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PubMed1996

A sensitive proliferation assay to determine the specific T cell response against HLA-A2.1-binding peptides.

A proliferation assay to detect a specific T cell response against HLA class I-binding peptides is reported. To establish the specificity and sensitivity of the assay we used a synthetic peptide derived from the CMV glycoprotein B containing the HLA-A2.1 ligand motif. Lymphocyte proliferation was measured following culture of PBMC in the presence or absence of peptide by BrdU uptake. Differing culture conditions were compared (cell number, time in culture, peptide concentration, +/- IL-2). A peptide-specific response was detected in 11 of 23 HLA-A2-positive and CMV IgG-positive donors (47.8%), and in 4 of 36 HLA-A2-positive and CMV IgG-negative donors (11.1%, p = 0.019) tested under optimized conditions. None of 22 HLA-A2-negative individuals tested showed a peptide-specific response and the reproducibility was high. Peptide-specific IFN-gamma-secreting T cells could be demonstrated in responding donors with the ELISPOT assay. This proliferation assay may be suitable for monitoring induction of a specific T cell response against known HLA class I-binding peptides following vaccination with tumor or viral antigens.

Antibodies, Viral↗

PubMed2002

Thermodynamics of peptide binding to the transporter associated with antigen processing (TAP).

The ATP-binding cassette (ABC) transporter TAP plays an essential role in antigen processing and immune response to infected or malignant cells. TAP translocates proteasomal degradation products from the cytosol into the endoplasmic reticulum, where MHC class I molecules are loaded with these peptides. Kinetically stable peptide-MHC complexes are transported to the cell surface for inspection by cytotoxic T lymphocytes. The transport cycle of TAP is initiated by peptide binding, which is responsible for peptide selection and for stimulation of ATP-hydrolysis and subsequent translocation. Here we have analysed the driving forces for the formation of the peptide-TAP complex by kinetic and thermodynamic methods. First, the apparent peptide association and dissociation rates were determined at various temperatures. Strikingly, very high activation energies for apparent association (E(a)(ass)=106 kJmol(-1)) and dissociation (E(a)(diss)=80 kJmol(-1)) of the peptide-TAP complex were found. Next, the temperature-dependence of the peptide affinity constants was investigated by equilibrium-binding assays. Along with calculations of free enthalpy deltaG, enthalpy deltaH and entropy deltaS, a large positive change in heat capacity was resolved (deltaC degrees =23 kJmol(-1)K(-1)), indicating a fundamental structural reorganization of the TAP complex upon peptide binding. The inspection of the conformational entropy reveals that approximately one-fourth of all TAP residues is rearranged. These thermodynamic studies indicate that at physiological temperature, peptide binding is endothermic and driven by entropy.

ATP-Binding Cassette Transporters↗

PubMed2004

Induction of adipophilin-specific cytotoxic T lymphocytes using a novel HLA-A2-binding peptide that mediates tumor cell lysis.

Identification of tumor-associated antigens and advances in tumor immunology resulted in the development of vaccination strategies to treat patients with malignant diseases. Using a novel approach that combines DNA chip analysis of tumor samples with isolation of peptides on the surface of tumor cells, a HLA-A*0201-binding peptide derived from the adipophilin protein was identified. Adipophilin is involved in lipid storage and was thought to be expressed only in adipocytes, but it can be found in other cell types such as macrophages or tumor cells. In the present study, we analyzed the possible use of this peptide as a T-cell epitope presented by malignant cells. To accomplish this, we induced CTL responses using this HLA-A*0201-binding peptide. The in vitro-induced CTLs efficiently lysed cells pulsed with the adipophilin peptide and HLA-matched tumor cell lines in an antigen-specific and HLA-restricted manner. Finally, the induced CTLs recognized autologous dendritic cells (DCs) pulsed with the antigenic peptide or transfected with tumor RNA purified from an adipophilin-expressing tumor cell line. To further analyze the possible use of this peptide in immunotherapies of human malignancies, we induced adipophilin-specific CTLs using peripheral blood mononuclear cells and DCs from HLA-A*0201-positive patients with chronic lymphatic leukemia and plasma cell leukemia. The in vitro-generated CTLs recognized autologous chronic lymphatic leukemia cells and malignant plasma cells, whereas they spared nonmalignant resting or activated B and T lymphocytes, monocytes, or DCs. Our results demonstrate that this peptide might represent an interesting candidate for the development of cancer vaccines designed to target adipophilin-derived epitopes in a wide range of malignancies.

