Analysis of novel streptavidin-binding peptides,identified using a phage display library,shows that amino acids external to a perfectly conserved consensus sequence and to the presented peptides contribute to binding

Summary Streptavidin-binding peptides containing the consensus amino acid sequence motif EPDW were identified using a phage display library. Phage presenting peptides containing these sequences bound streptavidin in a biotin-sensitive fashion and could be eluted with biotin. The previously identified streptag peptide sequence (AWRHPQGG) competed with phage presenting the EPDW consensus sequence for streptavidin binding. Furthermore, the EPDW sequence has two amino acids in common with yet another previously identified streptavidin-binding sequence, GDWVFI, which has similar biochemical properties. Binding inhibition studies revealed that residues flanking EPDW, as well as residues of the modified phage pIII product to which displayed peptides are fused, contributed to streptavidin binding. The derivation of small molecules based on the structure of peptides selected using display methods is a potentially important application of phage display technology. The relevance of the observations made here for that application are discussed. Finally, a group of nuisance peptides of the consensus sequence WHWWXW, whose binding specificity has not been fully elucidated, but which have been isolated in a number of biopanning experiments, including those that do not utilize streptavidin, are also described.     

Utilization of multiple phage display libraries for the identification of dissimilar peptide motifs that bind to a B7-1 monoclonal antibody

Summary Seven random peptide libraries (two displaying linear peptides and five displaying cysteine-constrained peptides) were constructed as gene III fusion proteins of the bacteriophage fd-tet. These libraries were used to screen a blocking monoclonal antibody raised against B7-1 (CD80), a human cell surface antigen that binds two T cell receptors, CD28 and CTLA-4. After three rounds of screening against the immobilized antibody, 1000-fold enrichment was observed in libraries displaying both linear and cysteineconstrained peptides. DNA sequencing of the enriched phage revealed two distinct consensus sequences: HXG(A/Y)XH and DVCXXGGPGC. Phage expressing these consensus sequences bound to L307.4 but not to an isotype matched antibody, indicating that binding was antibody specific. Synthetic peptides corresponding to both motifs inhibited phage binding to L307.4, indicating that the gene III protein is not required for peptide binding. In addition, the cyclized forms of synthetic peptides containing the DVCXXGGPGC motif were capable of inhibiting L307.4 binding to soluble B7-1/Fc fusion. Moreover, phage expressing only the HXG(A/Y)XH consensus sequence were inhibited from binding to L307.4 by the presence of chelating agents. These results indicate that the framework within which the peptide is presented on the surface of the phage may allow the identification of unique peptide motifs with distinct binding characteristics. These peptide motifs could be used for the design of peptidomimetics with therapeutic applications if they inhibit the binding of B7-1 to its T cell receptors.     

A combinatorial method for constructing libraries of long peptides displayed by filamentous phage

Summary We describe the construction and screening of a random peptide library displayed by filamentous phage. The peptides are expressed in multiple copies on the filamentous phage M13 as amino-terminal fusions with the major coat protein, the product of gene VIII. These libraries are efficiently screened for reactive peptides, using a combination of panning in solution followed by a plaque lift assay. Advantages of this system are that both high- and low-affinity phage clones are simultaneously identified and the analysis of non-reactive phage is minimized. The vector system utilized to construct this library enables it to be used for the construction of peptide libraries employing a combinatorial cloning strategy. This feature makes it especially suitable for construction of peptide libraries using codon-based oligonucleotide synthesis. The vectors also allow rapid optimization and modification of lead peptides by codon-based mutagenesis. A 20-amino acid long random peptide library of 1 × 10⁹ members was constructed and screened for peptides that bound to (i) a monoclonal antibody recognizing the amino-terminus of -endorphin; (ii) a monoclonal antibody recognizing a peptide epitope derived from the v -ros oncogene product; and (iii) the constant region of murine IgG2b. The approach described here provides a means for the construction of customized libraries that can be screened with a variety of target molecules.     

