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PubMed1996

Immunization with glycosylated Kb-binding peptides generates carbohydrate-specific, unrestricted cytotoxic T cells.

Cytotoxic T cells (CTL) recognize target proteins as short peptides presented by major histocompatibility complex (MHC) class I restriction elements. However, there is also evidence for peptide-independent T cell receptor (TCR) recognition of target proteins and non-protein structures. How such T cell responses are generated is presently unclear. We generated carbohydrate (CHO)-specific, MHC-unrestricted CTL responses by coupling di- and trisaccharides to Kb- or Db-binding peptides for direct immunization in mice. Four peptides and three CHO have been analyzed with the CHO either in terminal or central position on the carrier peptide. With two of these glycopeptides, with galabiose (Gal alpha 1-4Gal; Gal2) bound to a homocysteine (via an ethylene spacer arm) in position 4 or 6 in a vesicular stomatitis virus nucleoprotein-derived peptide (RGYVYQGL binding to Kb), CTL were generated which preferentially killed target cells treated with glycopeptide compared to those treated with the core peptide. Polyclonal CTL were also found to kill target cells expressing the same Gal2 epitope in a glycolipid. By fractionation of CTL, preliminary data indicate that glycopeptide-specific Kb-restricted CTL and unrestricted CHO-specific CTL belong to different T cell populations with regard to TCR expression. The results demonstrate that hapten-specific unrestricted CTL responses can be generated with MHC class I-binding carrier peptides. Different models that might explain the generation of such responses are discussed.

Amino Acid Sequence↗

PubMed2000

An automated prediction of MHC class I-binding peptides based on positional scanning with peptide libraries.

Specificities of three mouse major histocompatibility complex (MHC) class I molecules, Kb, Db, and Ld, were analyzed by positional scanning using combinatorial peptide libraries. The result of the analysis was used to create a scoring program to predict MHC-binding peptides in proteins. The capacity of the scoring was then challenged with a number of peptides by comparing the prediction with the experimental binding. The score and the experimental binding exhibited a linear correlation but with substantial deviations of data points. Statistically, for approximately 80% of randomly chosen peptides, MHC-binding capacity could be predicted within one log concentration of peptides for a half-maximal binding. Known cytotoxic T-lymphocyte epitope peptides could be predicted, with a few exceptions. In addition, frequent findings of MHC-binding peptides with incomplete or no anchor amino acid(s) suggested a substantial bias introduced by natural antigen processing in peptide selection by MHC class I molecules.

Animals↗

PubMed2004

An informatics search for the low-molecular weight chromium-binding peptide.

BACKGROUND: The amino acid composition of a low molecular weight chromium binding peptide (LMWCr), isolated from bovine liver, is reportedly E:G:C:D::4:2:2:2, though its sequence has not been discovered. There is some controversy surrounding the exact biochemical forms and the action of Cr(III) in biological systems; the topic has been the subject of many experimental reports and continues to be investigated. Clarification of Cr-protein interactions will further understanding Cr(III) biochemistry and provide a basis for novel therapies based on metallocomplexes or small molecules. RESULTS: A genomic search of the non-redundant database for all possible decapeptides of the reported composition yields three exact matches, EDGEECDCGE, DGEECDCGEE and CEGGCEEDDE. The first two sequences are found in ADAM 19 (A Disintegrin and Metalloproteinase domain 19) proteins in man and mouse; the last is found in a protein kinase in rice (Oryza sativa). A broader search for pentameric sequences (and assuming a disulfide dimer) corresponding to the stoichiometric ratio E:D:G:C::2:1:1:1, within the set of human proteins and the set of proteins in, or related to, the insulin signaling pathway, yields a match at an acidic region in the alpha-subunit of the insulin receptor (-EECGD-, residues 175-184). A synthetic peptide derived from this sequence binds chromium(III) and forms a metal-peptide complex that has properties matching those reported for isolated LMWCr and Cr(III)-containing peptide fractions. CONCLUSION: The search for an acidic decameric sequence indicates that LMWCr may not be a contiguous sequence. The identification of a distinct pentameric sequence in a significant insulin-signaling pathway protein suggests a possible identity for the LMWCr peptide. This identification clarifies directions for further investigation of LMWCr peptide fractions, chromium bio-coordination chemistry and a possible role in the insulin signaling pathway. Implications for models of chromium action in the insulin-signaling pathway are discussed.

Journal Article↗

PubMed2006

DynaPred: a structure and sequence based method for the prediction of MHC class I binding peptide sequences and conformations.