Antigen Presentation↗

PubMed1988

Isolation of mutants of Schizosaccharomyces pombe unable to synthesize cadystin, small cadmium-binding peptides.

Schizosaccharomyces pombe synthesize small cadmium-binding peptides cadystin, structure of which is (gamma-Glu-Cys)n-Gly, in response to cadmium. Mutants unable to synthesize cadystin were found in the mutants hypersensitive to cadmium. Some of them lack activity of either gamma-glutamylcysteine synthetase (EC 6.3.2.2) or glutathione synthetase (EC 6.3.2.3), enzyme involved in glutathione biosynthesis. Some mutants have the same activity levels of these enzymes as wild type has. These results indicate that some steps of cadystin biosynthesis are catalyzed by the enzymes catalyzing glutathione biosynthesis.

Cadmium↗

PubMed2005

Biosynthetic regulation of phytochelatins, heavy metal-binding peptides.

Phytochelatins (PCs) are heavy metal-binding peptides that play important roles in the detoxification of toxic heavy metals and the regulation of intracellular concentrations of essential metals in eukaryotes, including higher plants, fungi, and microalgae. Recently, PC synthase genes in higher plants and fission yeast have been identified and characterized, enabling molecular biological studies to unravel the mechanisms underlying PC synthesis. Moreover, recent routine database searches have unexpectedly identified genes that are similar to plant PC synthase genes in the genomes of worms and some prokaryotes. In this review, we introduce these recent advances in our understanding of the molecular mechanisms for PC biosynthesis and functions in order to supply basic information about the unique and attractive peptides applicable to various fields.

Aminoacyltransferases↗

PubMed2002

The beta-thymosins, small actin-binding peptides widely expressed in the developing and adult cerebellum.

The beta-thymosins are a highly conserved family of small polar peptides known to bind monomeric actin and inhibit its polymerization. The beta-thymosins show a high degree of sequence conservation among all vertebrate classes and they have been also identified in some invertebrate phyla. The most abundant beta-thymosins in mammals are thymosin beta4 (Tbeta4) and thymosin beta10 (Tbeta10), two ubiquitous small (43 amino acids) peptides sharing a high degree of sequence homology. Both beta-thymosins are present in virtually all mammalian tissues and cells studied, showing distinct patterns of expression in several tissues. The beta-thymosins are expressed in the developing and mature nervous system, indicating their participation with other actin-binding peptides in the control of actin polymerization. In the rat cerebellum the temporal and cellular patterns of expression of Tbeta4 and Tbeta10 are different, suggesting that each beta-thymosin could play a specific physiological function during cerebellum development. The possible roles of beta-thymosins in the developing mammalian cerebellum are discussed.

Animals↗

PubMedDate not supplied

Augmentation of the affinity of HLA class I-binding peptides lacking primary anchor residues by manipulation of the secondary anchor residues.

A direct binding assay has been used to investigate the effect of the secondary anchor residues on peptide binding to class I proteins of the major histocompatibility complex. Based on predictions from a previous chemometric approach, synthetic peptide analogues containing unnatural amino acids were synthesized and tested for B*2705 binding. Hydrophobic unnatural amino acids such as alpha-naphthyl- and cyclohexyl-alanine were found to be excellent substituents in the P3 secondary anchor position giving peptides with very high B*2705-binding affinity. The binding to B*2705 of peptides optimized for their secondary anchor residues, but lacking one of the P2 or P9 primary anchor residues was also investigated. Most such peptides did not bind, but one peptide, lacking the P2 Arg residue generally considered essential for binding to all B27 subtypes, was found to bind quite strongly. These findings demonstrate that peptide binding to class I proteins is due to a combination of all the anchor residues, which may be occupied also by unnatural amino acids-a necessary step towards the development of peptidic or non-peptidic antagonists for immunomodulation.

