Linear Peptide Sequences Research Articles

A proposed syntax for Minimotif Semantics, version 1

BackgroundOne of the most important developments in bioinformatics over the past few decades has been the observation that short linear peptide sequences (minimotifs) mediate many classes of cellular functions such as protein-protein interactions, molecular trafficking and post-translational modifications. As both the creators and curators of a database which catalogues minimotifs, Minimotif Miner, the authors have a unique perspective on the commonalities of the many functional roles of minimotifs. There is an obvious usefulness in standardizing functional annotations both in allowing for the facile exchange of data between various bioinformatics resources, as well as the internal clustering of sets of related data elements. With these two purposes in mind, the authors provide a proposed syntax for minimotif semantics primarily useful for functional annotation.ResultsHerein, we present a structured syntax of minimotifs and their functional annotation. A syntax-based model of minimotif function with established minimotif sequence definitions was implemented using a relational database management system (RDBMS). To assess the usefulness of our standardized semantics, a series of database queries and stored procedures were used to classify SH3 domain binding minimotifs into 10 groups spanning 700 unique binding sequences.ConclusionOur derived minimotif syntax is currently being used to normalize minimotif covalent chemistry and functional definitions within the MnM database. Analysis of SH3 binding minimotif data spanning many different studies within our database reveals unique attributes and frequencies which can be used to classify different types of binding minimotifs. Implementation of the syntax in the relational database enables the application of many different analysis protocols of minimotif data and is an important tool that will help to better understand specificity of minimotif-driven molecular interactions with proteins.

Formalin Fixation and Antigen Retrieval: Translating Insights To Clinical Innovation

Tissue fixation and antigen retrieval (AR) are important variables in evaluating protein expression in biopsies. Because of the complexity in modeling fixation and AR with whole proteins, we investigated antibody immunoreactivity to isolated peptide epitopes. We identified epitopes using phage‐displayed peptide combinatorial libraries. The epitopes were all linear peptide sequences from the native protein. Formalin fixation abrogated immunoreactivity if another (antigenically irrelevant) protein was present. AR restored immunoreactivity. Our data suggest a model of steric interference caused by formaldehyde‐induced cross‐linking. We recently translated these findings to practical use, as a QC tool for routine clinical laboratory use. Spots of formalin‐fixed or unfixed peptides, covalently attached to glass microscope slides, can serve as immunohistochemistry (IHC) controls. The peptides can be printed to specified concentrations, are reproducible (CV <8%), and amenable to mass production. In an initial study of 109 clinical IHC laboratories, approximately 18% demonstrated inadequate staining. Errors were more commonly associated with AR than the IHC stain. This technology was recently transferred for commercial production to ThermoFisher Corp. and will offer laboratories a new method for evaluating AR and IHC staining performance from day‐to‐day as well as relative to other laboratories.

Metathesis assisted synthesis of cyclic peptides

Installation of reversible, metathesis-active tethers into linear peptide sequences can be used to promote formation of cyclic peptide amides and esters.

Epitope mapping of anti-proteinase 3 and anti-myeloperoxidase antibodies.

Anti-proteinase 3 (PR3) and anti-myeloperoxidase (MPO) autoantibodies are present in many patients with Wegener's granulomatosis (WG) and microscopic polyarteritis. The aim of this study was to determine whether these antibodies bound to linear peptide sequences on their target antigens. If common linear epitopes were demonstrated, then these could be manufactured and used in diagnostic ELISAs for anti-PR3 and anti-MPO antibodies. In addition, any homology between these epitopes and bacterial or viral sequences might implicate those microorganisms in the development of these antibodies and the pathogenesis of the associated diseases. The presence of linear epitopes on PR3 and MPO was suggested by the binding of the corresponding autoantibodies to these proteins after they had been reduced with beta-mercaptoethanol (beta-ME) and denatured with SDS or boiling, and digested with proteases. Four of the 22 sera with anti-PR3 antibodies bound to PR3 in Western blots after treatment with SDS, beta-ME and boiling for 5 min. Thermal denaturation reduced the amount of binding more than other forms of denaturation. One serum with anti-PR3 antibodies bound to Lys-C and Glu-C-digested PR3 in dot blots. Linear epitopes could not be further defined by their binding in an ELISA using overlapping peptides corresponding to the PR3 molecule because of non-specific binding. Three of the five sera with anti-MPO antibodies bound to MPO in Western blots after treatment with SDS, beta-ME and boiling for 5 min. One serum with anti-MPO antibodies bound to Lys-C and Glu-C-digested MPO in dot blots. Again, linear epitopes could not be further defined using an ELISA with overlapping peptides because of non-specific binding. Some anti-PR3 and anti-MPO antibodies are likely to recognize linear epitopes, but these cannot be defined by use of a PIN ELISA system.