Selection of a cyclic nonapeptide inhibitor to α-chymotrypsin using a phage display peptide library

A cyclic nonapeptide library displayed on filamentous bacteriophages was selected 6 times against α-chymotrypsin (EC 3.4.21.1) at three different pH conditions (6.5, 7.0, and 7.5). Phage peptide clones from the sixth selection, at all three pH conditions, interacted more strongly with α-chymotrypsin than the original library and a wild-type phage did. DNA sequencing of the selected phage peptide clones showed that different cyclic nonapeptide sequences had been selected at the different pH conditions. The oxidized form of the synthetic peptide, Cys-Cys-Phe-Ser-Trp-Arg-Cys-Arg-Cys, selected at pH 7.5, could completely inhibit the enzymatic activity of α-chymotrypsin. The structurally related enzymes trypsin (bovine) and elastase (porcine) were only marginally inhibited by the same peptide under the same conditions. The inhibition constant for α-chymotrypsin was estimated to be 10^-6 M. Phage clones expressing this peptide had a lower affinity for phenylmethylsulfonylfluoride-modified α-chymotrypsin than for natural α-chymotrypsin as determined by an enzyme immunosorbent assay. This peptide phage clone was also competitively prevented from binding to α-chymotrypsin by the corresponding synthetic oxidized peptide. Collectively, the results suggest that the oxidized form of the selected peptide Cys-Cys-Phe-Ser-Trp-Arg-Cys-Arg-Cys interacts with the active site of α-chymotrypsin and acts as a specific inhibitor to the enzyme. To our knowledge, the selected sequence Cys-Cys-Phe-Ser-Trp-Arg-Cys-Arg-Cys has not been found in nature. This revised version was published online in August 2006 with corrections to the Cover Date.     

Effects of metal ion binding on an oncomodulin mutant containing a novel calcium-binding loop

The Ca²⁺-binding protein oncomodulin was altered by cassette mutagenesis of the CD site (CDOM33) with a sequence that was derived by a consensus method using over 250 known Ca²⁺-binding loop sequences. This mutant was studied using time-resolved and steady-state fluorescence from the Trp residue included at position 7 of the loop (position 57 of the protein sequence). The fluorescence characteristics of this species in the absence and presence of metal ions were compared to those of a tetradecapeptide containing the loop and the single Trp mutant of oncomodulin, Y57W. The fluorescence properties of CDOM33 were quite different from the peptide, both in the apo form and in response to metal binding. The consensus CD loop in CDOM33 exhibited the characteristics of a Ca²⁺/Mg²⁺ site in contrast to the Ca²⁺ specificity of the wild-type CD loop. The Trp analogue, 5-hydroxytryptophan (5HW), was incorporated into both oncomodulin mutants to produce Y75(5HW) and 5HW-CDOM33. Results showed that this intrinsic probe was relatively insensitive to structural changes in the mutants upon metal binding compared to Trp itself.     

Peptide mimotopes of phomopsins: Identification, characterization and application in an immunoassay

Peptide mimotopes of plant-associated toxins offer the potential for improving analytical and diagnostic methodologies as well as providing candidates for potential protective vaccines against plant poisoning diseases. Monoclonal antibody (mAb) C₃C₁₁, which recognizes the antimicrotubule phomopsin mycotoxins, was used to isolate peptide mimics of phomopsin A from a random 15-mer phage display peptide library. A total of 46 clones were isolated that showed specific reactivity with the mAb. Amino acid sequence analysis revealed four different types of mimotope sequences, all of which contained a common motif V-A-L/V-C. Of the 46 clones isolated, 44 contained the motif V-A-L-C while 2 contained the V-A-V-C motif. All four types of phage clones inhibited the reactivity of the mAb with phomopsin A in a competition ELISA. The clone with the mimotope sequence CT VALCNMYFGAKLD demonstrated the strongest binding. It was further shown that synthetic peptides containing these mimotope amino acid sequences were able to inhibit the mAb-phomopsin A interaction, indicating that the peptide mimotopes were responsible for the specific binding, independent of the phage framework. The results also suggest that the mimotope peptides bind to mAb C₃C₁₁ at the same site as phomopsin A. The application of recombinant phage particles carrying phomopsin mimotopes in immunoassay was evaluated and the results demonstrated approximately 100-fold increase in sensitivity in comparison with a conventional immunoassay using a chemically linked phomopsin-horseradish peroxidase conjugate.     

