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Results for “peptide binding”

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PubMed2006

Critical factors in the development of fluorescence polarization-based peptide binding assays: an equilibrium study monitoring specific peptide binding to soluble HLA-A*0201.

There is currently a significant interest in the identification and validation of HLA-restricted CTL epitopes, which are thought to have important implications for the development of preventive and/or therapeutic applications in bacterial or viral infections, autoimmune diseases, and cancer. To better facilitate epitope discovery and validation, we present a cell- and radioisotope-free HLA-A*0201 assay system which relies upon fluorescence polarization. The assay has the advantage of allowing real-time measurements in solution without separation steps. In this report, we directed our efforts towards enhancing the sensitivity and reproducibility of the assay by conducting an in-depth analysis of parameters critical for standardization. Initial experiments demonstrated that the attachment of a fluorescence moiety at positions 5 and 8 for 9-mers and positions 5 and 6 for 10-mers, respectively, does not interfere with ligand binding to soluble HLA-A*0201. In addition, it was found that their binding to HLA-A*0201 was very effective showing high affinity binding with K(d)'s between 10.7 to 21.8 nM and binding capacities of up to 37%. In order to deliver maximized responses, factors such as the regulation of thermal HLA activation parameters to initiate peptide exchange as well as the specific adjustment of assay components were identified. Overall, the results obtained clearly demonstrate high accuracy, sensitivity and reproducibility of the FP-based assay approach. With the need for both increased throughput and miniaturized volumes, this fully homogenous, fluorescent-type binding assay is expected to be useful for routine analysis of peptide binding to MHC class I as well as class II molecules.

Amino Acid Sequence↗

PubMed1994

The structural basis of sequence-independent peptide binding by OppA protein.

Specific protein-ligand interactions are critical for cellular function, and most proteins select their partners with sharp discrimination. However, the oligopeptide-binding protein of Salmonella typhimurium (OppA) binds peptides of two to five amino acid residues without regard to sequence. The crystal structure of OppA reveals a three-domain organization, unlike other periplasmic binding proteins. In OppA-peptide complexes, the ligands are completely enclosed in the protein interior, a mode of binding that normally imposes tight specificity. The protein fulfills the hydrogen bonding and electrostatic potential of the ligand main chain and accommodates the peptide side chains in voluminous hydrated cavities.

Amino Acid Sequence↗

PubMed1990

The kinetics of peptide binding to HLA-A2 and the conformation of the peptide-A2 complex can be determined by amino acid side chains on the floor of the peptide binding groove.

The ability of amino acid side chains in the floor of the peptide binding groove of HLA-A2 to affect the presentation of a viral peptide to peptide-specific cytotoxic T lymphocytes (CTL) has been examined. HLA-A2 molecules with naturally occurring single amino acid substitutions of Phe to Tyr at position 9 (HLA-A2.4a, Tyr9) and Tyr to Cys at position 99 (HLA-A2.4b, Cys99) and a site directed mutant with a Val to Leu substitution at position 95 (Leu95) were examined for their ability to present the influenza virus matrix M1 55-73 peptide and several sequence variants of the M1 peptide to a panel of 36 M1 55-73-specific HLA-A2.1-restricted CTL lines. The Leu95 molecule demonstrated enhanced kinetics of M1 peptide presentation and the ability to be sensitized by lower concentrations of the M1 peptide than the A2.1 molecule. The Tyr9 and Cys99 molecules exposed to M1 peptide were not recognized by 33 out of 36 CTL lines. The Tyr9 and Cys99 HLA-A2 molecules could bind the M1 55-73 peptide because at least one CTL line was found that could recognize each of these molecules that were exposed to the M1 peptide. CTL recognition patterns of variant M1 peptides presented by the Tyr9 molecule demonstrated that the amino acid at position 9 can be a critical determinant of the conformation of the peptide-A2 complex, and indicated that a particular peptide can bind in the HLA-A2 peptide binding groove in more than one conformation.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗

PubMed1995

An HLA class I peptide-binding assay based on competition for binding to class I molecules on intact human B cells. Identification of conserved HIV-1 polymerase peptides binding to HLA-A*0301.

