosis in recombinant-antigen commercial kits. In this study, we developed a sequence analysis in order to predict diagnostic peptide epitopes, followed by their spot synthesis on functionalized cellulose paper (Pepscan). This paper with synthetic peptides was tested against a sera pool of hepatitis A patients. Two peptide sequences, that have shown an antigenic recognition, were selected for greater scale synthesis on resin. A dimeric form of one of these peptides (IMT-1996), located in the C-Terminus region of protein VP1, was antigenic with a recognition frequency of 87-100% of anti-IgG antibodies and 100% of anti-IgM antibodies employing the immunological assays MABA and ELISA. We propose peptide IMT-1996, with less than twenty residues, as a cheaper alternative for prevalence studies and diagnosis of hepatitis A infection.
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Affiliation(s)
- A Gauna
- Sección de Biohelmintiasis, Instituto de Medicina Tropical, Facultad de Medicina, UCV, Caracas, Venezuela.
| | - S Losada
- Sección de Biohelmintiasis, Instituto de Medicina Tropical, Facultad de Medicina, UCV, Caracas, Venezuela.
| | - M Lorenzo
- Sección de Biohelmintiasis, Instituto de Medicina Tropical, Facultad de Medicina, UCV, Caracas, Venezuela.
| | - H Bermúdez
- Sección de Biohelmintiasis, Instituto de Medicina Tropical, Facultad de Medicina, UCV, Caracas, Venezuela.
| | - M Toledo
- Cátedra de Parasitología, Escuela de Medicina "Luis Razetti", Universidad Central de Venezuela, Venezuela.
| | - H Pérez
- Departamento de Virología, Instituto Nacional de Higiene-INH "Rafael Rangel", Venezuela.
| | - E Chacón
- Departamento de Virología, Instituto Nacional de Higiene-INH "Rafael Rangel", Venezuela.
| | - O Noya
- Sección de Biohelmintiasis, Instituto de Medicina Tropical, Facultad de Medicina, UCV, Caracas, Venezuela; Centro para Estudios Sobre Malaria, Instituto de Altos Estudios "Dr. Arnoldo Gabaldón" INH-Ministerio del Poder Popular para la Salud, Caracas, Venezuela.
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16
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SPOTing Acetyl-Lysine Dependent Interactions. MICROARRAYS 2015; 4:370-88. [PMID: 27600229 PMCID: PMC4996381 DOI: 10.3390/microarrays4030370] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 08/04/2015] [Accepted: 08/11/2015] [Indexed: 12/05/2022]
Abstract
Post translational modifications have been recognized as chemical signals that create docking sites for evolutionary conserved effector modules, allowing for signal integration within large networks of interactions. Lysine acetylation in particular has attracted attention as a regulatory modification, affecting chromatin structure and linking to transcriptional activation. Advances in peptide array technologies have facilitated the study of acetyl-lysine-containing linear motifs interacting with the evolutionary conserved bromodomain module, which specifically recognizes and binds to acetylated sequences in histones and other proteins. Here we summarize recent work employing SPOT peptide technology to identify acetyl-lysine dependent interactions and document the protocols adapted in our lab, as well as our efforts to characterize such bromodomain-histone interactions. Our results highlight the versatility of SPOT methods and establish an affordable tool for rapid access to potential protein/modified-peptide interactions involving lysine acetylation.
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17
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Kudithipudi S, Kusevic D, Weirich S, Jeltsch A. Specificity analysis of protein lysine methyltransferases using SPOT peptide arrays. J Vis Exp 2014:e52203. [PMID: 25489813 DOI: 10.3791/52203] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Lysine methylation is an emerging post-translation modification and it has been identified on several histone and non-histone proteins, where it plays crucial roles in cell development and many diseases. Approximately 5,000 lysine methylation sites were identified on different proteins, which are set by few dozens of protein lysine methyltransferases. This suggests that each PKMT methylates multiple proteins, however till now only one or two substrates have been identified for several of these enzymes. To approach this problem, we have introduced peptide array based substrate specificity analyses of PKMTs. Peptide arrays are powerful tools to characterize the specificity of PKMTs because methylation of several substrates with different sequences can be tested on one array. We synthesized peptide arrays on cellulose membrane using an Intavis SPOT synthesizer and analyzed the specificity of various PKMTs. Based on the results, for several of these enzymes, novel substrates could be identified. For example, for NSD1 by employing peptide arrays, we showed that it methylates K44 of H4 instead of the reported H4K20 and in addition H1.5K168 is the highly preferred substrate over the previously known H3K36. Hence, peptide arrays are powerful tools to biochemically characterize the PKMTs.
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18
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Schirwitz C, Loeffler FF, Felgenhauer T, Stadler V, Nesterov-Mueller A, Dahint R, Breitling F, Bischoff FR. Purification of high-complexity peptide microarrays by spatially resolved array transfer to gold-coated membranes. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2013; 25:1598-1602. [PMID: 23315653 DOI: 10.1002/adma.201203853] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Revised: 11/22/2012] [Indexed: 06/01/2023]
Abstract
A method for the one-step purification of high-complexity peptide microarrays is presented. The entire peptide library is transferred from the synthesis support to a gold coated polyvinylidenfluoride (PVDF) membrane, whereby only full-length peptides covalently couple to the receptor membrane via an N-terminally added cysteine. Highly resolved peptide transfer and purification of up to 10 000 features per cm(2) is demonstrated.