Design of peptide affinity ligands for S-protein: a comparison of combinatorial and de novo design strategies

Design of peptide affinity ligands against biological targets is important for a broad range of applications. Here, we report on de novo and combinatorial strategies for the design of high-affinity and high-specificity peptides against S-protein as a target. The peptide libraries employed in this study contain (1) consensus motif (CM) sequences identified from high-throughput phage combinatorial screening, (2) point mutations of CM sequences, and (3) de novo sequences rationally designed based on stereo-chemical information of the complex between S-protein and its natural ligand, S-peptide. In general, point mutations to CM allowed for modulating peptide affinity and specificity over a broad range. This is particularly useful in designing peptides with varying affinities and specificities for the target. De novo sequences, especially those based on the S-protein binding pocket, on average bound with higher affinities within a narrow range (10–100 nM) as compared to point mutations to CM (1 nM–2 $\mu $ M). As such, the approaches described here serve as a general guide for optimizing the design of peptide affinity ligands for a wide range of target proteins or applications.     

Construction and screening of M13 phage libraries displaying long random peptides

Summary We have constructed two phage display libraries expressing N-terminal pIII fusions in M13 composed of 37 and 43 random amino acid domains, respectively. The D38 library expresses 37 random amino acids with a central alanine residue, and the DC43 library contains 43 random amino acids with a central cysteine flanked by two glycine residues, giving the displayed peptide the potential to form disulfide loops of various sizes. We demonstrate that the majority of random sequences in both libraries are compatible in pentavalent display with phage viability. The M13 phage display vector itself has been engineered to contain a factor Xa protease cleavage site to provide an alternative to acid elution during affinity selection. An in-frame amber mutation has been inserted between the pIII cloning sites to allow for efficient selection against nonrecombinant phage in the library. These libraries have been panned against mAb 7E11-C5, which recognizes the prostate-specific membrane antigen (PSM). Isolated phage display a consensus sequence that is homologous to a region in the PSM molecule.     

Polymorphism of amyloid-β fibrils and its effects on human erythrocyte catalase binding

The Alzheimer's amyloid-β (Aβ) peptide exists as a number of naturally occurring forms due to differential proteolytic processing of its precursor molecule. Many of the Aβ peptides of different lengths form fibrils in vitro, which often show polymorphisms in the fibril structure. This study presents a TEM based analysis of fibril formation by eighteen different Aβ peptides ranging in length from 5 to 43 amino acids. Spectrophotometric analysis of Congo red binding to the fibrillar material has been assessed and the binding of human erythrocyte catalase (HEC) to Aβ fibrils has also been investigated by TEM. The results show that a diverse range of Aβ peptides form fibrils and also bind Congo red. The ability of both Aβ 1–28 and Aβ 29–40 to form fibrils indicates that there are at least two fibril-forming domains within the full-length Aβ 1–40 sequence, the ability of many Aβ peptides to form Congo red-binding aggregates suggests that there may be up to 4 possible aggregation promoting domains. The binding of HEC was limited to Aβ forms containing residues 29–32. The differing capacities of fibrillar and ribbon-like structures may reflect the accessibility of the 29–32 region and suggest that HEC may be able to discriminate between different forms of Aβ fibrils.     

Analysis of Lanthanide-Induced Conformational Change of the C-Terminal Domain on Centrin

Centrin, an EF-hand calcium-binding protein with high homology to calmodulin (CaM), is an essential component of microtubule-organizing center (MTOC). Lanthanide (Ln) ions can improve the stability, increase the amount and enhance the orderliness of microtubules, which are components of cytoskeleton. In order to investigate the structural basis of Ln ions on enhancing orderliness of microtubules, we characterized the binding properties of Ln ions with the isolated C-terminal domain of the Euplotes centrin (C-EoCen). Results suggested that Ln ions may occupy the canonical Ca²⁺ binding sites on C-EoCen with middle affinity. Near- and far-UV CD spectra of C-EoCen displayed pronounced differences before and after additing Ln ions. The asymmetry of microenvironments of Phe on C-EoCen was changed. Using 2-p-toluidinylnaphthalene-6- sulfonate (TNS) as probe, Ln ions induced C-EoCen to undergo conformational changes from closed state to open state, resulting in exposing hydrophobic patches to external environments. Ln ions have more obvious effect on the conformation of centrin than Ca²⁺. The differences found in the interactions of centrin binding with Ln ions/Ca²⁺ maybe provide some insights for structural basis of centrin functions in vivo.     