Amino Acid Sequence↗

PubMed2005

The R6A-1 peptide binds to switch II of Galphai1 but is not a GDP-dissociation inhibitor.

Heterotrimeric G-proteins are molecular switches that convert signals from membrane receptors into changes in intracellular physiology. Recently, several peptides that bind heterotrimeric G-protein alpha subunits have been isolated including the novel Galpha(i1).GDP binding peptides R6A and KB-752. The R6A peptide and its minimized derivative R6A-1 interact with Galpha(i1).GDP. Based on spectroscopic analysis of BODIPYFL-GTPgammaS binding to Galpha(i1), it has been reported that R6A-1 has guanine nucleotide dissociation inhibitor (GDI) activity against Galpha(i1) [W.W. Ja, R.W. Roberts, Biochemistry 43 (28) (2004) 9265-9275]. Using radioligand binding, we show that R6A-1 is not a GDI for Galpha(i1) subunits. Furthermore, we demonstrate that R6A-1 reduces the fluorescence quantum yield of the Galpha(i1)-BODIPYFL-GTPgammaS complex, thus explaining the previously reported GDI activity as a fluorescence artifact. We further show that R6A-1 has significant sequence similarity to the guanine nucleotide exchange factor peptide KB-752 that binds to switch II of Galpha(i1). We use competitive binding analysis to show that R6A-1 also binds to switch II of Galpha subunits.

Amino Acid Sequence↗

PubMed1992

Disparate interaction of peptide ligand with nascent versus mature class I major histocompatibility complex molecules: comparisons of peptide binding to alternative forms of Ld in cell lysates and the cell surface.

To determine the mechanism and structural consequences of peptide binding to class I molecules, we have studied the Ld molecule of the mouse. Previous studies have shown that a significant proportion of surface and intracellular Ld molecules can be detected in an alternative conformation designated Ldalt. Ldalt molecules are non-ligand associated and show weak if any beta 2-microglobulin (beta 2m) association. We report here that Ld molecules have a relatively rapid surface turnover compared with other class I molecules and that exogenous peptide dramatically prolongs Ld surface half-life. By contrast, Ldalt molecules are stably expressed on the surface and their half-life is unaffected by exogenous peptide. To study the surface interaction of peptide with Ld, live cells were incubated with iodinated peptides and Ld molecules were precipitated from cells precoated with monoclonal antibody before lysis. Using this assay, peptide binding to surface Ld molecules was found not to depend upon exchange with exogenous beta 2m, but did correlate with the level of beta 2m association. To study the intracellular interaction of peptide with Ld, cell lysates were used. In cell lysates, peptide was found to convert Ldalt molecules to properly folded Ld. This peptide-induced folding was almost complete at earlier but not later time points in pulse-chase analyses. Furthermore, conversion of Ldalt to Ld was found to affect almost exclusively immature (Endo Hs) class I molecules. Thus intrinsic properties of immature Ldalt molecules or their associated chaperonins are maintained in cell lysates that allow them to undergo de novo folding in vitro. These combined results demonstrate that immature Ldalt molecules are precursors awaiting constituents such as peptide and beta 2m that influence folding, whereas surface Ldalt molecules appear refractory to association with peptide, beta 2m, and consequent folding.

Animals↗

PubMed1990

The effect of mutations in the MHC class I peptide binding groove on the cytotoxic T lymphocyte recognition of the Kb-restricted ovalbumin determinant.