MOTIVATION: The binding of endogenous antigenic peptides to MHC class I molecules is an important step during the immunologic response of a host against a pathogen. Thus, various sequence- and structure-based prediction methods have been proposed for this purpose. The sequence-based methods are computationally efficient, but are hampered by the need of sufficient experimental data and do not provide a structural interpretation of their results. The structural methods are data-independent, but are quite time-consuming and thus not suited for screening of whole genomes. Here, we present a new method, which performs sequence-based prediction by incorporating information obtained from molecular modeling. This allows us to perform large databases screening and to provide structural information of the results. RESULTS: We developed a SVM-trained, quantitative matrix-based method for the prediction of MHC class I binding peptides, in which the features of the scoring matrix are energy terms retrieved from molecular dynamics simulations. At the same time we used the equilibrated structures obtained from the same simulations in a simple and efficient docking procedure. Our method consists of two steps: First, we predict potential binders from sequence data alone and second, we construct protein-peptide complexes for the predicted binders. So far, we tested our approach on the HLA-A0201 allele. We constructed two prediction models, using local, position-dependent (DynaPred(POS)) and global, position-independent (DynaPred) features. The former model outperformed the two sequence-based methods used in our evaluation; the latter shows a much higher generalizability towards other alleles than the position-dependent models. The constructed peptide structures can be refined within seconds to structures with an average backbone RMSD of 1.53 A from the corresponding experimental structures.

Algorithms↗

PubMedDate not supplied

A DNA-binding peptide from a phage display library.

A DNA-binding peptide was selected from a random peptide phage display library. For competitive elution using the DNA methyltransferase M.TaqI in the selection step, a biotin-labeled duplex oligodeoxyribonucleotide containing the 5'-TCGA-3' recognition sequence of M.TaqI was employed. Nine of ten phages selected were found to have the same deduced amino acid sequence SVSVGMKPSPRP. The selected phage binds to DNA, as demonstrated in an ELISA.

Amino Acid Sequence↗

PubMed1999

Peptide binding motifs and specificities for HLA-DQ molecules.

HLA-DQ molecules have been associated with susceptibility to a number of autoimmune and other diseases, possibly through the peptide repertoire that can be presented by different allelic products. It is thus of importance to understand which peptides can be bound by different HLA-DQ allelic products. Recently, a model for HLA-DQ has been described and used to derive peptide positional environments for HLA-DQ allelic products. By combining the peptide positional environments with known HLA-DQ peptide binding motifs, a set of predictions of likely anchor motifs for many of the products of HLA-DQ allelic variants are made and presented in a table referred to as a roadmap for HLA-DQ peptide binding specificities.

Antigen Presentation↗

PubMed2004

Comparative clinical evaluation of combination anorganic bovine-derived hydroxyapatite matrix (ABM)/cell binding peptide (P-15) and open flap debridement (DEBR) in human periodontal osseous defects: a 6 month pilot study.

A synthetic cell binding peptide (P-15) combined with anorganic bovine-derived hydroxyapatite bone matrix (ABM) was compared to open flap debridement (DEBR) in human periodontal osseous defects. Following initial preparation procedures, two osseous defects per patient were treated randomly with one of the two procedures after surgical preparation. Appropriate periodontal maintenance schedules were followed, and at 6 months clinical and radiographic assessments for soft tissue and hard tissue were performed for documentation and finalization of treatment. Statistical analysis using Student's paired t-test analyses of patient mean value from 10 patients revealed that the combination ABM/P-15 grafts demonstrated significantly better mean defect fill of 3.4+/-1.7 mm (73.2%) versus a mean defect fill of 0.6 mm (15.8%) for defects treated with DEBR. Soft tissue findings showed significant differences among treatments with ABM/P-15 compared to DEBR. These results suggest that the use of the P-15 synthetic cell-binding peptide combined with ABM yields better clinical results than DEBR.

Adult↗

PubMed1994

Peptide binding to surface class II molecules is the major pathway of formation of immunogenic class II-peptide complexes for viable antigen presenting cells.