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Affiliation(s)
- Christopher Schirwitz
- German Cancer Research Center (DKFZ), Functional Genome Analysis, Chip-based Peptide Libraries, Heidelberg, Germany.
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19
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Devarayan K, Hayashi T, Hachisu M, Araki J, Ohkawa K. Correlations between steric/thermochemical parameters and O-/N-acylation reactions of cellulose. Carbohydr Polym 2013; 94:468-78. [PMID: 23544564 DOI: 10.1016/j.carbpol.2012.12.074] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 11/29/2012] [Accepted: 12/31/2012] [Indexed: 11/26/2022]
Abstract
N(α)-t-Butyloxycarbonyl (Boc)-amino acids (Xaa = Gly, Ala, or β-Ala) were reacted with the cellulose hydroxyl groups (O-acylation) using N,N'-carbonyl diimidazole. The degrees of substitution toward the total hydroxyl groups (DS%(/OH)s) were 38% for O-(Boc-Gly)-Cellulose, 29% for O-(Boc-Ala)-Cellulose and 53% for O-(Boc-β-Ala)-Cellulose. The one-by-one N-acylation between the O-(Xaa)-Celluloses and Boc-Ala-Gly using a water-soluble carbodiimide yielded the conjugates N-(Boc-Ala-Gly)-Xaa-Celluloses with DS%(/NH2) values of 25% (Xaa = Gly), 35% (Ala), and 48% (β-Ala), respectively. The results were well correlated with ΔG and ΔEstrain profiles, which were predicted by semi-empirical thermochemical parameter calculation coupled with conformer search (R(2)>0.90). N-acylation of the O-(β-Ala)-Cellulose using various length of oligo-peptides, Boc-(Ala-Gly)n and Boc-(Gly-Ala)n (where, n = 0.5, 1.0, 1.5, 2.0, 3.0), suggested that the DS%(/NH2) was dependent on the structural features of the symmetric anhydrides as the N-acylating agents, including conformer populations and their transition energy.
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Affiliation(s)
- Kesavan Devarayan
- Institute of High Polymer Research, Faculty of Textile Science and Technology, Shinshu University, Tokida 3-15-1, Ueda 386-8567, Japan
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SRC Homology 2 Domain Binding Sites in Insulin, IGF-1 and FGF receptor mediated signaling networks reveal an extensive potential interactome. Cell Commun Signal 2012; 10:27. [PMID: 22974441 PMCID: PMC3514216 DOI: 10.1186/1478-811x-10-27] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Accepted: 08/01/2012] [Indexed: 12/31/2022] Open
Abstract
Specific peptide ligand recognition by modular interaction domains is essential for the fidelity of information flow through the signal transduction networks that control cell behavior in response to extrinsic and intrinsic stimuli. Src homology 2 (SH2) domains recognize distinct phosphotyrosine peptide motifs, but the specific sites that are phosphorylated and the complement of available SH2 domains varies considerably in individual cell types. Such differences are the basis for a wide range of available protein interaction microstates from which signaling can evolve in highly divergent ways. This underlying complexity suggests the need to broadly map the signaling potential of systems as a prerequisite for understanding signaling in specific cell types as well as various pathologies that involve signal transduction such as cancer, developmental defects and metabolic disorders. This report describes interactions between SH2 domains and potential binding partners that comprise initial signaling downstream of activated fibroblast growth factor (FGF), insulin (Ins), and insulin-like growth factor-1 (IGF-1) receptors. A panel of 50 SH2 domains screened against a set of 192 phosphotyrosine peptides defines an extensive potential interactome while demonstrating the selectivity of individual SH2 domains. The interactions described confirm virtually all previously reported associations while describing a large set of potential novel interactions that imply additional complexity in the signaling networks initiated from activated receptors. This study of pTyr ligand binding by SH2 domains provides valuable insight into the selectivity that underpins complex signaling networks that are assembled using modular protein interaction domains.
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21
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Sun Z, Li X, Massena S, Kutschera S, Padhan N, Gualandi L, Sundvold-Gjerstad V, Gustafsson K, Choy WW, Zang G, Quach M, Jansson L, Phillipson M, Abid MR, Spurkland A, Claesson-Welsh L. VEGFR2 induces c-Src signaling and vascular permeability in vivo via the adaptor protein TSAd. ACTA ACUST UNITED AC 2012; 209:1363-77. [PMID: 22689825 PMCID: PMC3405501 DOI: 10.1084/jem.20111343] [Citation(s) in RCA: 167] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
VEGFR2 activates c-Src and induces vascular permeability by binding to the adaptor protein TSAd Regulation of vascular endothelial (VE) growth factor (VEGF)–induced permeability is critical in physiological and pathological processes. We show that tyrosine phosphorylation of VEGF receptor 2 (VEGFR2) at Y951 facilitates binding of VEGFR2 to the Rous sarcoma (Src) homology 2-domain of T cell–specific adaptor (TSAd), which in turn regulates VEGF-induced activation of the c-Src tyrosine kinase and vascular permeability. c-Src was activated in vivo and in vitro in a VEGF/TSAd-dependent manner, and was regulated via increased phosphorylation at pY418 and reduced phosphorylation at pY527. Tsad silencing blocked VEGF-induced c-Src activation, but did not affect pathways involving phospholipase Cγ, extracellular regulated kinase, and endothelial nitric oxide. VEGF-induced rearrangement of VE–cadherin–positive junctions in endothelial cells isolated from mouse lungs, or in mouse cremaster vessels, was dependent on TSAd expression, and TSAd formed a complex with VE-cadherin, VEGFR2, and c-Src at endothelial junctions. Vessels in tsad−/− mice showed undisturbed flow and pressure, but impaired VEGF-induced permeability, as measured by extravasation of Evans blue, dextran, and microspheres in the skin and the trachea. Histamine-induced extravasation was not affected by TSAd deficiency. We conclude that TSAd is required for VEGF-induced, c-Src-mediated regulation of endothelial cell junctions and for vascular permeability.
