Peptide Arrays

Currently , a large community effort focuses on protein interaction data as a mean to explore uncharacterized proteins function, discover new pathways and identify potential drug targets. However, the redundant screenings carried out in the past four years in Saccharomyces cerevisae show a very weak overlap and underline the need of protein interaction data validation. Here we propose a new comparative genomic validation approach based on the conservation of binding sequences within orthologs alignments of fifteen closely related yeast species. Taking the 14-3-3 domains as a study case we explore the binding specificities of their ligand peptides taking advantage of mutagenesis analysis carried out by PepSpot experiments. Using these experimental results we create a prediction tool based on regular expression combined with position specific scoring matrix able to screen the full in S. cerevisae proteome and identify putative 14-3-3 domain ligands. The comparative genomic method together with other well established protein interaction validation approaches are benchmarked as filters to increase the accuracy of this prediction. We show that the conservation across several yeast species of 14-3-3 interacting sequences successfully discriminates binding sites from spurious regions matching by chance ligand consensus and increase the prediction accuracy of a four fold.

Phosphoprotein-binding domains (PPBDs) mediate many important cellular and molecular processes. Ten PPBDs have been known to exist in the human proteome, namely, 14-3-3, BRCT, C2, FHA, MH2, PBD, PTB, SH2, WD-40 and WW. PepCyber:P»PEP is a newly constructed database specialized in documenting human PPBD-containing proteins and PPBD-mediated interactions. Our motivation is to provide the research community with a rich information source emphasizing the reported, experimentally validated data for specific PPBD-PPEP interactions. This information is not only useful for designing, comparing and validating the relevant experiments, but it also serves as a knowledge-base for computationally constructing systems signaling pathways and networks. PepCyber:P»PEP is accessible through the URL, http://www.pepcyber.org/PPEP/. The current release of the database contains 7044 PPBDmediated interactions involving 337 PPBD-containing proteins and 1123 substrate proteins.

The N-terminal tails of histone proteins are massively decorated with post-translational modifications (PTMs), which play important roles in the regulation of gene expression. Several highly conserved chromatin interacting proteins can bind to histone modifications in a sequence and modification specific manner employing specific reading domains. These proteins often contain several reading domains, which can cooperate in the readout of different PTMs. To gain a better insight into the combinatorial readout of PTMs, we developed a method to study the binding of double reading domains to mixed peptide arrays containing two different peptides in each spot. For that, differently modified and unmodified peptides were prepared by SPOT synthesis and solubilized. Then, two peptides were mixed and spotted onto a glass slide creating peptide spots presenting two modifications on two different peptides. Different combinations of mixed spots containing modified and unmodified peptides were generated and incubated with recombinant double reading domains to study their synergistic binding. For validation of the method, we used the well-studied BPTF subunit of the NURF chromatin-remodeling complex. BPTF contains a plant homeodomain finger (PHD) and a Bromodomain recognizing H3K4me3 and H4K16ac, respectively. We first confirmed with peptide arrays and Fluorescence Anisotropy (FA) measurements that the BPTF PHD-Bromo (PB) domain interacts specifically with the expected modifications. Using our novel tool, we observed a strong and synergistic binding only to peptide spots containing both modifications, which was lost if one of the domains was inactivated by a mutation. These data indicate that BPTF-PB simultaneously interacts with both target modifications using its PHD and Bromodomain. In agreement with the synergistic peptide interaction on mixed peptide arrays, we also show that chromatin pulldown by BPTF-PB depends on the activity of both reading domains. We conclude that mixed peptide spot arrays are a powerful, cheap and novel method for screening the combinatorial interaction space of multidomain reading proteins. Using this approach hundreds of mixed peptide spots can be prepared and tested for binding in principle allowing for an unbiased medium throughput investigation.

A new method is described for the selective`in synthesis' labeling of peptides by rhodamine or biotin at a single, predetermined A-amino group of a lysine residue. The K-amino group and other lysyl residues of the peptide remain unmodified. Peptides are assembled by the Fmoc approach, which requires mild operative conditions for the final deprotection and cleavage, and ensures little damage of the reporter group. The labeling technique involves the previous preparation of a suitable Lysine derivative, easily obtained from commercially-available protected amino acids. This new derivative, where the reporter group (biotin, or rhodamine) acts now as permanent protection of lysyl side chain functions, is then inserted into the synthesis program as a conventional protected amino acid, and linked to the preceding residue by aid of carbodiimide. A simpler, alternative method is also described for the selective`in synthesis' labeling of peptides with N-terminal lysyl residues. Several applications of labeled peptides are reported.