Although studies on fixed APCs have demonstrated that peptide can bind to cell surface class II molecules, the mechanisms by which peptide-class II complexes are formed in viable cells is largely unexplored. To explore the possibility that peptide loading of class II molecules was occurring after endocytosis of peptides as well as by surface binding, we utilized an immunogenic hemagglutinin peptide (HAP 128-145) from the influenza strain A/Japan/57, and studied the appearance of surface complexes of HAP 128-145 bound to HLA-DRw11 molecules on human B-lymphoblastoid cells (BLCLs). Detection of the bound peptide was made possible by a rabbit anti-serum (alpha HAP) raised against HAP 128-145, which recognizes both the free peptide as well as peptide bound to DRw11 on living APCs. Pretreatment of the BLCLs with a variety of inhibitors of protein synthesis and intracellular trafficking failed to decrease the levels of HAP 128-145/DRw11 surface complexes. However, significant inhibition in the appearance of these complexes was caused by a decrease in the temperature at which the cells were incubated with peptide. Temperature-specific inhibition was also observed for fixed DRw11-positive APCs and purified DRw11 molecules indicating that the effect of temperature was directly on the class II molecules. We conclude that surface binding of peptide by class II molecules on human B cells is a major pathway of formation of immunogenic class II-peptide complexes for at least some soluble antigenic peptides, and that endocytosis of soluble peptides with subsequent binding of peptide by intracellular class II molecules plays little if any role in the formation of such complexes. Moreover, class II molecules have evolved to stably bind peptide optimally at physiologic temperatures, independent of cell metabolism.

Amino Acid Sequence↗

PubMed1998

Multi-center clinical evaluation of combination anorganic bovine-derived hydroxyapatite matrix (ABM)/cell binding peptide (P-15) as a bone replacement graft material in human periodontal osseous defects. 6-month results.

A synthetic cell-binding peptide (P-15) combined with anorganic bovine-derived hydroxyapatite bone matrix (ABM) was compared to demineralized freeze-dried bone allograft (DFDBA) and open flap debridement (DEBR) in human periodontal osseous defects in a controlled, monitored, multi-center trial. Following appropriate initial preparation procedures, flap surgery with defect and root debridement was performed. Three osseous defects per patient were treated randomly with one of three procedures after surgical preparation. Appropriate periodontal maintenance schedules were followed, and at 6 to 7 months re-entry flap surgery was performed for documentation and finalization of treatment. Analysis of variation (ANOVA) and t test analyses of patient mean values from 31 patients revealed that the combination ABM/P-15 grafts demonstrated significantly better mean defect fill of 2.8 +/- 1.2 mm (72.3%) versus a mean defect fill of 2.0 +/- 1.4 mm (51.4%) for defects treated with DFDBA (P <0.05) and a mean defect fill of 1.5 +/- 1.3 mm (40.3%) (P <0.05) for defects treated with DEBR. Other hard tissue findings showed similar clinically superior results with the use of ABM/P-15. Relative defect fill results showed 87% positive (50% to 100% defect fill) responses with ABM/P-15, 58% positive responses with DFDBA, and 41% positive responses with DEBR. There were 8 to 9 times more failures (minimal response) with DFDBA and DEBR (26% to 29% frequency) than with ABM/P-15. Soft tissue findings showed no significant differences among treatments except for greater clinical attachment level gain with ABM/P-15 compared to DEBR. These results suggest that the use of the P-15 synthetic cell-binding peptide combined with ABM yields better clinical results than either DFDBA or DEBR. Further studies are needed to determine the relative roles of the ABM and/or the P-15 in these improved results.

Adult↗

PubMed2006

A functional analysis of PCNA-binding peptides derived from protein sequence, interaction screening and rational design.

Proliferating cell nuclear antigen (PCNA) has no intrinsic enzymatic function, but functions as a sliding platform to mediate protein interactions with the DNA strand. Many proteins interact with PCNA through a small conserved motif with consensus QxxLxxFF. This work uses Schizosaccharomyces pombe and human cells to analyse the function of PCNA-binding peptides. Interacting peptides were identified using two-hybrid screening; one (pep102) binds directly to a physiologically relevant site on PCNA. The EGFP-pep102 overexpression phenotype is consistent with competitive blocking of PCNA-protein interactions. Various PCNA-binding peptides were all shown to inhibit PCNA function by competitive binding in both human and S. pombe cells as EGFP fusion proteins. The action of a p21(WAF1/Cip1)-derived peptide was complicated by the presence of additional functional domains and possible post-translational modification. The activity of pep102 was hampered by low expression in both model systems. The peptide derived from rational design (con1) was stable, highly active in inhibiting PCNA function both S. pombe and human cells and showed a high affinity for PCNA both in vitro and in vivo. These results validate the use of functional screening in yeast to identify peptide aptamers that are functional in mammalian cells; such aptamers provide excellent leads for small molecule antiproliferative therapies.

Amino Acid Sequence↗

PubMed2004

Peptide-binding motif of HLA-A*6603.

