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At least 1,207 records · Page 67Linked to original sources
PubMed1999

Monoclonal autoantibodies from patients with autoimmune diseases: synovial fluid B lymphocytes of a patient with rheumatoid arthritis produced an IgG lambda antibody recognizing J-sequences of Ig kappa chains in a conformation-dependent way.

Synovial fluid B cells from a patient with seronegative rheumatoid arthritis were immortalized by electrofusion. The specificity of clone FKN-E12 (IgG1 lambda) was analysed by screening a phage display random peptide library. One heptamer sequence was identified (RASFp1 = HLTFGPG). Three human IgG kappa antibodies contained a highly homologous sequence (xLTFGPG) at the junction of V- and J-regions. Homologies were also found in distinct humans (J kappa 3, J kappa 4) and murine (J kappa 5) J kappa-sequences (TFGPG, LTFGxG), and to a lower degree in all remaining J kappa-sequences (TFGxG). Binding and binding inhibition assays showed that FKN-E12 bound to kappa light chains tested in a conformation-dependent way: it reacted only with IgG kappa or IgA kappa chains adhered to a plastic surface, but not in soluble form. In conclusion, FKN-E12 detects a conformational epitope on probably all kappa light chains, which could be definded by screening a phage library displaying linear epitopes.

Amino Acid Sequence↗
PubMed1996

Identification of novel mdm2 binding peptides by phage display.

The oncogene mdm2 and its human homologue hdm2 bind to the tumour suppressor protein p53 and inactivate its function as a transcription factor. This has been implied as a possible mechanism for cancer development in several tumours including human sarcomas. The mdm2-p53 interaction is therefore a much persued target for the development of anti-cancer drugs. In order to find novel high affinity ligands for hdm2 which would interfere with its binding to p53 we screened phage display peptide libraries for mdm2 binding phage. We found a series of 12 and 15mer peptides which interact strongly with hdm2. The peptide sequences show striking homology with the previously established mdm2 binding site on p53, confirming that the peptide defined 18TFSDLW23 region is crucial for the interaction but that contact between the two molecules extends to position L26 on p53. Free synthetic peptides derived from the phage selected sequences proved to be up to 100 times stronger inhibitors of the p53-mdm2 interaction than the p53 derived wt-peptide in several ELISA-assays. This illustrates the potency of phage display libraries in the search for new peptide based lead structures designed to mimic or inhibit therapeutically important protein-protein interactions.

Bacteriophages↗
PubMed1998

Structural characterization and optimization of antibody-selected phage library mimotopes of an antigen associated with autoimmune recurrent thrombosis.

The presence of high titers of anti-cardiolipin antibodies (ACA's) of autoimmune origin, which are known to bind to plasma beta2-glycoprotein I (aka apolipoprotein H), correlates clinically with autoimmune recurrent thrombosis. Soluble beta2-glycoprotein I binds to solid-phase ACA (immobilized on a surface plasmon resonance chip) with a Kd of 1.4 microM, but if the reactants are reversed and beta2-glycoprotein I is on the solid-phase support, then the Kd is 52 nM. This 27-fold difference in affinity reflects the avidity/entropic advantage obtained for an antibody binding to an antigen that is made multivalent because it is attached to a solid phase. A mimotope of this antigen, selected from a phage display peptide library screen with an ACA, has been shown to bind to solid-phase ACA as a phage, using surface plasmon resonance. This peptide is representative of the motif from 37 peptides obtained in a previously reported phage library screen with this ACA (1). A synthetic version of this peptide, referred to as P4, has the sequence: A1G2P3C4I5L6L7A8R9D10R11C12P13G14, and binds to its selecting antibody with a Kd of 42 nM. NMR data indicate that proline-13 is present in both cis and trans configurations, and that these two geometries dramatically affect the overall tertiary structure of the molecule. The peptide lacking this proline binds severalfold better to the ACA, consistent with at least one of these structures having low affinity for binding ACA. Replacement of the arginine-9 position with a proline decreases binding affinity to ACA 10-fold. Another phage library-selected peptide has a proline in position 9, but also has a leucine in position 5, instead of isoleucine. Since its affinity for ACA is nearly as good as that for peptide P4, the phage library screening must have selected for a non-beta-branched amino acid in this position to compensate for the adverse effects of the arginine-9 to proline-9 substitution. The solution structure of a modified version of the antibody-selected phage peptide P4 with the central proline was determined. This peptide has one turn comprised of Ala-Pro-Asp-Arg, with the proline peptide bond in the cis configuration, and another turn that contains the disulfide and adjacent residues. If the disulfide is replaced by a thioether, and the central proline by an alpha-methyl proline, in an attempt to make the peptide more biologically stable, there is little adverse effect on affinity for ACA. The thioether bond/turn is fairly well defined with a Calpha to Calpha separation of 4.9 +/- 0.8 A. The alpha-methyl proline adopts the trans configuration, and this central Ala-(alpha-methyl-Pro)-Asp-Arg turn adopts a distorted type I turn conformation with a probable i to i+3 hydrogen bond. Modeling studies suggest that the proline peptide bond configuration switched from cis to trans in the presence of the alpha-methyl group on proline because of steric hindrance with the beta-carbon of the preceding residue. Overall, this peptidomimetic molecule is structurally very similar to the peptide with natural amino acids, with an rmsd difference of only 1.37 A, when comparing backbone atoms.

