Synthetic peptide arrays for investigating protein interaction domains

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.

[1]  Livia Perfetto,et al.  The protein interaction network mediated by human SH3 domains. , 2012, Biotechnology advances.

[2]  Yi Zhang,et al.  A map of WW domain family interactions , 2004, Proteomics.

[3]  N. Gray The possible and the actual, The Jessie and John Danz Lectures , 1996 .

[4]  C. Landgraf,et al.  Identification of a Novel, Intraperoxisomal Pex14-Binding Site in Pex13: Association of Pex13 with the Docking Complex Is Essential for Peroxisomal Matrix Protein Import , 2005, Molecular and Cellular Biology.

[5]  R. Frank Spot-synthesis: an easy technique for the positionally addressable, parallel chemical synthesis on a membrane support , 1992 .

[6]  P. Boisguérin,et al.  Evaluating the coupling efficiency of phosphorylated amino acids for SPOT synthesis , 2008, Journal of peptide science : an official publication of the European Peptide Society.

[7]  Jens Schneider-Mergener,et al.  The ScPex13p SH3 domain exposes two distinct binding sites for Pex5p and Pex14p. , 2003, Journal of molecular biology.

[8]  James R. Knight,et al.  A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae , 2000, Nature.

[9]  Carsten C. Mahrenholz,et al.  A study to assess the cross‐reactivity of cellulose membrane‐bound peptides with detection systems: an analysis at the amino acid level , 2010, Journal of peptide science : an official publication of the European Peptide Society.

[10]  Prisca Boisguerin,et al.  Characterization of a Putative Phosphorylation Switch: Adaptation of SPOT Synthesis to Analyze PDZ Domain Regulation Mechanisms , 2007, Chembiochem : a European journal of chemical biology.

[11]  H. Mihara,et al.  Peptide design based on an antibody complementarity-determining region (CDR): construction of porphyrin-binding peptides and their affinity maturation by a combinatorial method. , 2000, Chemistry.

[12]  P. Mcgeer,et al.  Protein labeling and biotinylation of peptides during spot synthesis using biotin p‐nitrophenyl ester (biotin‐ONp) , 2008, Proteomics.

[13]  R. Volkmer,et al.  Transformation of a biologically active Peptide into peptoid analogs while retaining biological activity. , 2006, Protein and peptide letters.

[14]  L. Castagnoli,et al.  Methods to reveal domain networks. , 2005, Drug discovery today.

[15]  Gavin MacBeath,et al.  A quantitative protein interaction network for the ErbB receptors using protein microarrays , 2006, Nature.

[16]  François Jacob The possible and the actual , 1982 .

[17]  R. Rickles,et al.  Identification of Src, Fyn, Lyn, PI3K and Abl SH3 domain ligands using phage display libraries. , 1994, The EMBO journal.

[18]  T. Stradal,et al.  Large-scale analysis of protein-protein interactions using cellulose-bound peptide arrays. , 2008, Advances in biochemical engineering/biotechnology.

[19]  R. Volkmer Synthesis and Application of Peptide Arrays: Quo Vadis SPOT Technology , 2009, Chembiochem : a European journal of chemical biology.

[20]  Jens Schneider-Mergener,et al.  Stable attachment of the HMB-linker to continuous cellulose membranes for parallel solid phase spot synthesis , 1997 .

[21]  H. M. Geysen,et al.  Use of peptide synthesis to probe viral antigens for epitopes to a resolution of a single amino acid. , 1984, Proceedings of the National Academy of Sciences of the United States of America.

[22]  A. Sparks,et al.  Identification and characterization of Src SH3 ligands from phage-displayed random peptide libraries. , 1994, The Journal of biological chemistry.

[23]  P. Bork,et al.  Functional organization of the yeast proteome by systematic analysis of protein complexes , 2002, Nature.

[24]  Chris Sander,et al.  A Specificity Map for the PDZ Domain Family , 2008, PLoS biology.

[25]  P. Schmieder,et al.  Chemical synthesis of the third WW domain of TCERG 1 by native chemical ligation , 2011, Journal of peptide science : an official publication of the European Peptide Society.

[26]  T. Kamradt,et al.  Cross-reactivity of T lymphocytes in infection and autoimmunity , 2004, Molecular Diversity.

[27]  R. Volkmer,et al.  Exploring and profiling protein function with peptide arrays. , 2009, Methods in molecular biology.