The peptide motif of HLA-A*6603 was determined and compared with the available data on the peptide motifs of A*6601 and A*6602. A*6601 differs from A*6602 by two amino acids at positions 90 (Asp90Ala; outer loop) and 163 (Arg163Glu; pocket A). A*6603 differs from A*6601 and A*6602 by a single amino-acid exchange at position 70 (His70Gln; pockets A, B and C). No significant differences were found between the A*6602 and A*6603 peptide motifs suggesting that the Gln70His variation is of minor importance. However, the auxiliary anchors at position P1 of peptides bound by A*6601 (polar/acidic: Asp, Glu) and A*6602/6603 (polar/neutral: Ser) had striking differences. This finding may be best explained by the Arg163Glu substitution that results in a shift towards higher acidity in pocket A of A*6602/6603, apparently leading to the loss of preference for acidic auxiliary anchors. The similarity of A*6602 and A*6603 peptide motifs suggests low allogenicity when mismatched in stem cell transplantation. Inversely, the differences in A*6601 versus A*6602/6603 peptide motifs suggest that mismatches will have a higher allogenicity. These data will contribute to both assessing permissive mismatches in the A*66 group and weighting the impact of this individual amino-acid variation for matching and peptide binding algorithms.

Amino Acid Motifs↗

PubMed1992

Assembly of MHC class I molecules in ex vivo carcinoma cells induced by IFN-gamma or by a binding peptide.

It has been reported that the assembly of MHC class I molecules in mutagenized cell lines could be induced by specific binding peptides. We have now demonstrated that the defect in assembly between heavy and light chains of class I molecules naturally occurred in tumor cells of one spontaneous ovarian carcinoma detected by one-dimensional isoelectric focusing of immunoprecipitates with anti-monomorphic class I MAb (W6/32) and by immunostaining with free heavy chain and beta 2m-specific MAbs. In vitro treatment of the tumor cells with IFN-gamma induced the assembly and surface expression of majority class I molecules (A2.1, B7, B15, Cw6, Cw7 out of A2.1, A2*, B7, B15, Cw6, Cw7). Moreover, assembly of A2 and Cw6 was induced by exposure of the tumor cells to a HLA A2-binding peptide K62 derived from influenza A matrix protein. Autologous blood T lymphocytes were activated in mixed lymphocyte-tumor cell culture (MLTC) by the IFN-gamma-treated but not by the unmanipulated tumor cells. Although activated lymphocytes damaged both IFN-gamma-treated and untreated tumor cells, the alpha class I MAb (W6/32) efficiently inhibited the lysis of IFN-gamma-treated targets, but not the untreated targets. These results indicate that the defect of MHC class I assembly may result in the escape of tumor cells from immune response.

Amino Acid Sequence↗

PubMed1987

Effects of buthionine sulfoximine on cd-binding Peptide levels in suspension-cultured tobacco cells treated with cd, zn, or cu.

Inhibition of cell growth and accumulation of Cd-binding peptide were measured in cultured tobacco cells exposed to buthionine sulfoximine. This inhibitor of glutathione metabolism caused little or no reduction of growth (at 0.1 millimolar) in the absence of Cd, but growth was greatly reduced in cultures exposed to buthionine sulfoximine and >/=22 micromolar Cd. Decreased cell growth was directly correlated with decreased levels of Cd-binding peptide and increased levels of what is thought to be free Cd. Zinc inhibited growth of tobacco cells only at the highest levels examined (900-1800 micromolar Zn), but buthionine sulfoximine had no additional significant effect. Similar results were observed for Cu (45-90 micromolar). Results suggest that synthesis of plant Cd-peptide involves gamma-glutamylcysteine synthetase or a related enzyme and that Zn accumulation in tobacco cells does not cause formation of significant Cd-peptide ligand.

Journal Article↗

PubMed1999

Substitution of aspartic acid at beta57 with alanine alters MHC class II peptide binding activity but not protein stability: HLA-DQ (alpha10201, beta10302) and (alpha10201, beta10303).

In class II major histocompatibility complex (MHC) proteins, residue beta57 is usually aspartic acid. Alleles carrying serine, valine, or alanine at this position are strongly correlated with the development of insulin-dependent diabetes mellitus (IDDM). Asp(beta)57 participates in a conserved salt bridge that bridges the alpha and beta subunits in the peptide-binding site. It has been proposed that the correlation between IDDM and MHC alleles lacking Asp(beta)57 may be due to an instability of the protein caused by loss of this salt bridge. Using a pair of HLA-DQ proteins (alpha1*0201, beta1*0302) and (alpha1*0201, beta1*0303) differing only in having aspartic acid or alanine at position beta57, we show that the polymorphism does not have a significant effect on protein stability for either the empty or peptide-loaded forms. However, the circular dichroism spectra indicate that empty and peptide-loaded Alabeta57 proteins display slightly different secondary structures relative to their Aspbeta57 counterparts. A set of three peptides shows different binding affinities for DQ(alpha1*0201, beta1*0302) relative to DQ(alpha1*0201, beta1*0303). We propose that substitution of Asp(beta)57 residue causes a local rearrangement within the DQ peptide-binding site that alters the peptide-binding specificity. This rearrangement may help to explain the previously observed differences in SDS stability between Asp and non-Asp(beta)57 DQ proteins.