Grb2 is an important regulator of normal vs. oncogenic cell signaling transduction. It plays a pivotal role on kinase-mediated signaling transduction by linking Receptor Tyrosine kinases to Ras/MAPK pathway which is known to bring oncogenic outcome. Coumarins are phenolic molecules found in several plants and seeds widely studied because of the antibiotic, anti-inflammatory, anticoagulant, vasodilator, and anti-tumor properties. Despite several studies about the anti-tumor properties of Coumarin in vivo and the role of Grb2 in signaling pathways related to cell proliferation, a molecular level investigation of the interaction between Grb2 and Coumarin is still missing. In this study, we performed a combined set of biophysical approaches to get insights on the interaction between Grb2 in a dimer state and Coumarin. Our results showed that Coumarin interacts with Grb2 dimer through its SH2 domain. The interaction is entropically driven, 1:1 molecular ratio and presents equilibrium constant of 10 5 M À1. In fact, SH2 is a well-known domain and a versatile signaling module for drug targeting which has been reported to bind compounds that block Ras activation in vivo. Despite we don't know the biological role coming from interaction between Grb2-SH2 domain and Coumarin, it is clear that this molecule could work in the same way as a SH2 domain inhibitor in order to block the link of Receptor Tyrosine kinases to Ras/MAPK pathway.

Members of the SH2 domain family modulate signal transduction by binding to short peptides containing phosphorylated tyrosines. Each domain displays a distinct preference for the sequence context of the phosphorylated residue. We have developed a high-density peptide chip technology that allows for probing of the affinity of most SH2 domains for a large fraction of the entire complement of tyrosine phosphopeptides in the human proteome. Using this technique, we have experimentally identified thousands of putative SH2-peptide interactions for more than 70 different SH2 domains. By integrating this rich data set with orthogonal context-specific information, we have assembled an SH2-mediated probabilistic interaction network, which we make available as a community resource in the PepspotDB database. A predicted dynamic interaction between the SH2 domains of the tyrosine phosphatase SHP2 and the phosphorylated tyrosine in the extracellular signal-regulated kinase activation loop was validated by experiments in living cells.

The last few years have witnessed a great improvement in methodologies for the synthesis and purification of biologically active peptides and selectively modified analogues. However, the lack of simple, effective and suitable devices for in-line control of the key reactions involved in solid-phase peptide synthesis (i.e., deprotection and coupling) has thus far hampered the development of truly automatic synthesizers. A prototype for solid-phase peptide synthesis equipped with reliable devices to monitor the extent of deprotection by conductimetric and spectrophotometric methods has been designed, realized and utilized for synthesizing a model peptide.

The adaptor protein CT10-Regulator of Kinase (CRK) and the closely related CRK-Like (CRKL) are adaptor proteins that play important roles in many signaling pathways regulating cell proliferation and cell motility. A notable example is their required role in Reelin signaling during development of the laminated structures of the vertebrate central nervous system, including the cerebral cortex, cerebellum, hippocampus, and retina. As adaptors, CRK/CRKL are important in coupling phosphotyrosine signaling to G protein activity to regulate both cell proliferation and changes in the actin cytoskeleton, thereby exerting control over cell motility, and migration. While many proteins that interact with CRK/CRKL have been identified, the diverse roles of these molecules suggest that more remain to be found. Herein is described a novel CRK/CRKL interacting protein, Src Homology 2 domain-containing protein D (SHD), which demonstrates a phosphorylation-dependent interaction with the CRK/CRKL SH2 domain in HEK 293 cells stimulated with hydrogen peroxide, which globally boosts tyrosine phosphorylation by inhibiting tyrosine phosphatases. Treatment with an inhibitor for Src family kinases (SFKs), Src-1, or an inhibitor of Abl/Arg kinases, STI571, reduces peroxide-induced binding of the CRKL-SH2 domain to SHD. We show that overexpression of Abl kinase, but not the SFK Fyn is sufficient to induce binding of the CRKL-SH2 to SHD and that this interaction requires at least one of the five tyrosines in YxxP motifs found in SHD. Using mass spectrometry, we found that Abl phosphorylates SHD on Y144, which is located in a YxxP motif. Mutation of this site to phenylalanine reduces, but does not prevent, Abl-induced binding of SHD to the CRKL-SH2 domain, suggesting that other YxxP sites also facilitate the interaction. A discussion of the cellular consequences of the interaction between SHD and CRK/CRKL is presented. To explore the biological role of SHD, we used the zebrafish to study shdb, a putative ortholog of human SHD. The expression of shdb was unknown and so we performed in situ hybridization and determined that shdb was expressed in the developing nervous system. To study the function of this gene, we used a morpholino to knock down expression of shdb which resulted in significantly reduced eye size. Possible roles of Shdb in eye development are discussed as is future research aimed to elucidate the cellular and developmental mechanisms by which Shdb functions in the developing eye. ii ACKNOWLEDGEMENTS Acknowledgements are one of those things that seem short and easy to write, and so it gets left until the last minute when you suddenly realize there is a long list people you have depended who deserve recognition. There is not space on one page to thank everyone who deserves it, but I will endeavor to thank those who contributed the most. First, I would like to thank my mentor Dr. Bryan A. Ballif, without whom this thesis would not have been possible. Bryan has an incredible commitment to seeing his students succeed and always finds time to help. He has taught me to think deeply and critically about questions, and to always start sentences with "surprisingly". I would like to thank my committee member and collaborator Dr. Alicia Ebert for her help with all things zebrafish, and for her puns (which are excellent). I would also like to thank the other members of my committee. Dr. Brent Lockwood has helped me to keep the larger picture in mind when I sometimes get stuck in the minutia. Dr. Diane Jaworski has pushed me to be a better scientist and encouraged me to stay focused. I appreciate all the help and support I have received. I also give thanks for the unconditional support from my family. I would also like to thank the members of the Ballif and Ebert lab for their constant support and assistance. And last, but far from least, I would like to thank by better half Susan Denton for her love, support, and baked goods, which have sustained me through my time as a graduate student. iii