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Affiliation(s)
- Zuyue Sun
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 751 85 Uppsala, Sweden
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22
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Volkmer R, Tapia V, Landgraf C. Synthetic peptide arrays for investigating protein interaction domains. FEBS Lett 2012; 586:2780-6. [PMID: 22576123 DOI: 10.1016/j.febslet.2012.04.028] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Revised: 04/16/2012] [Accepted: 04/17/2012] [Indexed: 11/28/2022]
Abstract
Synthetic peptide array technology was first developed in the early 1990s by Ronald Frank. Since then the technique has become a powerful tool for high throughput approaches in biology and biochemistry. Here, we focus on peptide arrays applied to investigate the binding specificity of protein interaction domains such as WW, SH3, and PDZ domains. We describe array-based methods used to reveal domain networks in yeast, and briefly review rules as well as ideas about the synthesis and application of peptide arrays. We also provide initial results of a study designed to investigate the nature and evolution of SH3 domain interaction networks in eukaryotes.
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Affiliation(s)
- Rudolf Volkmer
- Institut für Medizinische Immunologie Berlin, Molecular Libraries and Recognition Group, Charité-Universitätsmedizin Berlin, Hessische Str. 3-4, 10115 Berlin, Germany.
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Abstract
Enzymes are key molecules in signal-transduction pathways. However, only a small fraction of more than 500 human kinases, 300 human proteases and 200 human phosphatases is characterised so far. Peptide microarray based technologies for extremely efficient profiling of enzyme substrate specificity emerged in the last years. This technology reduces set-up time for HTS assays and allows the identification of downstream targets. Moreover, peptide microarrays enable optimisation of enzyme substrates. Focus of this review is on assay principles for measuring activities of kinases, phosphatases or proteases and on substrate identification/optimisation for kinases. Additionally, several examples for reliable identification of substrates for lysine methyl-transferases, histone deacetylases and SUMO-transferases are given. Finally, use of high-density peptide microarrays for the simultaneous profiling of kinase activities in complex biological samples like cell lysates or lysates of complete organisms is described. All published examples of peptide arrays used for enzyme profiling are summarised comprehensively.
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Transient protein-protein interaction of the SH3-peptide complex via closely located multiple binding sites. PLoS One 2012; 7:e32804. [PMID: 22457720 PMCID: PMC3310816 DOI: 10.1371/journal.pone.0032804] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Accepted: 02/05/2012] [Indexed: 01/20/2023] Open
Abstract
Protein-protein interactions play an essential role in cellular processes. Certain proteins form stable complexes with their partner proteins, whereas others function by forming transient complexes. The conventional protein-protein interaction model describes an interaction between two proteins under the assumption that a protein binds to its partner protein through a single binding site. In this study, we improved the conventional interaction model by developing a Multiple-Site (MS) model in which a protein binds to its partner protein through closely located multiple binding sites on a surface of the partner protein by transiently docking at each binding site with individual binding free energies. To test this model, we used the protein-protein interaction mediated by Src homology 3 (SH3) domains. SH3 domains recognize their partners via a weak, transient interaction and are therefore promiscuous in nature. Because the MS model requires large amounts of data compared with the conventional interaction model, we used experimental data from the positionally addressable syntheses of peptides on cellulose membranes (SPOT-synthesis) technique. From the analysis of the experimental data, individual binding free energies for each binding site of peptides were extracted. A comparison of the individual binding free energies from the analysis with those from atomistic force fields gave a correlation coefficient of 0.66. Furthermore, application of the MS model to 10 SH3 domains lowers the prediction error by up to 9% compared with the conventional interaction model. This improvement in prediction originates from a more realistic description of complex formation than the conventional interaction model. The results suggested that, in many cases, SH3 domains increased the protein complex population through multiple binding sites of their partner proteins. Our study indicates that the consideration of general complex formation is important for the accurate description of protein complex formation, and especially for those of weak or transient protein complexes.