The H-2Kb-restricted cytotoxic T lymphocyte (CTL) response directed against ovalbumin (OVA) is specific for a region contained within the sequence OVA253-276. In this study we have characterized this response by examining the class I-restricted presentation of OVA peptides by the naturally occurring Kb mutant (Kbm) glycoproteins Kbm1, Kbm3, Kbm5, Kbm8, Kbm10, Kbm11 and Kbm23. To facilitate this study we derived a series of somatic cell hybrid targets expressing the various Kbm class I molecules. Experiments using bulk OVA-specific CTL from C57BL/6 mice demonstrated that all the Kbm molecules except for Kbm1 and Kbm8 could present OVA peptides for effective T cell recognition. Clonal analysis revealed a more complex and relatively diverse pattern of CTL recognition of the Kbm/peptide combinations. This diversity is unlikely to result from the existence of multiple, independent Kb-restricted T cell determinants within OVA, since all CTL tested were specific for a single region between residues 259 and 273. Examination of the fine specificity of Kbm presentation identified individual changes at residues 77, 80 and 116 which affected T cell recognition. The results imply that these changes do not inhibit peptide binding since some clones could recognize peptide presented by a particular Kbm molecule, while other clones could not. All three residues reside within the peptide-binding cleft of the class I protein and are not expected to directly contact the T cell receptor. Although we did not formally demonstrate that OVA binding by Kbm vs. Kb is quantitatively identical, our results are best explained by postulating that the changes at residues 77, 80 and 116 indirectly affect T cell recognition by altering peptide conformation. Taken together our results suggest that changes within the class I binding site can profoundly modify peptide presentation without significantly inhibiting peptide-class I association.

Animals↗

PubMed2001

Peptide-binding G protein-coupled receptors: new opportunities for drug design.

Over the last decades distinct members of the G Protein-Coupled Receptor (GPCR) family emerged as prominent drug targets within pharmaceutical research, since approximately 60 % of marketed prescription drugs act by selectively addressing representatives of that class of transmembrane signal transduction systems. It is noteworthy that the majority of GPCR-targeted drugs elicit their biological activity by selective agonism or antagonism of biogenic monoamine receptors, while the development status of peptide-binding GPCR-addressing compounds is still in its infancy. Exemplified on selected medicinal chemistry projects, this review will focus on the opportunities of therapeutic intervention into a broad spectrum of disease processes through agonizing or antagonizing the functions of peptide-binding GPCRs. In this context, a brief overview of GPCR-mediated signal transduction pathways will be given in order to emphasize the biomedical relevance of a controlled modulation of receptor function. Modern trends on lead finding and optimization strategies for peptide-binding GPCR-targeted low-molecular weight compounds will be highlighted on the basis of current research programs conducted in the areas of angiotensin II, endothelin, bradykinin, neurokinin, neuropeptide Y, LHRH, C5a antagonists, and somatostatin agonists, respectively. Special emphasis will be laid on the elaboration and utilization of structural rationales on the potential drug candidates, thus facilitating more detailed insights into the underlying molecular recognition event.

Animals↗

PubMed2000

Ligand interactions in the adenosine nucleotide-binding domain of the Hsp90 chaperone, GRP94. II. Ligand-mediated activation of GRP94 molecular chaperone and peptide binding activity.

The N-terminal domain of eukaryotic Hsp90 proteins contains a conserved adenosine nucleotide binding pocket that also serves as the binding site for the Hsp90 inhibitors geldanamycin and radicicol. Although this domain is essential for Hsp90 function, the molecular basis for adenosine nucleotide-dependent regulation of GRP94, the endoplasmic reticulum paralog of Hsp90, remains to be established. We report that bis-ANS (1,1'-bis(4-anilino-5-napthalenesulfonic acid), an environment sensitive fluorophore known to interact with nucleotide-binding domains, binds to the adenosine nucleotide-binding domain of GRP94 and thereby activates its molecular chaperone and peptide binding activities. bis-ANS was observed to elicit a tertiary conformational change in GRP94 similar to that occurring upon heat shock, which also activates GRP94 function. bis-ANS activation of GRP94 function was efficiently blocked by radicicol, an established inhibitory ligand for the adenosine nucleotide binding pocket. Confirmation of the N-terminal nucleotide binding pocket as the bis-ANS-binding site was obtained following covalent incorporation of bis-ANS into GRP94, trypsinolysis, and sequencing of bis-ANS-labeled limit digestion products. These data identify a ligand dependent regulation of GRP94 function and suggest a model whereby GRP94 function is regulated through a ligand-dependent conversion of GRP94 from an inactive to an active conformation.