Herein we report a practical approach for peptide synthesis using second-generation fibrous polyacrylamide resin (Li-resin, “Li” is coming from the name of its inventor, Yongfu Li). This resin with the corresponding handle was used for solid phase peptide synthesis (SPPS) using a fluorenylmethoxycarbonyl (Fmoc) approach. We reveal that the most appropriate mixing and filtration strategy when using amino-Li-resin in SPPS is via shaking and gravity filtration, instead of mechanical stirring and suction filtration used with other resins. The strategy was demonstrated with the SPPS of H-Tyr-Ile-Ile-Phe-Leu-NH2, which contains the difficult sequence Ile-Ile. The peptide was obtained with excellent purity and yield. We are confident that this strategy will be rapidly implemented by other peptide laboratories.

SH3 domains are protein modules that mediate protein-protein interactions in many eukaryotic signal transduction pathways. The majority of SH3 domains studied thus far act by binding to proline-rich sequences in partner proteins, but a growing number of studies have revealed alternative recognition mechanisms. We have comprehensively surveyed the specificity landscape of human SH3 domains in an unbiased manner using peptide-phage display and deep sequencing. Based on $70,000 unique binding peptides, we obtained 154 specificity profiles for 115 SH3 domains, which reveal that roughly half of the SH3 domains exhibit non-canonical specificities and collectively recognize a wide variety of peptide motifs, most of which were previously unknown. Crystal structures of SH3 domains with two distinct non-canonical specificities revealed novel peptide-binding modes through an extended surface outside of the canonical proline-binding site. Our results constitute a significant contribution toward a complete understanding of the mechanisms underlying SH3-mediated cellular responses.

CRK and CRKL adapter proteins play essential roles in development and cancer through their SRC homology 2 and 3 (SH2 and SH3) domains. To gain insight into the origin of their shared functions, we have investigated their evolutionary history. We propose a term, crk/crkl ancestral (crka), for orthologs in invertebrates before the divergence of CRK and CRKL in the vertebrate ancestor. We have isolated two orthologs expressed in the choanoflagellate Monosiga brevicollis, a unicellular relative to the metazoans. Consistent with its highly-conserved three-dimensional structure, the SH2 domain of M. brevicollis crka1 can bind to the mammalian CRK/CRKL SH2 binding consensus phospho-YxxP, and to the SRC substrate/focal adhesion protein BCAR1 (p130(CAS)) in the presence of activated SRC. These results demonstrate an ancient origin of the CRK/CRKL SH2-target recognition specificity. Although BCAR1 orthologs exist only in metazoans as identified by an N-terminal SH3 domain, YxxP motifs, and a ...

Lipids are susceptible to damage by reactive oxygen species, and from lipid oxidation reactions many short chain lipid peroxidation products can be formed. 4-Hydroxy-2-nonenal (HNE) is one of the most abundant and cytotoxic lipid oxidation products and is known to form covalent adducts with nucleophilic amino acids of proteins. HNE-modified proteins have value as biomarkers and can be detected by antibody-based techniques, but most commercially available antibodies were raised against HNE-keyhole limpet hemocyanin. We used HNE-treated human serum albumin (HSA) to raise sheep antiserum and report for the first time the use of covalently modified peptide arrays to assess epitope binding of antibodies (Abs). Peptide arrays covering the sequence of HSA and treated post peptide synthesis with HNE were used to compare the different binding patterns of a commercial polyclonal antibody (pAb) raised against HNEtreated KLH and an in-house anti-HNE enriched pAb. The results were correlated with analysis of HNE-modified HSA by high-resolution tandem mass spectrometry. Both anti-HNE pAbs were found to bind strongly to eight common peptides on the HNE-treated HSA membranes, suggesting that HNE adducts per se induced an immune response in both cases even though different immunogens were used. Both antibodies bound with the highest affinity to the peptide 365 DPHECYAKVFDEFKPLV 381 , which contains K378 and was also shown to be modified by the mass spectrometry analysis. Overall, the commercial anti-HNE pAb showed better specificity, recognizing nine out of the eleven adducts found by MS/MS, while the in-house enriched pAb only recognizes six. Nevertheless, the in-house pAb recognized specific peptides that were not recognized by the commercial pAb, which suggests the presence of clones uniquely specific to HNE adducts on HSA.