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25
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Shelburne SA, Olsen RJ, Makthal N, Brown NG, Sahasrabhojane P, Watkins EM, Palzkill T, Musser JM, Kumaraswami M. An amino-terminal signal peptide of Vfr protein negatively influences RopB-dependent SpeB expression and attenuates virulence in Streptococcus pyogenes. Mol Microbiol 2011; 82:1481-95. [PMID: 22040048 DOI: 10.1111/j.1365-2958.2011.07902.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
Streptococcal pyrogenic exotoxin B (SpeB) is an extracellular cysteine protease that is a critical virulence factor made by the major human pathogen group A Streptococcus (GAS). speB expression is dependent on the regulator of proteinase B (RopB) and is upregulated with increasing cell density and during infection. Because computer modelling suggested significant structural similarity between RopB and peptide-sensing regulatory proteins made by other Gram-positive bacteria, we hypothesized that speB expression is influenced by RopB-peptide interactions. Inactivation of the gene (vfr) encoding the virulence factor related (Vfr) protein resulted in increased speB transcript level during the exponential growth phase, whereas provision of only the amino-terminal region of Vfr comprising the secretion signal sequence in trans restored a wild-type speB expression profile. Addition of the culture supernatant from a Vfr signal peptide-expressing GAS strain restored wild-type speB transcript level to a vfr-inactivated isogenic mutant strain. A distinct peptide in the Vfr secretion signal sequence specifically bound to recombinant RopB. Finally, overexpression of the Vfr secretion signal sequence significantly decreased speB transcript level and attenuated GAS virulence in two mouse models of invasive infection. Taken together, these data delineate a previously unknown small peptide-mediated regulatory system that controls GAS virulence factor production.
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Affiliation(s)
- Samuel A Shelburne
- Department of Infectious Diseases, MD Anderson Cancer Center, Houston, TX, USA
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26
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Schiefner A, Chatwell L, Körner J, Neumaier I, Colby DW, Volkmer R, Wittrup KD, Skerra A. A disulfide-free single-domain V(L) intrabody with blocking activity towards huntingtin reveals a novel mode of epitope recognition. J Mol Biol 2011; 414:337-55. [PMID: 21968397 DOI: 10.1016/j.jmb.2011.09.034] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Revised: 09/19/2011] [Accepted: 09/20/2011] [Indexed: 10/17/2022]
Abstract
We present the crystal structure and biophysical characterization of a human V(L) [variable domain immunoglobulin (Ig) light chain] single-domain intrabody that binds to the huntingtin (Htt) protein and has been engineered for antigen recognition in the absence of its intradomain disulfide bond, otherwise conserved in the Ig fold. Analytical ultracentrifugation demonstrated that the αHtt-V(L) 12.3 domain is a stable monomer under physiological conditions even at concentrations >20 μM. Using peptide SPOT arrays, we identified the minimal binding epitope to be EKLMKAFESLKSFQ, comprising the N-terminal residues 5-18 of Htt and including the first residue of the poly-Gln stretch. X-ray structural analysis of αHtt-V(L) both as apo protein and in the presence of the epitope peptide revealed several interesting insights: first, the role of mutations acquired during the combinatorial selection process of the αHtt-V(L) 12.3 domain-initially starting from a single-chain Fv fragment-that are responsible for its stability as an individually soluble Ig domain, also lacking the disulfide bridge, and second, a previously unknown mode of antigen recognition, revealing a novel paratope. The Htt epitope peptide adopts a purely α-helical structure in the complex with αHtt-V(L) and is bound at the base of the complementarity-determining regions (CDRs) at the concave β-sheet that normally gives rise to the interface between the V(L) domain and its paired V(H) (variable domain Ig heavy chain) domain, while only few interactions with CDR-L1 and CDR-L3 are formed. Notably, this noncanonical mode of antigen binding may occur more widely in the area of in vitro selected antibody fragments, including other Ig-like scaffolds, possibly even if a V(H) domain is present.
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Affiliation(s)
- André Schiefner
- Munich Center for Integrated Protein Science and Lehrstuhl für Biologische Chemie, Technische Universität München, 85350 Freising-Weihenstephan, Germany
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27
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Borja MS, Piotukh K, Freund C, Gross JD. Dcp1 links coactivators of mRNA decapping to Dcp2 by proline recognition. RNA (NEW YORK, N.Y.) 2011; 17:278-90. [PMID: 21148770 PMCID: PMC3022277 DOI: 10.1261/rna.2382011] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2010] [Accepted: 11/08/2010] [Indexed: 05/20/2023]
Abstract
Cap hydrolysis is a critical step in several eukaryotic mRNA decay pathways and is carried out by the evolutionarily conserved decapping complex containing Dcp2 at the catalytic core. In yeast, Dcp1 is an essential activator of decapping and coactivators such as Edc1 and Edc2 are thought to enhance activity, though their mechanism remains elusive. Using kinetic analysis we show that a crucial function of Dcp1 is to couple the binding of coactivators of decapping to activation of Dcp2. Edc1 and Edc2 bind Dcp1 via its EVH1 proline recognition site and stimulate decapping by 1000-fold, affecting both the K(M) for mRNA and rate of the catalytic step. The C-terminus of Edc1 is necessary and sufficient to enhance the catalytic step, while the remainder of the protein likely increases mRNA binding to the decapping complex. Lesions in the Dcp1 EVH1 domain or the Edc1 proline-rich sequence are sufficient to block stimulation. These results identify a new role of Dcp1, which is to link the binding of coactivators to substrate recognition and activation of Dcp2.