Antibodies, Anticardiolipin↗
PubMed2005

Functional specificity of artificial transcriptional activators.

Misregulated transcription is linked to many human diseases, and thus artificial transcriptional activators are highly desirable as mechanistic tools and as replacements for their malfunctioning natural counterparts. We previously reported two artificial transcriptional activation domains obtained from synthetic peptide libraries screened for binding to the yeast transcription protein Med15(Gal11). Here we demonstrate that the transcriptional potency of the Med15 ligands is increased through straightforward structural alterations. These artificial activation domains upregulate transcription via specific Med15 binding interactions and do not function in mammalian cells, which lack Med15. This functional specificity stands in contrast to most natural or artificial activation domains that function across all eukaryotic cell types. The results indicate that the screening strategy holds excellent promise for identifying peptide and small molecule transcriptional activators that function by unique mechanisms with advantageous specificity properties.

Binding Sites↗
PubMed1999

Systematic study of the substituted active C-terminus of hirudin.

Hirudin, a potent clinical thrombin inhibitor from Hirudo medicinalis, consists of 65 amino acids in a single chain. In this paper, we systematically synthesize a series of C-terminal (desulfo hirudin45-65) peptides substituted by 20 natural L-amino acids via the Multipin method. The resulting peptide library is subsequently screened using an alpha-thrombin-mediated fibrinogen clotting assay and alpha-thrombin-induced amidolytic hydrolysis assay.

Amides↗
PubMed1998

CSF-enriched antibodies do not share specificities among MS patients.

The specificity of the oligoclonal immunoglobulins found in MS CSF is unknown. We have previously shown that random peptide libraries displayed on phage can be used to identify specific ligands for CSF antibodies. Here we describe the use of this tool in the attempt to identify MS-specific CSF-enriched antibody reactivities with potential pathogenic, diagnostic or prognostic value. Applying different experimental strategies, several ligands reacting with CSF-enriched antibodies were identified. When tested against a panel of 55 MS patients, none of the ligands found were recognized by antibodies shared by any two patients. We used the selected peptides to demonstrate the stability in time of CSF-enriched antibodies notwithstanding disease progression.

Adult↗
PubMed2003

[Analysis on patial amino acid sequence of a novel glycoprotein binding to antiherpes simplex virus monoclonal antibody CHA9].