In this review, we summarize the development and applications of synthetic peptide based tools to identify and characterize binding proteins of histone posttranslational modifications (PTMs). The limitation of peptide-based approaches is then discussed, followed by a brief description on recent development of nucleosome-based tools.

Reactions that can selectively modify amino acid sequences within peptides and proteins are important for preparing protein reagents, immobilizing proteins, and making antibody-drug conjugates. The development of new reactions often begins with known chemistries and optimizes yields using a small set of peptide reactants. This article describes the use of peptide arrays and selfassembled monolayers for matrix-assisted laser desorption/ionization mass spectrometry (SAMDI-MS) to discover and characterize unanticipated sequence-selective reactions of peptides. This work reports the selective acetylation of HY (histidine-tyrosine) and YH (tyrosine-histidine) dyads when treated with acetic anhydride in aqueous conditions. More broadly, this example illustrates the benefits of using peptide arrays and a label-free analysis method to discover peptide-modifying reactions and gain mechanistic insight into their sequence specificity.

Emerging peptide array technologies are able to profile molecular activities within cell lysates. However, the structural diversity of peptides leads to inherent differences in peptide signal-to-noise ratios (S/N). These complex effects can lead to potentially unrepresentative signal intensities and can bias subsequent analyses. Within mass spectrometry-based peptide technologies, the relation between a peptide's amino acid sequence and S/N remains largely nonquantitative. To address this challenge, we present a method to quantify and analyze mass spectrometry S/N of two peptide arrays, and we use this analysis to portray quality of data and to design future arrays for SAMDI mass spectrometry. Our study demonstrates that S/N varies significantly across peptides within peptide arrays, and variation in S/N is attributable to differences of single amino acids. We apply supervised machine learning to predict peptide S/N based on amino acid sequence, and identify specific physical properties of the amino acids that govern variation of this metric. We find low peptide−S/N concordance between arrays, demonstrating that different arrays require individual characterization and that global peptide−S/N relationships are difficult to identify. However, with proper peptide sampling, this study illustrates how machine learning can accurately predict the S/N of a peptide in an array, allowing for the efficient design of arrays through selection of high S/N peptides.

The N-terminal tails of histone proteins are massively decorated with post-translational modifications (PTMs), which play important roles in the regulation of gene expression. Several highly conserved chromatin interacting proteins can bind to histone modifications in a sequence and modification specific manner employing specific reading domains. These proteins often contain several reading domains, which can cooperate in the readout of different PTMs. To gain a better insight into the combinatorial readout of PTMs, we developed a method to study the binding of double reading domains to mixed peptide arrays containing two different peptides in each spot. For that, differently modified and unmodified peptides were prepared by SPOT synthesis and solubilized. Then, two peptides were mixed and spotted onto a glass slide creating peptide spots presenting two modifications on two different peptides. Different combinations of mixed spots containing modified and unmodified peptides were generated and incubated with recombinant double reading domains to study their synergistic binding. For validation of the method, we used the well-studied BPTF subunit of the NURF chromatin-remodeling complex. BPTF contains a plant homeodomain finger (PHD) and a Bromodomain recognizing H3K4me3 and H4K16ac, respectively. We first confirmed with peptide arrays and Fluorescence Anisotropy (FA) measurements that the BPTF PHD-Bromo (PB) domain interacts specifically with the expected modifications. Using our novel tool, we observed a strong and synergistic binding only to peptide spots containing both modifications, which was lost if one of the domains was inactivated by a mutation. These data indicate that BPTF-PB simultaneously interacts with both target modifications using its PHD and Bromodomain. In agreement with the synergistic peptide interaction on mixed peptide arrays, we also show that chromatin pulldown by BPTF-PB depends on the activity of both reading domains. We conclude that mixed peptide spot arrays are a powerful, cheap and novel method for screening the combinatorial interaction space of multidomain reading proteins. Using this approach hundreds of mixed peptide spots can be prepared and tested for binding in principle allowing for an unbiased medium throughput investigation.