Adenine Nucleotides↗

PubMed2006

Optimally-connected hidden markov models for predicting MHC-binding peptides.

Hidden Markov models (HMMs) are one of various methods that have been applied to prediction of major histo-compatibility complex (MHC) binding peptide. In terms of model topology, a fully-connected HMM (fcHMM) has the greatest potential to predict binders, at the cost of intensive computation. While a profile HMM (pHMM) performs dramatically fewer computations, it potentially merges overlapping patterns into one which results in some patterns being missed. In a profile HMM a state corresponds to a position on a peptide while in an fcHMM a state has no specific biological meaning. This work proposes optimally-connected HMMs (ocHMMs), which do not merge overlapping patterns and yet, by performing topological reductions, a model's connectivity is greatly reduced from an fcHMM. The parameters of ocHMMs are initialized using a novel amino acid grouping approach called "multiple property grouping." Each group represents a state in an ocHMM. The proposed ocHMMs are compared to a pHMM implementation using HMMER, based on performance tests on two MHC alleles HLA (Human Leukocyte Antigen)-A*0201 and HLA-B*3501. The results show that the heuristic approaches can be adjusted to make an ocHMM achieve higher predictive accuracy than HMMER. Hence, such obtained ocHMMs are worthy of trial for predicting MHC-binding peptides.

Amino Acid Sequence↗

PubMed2005

[Screening the antibody mimic peptide binding to hepatocellular carcinoma cells by phage display technique].

AIM: To screen the antibibody mimic peptide binding to hepatocellular carcinoma (HCC) from the circular 7-mer peptide libraries. METHODS: The enrichment of phage was achieved by repetitious biopanning. The affinity of peptide was evaluated by ELISA, and the binding site of the peptide was analysed by the competition ELISA. RESULTS: The output of phage gradually rose along with increasing of biopanning times. The obtained circular 7-mer peptide showed good binding activity to hepatocellular carcinoma cell lines SMMC-7721 and BEL-7402 (P<0.05), and its affinity to SMMC-7721 cells was superior to that of BEL-7402 (P<0.05). At the level of alpha=0.01, the screened 7-mer peptide monoclonal stocks could obviously compete with scFv to bind SMMC-7721 cells (0.005<P<0.01). As the concentration of scFv gradually fell, the competition inhibition rate dropped accordingly. Sequence analysis showed that the sequences of 7-mer positive monoclonal stocks were identical. CONCLUSION: The peptide obtained through biopanning was specific and effective, which may provide further support for target therapy of HCC.

Antibodies↗

PubMed1994

HLA-A2-binding peptides cross-react not only within the A2 subgroup but also with other HLA-A-locus allelic products.

Seven A2-binding peptides were tested by the HLA class I alpha-chain refolding assay previously described for their direct binding to HLA class I alpha chains derived from a panel of 18 HLA-homozygous B-cell lines of various HLA specificities, including four A2 subtypes: A*0201, A*0204, A*0205, and A*0206. All but one test peptide possessed the major anchor residue motifs, L-V, L-L, or I-L, of A2(A*0201)/A2(A*0205)-binding peptides or the closely related motifs, I-V or V-V. This cell panel analysis confirmed the high A2 allele specificity of the test peptides, but also revealed the existence of a broad cross-binding within the A2 subgroup. Most peptides bound to the alpha chains of the A2 subtypes tested, although their binding patterns showed differences. Furthermore, the A2-binding peptides carrying the I-V or V-V motif were found to cross-react also outside of the A2 subtypes, probably with A24, A26, A28, and A29. Other A-locus allelic products, A1, A3, A11, A30, and A31, and the B-locus allelic products carried by the cells tested were essentially negative, although a few exceptions were seen.

Alleles↗

PubMed1987

Properties of tobacco (Nicotiana tabacum) cadmium-binding peptide(s). Unique non-metallothionein cadmium ligands.