AIM: To acquire the characteristic amino acid sequence of a novel glycoprotein of herpes simplex virus (HSV), so as to localize gene encoding the novel glycoprotein accurately. METHODS: A 12-mer phage peptide library was screened for 3 rounds by using biotinylated mAb CHA9 against new glycoprotein g30k of HSV-2. Positive phage clones were detected by ELISA. 10 positive clones were selected randomly for sequencing. Sequence alignment and hydrophobic cluster analysis were carried out. RESULTS: Most of the sequences of 10 positive phage clones were highly homologous with a core-PH/KHXHXGS-. Phages containing this motif could react specifically with the mAb CHA9 and not cross-react with other IgG. Hydrophobic cluster analysis showed that the peptide was likely to form an epitope. CONCLUSION: We obtained a characteristic short peptide which shows some characters of g30K amino acid sequence. It provides valuable clue for prediction of the open reading frame of g30K gene and will be useful to explore biological characteristics of the new glycoprotein.

Amino Acid Sequence↗
PubMed2004

[Screening of dominant epitopes of antigens related to antibodies in the sera of patients with nasopharyngeal carcinoma].

BACKGROUND & OBJECTIVE: Epstein-Barr virus (EBV) is closely related to nasopharyngeal carcinoma (NPC). Many kinds of methods can be used to examine antibodies in NPC patients sera. This study was to screen the dominant epitopes from random peptide libraries (RPLs) displayed on phage using the EBV-related antibodies purified from the sera of NPC patients, and find new antigens at the epitope level. METHODS: The EBV-related antibodies were eluted from the sera of NPC patients using B95-8 cell EBV proteins as antigen, and the phages from 12-mer RPLs were elutriated for 3 rounds with the antibodies. The positive clones were gained by sandwich ELISA, and competitive inhibition assay from the third elution. The positive clones were sequenced, and the peptide coded by the inserted DNA were blasted with the antigen region of EBV proteins. RESULTS: Sixty-four phage clones were randomly picked up from the third eluate,25 positive clones were picked up using sandwich ELISA assay, the positive percentage was 39.06%. Thirteen clones were picked up for competitive ELISA assay,11 clones showed inhibitory phenomena,the inhibitory rates were between 18.09% and 65.94%. Five positive clones with high absorbency value, and high inhibitory rates were selected out, the sequences of peptides displayed on these clones were -A-T-S-H-L-H-V-R-L-P-W-T- (d15, and d18), -G-S-T-H-K-H-N-H-F-N-K-T- (d19), -K-P-I-H-E-H-P-H-R-F-K-S- (e8), -H-T-H-K-I-K-I-P-L-P-I-Q- (e23). These peptide sequences showed similarity with the amino acid sequences located in antigen regions of EBV integral membrane protein (d15, and d18), EBV thymidine kinase (d19), and EBV major capsid protein (e8, and e23). CONCLUSION: EBV-related epitopes could be obtained by screening the phages from RPLs with polyclonal antibodies purified from the sera of NPC patients, which may offer new methods of antigen preparation for sera diagnosis of NPC.

Amino Acid Sequence↗
PubMed2005

Differentiation of a passive vaccine and the humoral immune response toward infection: analysis of phage displayed peptides.

Antibody-genes undergo molecular events that produce unique binding-sites that recognize specific epitopes, thus, leading to B-cell clonal variation. As a result, different binding-site structures (paratope internal images) are produced even when two distinct B-cells bind one and the same epitope. Paratope structural variation can be exploited to enable one to evaluate antibody-diversity in a single polyclonal serum sample. This is accomplished through the selection of antibody-specific peptides isolated from combinatorial phage displayed peptide libraries. As an example, we demonstrate the analysis of macaque sera containing passively administered antibodies, given as a therapeutic vaccine and antibodies actively produced by the virus-infected monkeys.

Animals↗
PubMed2003

The mapping and reconstitution of a conformational discontinuous B-cell epitope of HIV-1.

A method for the discovery of the structure of conformational discontinuous epitopes of monoclonal antibodies (mAbs) is described. The mAb is used to select specific phages from combinatorial phage-display peptide libraries that in turn are used as an epitope-defining database that is applied via a novel computer algorithm to analyze the crystalline structure of the original antigen. The algorithm is based on the following: (1) Most contacts between a mAb and an antigen are through side-chain atoms of the residues. (2) In the three-dimensional structure of a protein, amino acid residues remote in linear sequence can juxtapose to one another through folding. (3) Tandem amino acid residues of the selected phage-displayed peptides can represent pairs of juxtaposed amino acid residues of the antigen. (4) Contact residues of the epitope are accessible to the antigen surface. (5) The most frequent tandem pairs of amino acid residues in the selected phage-displayed peptides can reflect pairs of juxtaposed amino acid residues of the epitope. Application of the algorithm enabled prediction of epitopes. On the basis of these predictions, segments of an antigen were used to reconstitute an antigenic epitope mimetic that was recognized by its original mAb.