[28]  M. Gerstein,et al.  Global Analysis of Protein Activities Using Proteome Chips , 2001, Science.

[29]  Giovanni Cesareni,et al.  Modular protein domains , 2005 .

[30]  I. Kretzschmar,et al.  Probing the Ligand‐Binding Specificity and Analyzing the Folding State of SPOT‐Synthesized FBP28 WW Domain Variants , 2006, Chembiochem : a European journal of chemical biology.

[31]  Prisca Boisguerin,et al.  An improved method for the synthesis of cellulose membrane-bound peptides with free C termini is useful for PDZ domain binding studies. , 2004, Chemistry & biology.

[32]  S. P. Fodor,et al.  Light-directed, spatially addressable parallel chemical synthesis. , 1991, Science.

[33]  P Bork,et al.  Cytoplasmic signalling domains: the next generation. , 1997, Trends in biochemical sciences.

[34]  T. Pawson,et al.  Assembly of Cell Regulatory Systems Through Protein Interaction Domains , 2003, Science.

[35]  R. Nussinov,et al.  Protein–protein interactions: Structurally conserved residues distinguish between binding sites and exposed protein surfaces , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[36]  Sachdev S Sidhu,et al.  Studying binding specificities of peptide recognition modules by high-throughput phage display selections. , 2011, Methods in molecular biology.

[37]  David B. Searls,et al.  Linguistic approaches to biological sequences , 1997, Comput. Appl. Biosci..

[38]  Xiaodong Cheng,et al.  Protein lysine methyltransferase G9a acts on non-histone targets. , 2008, Nature chemical biology.

[39]  Gary D Bader,et al.  A Combined Experimental and Computational Strategy to Define Protein Interaction Networks for Peptide Recognition Modules , 2001, Science.

[40]  A. Poustka,et al.  Combinatorial synthesis of peptide arrays with a laser printer. , 2008, Angewandte Chemie.

[41]  T. Clackson,et al.  A hot spot of binding energy in a hormone-receptor interface , 1995, Science.

[42]  P. Bork,et al.  Characterization of a novel protein‐binding module — the WW domain , 1995, FEBS letters.

[43]  D. Searls,et al.  Robots in invertebrate neuroscience , 2002, Nature.

[44]  Annalisa Pastore,et al.  Y65C Missense Mutation in the WW Domain of the Golabi-Ito-Hall Syndrome Protein PQBP1 Affects Its Binding Activity and Deregulates Pre-mRNA Splicing* , 2010, The Journal of Biological Chemistry.

[45]  S. Schreiber,et al.  Printing proteins as microarrays for high-throughput function determination. , 2000, Science.

[46]  Carsten C. Mahrenholz,et al.  Sorting and pooling strategy: a novel tool to map a virus proteome for CD8 T-cell epitopes. , 2007, Biopolymers.

[47]  Jens Schneider-Mergener,et al.  Highly parallel nano-synthesis of cleavable peptide-dye conjugates on cellulose membranes , 2000 .

[48]  A. Jungbauer,et al.  Evaluation of a sensitive detection method for peptide arrays prepared by SPOT synthesis. , 2006, Journal of biochemical and biophysical methods.

[49]  Stephan Lorenzen,et al.  Peroxisomal membrane proteins contain common Pex19p-binding sites that are an integral part of their targeting signals. , 2004, Molecular biology of the cell.

[50]  A. Wittinghofer,et al.  Systematic Peptide Array-based Delineation of the Differential β-Catenin Interaction with Tcf4, E-Cadherin, and Adenomatous Polyposis Coli* , 2005, Journal of Biological Chemistry.

[51]  G. Baillie,et al.  Scanning peptide array analyses identify overlapping binding sites for the signalling scaffold proteins, beta-arrestin and RACK1, in cAMP-specific phosphodiesterase PDE4D5. , 2006, The Biochemical journal.

[52]  A. Gingras,et al.  Histone Recognition and Large-Scale Structural Analysis of the Human Bromodomain Family , 2012, Cell.

[53]  D. Laune,et al.  Improved performances of spot multiple peptide synthesis. , 1996, Peptide research.

[54]  John Maynard Smith,et al.  Natural Selection and the Concept of a Protein Space , 1970, Nature.