Web Server To Identify Similarity of Amino Acid Motifs to Compounds (SAAMCO)

Protein-protein interactions are fundamental in mediating biological processes including metabolism, cell growth, and signaling. To be able to selectively inhibit or induce protein activity or complex formation is a key feature in controlling disease. For those situations in which protein-protein interactions derive substantial affinity from short linear peptide sequences, or motifs, we can develop search algorithms for peptidomimetic compounds that resemble the short peptide's structure but are not compromised by poor pharmacological properties. SAAMCO is a Web service ( http://bioware.ucd.ie/ approximately saamco) that facilitates the screening of motifs with known structures against bioactive compound databases. It is built on an algorithm that defines compound similarity based on the presence of appropriate amino acid side chain fragments and a favorable Root Mean Squared Deviation (RMSD) between compound and motif structure. The methodology is efficient as the available compound databases are preprocessed and fast regular expression searches filter potential matches before time-intensive 3D superposition is performed. The required input information is minimal, and the compound databases have been selected to maximize the availability of information on biological activity. "Hits" are accompanied with a visualization window and links to source database entries. Motif matching can be defined on partial or full similarity which will increase or reduce respectively the number of potential mimetic compounds. The Web server provides the functionality for rapid screening of known or putative interaction motifs against prepared compound libraries using a novel search algorithm. The tabulated results can be analyzed by linking to appropriate databases and by visualization.

G Protein–Coupled Receptor Sorting to Endosomes and Lysosomes

The heptahelical G protein-coupled receptors (GPCRs) belong to the largest family of cell surface signaling receptors encoded in the human genome. GPCRs signal to diverse extracellular stimuli and control a vast number of physiological responses, making this receptor class the target of nearly half the drugs currently in use. In addition to rapid desensitization, receptor trafficking is crucial for the temporal and spatial control of GPCR signaling. Sorting signals present in the intracytosolic domains of GPCRs regulate trafficking through the endosomal-lysosomal system. GPCR internalization is mediated by serine and threonine phosphorylation and arrestin binding. Short, linear peptide sequences including tyrosine- and dileucine-based motifs, and PDZ ligands that are recognized by distinct endocytic adaptor proteins also mediate internalization and endosomal sorting of GPCRs. We present new data from bioinformatic searches that reveal the presence of these types of sorting signals in the cytoplasmic tails of many known GPCRs. Several recent studies also indicate that the covalent modification of GPCRs with ubiquitin serves as a signal for internalization and lysosomal sorting, expanding the diversity of mechanisms that control trafficking of mammalian GPCRs.

The minimum element of a synthetic peptide required to block prostate tumor cell migration

Human prostate tumor cell invasion and metastasis is dependent in part on cell adhesion to extracellular matrix proteins and cell migration. We previously identified a synthetic D-amino acid tumor cell adhesion peptide called HYD1 (kikmviswkg) that supported adhesion of tumor cells derived from breast, prostate, ovary and pancreas tissue. Alanine substitution analysis and a peptide deletion strategy were used to determine the minimal element of HYD1 necessary for bioactivity in a prostate cancer cell line called PC3N. Bioactivity was measured by assays of cell adhesion, migration and ERK signaling. The most potent element of HYD1 necessary to support cell adhesion was kmvixw, the block to migration required xkmviswxx and activation of ERK signaling required ikmviswxx. The shortest sequence active in all three assays was iswkg. The HYD1 peptide contains overlapping elements required for adhesion, blocking migration and the activation of ERK signaling. These linear peptide sequences provide the starting point for development of novel compounds to target cancer cell adhesion and migration.

Targeting Beta-3 Integrin Using a Linear Hexapeptide Labeled with a Near-Infrared Fluorescent Molecular Probe

Biomolecules containing the RGD peptide sequence are known to bind integrins with high affinity. Studies of hexa-and hepta-peptides labeled with a near-infrared fluorescent probe (cypate) showed that rearranging the glycine in a linear RGD peptide sequence to form the GRD analogue favored the uptake of the GRD compound by alphavbeta3 integrin receptor (ABIR)-positive A549 tumor cells and tissue. The internalization of the GRD compound in A549 cells and tumor uptake in mice were inhibited by ABIR-avid peptides, suggesting its recognition by this receptor. Further studies with functional blocking antibodies and beta3 knockout cells revealed that beta3 integrin mediates the internalization of the cypate-GRD peptide. Molecular modeling studies supported preferential interaction of the probe with the beta3 subunit of integrins relative to the alphav subunit. The results demonstrate that the cypate-GRD peptide targets beta3 integrin, thereby providing a strategy to monitor drug delivery and efficacy, and physiopathologic processes mediated by this protein.