Using a combinatorial peptide library that is based on the one-bead one-peptide approach we identified 14 peptide substrates for the c-ABL protein tyrosine kinase, which define three distinct consensus sequence groups. This is distinct from many serine/threonine kinases, which often phosphorylate only one major consensus sequence. The three consensus sequences accurately predict phosphorylation sites in cellular ABL substrates proven to play a role in cell signaling. Our data suggest that protein tyrosine kinases have evolved to recognize multiple substrate motifs.

The mechanisms underlying development of ribonucleoprotein (RNP) autoantibodies are unclear. The U1-70K protein is the predominant target of RNP autoantibodies, and the RNA binding domain has been shown to be the immunodominant autoantigenic region of U1-70K, although the specific epitopes are not known. To precisely map U1-70K epitopes, we developed silicon-based peptide microarrays with >5700 features, corresponding to 843 unique peptides derived from the U1-70K protein. The microarrays feature overlapping peptides, with single-amino acid resolution in length and location, spanning amino acids 110-170 within the U1-70K RNA binding domain. We evaluated the serum IgG of a cohort of patients with systemic lupus erythematosus (SLE; n = 26) using the microarrays, and identified multiple reactive epitopes, including peptides 116-121 and 143-148. Indirect peptide ELISA analysis of the sera of patients with SLE (n = 88) revealed that ∼14% of patients had serum IgG reactivity to 116-121...

Whether RET is able to directly phosphorylate and activate downstream targets independently of the binding of proteins that contain Src homology 2 or phosphotyrosine binding domains and whether mechanisms in trans by cytoplasmic kinases can modulate RET function and signaling remain largely unexplored. In this study, oligopeptide arrays were used to screen substrates directly phosphorylated by purified recombinant wild-type and oncogenic RET kinase domain in the presence or absence of small molecule inhibitors. The results of the peptide array were validated by enzyme kinetics, in vitro kinase, and cell-based experiments. The identification of focal adhesion kinase (FAK) as a direct substrate for RET kinase revealed (i) a RET-FAK transactivation mechanism consisting of direct phosphorylation of FAK Tyr-576/577 by RET and a reciprocal phosphorylation of RET by FAK, which crucially is able to rescue the kinase-impaired RET K758M mutant and (ii) that FAK binds RET via its FERM domain. Interestingly, this interaction is abolished upon RET phosphorylation, indicating that RET binding to the FERM domain of FAK is a priming step for RET-FAK transactivation. Finally, our data indicate that FAK inhibitors could be used as potential therapeutic agents for patients with multiple endocrine neoplasia type 2 tumors because both, treatment with the FAK kinase inhibitor NVP-TAE226 and FAK down-regulation by siRNA reduced RET phosphorylation and signaling as well as the proliferation and survival of tumor and transfected cell lines expressing oncogenic RET. Receptor tyrosine kinases (RTKs) 2 are key molecules for the recognition and transduction of external signals across the * This work was supported by grants from Breakthrough Breast Cancer (to C. M. I.), Ministerio de Educació n y Ciencia of Spain Grant EX2006_1341 (to I. P.-M.), and Cancer Research UK (to I. P.-M. and N. Q. M.).

Grb2 is an important regulator of normal vs. oncogenic cell signaling transduction. It plays a pivotal role on kinase-mediated signaling transduction by linking Receptor Tyrosine kinases to Ras/MAPK pathway which is known to bring oncogenic outcome. Coumarins are phenolic molecules found in several plants and seeds widely studied because of the antibiotic, anti-inflammatory, anticoagulant, vasodilator, and anti-tumor properties. Despite several studies about the anti-tumor properties of Coumarin in vivo and the role of Grb2 in signaling pathways related to cell proliferation, a molecular level investigation of the interaction between Grb2 and Coumarin is still missing. In this study, we performed a combined set of biophysical approaches to get insights on the interaction between Grb2 in a dimer state and Coumarin. Our results showed that Coumarin interacts with Grb2 dimer through its SH2 domain. The interaction is entropically driven, 1:1 molecular ratio and presents equilibrium constant of 10 5 M À1. In fact, SH2 is a well-known domain and a versatile signaling module for drug targeting which has been reported to bind compounds that block Ras activation in vivo. Despite we don't know the biological role coming from interaction between Grb2-SH2 domain and Coumarin, it is clear that this molecule could work in the same way as a SH2 domain inhibitor in order to block the link of Receptor Tyrosine kinases to Ras/MAPK pathway.

A new method is described for the selective`in synthesis' labeling of peptides by rhodamine or biotin at a single, predetermined A-amino group of a lysine residue. The K-amino group and other lysyl residues of the peptide remain unmodified. Peptides are assembled by the Fmoc approach, which requires mild operative conditions for the final deprotection and cleavage, and ensures little damage of the reporter group. The labeling technique involves the previous preparation of a suitable Lysine derivative, easily obtained from commercially-available protected amino acids. This new derivative, where the reporter group (biotin, or rhodamine) acts now as permanent protection of lysyl side chain functions, is then inserted into the synthesis program as a conventional protected amino acid, and linked to the preceding residue by aid of carbodiimide. A simpler, alternative method is also described for the selective`in synthesis' labeling of peptides with N-terminal lysyl residues. Several applications of labeled peptides are reported.