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Affiliation(s)
- Mark S Borja
- Program in Chemistry and Chemical Biology, University of California, San Francisco, California 94158, USA
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28
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Katz C, Levy-Beladev L, Rotem-Bamberger S, Rito T, Rüdiger SGD, Friedler A. Studying protein–protein interactions using peptide arrays. Chem Soc Rev 2011; 40:2131-45. [DOI: 10.1039/c0cs00029a] [Citation(s) in RCA: 147] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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29
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Hahn R, Seifert M, Greinstetter S, Kanatschnig B, Berger E, Kaar W, Jungbauer A. Peptide affinity chromatography media that bind Npro fusion proteins under chaotropic conditions. J Chromatogr A 2010; 1217:6203-13. [DOI: 10.1016/j.chroma.2010.07.074] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2010] [Revised: 07/27/2010] [Accepted: 07/28/2010] [Indexed: 10/19/2022]
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30
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Vedadi M, Arrowsmith CH, Allali-Hassani A, Senisterra G, Wasney GA. Biophysical characterization of recombinant proteins: a key to higher structural genomics success. J Struct Biol 2010; 172:107-19. [PMID: 20466062 PMCID: PMC2954336 DOI: 10.1016/j.jsb.2010.05.005] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2010] [Revised: 03/26/2010] [Accepted: 05/06/2010] [Indexed: 01/12/2023]
Abstract
Hundreds of genomes have been successfully sequenced to date, and the data are publicly available. At the same time, the advances in large-scale expression and purification of recombinant proteins have paved the way for structural genomics efforts. Frequently, however, little is known about newly expressed proteins calling for large-scale protein characterization to better understand their biochemical roles and to enable structure-function relationship studies. In the Structural Genomics Consortium (SGC), we have established a platform to characterize large numbers of purified proteins. This includes screening for ligands, enzyme assays, peptide arrays and peptide displacement in a 384-well format. In this review, we describe this platform in more detail and report on how our approach significantly increases the success rate for structure determination. Coupled with high-resolution X-ray crystallography and structure-guided methods, this platform can also be used toward the development of chemical probes through screening families of proteins against a variety of chemical series and focused chemical libraries.
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Affiliation(s)
- Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, Room 839, MaRS Center, South Tower, Toronto, Ontario, Canada.
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Sereda MJ, Hartmann S, Büttner DW, Volkmer R, Hovestädt M, Brattig N, Lucius R. Characterization of the allergen filarial tropomyosin with an invertebrate specific monoclonal antibody. Acta Trop 2010; 116:61-7. [PMID: 20525500 DOI: 10.1016/j.actatropica.2010.05.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2010] [Revised: 05/25/2010] [Accepted: 05/27/2010] [Indexed: 10/19/2022]
Abstract
Tropomyosins of invertebrates are pan-allergens responsible for wide spread allergic reactions against seafood and arthropods. As invertebrate tropomyosins are highly conserved, helminth tropomyosins are likely to show properties similar to these medically important allergens. Studies with a monoclonal antibody, NR1, raised against tropomyosin of the rodent filarial nematode Acanthocheilonema viteae revealed a B cell epitope common to helminths and marine mollusks, which does not occur in vertebrate tropomyosin. This antibody detected tropomyosin of A. viteae, other filariids, nematodes, trematodes and a cestode, and recognized as well tropomyosin of oyster, squid and octopus, but not of arthropods and vertebrates. Immunohistological analyses of A. viteae, Onchocerca volvulus and other nematodes using NR1 showed that tropomyosin is located in the fibrillar part of the body wall muscles and the uterus, and is also conspicuous in muscles of the pharynx, the vagina and other organs of the nematodes. The abundance of a pan-allergen like tropomyosin in parasitic worms and the counterintuitive, but well documented protection against allergic reactivity by some chronic helminth infections is discussed.
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32
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Ruppel E, Aÿ B, Boisguerin P, Dölle S, Worm M, Volkmer R. Identification of IgE Binding to Api g 1-Derived Peptides. Chembiochem 2010; 11:2283-93. [DOI: 10.1002/cbic.201000322] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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33
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Mahrenholz CC, Tapia V, Stigler RD, Volkmer R. A study to assess the cross-reactivity of cellulose membrane-bound peptides with detection systems: an analysis at the amino acid level. J Pept Sci 2010; 16:297-302. [PMID: 20474041 DOI: 10.1002/psc.1237] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The growing demand for binding assays to study protein-protein interaction can be addressed by peptide array-based methods. The SPOT technique is a widespread peptide-array technology, which is able to distinguish semi-quantitatively the binding affinities of peptides to defined protein targets within one array. The quality of an assay system used for probing peptide arrays depends on the well-balanced combination of screening and read-out methods. The former address the steady-state of analyte capture, whereas the latter provide the means to detect captured analyte. In all cases, however, false-positive results can occur when challenging a peptide array with analyte or detecting captured analyte with label conjugates. Little is known about the cross-reactivity of peptides with the detection agents. Here, we describe at the amino acid level the potential of (i) 5-(and 6)-carboxytetramethylrhodamine (5(6)-TAMRA), (ii) fluoresceinisothiocyanate in form of the peptide-bound fluorescein-substituted thiourea derivative (FITC), and (iii) biotin/streptavidin-POD to cross-react with individual amino acids in a peptide sequence.