Alanine↗

PubMed1993

Positive selection of CD8+ T cells induced by major histocompatibility complex binding peptides in fetal thymic organ culture.

We have used an in vitro system to study the effects of major histocompatibility complex class I binding peptides on thymic development. Fetal thymus lobes from mice deficient in the class I light chain (beta 2 microglobulin or beta 2 M-/-) were cultured for 10 d in vitro, during which time T cell precursors develop into mature T cells. In these organ cultures, as in the adult or neonatal beta 2 M-/- thymus, CD8+ mature T cells did not develop, demonstrating that the mature T cells seen during early murine thymic development are the result of the positive selection process. To these cultures we added various class I binding peptides with or without a source of exogenous beta 2M. CD8+ T cells developed to various degrees only in the presence of beta 2M and peptides. Using peptide mixtures of differing complexity, we showed that the efficiency of this process is dependent more on peptide complexity than on peptide concentration. These data argue for a specific role for peptides in the process of positive selection. Furthermore, this culture system should be useful in identifying peptides that can promote positive selection of cells expressing a specific T cell receptor (TCR) in TCR transgenic mice.

Amino Acid Sequence↗

PubMed1987

Increased atrial natriuretic peptide binding sites in the rat subfornical organ after water deprivation.

Binding sites for rat atrial natriuretic peptide (99-126) were localized and quantified in the subfornical organ and choroid plexus of control and water-deprived rats. Brain sections were analyzed after incubation with 125I-rat atrial natriuretic peptide (99-126), autoradiography, computerized microdensitometry and comparison to 125I-standards. Higher numbers of atrial natriuretic peptide binding sites were present in both the subfornical organ and the choroid plexus after 4 days of water deprivation. Our results indicate a central role for atrial natriuretic peptide in the regulation of water balance.

Animals↗

PubMed1999

Kinetic analysis of peptide binding to the TAP transport complex: evidence for structural rearrangements induced by substrate binding.

The transporter associated with antigen processing (TAP) plays a key role in the class I major histocompatibility complex (MHC) mediated immune surveillance. It translocates peptides generated by the proteasome complex into the endoplasmic reticulum (ER) for loading onto MHC class I molecules. At the cell surface these MHC complexes are monitored for their antigenic cargo by cytotoxic T-lymphocytes. Peptide binding to TAP is the essential step for peptide selection and for subsequent ATP-dependent translocation into the ER lumen. To examine the pathway of substrate recognition by TAP, we employed peptide epitopes, which were labeled with an environmentally sensitive fluorophore. Upon binding to TAP, a drastic fluorescence quenching of the fluorescent substrate was detected. This allowed us to analyze TAP function in real-time by using a homogeneous assay. Formation of the peptide-TAP complex is composed of a fast association step followed by a slow isomerization of the transport complex. Proton donor groups moving in proximity to the fluorescence label cause fluorescence quenching. Taken together, this peptide-induced structural reorganization may reflect the crosstalk of structural information between the peptide binding site and both nucleotide-binding domains within the TAP complex.

ATP Binding Cassette Transporter, Subfamily B, Mem↗

PubMed1993

Identification of the peptide binding domain of hsc70. 18-Kilodalton fragment located immediately after ATPase domain is sufficient for high affinity binding.

Recombinant hsc70, a purified glutathione S-transferase (GST) fusion protein containing the C-terminal domain of hsc70 (GST-Ct), and an internal 18-kDa polypeptide located immediately after the 44-kDa ATPase domain of hsc70 were investigated for their peptide binding properties. The dissociation constants of the S-peptide for native hsc70 (Kd = 5-8 microM), GST-Ct (Kd = 6.5 microM), and the 18-kDa fragment (Kd = 8.1 microM) are virtually identical. In addition, polylysine and (Pro-Pro-Gly)5 do not show high affinity toward hsc70, GST-Ct, and the 18-kDa fragment, whereas peptide GT4 and P3a show comparably high affinity toward these polypeptides. These observations indicate that the peptide binding domain of hsc70 is confined in the internal 18-kDa fragment.

Adenosine Triphosphatases↗