Study on the relationship between structure and taste activity of the umami peptide of Stropharia rugosoannulata prepared by ultrasound

Through virtual screening, electronic tongue verification, and molecular docking technology, the structure-taste activity relationship of 47 kinds of umami peptides (octapeptide - undecapeptide) from Stropharia rugosoannulata prepared by simultaneous ultrasonic-assisted directional enzymatic hydrolysis was analyzed. The umami peptides of S.rugosoannulata can form hydrogen bond interaction and electrostatic interaction with umami receptors T1R1/T1R3. The amino acid residues at the peptides' N-terminal and C-terminal play a vital role in binding with the receptors to form a stable complex. D, E, and R are the primary amino acids in the peptides that easily bind to T1R1/T1R3. The basic amino acid in the peptides is more easily bound to T1R1, and the acidic amino acid is more easily bound to T1R3. The active amino acid sites of the receptors to which the peptides bind account for 42%−65% of the total active amino acid residues in the receptors. ASP147 and ASP219 are the critical amino acid residues for T1R1 to recognize the umami peptides, and ARG64, GLU45, and GLU48 are the critical amino acid residues for T1R3 to recognize the umami peptides. The increase in the variety and quantity of umami peptides is the main reason for improving the umami taste of the substrate prepared by synchronous ultrasound-assisted directional enzymatic hydrolysis. This study provides a theoretical basis for understanding simultaneous ultrasound-assisted directional enzymatic hydrolysis for preparing umami peptides from S.rugosoannulata, enhancing the flavor of umami, and the relationship between peptide structure and taste activity.     

稀土离子Tb3+与拟南芥钙调素相互作用的荧光光谱及分析应用

钙调素 (CaM)是一种普遍存在的钙受体蛋白 ,它调节了许多细胞生物学功能。钙调素分子有 4个金属结合位点 ,而植物钙调素Ⅰ ,Ⅱ ,Ⅲ位点不含酪氨酸残基 ,只有第 4位点含一个酪氨酸残基。与动物体不同的是 ,植物能表达多种功能不同的钙调素亚型。文章利用Tb3 荧光探针 ,采用直接激发 ( 2 2 1nm)或敏化激发 ( 2 80nm)并测量 5 4 5nm处的荧光发射强度 ,研究拟南芥CaM与Tb3 的结合作用及分析应用。直接激发 ( 2 2 1nm)Tb3 CaM络合物时 ,Tb3 的发光显著增强 ,这归因于CaM中配位基取代了Tb3 的配位水分子 ,从而导致荧光速率常数增加。直接激发滴定曲线中 ,当cTb3 /cCaM <4时 ,荧光强度呈不断上升的直线 ,之后出现平台区 ,这与CaM只结合 4个钙离子的结论一致。而间接激发滴定曲线近似为S型 ,且荧光强度较弱 ;其中当cTb3 /cCaM≤ 2时 ,荧光强度增加较弱 ;当 2 相似文献   

A theoretical prediction on the ground‐state complexes bound by metal ions to thymine base isomers

Stability orderings of 150 stable complexes formed by metal ions (Na⁺, K⁺, Ca²⁺, Mg²⁺, and Zn²⁺) and 13 stable thymine tautomers in both solvent and gas phases are obtained, and the optimal binding site for a metal ion in a specific thymine tautomer is identified. Results indicate that the complex with the canonical thymine tautomer (T1) is more stable than those with the rare ones, and the monodentate complex M–T1o4(o2) are their ground‐state form in the solvent phase. The ground‐state thymine complexes bound by Ca²⁺, Mg²⁺, or Zn²⁺ become bidentate M–T3o4lo2,n3, which is derived from a rare thymine tautomer T3o4l, whereas those bound by Na⁺ and K⁺ are still monodentate complexes M–T1o4(o2), however, in the gas phase. The differences in stability are discussed in detail from the binding strength of metal ions, relative energy of the corresponding thymine tautomers, and solution effect. Copyright © 2011 John Wiley & Sons, Ltd.     