The changes in signal transduction associated with the acquisition of specific cell fates remain poorly understood. We performed massive parallel assessment of kinase signatures of the radiations of the hematopoietic system, including long-term repopulating hematopoietic stem cells (LT-HSC), short-term repopulating HSC (ST-HSC), immature natural killer (iNK) cells, NK cells, B cells, T cells and myeloid cells. The LT-HSC kinome is characterised by non-canonical Wnt, Ca 2+ and classical protein kinase C (PKC)-driven signalling, which is lost upon the transition to ST-HSC, whose kinome signature prominently features receptor tyrosine kinase (RTK) activation of the Ras/MAPK signalling cassette. Further differentiation to iNK maintains signalling through this cassette but simultaneously leads to activation of a PI3K/PKB/Rac signalling, which becomes the dominant trait in the kinase signature following full differentiation towards NK cells. Differentiation along the myeloid and B cell lineages is accompanied by hyperactivation of both the Ras/MAPK and PI3K/PKB/Rac signalling cassette. T cells, however, deactivate signalling and only display residual G protein-coupled pathways. Thus, differentiation along the hematopoietic lineage is associated with major remodelling of cellular kinase signature.

Protein-peptide interactions form an important subset of the total protein interaction network in the cell and play key roles in signaling and regulatory networks, and in major biological processes like cellular localization, protein degradation, and immune response. In this work, we have described the LMDIPred web server, an online resource for generalized prediction of linear peptide sequences that may bind to three most prevalent and well-studied peptide recognition modules (PRMs)-SH3, WW and PDZ. We have developed support vector machine (SVM)-based prediction models that achieved maximum Matthews Correlation Coefficient (MCC) of 0.85 with an accuracy of 94.55% for SH3, MCC of 0.90 with an accuracy of 95.82% for WW, and MCC of 0.83 with an accuracy of 92.29% for PDZ binding peptides. LMDIPred output combines predictions from these SVM models with predictions using Position-Specific Scoring Matrices (PSSMs) and string-matching methods using known domain-binding motif instances and regular expressions. All of these methods were evaluated using a five-fold cross-validation technique on both balanced and unbalanced datasets, and also validated on independent datasets. LMDIPred aims to provide a preliminary bioinformatics platform for sequence-based prediction of probable binding sites for SH3, WW or PDZ domains.

Peptide recognition domains (PRD) bind to short linear motifs on their biological partners and are found in several cellular pathways including those found to be critical in tumorigenesis. In this study, I aimed to generate peptide probes against PRDs present on proteins involved in ovarian cancer. Using bioinformatics, I identified 66 potential PRDs present on these proteins. I then used peptide phage display to successfully generate peptides against 27 of the 66 domains.

The forkhead-associated (FHA) domain is a protein module found in many proteins involved in cell signaling in response to DNA damage. It has been suggested to bind to pThr sites of its target protein. Recently we have determined the ®rst structure of an FHA domain, FHA2 from the yeast protein Rad53, and demonstrated that FHA2 binds to a pTyrcontaining peptide 826 EDI(pY)YLD 832 from Rad9, with a moderate af®nity (K d ca. 100 mM). We now report the solution structure of the complex of FHA2 bound with this pTyr peptide. The structure shows that the phosphate group of pTyr interacts directly with three arginine residues (605, 617, and 620), and that the leucine residue at the 2 position from the pTyr interacts with a hydrophobic surface on FHA2. The sequence speci-®city of FHA2 was determined by screening a combinatorial pTyr library. The results clearly show that FHA2 recognizes speci®c sequences C-terminal to pTyr with the following consensus: XX(pY)N 1 N 2 N 3 , where N 1 Leu, Met, Phe, or Ile, N 2 Tyr, Phe, Leu, or Met, and N 3 Phe, Leu, or Met. Two of the selected peptides, GF(pY)LYFIR and DV(pY)FY-MIR, bind FHA2 with K d values of 1.1 and 5.0 mM, respectively. The results, along with other recent reports, demonstrate that the FHA domain is a new class of phosphoprotein-binding domain, capable of binding both pTyr and pThr sequences.

Peptide microarrays serve as ah igh-throughput tool for the readout of protein-peptide interactions. We present am ulti-step purification of high-complexity peptide microarrays by transfer to specialized surfaces. Only correctly synthesized peptides are transferred from the synthesis surface to variouss ubstrates where they can be immobilizedb y av ariety of different anchor molecules.H ere, we demonstrate the transfert or igid streptavidin, epoxide, gold, and azide surfaces. The reportedm ethod reduces the cost of purified peptidea rray production through the reproduction of one array several times.