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Affiliation(s)
- Carsten C Mahrenholz
- Institut für Medizinische Immunologie, Charité-Universitätsmedizin Berlin, Berlin, Germany
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34
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High throughput T epitope mapping and vaccine development. J Biomed Biotechnol 2010; 2010:325720. [PMID: 20617148 PMCID: PMC2896667 DOI: 10.1155/2010/325720] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2009] [Revised: 02/18/2010] [Accepted: 04/20/2010] [Indexed: 11/22/2022] Open
Abstract
Mapping of antigenic peptide sequences from proteins of relevant pathogens recognized by T helper (Th) and by cytolytic T lymphocytes (CTL) is crucial for vaccine development. In fact, mapping of T-cell epitopes provides useful information for the design of peptide-based vaccines and of peptide libraries to monitor specific cellular immunity in protected individuals, patients and vaccinees. Nevertheless, epitope mapping is a challenging task. In fact, large panels of overlapping peptides need to be tested with lymphocytes to identify the sequences that induce a T-cell response. Since numerous peptide panels from antigenic proteins are to be screened, lymphocytes available from human subjects are a limiting factor. To overcome this limitation, high throughput (HTP) approaches based on miniaturization and automation of T-cell assays are needed. Here we consider the most recent applications of the HTP approach to T epitope mapping. The alternative or complementary use of in silico prediction and experimental epitope definition is discussed in the context of the recent literature. The currently used methods are described with special reference to the possibility of applying the HTP concept to make epitope mapping an easier procedure in terms of time, workload, reagents, cells and overall cost.
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35
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Singh P, LeBeau AM, Lilja H, Denmeade SR, Isaacs JT. Molecular insights into substrate specificity of prostate specific antigen through structural modeling. Proteins 2010; 77:984-93. [PMID: 19705489 DOI: 10.1002/prot.22524] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Prostate Specific Antigen's (PSA) role as a biomarker for prostate cancer is well established but the physiological role of its serine protease activity in the pathobiology of normal prostate and prostate carcinogenesis remains largely unknown. In light of recent studies that implicate PSA's enzymatic activity in the initiation and/or progression of prostate cancer, we performed a molecular modeling study of substrate binding at the catalytic site of PSA wherein a PSA-selective substrate (HSSKLQ) was docked in an acyl-enzyme conformation to a three-dimensional homology model of PSA. Additionally, virtual positional scanning studies were conducted to gain mechanistic insights into substrate recognition of PSA. Subsequently, 13 novel peptide substrates of 6-aa length and four peptide substrates with varying length were synthesized and assayed for PSA hydrolysis to evaluate the experimental validity of docking insights. Additionally, six novel aldehyde-containing transition state analog inhibitors were synthesized and tested for their inhibitory potencies. The experimental data on the hydrolysis rates of the newly synthesized substrates and inhibitory potencies of the aldehyde peptides agreed with the docking predictions, providing validation of the docking methodology and demonstrating its utility towards the design of substrate-mimetic inhibitors that can be used to explore PSA's role in the pathobiology of prostate cancer.
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Affiliation(s)
- Pratap Singh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore, Maryland 21218, USA.
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36
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Abstract
Development of array technologies started in the late 1980s and was first extensively applied to DNA arrays especially in the genomic field. Today this technique has become a powerful tool for high-throughput approaches in biology and chemistry. Progresses were mainly driven by the human genome project and were associated with the development of several new technologies, which led to the onset of additional "omic" topics like proteomics, glycomics, antibodyomics or lipidomics. The main characteristics of the array technology are (i) spatially addressable immobilization of a huge number of different capture molecules; (ii) probing the array in a simultaneous and highly parallel manner with a biological sample; (iii) tendency towards miniaturization of the arrays; and (iv) software-supported read-out and data analysis. We review some general concepts about peptide arrays on planar supports and point out technical aspects concerning the generation of peptide microarrays. Finally, we discuss recent applications by describing relevant literature.
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37
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Abstract
Developing new lead structures for drugs against multiresistant bacteria is an urgent need for modern medicine. Antimicrobial peptides are a class of drugs that can be used to discover such structures. In order to support development of this research, a fast, easy, and inexpensive method to synthesize peptides is necessary. The SPOT synthesis has the potential to produce the required peptide arrays, synthesizing up to 8,000 peptides, peptide mixtures, or other organic compounds on cellulose or other planar surfaces in a positionally addressable and multiple manner. Protocols for the preparation of cellulose membranes and the SPOT synthesis as well as cleavage of peptides from the support are described.
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Affiliation(s)
- Dirk F H Winkler
- Brain Research Centre, University of British Columbia, Vancouver, BC, Canada
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38
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Volkmer R. Synthesis and application of peptide arrays: quo vadis SPOT technology. Chembiochem 2009; 10:1431-42. [PMID: 19437530 DOI: 10.1002/cbic.200900078] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Rudolf Volkmer
- Institut für Medizinische Immunologie, AG Molekulare Bibliotheken, Charité-Universitätsmedizin Berlin, Hessische Strasse 3-4, 10115 Berlin, Germany.
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Abstract
Enzymes are key molecules in signal transduction pathways. However, only a small fraction of more than 500 predicted human kinases, 250 proteases and 250 phosphatases is characterized so far. Peptide microarray-based technologies for extremely efficient profiling of enzyme substrate specificity emerged in the last years. Additionally, patterns of enzymatic activities could be used to fingerprint the status of cells or organisms. This technology reduces set-up time for HTS assays and allows the identification of downstream targets. Moreover, peptide microarrays enable optimization of enzyme substrates. A comprehensive overview regarding enzyme profiling using peptide microarrays is presented with special focus on assay principles.
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Affiliation(s)
- Alexandra Thiele
- Max Planck Research Unit for Enzymology of Protein Folding, Halle, Germany
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40
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Abstract
Peptide synthesis on cellulose using the SPOT technology follows the standard Fmoc-chemistry and can be performed manually or automated. This method allows the synthesis of low-cost peptide arrays containing around 900 large spots of addressable peptides on a cellulose sheet of 19 cm x 29 cm. These peptides can be cleaved from the cellulose support by ammonia gas and afterward spotted on glass microchips. Alternatively, the peptides can be synthesized on modified cellulose discs and CelluSpot microarrays can be produced.