The chemical and physical characteristics of Cd-binding peptides isolated from tobacco (Nicotiana tabacum) leaves and suspension-cultured tobacco cells were determined and compared with properties of rat liver Cd,Zn-thionein. Some emphasis was placed on metal-binding and specificity properties. Cd-peptides of apparent Mr 6000 and 2000 were induced in tobacco leaves by growth of plants with 90 microM-Cd. Only the apparent-Mr-2000 Cd-peptide was induced in the leaves of tobacco plants grown in the presence of 3 microM-Cd. In cultured tobacco cells exposed to a wide range of Cd levels (3-180 microM), a peptide of apparent Mr 2000 was observed. Under denaturing conditions [6 M-guanidinium chloride (GdmCl) with or without 100 mM-2-mercaptoethanol], all of the above forms were shown to have an Mr of approx. 1300, compared with an Mr of 6000 for Cd,Zn-thionein. The apparent disaggregation of the Mr-6000 form by GdmCl to what appears to be the unit Cd-binding peptide was reversible. Tobacco-derived Cd-peptide contained approx. 40, 35 and 15 residues of glutamate/glutamine, cysteine and glycine respectively, with serine, lysine, and aromatic residues being absent. Tobacco Cd-peptide had an isoelectric point (pI) of 3.15, which is lower than the pI greater than or equal to 4 reported for metallothionein. A 50% dissociation of Cd occurred at pH 5 and 3.5 for the tobacco Cd-peptide and Cd,Zn-thionein respectively, and GdmCl was shown to cause Cd dissociation from tobacco peptide, but not from metallothionein. No evidence was obtained for Zn induction in vivo of, or Zn binding in vitro to, tobacco Cd-peptide. Copper induced a low-Mr metal-binding component in cultured tobacco cells which did not appear to be identical with the peptide induced by Cd. Properties of tobacco Cd-peptide and Cd,Zn-thionein, including metal affinity and selectivity, are greatly different, except for the common presence of 30 residues of cysteine/100 residues.

Amino Acids↗

PubMed1991

Peptide-binding specificity of the molecular chaperone BiP.

Members of the heat-shock protein family (hsp70s) can distinguish folded from unfolded proteins. This property is crucial to the role of hsp70s as molecular chaperones and is attributable to the amino-acid specificity of the peptide-binding site. The specificity for peptide ligands is investigated using a set of peptides of random sequence but defined chain length. The peptide-binding site selects for aliphatic residues and accommodates them in an environment energetically equivalent to the interior of a folded protein.

Adenosine Triphosphatases↗

PubMed1992

In vitro peptide binding to soluble empty class I major histocompatibility complex molecules isolated from transfected Drosophila melanogaster cells.

A soluble form of a mouse class I major histocompatibility antigen (H-2Kb) has been expressed in transfected Drosophila melanogaster cells. These molecules were efficiently secreted (up to 4 mg/liter) as noncovalent heterodimers and purified to homogeneity from cell supernatants. The isolated soluble Kb molecules were devoid of endogenous peptides. Using these molecules, we have characterized the Kb heavy chain-beta 2-microglobulin (beta 2m) assembly as well as peptide binding in vitro. In detergent-free solution the heavy chains readily re-assembled with beta 2m even in the absence of peptides. Kinetic analyses showed that the peptide binding is rapid and reversible and dependent on the heavy chains being assembled with beta 2m. Likewise, peptide dissociated from Kb molecules without the displacement of beta 2m. Equilibrium binding experiments using various peptides confirmed that octapeptides bind to Kb molecules with the highest affinity and form the most stable complexes. However, in contrast to earlier studies, the amino-terminal positioning of peptide to Kb molecules was more crucial than the carboxyl-terminal positioning and amidation of the peptide carboxylate did not affect the binding. Soluble Kb molecules could selectively bind allele-specific peptides among a mixture of randomly synthesized octapeptides in vitro; however, no dominant residue was observed at the carboxyl terminus of bound peptides. This suggests that the previously observed hydrophobic residues at the carboxyl terminus of peptides may reflect the specificity of enzyme(s) or protein(s) involved in peptide processing in vivo.

Amino Acid Sequence↗