Algorithms↗
PubMed2002

Mutant tyrosine kinases with unnatural nucleotide specificity retain the structure and phospho-acceptor specificity of the wild-type enzyme.

The direct substrates of one protein kinase in a cell can be identified by mutation of the ATP binding pocket to allow an unnatural ATP analog to be accepted exclusively by the engineered kinase. Here, we present structural and functional assessment of peptide specificity of mutant protein kinases with unnatural ATP analogs. The crystal structure (2.8 A resolution) of c-Src (T338G) with N(6)-(benzyl) ADP bound shows that the creation of a unique nucleotide binding pocket does not alter the phospho-acceptor binding site of the kinase. A panel of optimal peptide substrates of defined sequence, as well as a degenerate peptide library, was utilized to assess the phospho-acceptor specificity of the engineered "traceable" kinases. The specificity profiles for the mutant kinases were found to be identical to those of their wild-type counterparts.

Amino Acid Sequence↗
PubMed2006

[Development of nanomedicine using intracellular DDS].

In recent years, sustained release and targeting system using nanospheres or microspheres is noticed in systemic pharmacokinetics. However, in the near future, not only "systemic pharmacokinetics" but also "intracellular pharmacokinetics" seems to be important in Drug Delivery System research. In this context, we have tried to develop the novel cytoplasmic nanoparticle (NP) delivery methods using fusogenic liposomes (FL) and protein transduction domain (PTD). In this study, we demonstrated that the FL efficiently delivered the encapsulated NP to the cytoplasm directly in a fusion -dependent. Oligonucleotides attached to NP were gradually released in the cytoplasm after its efficient delivery using FL. Furthermore, we have succeeded in identifying the novel PTD using phage displayed random peptide library. In near future, this novel PTDs are applied to cytoplasmic NP delivery carrier. From these results, we suggested that this technology is very important to control the intracellular pharmacokinetics, and can be also applied to any NP which will be produced by the nanotechnology in the future.

Cytoplasm↗
PubMed2002

Identification of antigenic peptide recognized by the anti-JL1 leukemia-specific monoclonal antibody from combinatorial peptide phage display libraries.

PURPOSE: In the present study an antigen-mimetic peptide of the anti-JL1 leukemia-specific monoclonal antibody (mAb) was identified and characterized. METHODS: From combinatorial peptide phage display libraries displaying the random linear heptapeptides and dodecapeptides, we selected clones with affinity to anti-JL1 mAb through repeated rounds of panning on a mAb-coated ELISA plate. The antigenicity and immunogenicity of the peptide epitopes were then studied using chemically synthesized peptides. RESULTS: The selected clones had the LXPSIP consensus sequence. Two synthetic peptides LPPSIPFGLTVGGGGS and LLPSIPNQAYLGGGGS specifically reacted with anti-JL1 mAb in ELISA. These two peptides were found to inhibit the interaction between anti-JL1 mAb and JL1 antigen-positive Molt-4 cells. Although the immune sera raised against the keyhole limpet hemocyanin-conjugated peptides failed to react with Molt-4 cells, it showed strong reactivity to the peptide epitope. However, one mAb raised by peptide immunization successfully bound to Molt-4 cells. CONCLUSION: An epitope-mimetic peptide of anti-JL1 mAb was found using combinatorial peptide phage display libraries. It induced strong humoral response against itself, but only a limited fraction of this humoral response was cross-reactive with the original JL1 antigen.

Amino Acid Sequence↗
PubMed2003

Combinatorial peptide microarrays for the rapid determination of kinase specificity.