Understanding of the role of estrogen receptors (ER␣ and ER␤) in the pathophysiology of breast cancer (BC) has considerably increased in last decades. Despite sharing a similar structure, these two transcription factors often exert opposite roles in BC. In addition, it has been shown that their transcriptional activity is not strictly associated to ligand activation and that unliganded ERs are able to "have a life on their own." This appears to be mainly due to ligandindependent mechanisms leading to ERs PTMs or to their recruitment to specific protein complexes, dependent on cellular context. Furthermore, a significant unliganded ER activity, probably independent by the activation of other pathways, has been recently reported to affect gene transcription, microRNA expression, and downstream proteome. In this review, we describe recent findings on nuclear and cytoplasmic unliganded ER␣ and ER␤ activity. We focus on functional genomics, epigenomics, and interaction proteomics data, including PTM induced by ERs-modulated miRNAs in the BC context. A better comprehension of the molecular events controlled by unliganded ERs activity in BC pathogenesis is crucial since it may impact the therapeutic approach to the initial or acquired resistance to endocrine therapies, frequently experienced in the treatment of BC.

Proteins are the main perpetrators of most cellular tasks. However, they seldom act alone and most biological processes are carried out by macromolecular assemblies and regulated through a complex network of protein-protein interactions. Thus, modern molecular and cell biology no longer focus on single macromolecules but now look into complexes, pathways or even entire organisms. The many genomesequencing initiatives have provided a near complete list of the components present in an organism, and post-genomic projects have aimed to catalogue the relationships between them. The emerging field of systems biology is now centred mainly on unraveling these relationships. However, all these interaction maps lack molecular details: they tell us who interacts with whom, but not how. A full understanding of how molecules interact can be attained only from high resolution three-dimensional (3D) structures, since these provide crucial atomic details about binding. These details allow a more ra...

Chemical modifications on histones and DNA/RNA constitute a fundamental mechanism for epigenetic regulation. These modifications often function as docking marks to recruit or stabilize cognate "reader" proteins. So far, a platform for quantitative and high-throughput profiling of the epigenetic interactome is urgently needed but still lacking. Here, we report a 3D-carbene chip-based surface plasmon resonance imaging (SPRi) technology for this purpose. The 3D-carbene chip is suitable for immobilizing versatile biomolecules (e.g., peptides, antibody, DNA/RNA) and features low nonspecific binding, random yet function-retaining immobilization, and robustness for reuses. We systematically profiled binding kinetics of 1,000 histone "reader-mark" pairs on a single 3D-carbene chip and validated two recognition events by calorimetric and structural studies. Notably, a discovery on H3K4me3 recognition by the DNA mismatch repair protein MSH6 in Capsella rubella suggests a m...

Members of the SH2 domain family modulate signal transduction by binding to short peptides containing phosphorylated tyrosines. Each domain displays a distinct preference for the sequence context of the phosphorylated residue. We have developed a high-density peptide chip technology that allows for probing of the affinity of most SH2 domains for a large fraction of the entire complement of tyrosine phosphopeptides in the human proteome. Using this technique, we have experimentally identified thousands of putative SH2-peptide interactions for more than 70 different SH2 domains. By integrating this rich data set with orthogonal context-specific information, we have assembled an SH2-mediated probabilistic interaction network, which we make available as a community resource in the PepspotDB database. A predicted dynamic interaction between the SH2 domains of the tyrosine phosphatase SHP2 and the phosphorylated tyrosine in the extracellular signal-regulated kinase activation loop was validated by experiments in living cells.

To reduce the errors associated with identifying false-positives, non-specific interacting peptides (so-called 'sticky'peptides) were identified in two ways. Peptides that bound to GST, reflected by an intensity above the mean in two out of three separate trials, were tagged as non-specific binding peptides. Alternatively, peptides that exhibited above-mean binding to the majority of individual SH2 domains were used to corroborate an assessment of “non-specific”. This latter method relies upon the data-distribution properties obtained by ...

A peptide thioester is a key building block for protein synthesis by a ligation method, such as the thioester method and native chemical ligation. Combining these ligation methods offers flexibility in the choice of the condensation sites in a sequential ligation strategy. We describe herein a novel strategy, in which native chemical ligation followed by the thioester method are utilized, based on the use of a peptide containing a CysPro ester (CPE) autoactivating unit at the C-terminus as a peptide thioester precursor. This sequential ligation strategy was applied to the synthesis of histone H3, which consists of 135 amino acid residues and contains a trimethyl Lys 9 residue.