A peptide-binding assay employing the HLA class I molecules on intact human B cells is described. The peptide antigens are stripped from the HLA class I molecules by mild acid treatment, after which the cells are incubated with a FL-labeled reference peptide together with different concentrations of the peptide of interest. The effectiveness by which the latter peptide competes for binding to the HLA class I molecules is assayed by measuring the amount of HLA-bound FL-labeled reference peptide with FACscan analysis. The assay is easy to perform because there is no need to purify HLA class I molecules, or to transfect cells with HLA class I molecules, and no radioactive label is used. Moreover, large panels of HLA-typed human B-cell lines are available as tools for peptide binding to a vast array of HLA molecules. The binding assay was optimized and validated with peptides of known binding capacity to either HLA-A*0201 or HLA-A*0301. The kinetics of peptide binding in this assay were shown to be comparable to that in assays employing soluble HLA class I molecules. Application of the assay in the search for potential HLA-A*0301 restricted CTL epitopes, derived from HIV-1 polymerase, resulted in the identification of five high-affinity binding peptides.

Amino Acid Sequence↗

PubMed2000

An N-acetylated natural ligand of human histocompatibility leukocyte antigen (HLA)-B39. Classical major histocompatibility complex class I proteins bind peptides with a blocked NH(2) terminus in vivo.

Sequence-independent interactions involving the free peptidic NH(2) terminus are thought to be an essential feature of peptide binding to classical major histocompatibility complex (MHC) class I proteins. Challenging this paradigm, a natural Nalpha-acetylated ligand of human histocompatibility leukocyte antigen (HLA)-B39 was identified in this study. It matched the NH(2)-terminal sequence of two human helicases, was resistant to aminopeptidase M, and was produced with high yield from a synthetic 30 mer with the sequence of the putative parental protein by the 20S proteasome. This is the first reported natural ligand of classical MHC class I antigens that has a blocked NH(2) terminus.

Acetylation↗

PubMed1999

GRP94, an ER chaperone with protein and peptide binding properties.

GRP94 is the ER representative of the HSP90 family of stress-induced proteins. It binds to a limited number of proteins in the secretory pathway, apparently by recognizing advanced folding intermediates or incompletely assembled proteins, GRP94 also binds peptides and can act as a tumor vaccine, delivering the peptides for presentation to T lymphocytes. Here, we review the current data about GRP94 and propose a structural model that integrates the biochemical data and known functions of the protein.

Adenosine Triphosphate↗

PubMed1994

Scheme for ranking potential HLA-A2 binding peptides based on independent binding of individual peptide side-chains.

A method to predict the relative binding strengths of all possible nonapeptides to the MHC class I molecule HLA-A2 has been developed based on experimental peptide binding data. These data indicate that, for most peptides, each side-chain of the peptide contributes a certain amount to the stability of the HLA-A2 complex that is independent of the sequence of the peptide. To quantify these contributions, the binding data from a set of 154 peptides were combined together to generate a table containing 180 coefficients (20 amino acids x 9 positions), each of which represents the contribution of one particular amino acid residue at a specified position within the peptide to binding to HLA-A2. Eighty peptides formed stable HLA-A2 complexes, as assessed by measuring the rate of dissociation of beta 2m. The remaining 74 peptides formed complexes that had a half-life of beta 2m dissociation of less than 5 min at 37 degrees C, or did not bind to HLA-A2, and were included because they could be used to constrain the values of some of the coefficients. The "theoretical" binding stability (calculated by multiplying together the corresponding coefficients) matched the experimental binding stability to within a factor of 5. The coefficients were then used to calculate the theoretical binding stability for all the previously identified self or antigenic nonamer peptides known to bind to HLA-A2. The binding stability for all other nonamer peptides that could be generated from the proteins from which these peptides were derived was also predicted. In every case, the previously described HLA-A2 binding peptides were ranked in the top 2% of all possible nonamers for each source protein. Therefore, most biologically relevant nonamer peptides should be identifiable using the table of coefficients. We conclude that the side-chains of most nonamer peptides to the first approximation bind independently of one another to the HLA-A2 molecule.

Amino Acid Sequence↗

PubMed2005

Energetics and cooperativity of the hydrogen bonding and anchor interactions that bind peptides to MHC class II protein.