Identification of a Two-Partner Secretion Locus of Enterotoxigenic Escherichia coli

Enterotoxigenic Escherichia coli (ETEC) remains a formidable cause of diarrheal illness worldwide. At present, there is no vaccine that provides broad-based protection against ETEC. A 'phoA-based self-cloning mutagenesis system, TnphoA.ts, employed to identify novel ETEC surface antigens, led to identification of an ETEC two-partner secretion locus (etpBAC) on the pCS1 virulence plasmid of prototype strain H10407. Cloning and expression of etpBAC in recombinant E. coli LMG194(pJY019) resulted in secretion of a high-molecular-weight (HMW) glycosylated exoprotein. This glycoprotein, EtpA, exhibits linear peptide sequence and predicted structural homologies with known HMW adhesins produced by other two-partner secretion loci. Antibodies directed against recombinant EtpA (anti-rEtpA.6H) recognized an HMW protein in culture supernatants of ETEC strains H10407 and LMG194(pJY019) but not in culture supernatant of strain H10407-P, which lacks the 92-kb pCS1 plasmid, or an isogenic etpA mutant. etpA mutants were deficient in adherence to intestinal epithelial cells in vitro, and anti-rEtpA.6H antibodies inhibited association of H10407 with target epithelial cells. Cloning and expression of etpB in recombinant E. coli were sufficient to confer adherence. Screening of multiple ETEC isolates for the etpBAC locus by colony hybridization and by EtpA immunoblotting suggested that EtpA is one of the most common antigens secreted by these pathogens. Together, these results indicate that the newly identified ETEC two-partner secretion locus directs the secretion of a high-molecular-weight glycosylated protein, EtpA, that in concert with the putative EtpB transporter participates in adherence of H10407 to epithelial cells, thereby expanding the repertoire of potential ETEC virulence proteins and vaccine candidates.

The Cyclization of High Diversity mRNA Display Libraries

The cyclization of linear peptide sequences shows enormous promise for the development of novel pharmacaphores, owing in part to the loss in conformational entropy upon cyclization. Directed evolution of cyclic peptides in a biological display context has previously been limited to disulfide formation as the sole means to generate peptide macrocycles. The primary disadvantage of this methodology is the inherent instability of the disulfide bond in a reducing intracellular environment. To address this, we have developed a chemical approach to generating covalently cyclized mRNA display libraries based on the cross-linking of primary amines in the linear peptide sequence. MALDI-TOF MS has been employed to verify the specificity of the post-translational cross-linking reaction in a model mRNA- peptide fusion. The incorporation of α-hydroxy phenylalanine via nonsense suppression was used to generate a second model peptide fusion, whose cyclization efficiency could be assayed by hydrolysis of the non-natural ester linkage. Finally, this methodology was used to construct a series of covalently cyclized libraries of varying lengths whose cyclization efficiencies could be directly measured. The largest of these libraries contains >1013 sequences and was found to be ~30% cyclized, effectively the largest cyclic library assembled in a biological display context.

3D‐Epitope‐Explorer (3DEX): Localization of conformational epitopes within three‐dimensional structures of proteins

Neutralizing antibodies often recognize conformational, discontinuous epitopes. Linear peptides mimicking such conformational epitopes can be selected from phage display peptide libraries by screening with the respective antibodies. However, it is difficult to localize these "mimotopes" within the three-dimensional (3D) structures of the target proteins. Knowledge of conformational epitopes of neutralizing antibodies would help to design antigens able to elicit protective immune responses. Therefore, we provide here a software that allows to localize linear peptide sequences within 3D structures of proteins. The 3D-Epitope-Explorer (3DEX) software allows to map conformational epitopes in 3D protein structures based on an algorithm that takes into account the physicochemical neighborhood of C(alpha)- or C(beta)-atoms of individual amino acids. A given amino acid of a peptide sequence is localized within the protein and the software searches within predefined distances for the amino acids neighboring that amino acid in the peptide. Surface exposure of the amino acids can also be taken into consideration. The procedure is then repeated for the remaining amino acids of the peptide. The introduction of a joker function allows to map peptide mimotopes, which do not necessarily have 100% sequence homology to the protein. Using this software we were able to localize mimotopes selected from phage displayed peptide libraries with polyclonal antibodies from HIV-positive patient plasma within the 3D structure of gp120, the exterior glycoprotein of HIV-1. We also analyzed two recently published peptide sequences corresponding to known conformational epitopes to further confirm the integrity of 3DEX.