[55]  R. Ozawa,et al.  A comprehensive two-hybrid analysis to explore the yeast protein interactome , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[56]  A. Kramer,et al.  Spot synthesis: observations and optimizations. , 1999, The journal of peptide research : official journal of the American Peptide Society.

[57]  J. Schneider-Mergener,et al.  Coherent membrane supports for parallel microsynthesis and screening of bioactive peptides. , 2000, Biopolymers.

[58]  F. Cohen,et al.  An evolutionary trace method defines binding surfaces common to protein families. , 1996, Journal of molecular biology.

[59]  Sarah A. Teichmann,et al.  Principles of protein-protein interactions , 2002, ECCB.

[60]  Armin A. Weiser,et al.  SPOT synthesis: reliability of array-based measurement of peptide binding affinity. , 2005, Analytical biochemistry.

[61]  H. Blackwell,et al.  Small molecule macroarray construction via Ugi four-component reactions. , 2005, Organic letters.

[62]  J. Schneider-Mergener,et al.  Peptide Arrays in Proteomics and Drug Discovery , 2006 .

[63]  Gary D. Bader,et al.  Bayesian Modeling of the Yeast SH3 Domain Interactome Predicts Spatiotemporal Dynamics of Endocytosis Proteins , 2009, PLoS biology.

[64]  Marius Sudol,et al.  From Src Homology domains to other signaling modules: proposal of the `protein recognition code' , 1998, Oncogene.

[65]  J. Schneider-Mergener,et al.  Spatially addressed synthesis of amino- and amino-oxy-substituted 1, 3,5-triazine arrays on polymeric membranes. , 2000, Journal of combinatorial chemistry.

[66]  A. Kramer,et al.  Antigen sequence- and library-based mapping of linear and discontinuous protein-protein-interaction sites by spot synthesis. , 1999, Current topics in microbiology and immunology.

[67]  A. Bogan,et al.  Anatomy of hot spots in protein interfaces. , 1998, Journal of molecular biology.

[68]  Mario Gimona,et al.  Protein linguistics — a grammar for modular protein assembly? , 2006, Nature Reviews Molecular Cell Biology.

[69]  Carsten C. Mahrenholz,et al.  A network of coiled-coil associations derived from synthetic GCN4 leucine-zipper arrays. , 2007, Angewandte Chemie.

[70]  J. Koch,et al.  Peptide Arrays on Membrane Supports. Synthesis and Applications , 2002 .

[71]  Gary D Bader,et al.  Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry , 2002, Nature.

[72]  Prisca Boisguerin,et al.  Engineering peptide inhibitors to overcome PDZ binding promiscuity. , 2010, Angewandte Chemie.

[73]  L. Castagnoli,et al.  Protein Interaction Networks by Proteome Peptide Scanning , 2004, PLoS biology.

[74]  A. Barabasi,et al.  Functional and topological characterization of protein interaction networks , 2004, Proteomics.

[75]  S Das,et al.  Identifying nature's protein Lego set. , 2000, Advances in protein chemistry.

[76]  J. Maynard Smith Natural Selection and the Concept of a Protein Space , 1970 .

[77]  S. Fields,et al.  A novel genetic system to detect protein–protein interactions , 1989, Nature.

[78]  C Sander,et al.  Dictionary of recurrent domains in protein structures , 1998, Proteins.

[79]  R. Micura,et al.  Atomic mutagenesis reveals A2660 of 23S ribosomal RNA as key to EF-G GTPase activation. , 2010, Nature chemical biology.

[80]  Jens Schneider-Mergener,et al.  Synthesis and screening of peptoid arrays on cellulose membranes , 2003 .

[81]  J. Wells,et al.  High-resolution epitope mapping of hGH-receptor interactions by alanine-scanning mutagenesis. , 1989, Science.

[82]  M. Bradley,et al.  Functional peptide arrays for high-throughput chemical biology based applications. , 2007, Current opinion in biotechnology.

[83]  R. Hoffmann,et al.  In situ stimulation of a T helper cell hybridoma with a cellulose-bound peptide antigen. , 2000, Journal of immunological methods.

[84]  Ulf Reimer,et al.  Peptide arrays: from macro to micro. , 2002, Current Opinion in Biotechnology.

[85]  A stabilizing influence: CAL PDZ inhibition extends the half-life of ΔF508-CFTR. , 2010, Angewandte Chemie.

[86]  S. Fields,et al.  Protein analysis on a proteomic scale , 2003, Nature.