Spectroscopic Study of Some Alkali and Alkaline Earth Complexes with Benzo Crown Ethers in Ethanol Solution

The interaction between Na⁺, K⁺, Mg²⁺ and Ca²⁺ ions and benzo crown ethers B15C5, DB18C6, DB21C7, DB24C8 and DB30C10 in ethanol solution has been studied spectrophotometrically at 25°C. The formation constants for 1:1 complexes were determined by computer fitting of the resulting UV-absorbance-mole ratio data. In the case of all crown ethers used, K⁺ ion was found to form the most stable complexes. The observed selectivities of different benzo crowns for the cations used are discussed in terms of the cavity-cation size ratio, number of the donating oxygens participating in the cation binding, conformations of the free and complexed ligands and ionic solvation.     

Multiplexed sorting of libraries on libraries: A novel method for empirical protein design by affinity-driven phage enrichment on synthetic peptide arrays

Chemically synthesized peptide arrays on planar cellulose carriers are proposed as libraries of ligands suitable for the multiplexed simultaneous capture of peptide-specific acceptor proteins from a large randomly mutagenized library of acceptor proteins presented on bacteriophage M13 particles. This experimental set-up can be exploited to rapidly screen for individual new, distinct binding partners from two complementary libraries (two-dimensional screening). The technical feasibility of this empirical protein design approach was demonstrated with calmodulin as an aceptor protein using an array of mastoparan variants for multiplexed phage affinity enrichment.     

Influence on drug efficacy of the binding behavior of pioglitazone hydrochloride with tryptophan residues,and tyrosine residues in bovine transferrin

Abstract

The interaction of pioglitazone hydrochloride bound to tryptophan residues and tyrosine residues in bovine transferrin was investigated using synchronous fluorescence spectroscopy at various temperatures (298, 310, and 318?K). From binding constants and thermodynamic parameters, it was shown that 1:1 stable compound was formed by the electrostatic force interaction of pioglitazone hydrochloride bound to tryptophan residues and tyrosine residues in bovine transferrin. The extent of binding between pioglitazone hydrochloride and tryptophan residues in bovine transferrin was more than that between pioglitazone hydrochloride and tyrosine residues in bovine transferrin. At 310?K, the fluorescence quenching ratio number of tyrosine residues and tryptophan residues in bovine transferrin were 47.52% and 54.19%, respectively, which indicated that the fluorescence contribution of tryptophan residues was greater. At 310?K, pioglitazone hydrochloride-tyrosine residues(in bovine transferrin) binding rate were 55.60–73.82%, and the combined model was W?=??0.0315R²???0.1520R?+?0.7385. The value of Hill’s coefficients was greater than 1, which suggested that there was a positive cooperativity between pioglitazone hydrochloride and subsequent ligands. The results of molecular docking were consistent with that of experimental calculation.     

Peptomers: A Versatile Approach for the Preparation of Diverse Combinatorial Peptidomimetic Bead Libraries

This report describes a versatile approach in thegeneration of peptidomimetic bead libraries. Themethod is based on the preparation of peptide–peptoidhybrids using the portioning–mixing procedure, whichgives diverse peptidomimetic bead libraries composedof peptides, peptoids and peptide–peptoid hybrids. Weterm these peptomers, from peptide–peptoidhybrid polymers. The synthesis of the peptomersis easily accomplished by adapting the peptoidsynthesis strategy, in which a primary amine reactswith bromoacetic acid, and we combine this methodologywith conventional peptide synthesis. The sequence ofthe active compound is deduced by conventionalmicrosequencing using Edman degradation chemistry,thus avoiding the synthesis of a coding structure orthe addition of molecular tags. We demonstrate theutility of the peptomer approach by the synthesis ofa bead library together with the identification ofnovel peptidomimetic ligands binding to themacromolecular targets streptavidin and the insulin receptor.     