Identification of multiple linear epitopes of the plasminogen activator A (PauA) of Streptococcus uberis with murine monoclonal antibodies

Streptococcus (S.) uberis is a common cause of mastitis in cattle. A protein (PauA) secreted by this bacterium is capable of activating plasminogen from sheep and cattle. The PauA first binds to bovine plasminogen (b-plg) to form a PauA-plasminogen complex that subsequently binds to and activates b-plg to form plasmin. We have identified several linear epitopes of PauA that are recognized by murine monoclonal antibodies to PauA. Two of the monoclonal antibodies which neutralized the enzymatic activity of PauA, EC3 and 2.22, recognized common linear peptide sequences with similar charge and spacing patterns. These neutralization epitopes are located in the predicted alpha-domain of the PauA molecule. Further, these same epitopes are in critical structure/function domains identified in other studies. These characterizations may facilitate the design of an efficacious vaccine for streptococcal mastitis in the dairy cow.

Structure-based development of a novel collagen inhibitor for MMP-1: re-designing the functions of a matrix protein.

Collagenases are a highly specific class of enzymes. In their native states, collagenases cleave only native triple helical collagen molecules at a single peptide bond between Gly775-Leu776 for Type I collagen and Gly775-Ile776 for Type II collagen. The linear sequence of collagen is about 1050 amino acids in length, where three linear peptide sequences are required to form a triple helical collagen molecule. At present, there exist no crystallographic structures of collagenase bound to native triple helical collagen; nor has it been shown that collagenase recognizes the triple helical conformation of collagen. In our study, we have used an inhibitor design structure-activity based approach to show that collagenase recognizes and cleaves triple helical collagen conformations in preference to non-triple helical collagen conformations.

Mimicking the Biologically Active Part of the Cyclopeptides Segetalin A and B by “Clipping” of a Linear Tripeptide Derivative by Metal Coordination

A new method for the conformational fixation of bioactive loop-type peptide structures is presented. Hereby, ligand moieties are attached to the termini of a linear peptide sequence. Upon metal complexation, a macrocyclic structure with a loop-type conformation of the peptide is formed. As a representative example, the preparation of a WAG-bridged dicatechol derivative is described which mimics the active part of the natural products Segetalin A and Segetalin B.

Studies on the synthetic methodology of head to tail cyclization of linear peptides

Our recent studies on the synthetic methodology of head to tail cyclization of linear peptides are summarized in this paper. Ten cyclopeptides including six cyclopentapeptides as candidates of LHRH antagonists, two cyclopentapeptides, and two cycloheptapeptides which were isolated from Chinese medicinal herbs were synthesized using an organic phosphorus reagent, DEPBT, and were selected as model peptides for studying the factors that influence the cyclization yields. Our results show that the coupling reagent choice and linear peptide sequence are the two most important considerations that determine the success or failure for a cyclization reaction. Effects of different metal ions on the cyclization were also studied. The results suggest that Na+ is suitable for promoting the cyclization of linear pentapeptides while bigger Cs+ is better for promotion of the ring closure of linear heptapeptides. Application of Pac ester in thioester method for synthesis of cyclopeptides was studied. N-protected amino acid and peptide thioesters with Pac group were readily purified in each step of synthesis. The Pac group was easy to remove with zinc powder in acetic acid and its flexibility allows elongatation of the peptide chain from either N-or C-terminal.

Molecular interaction studies of hemostasis: fibrinogen ligand–human platelet receptor interactions

The interactions between fibrinogen ligands and platelet receptor α IIb β 3 were studied under physiological conditions by atomic force microscopy (AFM). Two linear peptide sequences in fibrinogen, RGD and HHLGGAKQ AGD V, play central roles in the regulation of hemostasis and thrombosis by facilitating adhesion and aggregation of platelets. In order to measure the interactions (i.e., debonding force), oligopeptides, GSSSGaaa, where aaa is - RGD SPA or -HHLGGAKQ AGD V, were synthesized and grafted on to the surface of AFM probe tips. The interaction forces between a peptide-modified AFM probe tip and platelet surface were determined from pN to nN levels using AFM force measurements. Our results show that the zero kinetic off-rate, K off(0) , for RGDSPA is significantly smaller than that for HHLGGAKQ AGD V, under the consideration of flexible receptor surfaces. From our analysis, the K off(0), the single molecular binding energy E b, and the transition state x b, were extracted from the data, and estimated to be 1.53 s −1, −2.64×10 −20 J and 1.03 Å for the RGD– α IIb β 3 system, and 47.58 s −1, 2.67×10 −20, 1.09 Å for the HHLGGAKQAGDV– α IIb β 3 system, respectively.