The complexity of the interaction between major histocompatibility complex class II (MHC II) proteins and peptide ligands has been revealed through structural studies and crystallographic characterization. Peptides bind through side-chain "anchor" interactions with MHC II pockets and an extensive array of genetically conserved hydrogen bonds to the peptide backbone. Here we quantitatively investigate the kinetic hierarchy of these interactions. We present results detailing the impact of single side-chain mutations of peptide anchor residues on dissociation rates, utilizing two I-A(d)-restricted peptides, one of which has a known crystal structure, and 24 natural and non-natural amino acid mutant variants of these peptides. We find that the N-terminal P1, P4 and P6 anchor-pocket interactions can make significant contributions to binding stability. We also investigate the interactions of these peptides with four I-A(d) MHC II proteins, each mutated to disrupt conserved hydrogen bonds to the peptide backbone. These complexes exhibit kinetic behavior suggesting that binding energy is disproportionately invested near the peptide N terminus for backbone hydrogen bonds. We then evaluate the effects of simultaneously modifying both anchor and hydrogen bonding interactions. A quantitative analysis of 71 double mutant cycles reveals that there is little apparent cooperativity between anchor residue interactions and hydrogen bonds, even when they are directly adjacent (<5A).

Alanine↗

PubMed2006

Screening and identification of vascular-endothelial-cell-specific binding peptide in gastric cancer.

Antiangiogenesis therapy has become a hot field in cancer research. Blood vessels of tumor carry specific markers that are usually related to angiogenesis. Study of these heterogeneous molecules in different tumor vessels may be beneficial for promoting antiangiogenic therapy. In this study, we established an in vitro co-culture model of human umbilical vein endothelial cells (HUVECs) and gastric adenocarcinoma cell line SGC7901, screened the peptides binding specifically to the HUVECs co-cultured with gastric cancer cells (Co-HUVECs) using phage display peptides library, and studied the affinity of these peptides to gastric cancer vascular endothelial cells. After four rounds of panning, there was an obvious enrichment for the phages specifically binding to the Co-HUVECs, and the output/input ratio of Co-HUVECs increased about 590-fold (from 0.95x10(-7) to 561.25x10(-7)). Five phage clones (M6, M3, M9, IN12, IN11), which could strongly bind to Co-HUVECs instead of wild-type HUVECs, were characterized by ELISA. In vitro cellular binding assay showed that phage IN11 preferably bound to Co-HUVECs rather than control HUVECs, and the number of the phage IN11 recovered from Co-HUVECs was 5.7- and 16.9-folds, respectively, as much as those from control HUVECs and GES cells. Immunocytochemical and immunohistochemical staining confirmed that phage IN11 could specifically bind to Co-HUVECs as well as vascular endothelial cells in gastric cancer tissue sections. Competitive and inhibitory assay revealed the synthetic peptide GEBP11 (CTKNSYLMC) displayed on phage IN11 could competitively inhibit binding of the phage IN11 to Co-HUVECs. Immunofluorescence microscopy showed that the fluorescence-labeled peptide GEBP11 was located at the membrane and perinuclear cytoplasm of Co-HUVECs. Meanwhile, GEBP11 was found to be able to target the gastric cancer vascular endothelial cells. Therefore, GEBP11 may be a potential candidate for targeted drug delivery in antivascular therapy and diagnosis of gastric cancer.

Amino Acid Sequence↗

PubMed2001

Peptide binding to active class II MHC protein on the cell surface.

Solution studies have demonstrated the existence of two functionally distinct isomers of empty class II MHC: an active isomer that binds peptide and an inactive isomer that does not. Empty MHC molecules on the surface of APCs can load antigenic peptides directly from the extracellular medium, facilitating the generation of a diverse peptide repertoire for T cell presentation. In this report, we examine I-Ek on the surface of Chinese hamster ovary cells with respect to the active and inactive isomers. As in the case of purified soluble active I-Ek, active I-Ek on the cell surface is unstable, decaying to the inactive form in approximately 14 min. Evidence is presented suggesting that at steady state <1% of the total cell surface I-Ek is active and that a significant fraction of these active molecules originates from intracellular pools as well as reactivation of inactive cell surface I-EK.

Amino Acid Sequence↗

PubMed2006

An integrated machine learning system to computationally screen protein databases for protein binding peptide ligands.