We report a rapid method for profiling of kinases using a strategy that couples the merits of combinatorics (in rapid diversity generation) with the throughput attainable using microarrays (in parallel screening). Alanine-scanning, deletion and positional-scanning peptide libraries of a kinase substrate were synthesized and site-specifically arrayed onto glass slides. The phosphorylation pattern of target sequences detected using fluorescently-labeled antiphosphoamino acid antibodies revealed the substrate preference of the kinase through its activity profile.

Amino Acid Sequence↗
PubMed2005

Identification of a novel B cell epitope on the nucleocapsid protein of porcine reproductive and respiratory syndrome virus by phage display.

A phage display peptide library targeting the nucleocapsid (N) protein of porcine reproductive and respiratory syndrome virus (PRRSV) strain CH-1a was generated and used for epitope mapping. After 3 rounds of biopanning with the monoclonal antibody (MAb) N3H2 directed against the N protein, 3 positive phages were screened and sequenced. These phages share a consensus sequence, IQTAFNQGA, which corresponds to the amino acid (AA) 79-87 segment of the CH-1a N protein. A small DNA fragment coding for IQTAFNQGA was expressed as a fusion product, and reacted to N3H2 in Western blots and indirect ELISA. Four truncated peptides (IQTAFNQG, IQTAFNQ, QTAFNQGA, and TAFNQGA) expressed as GST fusion products failed to react with N3H2. The sequences around the N3H2-binding site among the N proteins of 57 PRRSV strains were compared. Our results indicate that the IQTAFNQGA motif is highly conserved among North American and European isolates. We concluded that the precisely defined nona-peptide epitope is a novel conserved Linear B cell epitope on the N protein of PRRSV.

Amino Acid Sequence↗
PubMed1997

The neuronal nitric oxide synthase PDZ motif binds to -G(D,E)XV* carboxyterminal sequences.

PDZ motifs are small protein-protein interaction modules that are thought to play a role in the clustering of submembranous signalling molecules. The specificity and functional consequences of their associative actions is still largely unknown. Using two-hybrid methodology we here demonstrate that the PDZ motif of neuronal nitric oxide synthase (nNOS) can mediate the binding to several other proteins in brain. Peptide library screening showed that proteins bearing a carboxy-terminal G(D,E)XV* sequence are preferred targets for the nNOS amino-terminal PDZ motif. Potential nNOS targets include a melanoma-associated antigen, cyclophilins and the alpha1C-adrenergic receptor.

Amino Acid Sequence↗
PubMed2003

Bispecific monoclonal antibodies against a viral and an enzyme: utilities in ultrasensitive virus ELISA and phage display technology.

A quadroma (hybrid-hybridoma) secreting bispecific antibodies with one paratope specific for M13 bacteriophage coat protein and another paratope specific for alkaline phosphatase (AP) was developed by electro-fusion of the two parental hybridomas and selected by a fluorescence activated cell sorter (FACS). The anti-phage M13/anti-AP bsMAbs were purified from anti-phage M13 monospecific MAb by a novel affinity method using Mimetic Blue A6XL as immune complexes with AP. The purified bsMAbs with potentially every molecule uniformly bound with AP generated an immuno-probe with the theoretical highest specificity. An ultrasensitive sandwich ELISA for detecting viruses was developed by using this bsMAb coupled with an amplified ELISA procedure. The sensitivity of the assay was increased 1000 times compared with conventional ELISA to achieve detection of 100 phage particles which is approximately 2.3 fg of phage coat protein. This type of bsMAb probe and ELISA format can be used to design new body fluid assays for viral load of HIV, hepatitis and other human pathogens as rapid and inexpensive alternatives to the PCR based method. This unique bispecific probe also allowed rapid and sensitive detection of bound M13/fd phage clones while panning for specific phages displaying peptide mimics against an antigen from a phage display peptide library. Furthermore, we demonstrate the principle virus purification using bsMAb as affinity ligand with a mild phosphate buffer elution. The results indicate that bsMAb could be used to develop affinity chromatography for purifying highly contagious and pathogenic viruses avoiding procedures employing prolonged high-speed centrifugation.

Alkaline Phosphatase↗