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Abstract
Information at the amino acid level about the epitopes of proteins recognized by antibodies or antibody fragments is important for their use as biological and diagnostic tools, therapeutic molecules, and for understanding molecular recognition events in general. The use of chemically prepared arrays of short peptides has emerged as a powerful tool to identify and characterize antibody epitopes. In this chapter the SPOT synthesis technique is described in detail. In addition, three different types of peptide libraries and their applications are described: protein sequence-derived scans of overlapping peptides (peptide scans) used to locate epitopes within the protein sequence, truncation libraries used to identify the minimal peptide length required for antibody binding, and complete substitutional analyses to identify the key residues important for antibody binding.
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42
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The spot technique: synthesis and screening of peptide macroarrays on cellulose membranes. Methods Mol Biol 2008; 494:47-70. [PMID: 18726568 DOI: 10.1007/978-1-59745-419-3_4] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Peptide arrays are a widely used tool for drug development. For peptide-based drug design it is necessary to screen a large number of peptides. However, there are often difficulties with this approach. Most common peptide synthesis techniques are able to simultaneously synthesize only up to a few hundred single peptides. Spot synthesis is a positionally addressable, multiple synthesis technique offering the possibility of synthesizing and screening up to 10,000 peptides or peptide mixtures on cellulose or other membrane surfaces. In this chapter we present the basic procedures and screening methods related to spot synthesis and outline protocols for easy-to-use detection methods on these peptide arrays.
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43
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Nady N, Min J, Kareta MS, Chédin F, Arrowsmith CH. A SPOT on the chromatin landscape? Histone peptide arrays as a tool for epigenetic research. Trends Biochem Sci 2008; 33:305-13. [PMID: 18538573 DOI: 10.1016/j.tibs.2008.04.014] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2008] [Revised: 04/18/2008] [Accepted: 04/23/2008] [Indexed: 12/23/2022]
Abstract
Post-translational modifications of histones serve as docking sites and signals for effector proteins and chromatin-remodeling enzymes, thereby influencing many fundamental cellular processes. Nevertheless, there are huge gaps in the knowledge of which proteins read and write the 'histone code'. Several techniques have been used to decipher complex histone-modification patterns. However, none is entirely satisfactory owing to the inherent limitations of in vitro studies of histones, such as deficits in the knowledge of the proteins involved, and the associated difficulties in the consistent and quantitative generation of histone marks. An alternative technique that could prove to be a useful tool in the study of the histone code is the use of synthetic peptide arrays (SPOT blot analysis) as a screening approach to characterize macromolecules that interact with specific covalent modifications of histone tails.
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Affiliation(s)
- Nataliya Nady
- Ontario Cancer Institute and Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, Ontario, M5G 1L7, Canada
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44
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Large-scale analysis of protein-protein interactions using cellulose-bound peptide arrays. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2008; 110:115-52. [PMID: 18418558 DOI: 10.1007/10_2008_096] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Peptide arrays for screening large numbers of peptide fragments and probing with large numbers of samples is discussed.
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45
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Kim DH, Shin DS, Lee YS. Spot arrays on modified glass surfaces for efficient SPOT synthesis and on-chip bioassay of peptides. J Pept Sci 2007; 13:625-33. [PMID: 17694567 DOI: 10.1002/psc.884] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
To make SPOT synthesis of peptides and their assays on glass surfaces more convenient, a simple method for making spot arrays on a slide glass was designed through patterning with a photoresist and perfluorination followed by amination with various silane compounds and polymers. With these spot-arrayed glass surfaces, we could measure the coupling completion of each Fmoc amino acid on the glass surface by direct fluorescence analysis after fluorescence-labeling the amino groups on the surface of each spot. Then we synthesized several types of decapeptides and HPQ-pentapeptides on the spot-arrayed glasses and identified the optimal surface condition for stepwise peptide coupling and on-chip bioassay. After optimizing the surface conditions, we synthesized a model library of biotin-Gly-Ala-P(1)-Gly (P(1): one of 19 amino acids) and successfully replicated the well-known alpha-chymotrypsin subsite specificities through Cy5-streptavidin binding to the remaining biotin on the surface after the enzymatic digestion.
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Affiliation(s)
- Do-Hyun Kim
- School of Chemical and Biological Engineering, Seoul National University, Seoul 151-744, Republic of Korea
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46
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Hilpert K, Hancock REW. Use of luminescent bacteria for rapid screening and characterization of short cationic antimicrobial peptides synthesized on cellulose using peptide array technology. Nat Protoc 2007; 2:1652-60. [PMID: 17641630 DOI: 10.1038/nprot.2007.203] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The increasing multi-resistance of pathogenic bacteria requires the development of novel classes of antibiotics. Antimicrobial host defense peptides represent one promising class. Here we describe a protocol for screening large numbers of peptides against any microbe of interest. Peptides synthesized on a cellulose support by peptide array technology can be added to a microbe that expresses the luxCDABE (luciferase) gene cassette. Any substance that decreases the energy level within the microbe will cause a quantifiable decrease in light production. The potency of the compound, at different concentrations, is reflected by the rate of decrease in luminescence. In conjunction with peptide array technology, the screening assay is rapid and high throughput and demonstrates good correlation with conventional killing or minimal inhibitory concentration assays performed with the same peptides synthesized by standard solid-phase peptide synthesis. The protocol can be completed in 3 d.