A fairly large set of protein interactions is mediated by families of peptide binding domains, such as Src homology 2 (SH2), SH3, PDZ, major histocompatibility complex, etc. To identify their ligands by experimental screening is not only labor-intensive but almost futile in screening low abundance species due to the suppression by high abundance species. An ideal way of studying protein-protein interactions is to use high throughput computational approaches to screen protein sequence databases to direct the validating experiments toward the most promising peptides. Predictors with only good cross-validation were not good enough to screen protein databases. In the current study we built integrated machine learning systems using three novel coding methods and screened the Swiss-Prot and GenBank protein databases for potential ligands of 10 SH3 and three PDZ domains. A large fraction of predictions has already been experimentally confirmed by other independent research groups, indicating a satisfying generalization capability for future applications in identifying protein interactions.

Amino Acid Motifs↗

PubMed1995

Tolerance to amino acid variations in peptides binding to the major histocompatibility complex class I protein H-2Kb.

Major histocompatibility complex (MHC) class I molecules are cell-surface glycoproteins that bind peptides and present them to T cells. The formation of a peptide-MHC complex is the initial step in specific, T cell-mediated immune responses. But, unlike other receptor-ligand systems, peptides are essential for a stable conformation of the MHC proteins. To investigate the contribution of every amino acid of octapeptides to the stability and antigenic integrity of MHC proteins, complex octapeptide libraries with one defined amino acid and mixtures of 19 amino acids in the remaining seven positions were synthesized and tested for their capacity to stabilize the conformation of the mouse MHC class I molecule H-2Kb. Peptide transporter-deficient RMA-S cells were employed in this study. Amino acid preferences found for the eight sequence positions reveal constitutional, volumetric, and steric constraints that govern peptide selection by MHC molecules. The pattern of amino acid preferences indicates that the peptides behave as integral parts of the MHC proteins and follow rules established for the interrelationship of primary sequence and the conformation and stability of proteins in general.

Amino Acid Sequence↗

PubMed1994

A lactate dehydrogenase (LDH)-based immunoassay for detection of cell surface antigens and its application to the study of MHC class I-binding peptides.

A lactate dehydrogenase (LDH)-based immunoassay, referred to as CPEIA (cell panning enzyme immunoassay), has been developed for the detection of cell-surface antigens. CPEIA is similar to a panning assay, in that it is based on the capture of cells bearing an antigen of interest by means of an antibody immobilized to a 96-well microtiter plate. Attachment of the cells is then measured by addition of a substrate for the intracellular enzyme lactate dehydrogenase. The substrate solution also contains the nonionic detergent Triton X-100 to lyse the cells and release LDH, which converts the substrate p-iodonitrotetrazolium violet (INT) from yellow to red. The intensity of the color resulting from the LDH-catalyzed reaction is proportional to the number of cells bound to the plate. The procedure does not require fixation of the cells, centrifugation, and blocking steps, resulting in a more convenient assay. CPEIA has been used for the detection of MHC class I antigens and other molecules on the surfaces of mouse cell lines and concanavalin A (ConA)-stimulated T lymphocytes. In addition, the assay has been used to detect peptide binding to Db and Kb MHC class I molecules on the surface of the mutant cell line RMA-S. The half-maximal responses for peptide-MHC class I interactions at different peptide concentrations can be determined with the assay, allowing the apparent dissociation constants to be calculated.

Amino Acid Sequence↗

PubMed1995

Dependence of peptide binding by MHC class I molecules on their interaction with TAP.

Major histocompatibility complex (MHC) class I molecules bind peptides that are delivered from the cytosol into the endoplasmic reticulum by the MHC-encoded transporter associated with antigen processing (TAP). Peptide capture by immature heterodimers of class I heavy chains and beta 2-microglobulin may be facilitated by their physical association with TAP. A genetic defect in a human mutant cell line causes the complete failure of diverse class I heterodimers to associate with TAP. This deficiency impairs the ability of the class I heterodimers to efficiently capture peptides and results from loss of function of an unidentified gene or genes linked to the MHC.

ATP Binding Cassette Transporter, Subfamily B, Mem↗

PubMed1998

Fibronectin-binding peptides. I. Isolation and characterization of two unique fibronectin-binding peptides from gelatin.