Tyrosine phosphorylation and protein recognition, mediated by phosphotyrosine containing peptides, play an important role in determining the speci®c response of a cell, when stimulated by external signals. We have used peptide repertoires displayed by ®lamentous phage as a tool to study the substrate speci®city of the protein tyrosine kinase (PTK) p55 fyn (Fyn). Peptide libraries were incubated for a short time in the presence of Fyn and phages displaying ef®ciently phosphorylated peptides were selected by panning over anti-phosphotyrosine antibodies. The characterization of the peptides enriched after three phosphorylation/selection rounds allowed us to de®ne a canonical substrate sequence for the kinase Fyn, E±(j/T)YGxj, where j represents any hydrophobic residue. A peptide conforming to this sequence is a better substrate than a second peptide designed to be in accord with the consensus sequence recognised by the Fyn SH2 domain. When the library phosphorylation reaction is carried out in saturation conditions, practically all the tyrosine containing peptides are phosphorylated, irrespective of their context. These``fully modi®ed'' peptide libraries are a valuable tool to study the speci®city of phosphotyrosine mediated protein recognition. We have used this new tool to identify a family of peptides that bind the PTB domain of the adapter protein Shc. Comparison of the peptide sequences permits us to con®rm the essential role of N at position À3, while P often found at position À2 in natural targets is not absolutely required. Furthermore, our approach permits us to reveal an``extended'' consensus indicating that residues that do not seem to in¯uence binding in natural peptides can make productive contacts, at least in linear peptides.

The study of proteomics succeeds the deciphering of the genetic code; this growing burgeoning area is set to dominate scientific research well into the next decade. Current tools employed in studying protein-protein interactions include antibodies, non-protein scaffolds, fluorescence imaging, split enzymes and the relatively new tool termed Adhirons designed by researchers at Leeds University. Antibodies have been used extensively in protein studies due to the high degree of affinity and specificity however the rise in cost and the length of time required to make antibodies has fuelled efforts to find better alternatives. In this work we report whether Adhirons owing to their small size and high stability can be adapted to assay interactions in cells. It will explore whether current tools widely used in protein studies can debunk the davinchi code for protein-protein interactions. Most biological processes are governed by protein interactions and at the heart of most disease states particularly cancer lies a signalling cascade triggered by a plethora of protein interactions. We review current research into proteomics to evaluate and appreciate the work achieved thus far by international scientist crossing east and west divide. The journey into proteomics has already begun and at the present juncture has made significant milestones.

The N-terminal 25 residue segment of human surfactant protein B (SP-B 1-25) was synthesised in 26% yield by manual Fmoc solid-phase peptide synthesis (Fmoc SPPS) using low-loading Fmoc-Gly-Wang resin. Substantial oxidation of Met 21 occurred during the synthesis, and the addition of Bu 4 NBr to a TFA/water/EDT/TIS cleavage cocktail enabled facile reduction of Met(O) 21-SP-B 1-25 to SP-B 1-25. The methods described herein are generally applicable to the Fmoc SPPS of difficult sequences containing methionine.

Members of the SH2 domain family modulate signal transduction by binding to short peptides containing phosphorylated tyrosines. Each domain displays a distinct preference for the sequence context of the phosphorylated residue. We have developed a high-density peptide chip technology that allows for probing of the affinity of most SH2 domains for a large fraction of the entire complement of tyrosine phosphopeptides in the human proteome. Using this technique, we have experimentally identified thousands of putative SH2-peptide interactions for more than 70 different SH2 domains. By integrating this rich data set with orthogonal context-specific information, we have assembled an SH2-mediated probabilistic interaction network, which we make available as a community resource in the PepspotDB database. A predicted dynamic interaction between the SH2 domains of the tyrosine phosphatase SHP2 and the phosphorylated tyrosine in the extracellular signal-regulated kinase activation loop was validated by experiments in living cells.

This review is devoted to describing, summarizing, and analyzing of dynamic proteomics data obtained over the last few years and concerning the role of protein-protein interactions in modeling of the living cell. Principles of modern high-throughput experimental methods for investigation of protein-protein interactions are described. Systems biology approaches based on integrative view on cellular processes are used to analyze organization of protein interaction networks. It is proposed that finding of some proteins in different protein complexes can be explained by their multi-modular and polyfunctional properties; the different protein modules can be located in the nodes of protein interaction networks. Mathematical and computational approaches to modeling of the living cell with emphasis on molecular dynamics simulation are provided. The role of the network analysis in fundamental medicine is also briefly reviewed.

Identifying associated partners is critical to understanding the potential function and upstream and downstream pathways of the molecule being studied. The Src homology 2 (SH2) domain is a binding module for peptides containing a phosphotyrosine residue, which is a posttranslational modification that is heavily involved in signal transduction. A paper in this issue shows how "reverse interactomics" can be exploited to identify binding partners of the SH2 domain of tensin.