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Affiliation(s)
- Kai Hilpert
- Centre for Microbial Diseases and Immunity Research, University of British Columbia, no. 2259 Lower Mall Research Station, Vancouver, British Columbia, V6T 1Z3, Canada
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47
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Hilpert K, Winkler DFH, Hancock REW. Peptide arrays on cellulose support: SPOT synthesis, a time and cost efficient method for synthesis of large numbers of peptides in a parallel and addressable fashion. Nat Protoc 2007; 2:1333-49. [PMID: 17545971 DOI: 10.1038/nprot.2007.160] [Citation(s) in RCA: 203] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Peptide synthesis on cellulose using SPOT technology allows the parallel synthesis of large numbers of addressable peptides in small amounts. In addition, the cost per peptide is less than 1% of peptides synthesized conventionally on resin. The SPOT method follows standard fluorenyl-methoxy-carbonyl chemistry on conventional cellulose sheets, and can utilize more than 600 different building blocks. The procedure involves three phases: preparation of the cellulose membrane, stepwise coupling of the amino acids and cleavage of the side-chain protection groups. If necessary, peptides can be cleaved from the membrane for assays performed using soluble peptides. These features make this method an excellent tool for screening large numbers of peptides for many different purposes. Potential applications range from simple binding assays, to more sophisticated enzyme assays and studies with living microbes or cells. The time required to complete the protocol depends on the number and length of the peptides. For example, 400 9-mer peptides can be synthesized within 6 days.
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Affiliation(s)
- Kai Hilpert
- Centre for Microbial Diseases and Immunity Research, University of British Columbia, #2259 Lower Mall Research Station, Vancouver, British Columbia, Canada V6T 1Z3.
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48
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Hilpert K, Winkler DFH, Hancock REW. Cellulose-bound Peptide Arrays: Preparation and Applications. Biotechnol Genet Eng Rev 2007; 24:31-106. [DOI: 10.1080/02648725.2007.10648093] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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49
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Smith MJ, Hardy WR, Murphy JM, Jones N, Pawson T. Screening for PTB domain binding partners and ligand specificity using proteome-derived NPXY peptide arrays. Mol Cell Biol 2006; 26:8461-74. [PMID: 16982700 PMCID: PMC1636785 DOI: 10.1128/mcb.01491-06] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Modular interaction domains that recognize peptide motifs in target proteins can impart selectivity in signaling pathways. Phosphotyrosine binding (PTB) domains are components of cytoplasmic docking proteins that bind cell surface receptors through NPXY motifs. We have employed a library of human proteome-derived NXXY sequences to explore PTB domain specificity and function. SPOTS peptide arrays were used to create a comprehensive matrix of receptor motifs that were probed with a set of 10 diverse PTB domains. This approach confirmed that individual PTB domains have selective and distinct recognition properties and provided a means to explore over 2,500 potential PTB domain-NXXY interactions. The results correlated well with previously known associations between full-length proteins and predicted novel interactions, as well as consensus binding data for specific PTB domains. Using the Ret, MuSK, and ErbB2 receptor tyrosine kinases, we show that interactions of these receptors with PTB domains predicted to bind by the NXXY arrays do occur in cells. Proteome-based peptide arrays can therefore identify networks of receptor interactions with scaffold proteins that may be physiologically relevant.
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Affiliation(s)
- Matthew J Smith
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada M5G 1X5
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50
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Beyer M, Felgenhauer T, Ralf Bischoff F, Breitling F, Stadler V. A novel glass slide-based peptide array support with high functionality resisting non-specific protein adsorption. Biomaterials 2006; 27:3505-14. [PMID: 16499964 DOI: 10.1016/j.biomaterials.2006.01.046] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2005] [Accepted: 01/30/2006] [Indexed: 11/18/2022]
Abstract
Glass slides have been modified with a multifunctional poly(ethylene glycol) (PEG)-based polymer with respect to array applications in the growing field of proteome research. We systematically investigated the stepwise synthesis of the PEG films starting from self-assembled alkyl silane monolayers via monolayer peroxidation and subsequent graft polymerization of PEG methacrylate (PEGMA). Chemical composition was examined by X-ray photoelectron spectroscopy (XPS); infrared spectroscopy provided information about order and composition of the films as well; film thickness was determined by ellipsometry; using fluorescence microscopy and again XPS, the amount of proteins adsorbed on the slides was investigated. The novel support material allows a versatile modification of the amino group surface density up to 40 nmol/cm(2) for the linkage of probe molecules. Further on, we carried out standard peptide synthesis based on the well-established 9-fluorenylmethoxycarbonyl (Fmoc) chemistry, which was monitored by UV/Vis quantification of the Fmoc deblocking and mass spectrometry. The polymer coating is stable with respect to a wide range of chemical and thermal conditions, and prevents the glass surface from unspecific protein adsorption. Finally, we applied our modified glass slides in immunoassays and thus examined specific interactions of monoclonal antibodies with appropriate peptide epitopes.
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Affiliation(s)
- Mario Beyer
- Department Chip-Based Peptide Libraries, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
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