Gelatin binds to fibronectin with a high affinity although the fibronectin-binding components have not been located. Fibronectin plays an important role in tumor cell metastasis and gelatin may have a profound effect on the metastatic process. In this study, fractionated acid-washed gelatin was cleaved with trypsin and resultant peptides fractionated by fibronectin-Sepharose affinity chromatography. After further purification using size exclusion HPLC and then reverse-phase HPLC, two unique peptides were obtained and sequenced. The binding affinities of these two peptides to fibronectin were evaluated by an ELISA method developed during this study and compared with the gelatin. Both possessed significantly higher binding affinities to fibronectin than gelatin alone.

Amino Acid Sequence↗

PubMed1990

Subcellular localization of cadmium and cadmium-binding peptides in tobacco leaves : implication of a transport function for cadmium-binding peptides.

The synthesis of Cd-binding peptides (CdBPs) was induced upon addition of 20 micromolar CdCl(2) (nonphytotoxic level) to the nutrient solution of hydroponically grown tobacco seedlings (Nicotiana rustica var Pavonii). Amino acid analysis showed that the main components were gamma-(Glu-Cys)(3)-Gly and gamma-(Glu-Cys)(4)-Gly. Seedlings exposed to the metal for 1 week contained similar glutathione levels as found in the controls (about 0.18 micromole per gram fresh weight). If, as has been proposed, CdBPs are involved in Cd-detoxification by chelation, both metal and ligand must be localized in the same cellular compartment. To directly determine the localization of Cd and CdBPs, protoplasts and vacuoles were isolated from leaves of Cd-exposed seedlings. Purified vacuoles contained virtually all of the CdBPs and Cd found in protoplasts (104% +/- 8 and 110% +/- 8, respectively). CdBPs were associated with the vacuolar sap and not with the tonoplast membrane. Glutathione was observed in leaves and protoplasts but not in vacuoles. The probability that CdBPs are synthesized extravacuolarly and our finding that they and Cd are predominantly located in the vacuole suggest that these molecules might be involved in transport of Cd to the vacuole. Our results also suggest that a simple cytoplasmic chelator role for CdBPs in Cd tolerance cannot be assumed.

Journal Article↗

PubMed2000

Development of an antibody against a 40,000 mol. wt brain injury-derived neurotrophic peptide-binding protein and identification of a 40,000 mol. wt brain injury-derived neurotrophic peptide-binding protein in hippocampal neurons.

Brain injury-derived neurotrophic peptide is a 13-amino acid peptide derived from a 15,000 mol. wt neurotrophic factor released from sites of mechanical injury in neonatal rat brain. This peptide promotes survival of septal cholinergic neurons and mesencephalic dopaminergic neurons, and protects hippocampal neurons from glutamate-induced neurotoxicity. In this study, we have developed a monoclonal antibody against a brain injury-derived neurotrophic peptide-binding protein by immunizing mice with septal synaptosomes from five-week-old rat brain. Monoclonal antibodies were screened for inhibition of the binding of a 125I-labeled analogue of brain injury-derived neurotrophic peptide to rat brain synaptosomes. The monoclonal antibody 6A22 suppressed the biological activity of brain injury-derived neurotrophic peptide and abolished the protective effect of the neurotrophic peptide against glutamate-induced neurotoxicity. This monoclonal antibody recognized a 40,000 mol. wt brain injury-derived neurotrophic peptide-binding protein, which was also identified by cross-linking experiments. Immunohistochemical studies showed that the 6A22 antibody bound to the cell surfaces of a subpopulation (about 60%) of hippocampal neurons in culture. These results are consistent with the possibility that the 40,000 mol. wt protein belongs to brain injury-derived neurotrophic peptide receptors.

Animals↗

PubMed1997

A roadmap for HLA-DR peptide binding specificities.

Peptide residue positional environments have previously been defined for class I MHC allelic products. These environments provide a less restrictive description of the traditional peptide binding pockets of class I molecules. When combined with the peptide anchor motifs that have been identified for some class I molecules, predictions as to likely motifs for other MHC molecules, which share the same potential environment can be made. Here, the same approach is used to derive peptide residue positional environments for class II MHC molecules. The environments are used to make predictions as to likely binding motifs for HLA-DR allelic products. The predictions are presented in the form of a Table and shown to have concordance with experimental results.

Alleles↗