A powerful combinatorial screen to identify high-affinity terbium(III)-binding peptides.

Lanthanide-binding tags (LBTs) are protein fusion partners consisting of encoded amino acids that bind lanthanide ions with high affinity. Herein, we present a new screening methodology for the identification of new LBT sequences with high affinity for Tb(3+) ions and intense luminescence properties. This methodology utilizes solid-phase split-and-pool combinatorial peptide synthesis. Orthogonally cleavable linkers allow an efficient two-step screening procedure. The initial screen avoids the interference caused by on-bead screening by photochemically releasing a portion of the peptides into an agarose matrix for evaluation. The secondary screen further characterizes each winning sequence in a defined aqueous solution. Employment of this methodology on a series of focused combinatorial libraries yielded a linear peptide sequence of 17 encoded amino acids that demonstrated a 140-fold increase in affinity (57 nM dissociation constant, K(D)) over previously reported lanthanide-binding peptides. This linear sequence was macrocyclized by introducing a disulfide bond between flanking cysteine residues to produce a peptide with a 2-nM apparent dissociation constant for Tb(3+) ions.Supporting information for this article is available on the WWW under http://www.chemphyschem.org or from the author.

Methionine anchoring applied to the solid-phase synthesis of lysine-containing ‘head-to-tail’ cyclic peptides

Lysine-containing ‘head-to-tail’ cyclic peptides can be prepared via a side-chain anchoring solid-phase synthesis strategy. A handle is prepared using a methionine residue, theCα-carboxyl of which forms an, amide with theNe-amine of lysine. Subsequently, the linear peptide sequence is assembled, appropriate deblocking steps are carried out, and on-resin head-to-tail cyclization follows. Optionally, acid-labile protecting groups may be removed while the peptide remains resin-bound. The final cleavage step uses CNBr, and releases the free or protected cyclic peptide into solution.

Sequence and structure-activity relationship of a scorpion venom toxin with nitrergic activity in rabbit corpus cavernosum.

An alpha-toxin responsible for nitric oxide (NO) release in rabbit corpus cavernosum (RbCC) was isolated from Tityus serrulatus venom (TSV). The isolated peptide (molecular mass of 7427.66+/-0.15 Da) was identified as Ts3 after determination of Cys residues, N-terminal amino acid analysis, and proteolytic peptide mapping. Ts3 (30 nM) markedly relaxed the RbCC; this response was blocked by the NO synthesis inhibitor N(omega)-nitro-L-arginine methyl ester (100 microM) and the Na+ channel blocker tetrodotoxin (100 nM). Synthetic peptides based on either Ts3 (P1-16, P17-32, P33-48, P49-64, P9-24, P25-40, P41-56, YGLPDKVPTKT) or Bukatoxin (isolated from Buthus martensi Karsch scorpion venom) sequence (Buka11, Buka11-B, PDKVP, PDSEP) were assayed. These peptides slightly relaxed the RbCC, and such an effect was independent of Na+ channel activation or NO release. Our results indicate that Ts3 exerts nitrergic actions and contributes to the relaxing activity of TSV in RbCC, thus providing a valuable tool to investigate the mechanisms underlying nerve activation in erectile tissues, because NO released from nitrergic fibers plays a key role in the erectile process. Our findings revealed the key importance of the Ts3 structure three-dimensional conformation maintenance for biological activity, because linear peptide sequences neither presented substantial relaxations nor was this effect related to nitrergic activity.

Selection and characterization of peptide memitopes binding to ricin.

A combinatorial random peptide display library expressed in E. coli was employed to identify short, linear peptide sequences that showed affinity for ricin and could be used as reagents for detection and identification of ricin. One peptide, P3, from a collection of four short peptides showed specific binding to ricin. The kinetic analysis of this peptide binding to the ricin showed lower equilibrium binding constants for the peptide P3 than monoclonal antibody. This is attributed due to both slower association and faster dissociation rates for the peptide P3. The random ricin peptide P3 binds to ricin with a KD of 1 microM versus the antibody's KD of 14 nM. This particular peptide memitope P3 against ricin showed specific binding to ricin without any significant cross-reactivity against other proteins such as bovine serum albumin (BSA), lysozyme and natural bacterial toxins such as Staphylococcal enterotoxins A and B. The results provided proof-of-principal that peptide memitopes are another choice of reagents due to ease in production to be used for the detection of highly toxic bio-threat or biowarfare agents such as ricin.