Binding properties of SH3 peptide ligands identified from phage-displayed random peptide libraries

Summary Combinatorial libraries have yielded high-affinity ligands for SH3 domains of a number of different proteins. We have shown that synthetic peptides containing these SH3 ligand sequences serve as specific probes of SH3 domains. Direct binding of the N-terminal biotinylated peptide ligands was conveniently detected in ELISA, filter-blotting, and dot-blotting experiments with the use of streptavidin-conjugated enzymes. In some cases, detection of peptide-SH3 interactions required that the biotinylated peptides first were preconjugated with streptavidin to form a multivalent complex. Interestingly, these nominally tetravalent SH3 peptide ligands cross-react to varying degrees with different SH3 domains. We have used such complexes to screen cDNA expression libraries and have isolated clones that encode both known and novel SH3-domain-containing proteins. Based on the success of this methodology, we propose a general strategy by which ligands of a modular domain-containing protein can be isolated from random peptide libraries and used to screen cDNA expression libraries systematically for novel modular domain-containing proteins.     

Effect of core epitope modification on the antibody recognition of a MUC2 mucin peptide

Identification of protein epitopes via combinatorial chemistry was one of the most important discoveries of the past three decades. Mapping of linear antibody epitopes can be achieved rapidly and cost-effectively by the polymer pin-bound peptide approach. In this article, the determination of the fine epitope structure of MUC2 mucin glycoprotein is described by using specific monoclonal antibody. We have used positional scanning combinatorial approach, and also parallel synthesis. The residues within the MUC2 epitope ¹⁸PTGTQ²² of MAb 996 were replaced by all other proteinogenic amino acids on pin-bound peptide libraries, and their antibody binding was studied in modified ELISA. Thr¹⁹ was the least important of the residues in antibody recognition; most of the other amino acids could be replaced, except Pro. The other residues cannot be replaced without loss of antibody binding, where both the size and character of the amino acids were important. The significance of the non-chiral Gly²⁰ residue was further studied by competitive ELISA of parallelly synthesized soluble peptides containing l- or d-Ala instead of Gly residue. However, the d-Ala-containing oligopeptides showed no antibody binding; therefore, the backbone conformation is characteristic of that of l-amino acid containing peptides in this position as well. With the combinatorial approach we obtained relevant information about the contribution of individual amino acid side chains to the MAb 996 antibody binding within the PTGTQ predominant MUC2 mucin epitope. These results could be utilized for the design of synthetic antigens for detection of MUC2 protein core-specific antibodies related to carcinoma(s).     

Effective combinatorial strategy to increase affinity of carbohydrate binding by peptides

The Thomsen-Friedenreich antigen, a carcinoma-associated disaccharide involved in carcinoma cell homotypic aggregation and increased metastatic potential, has clinical value as a prognostic indicator and a marker of metastasized cells. Hence, it can reasonably be predicted that antigen-binding macromolecules are valuable clinical in vivo diagnostic/therapeutic targeting agents. Recently, we have selected first-generation antigen-binding peptides from a random peptide bacteriophage display library and have applied combinatorial affinity maturation to select functionally-maturated peptides, which target cultured carcinoma cells and inhibit carcinoma cell aggregation. In the current study we hypothesize that a targeted search of sequence space surrounding the antigen-binding consensus sequence will select unpredictable amino acid sequences in the non-consensus portions of the peptides, leading to increased affinity for the carbohydrate and greater solubility in physiological buffers. This comprehensive in vitro analysis demonstrates that preferential evolution of the amino-terminal sequence of the peptides occurred, which correlated, in structure/function studies, with the acquisition of maturated function. The maturated peptides are more soluble than the earlier peptides. Studies of peptide binding to the disaccharide indicate that two maturated peptides (P-30-1, F03) have higher affinity for the antigen and bind with higher intensity to the surface of cultured human carcinoma cells than the first-generation peptides. The results support our hypothesis that affinity maturation can improve carbohydrate binding by peptides and have theoretical importance as the first report of maturation of carbohydrate-binding affinity in a small, soluble peptide.