Relevant bibliographies by topics / Presentation of peptides

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Academic literature on the topic 'Presentation of peptides'

Author: Grafiati
Published: 30 November 2024

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Journal articles on the topic "Presentation of peptides"

1

Wen, R., G. A. Cole, S. Surman, M. A. Blackman, and D. L. Woodland. "Major histocompatibility complex class II-associated peptides control the presentation of bacterial superantigens to T cells." Journal of Experimental Medicine 183, no. 3 (March 1, 1996): 1083–92. http://dx.doi.org/10.1084/jem.183.3.1083.

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Recent studies have shown that only a subset of major histocompatibility complex (MHC) class II molecules are able to present bacterial superantigens to T cells, leading to the suggestion that class-II associated peptides may influence superantigen presentation. Here, we have assessed the potential role of peptides on superantigen presentation by (a) analyzing the ability of superantigens to block peptide-specific T cell responses and (b) analyzing the ability of individual peptides to promote superantigen presentation on I-Ab-expressing T2 cells that have a quantitative defect in antigen processing. A series of peptides is described that specifically promote either toxic shock syndrome toxin (TSST) 1 or staphylococcal enterotoxin A (SEA) presentation. Whereas some peptides promoted the presentation of TSST-1 (almost 5,000-fold in the case of one peptide), other peptides promoted the presentation of SEA. These data demonstrate that MHC class II-associated peptides differentially influence the presentation of bacterial superantigens to T cells.
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Zandvliet, Maarten L., J. H. Frederik Falkenburg, Michel G. D. Kester, Arnoud H. de Ru, Peter A. van Veelen, Roelof Willemze, Henk-Jan Guchelaar, and Pauline Meij. "Sequence Dependent Efficiency of Cross-Presentation in MHC Class I Requires Rational Design of Long Synthetic Peptides for Vaccination or Ex Vivo Activation." Blood 112, no. 11 (November 16, 2008): 3904. http://dx.doi.org/10.1182/blood.v112.11.3904.3904.

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Abstract For the induction or boosting of antigen-specific CD8+ T cell responses, long synthetic peptides have been used in vaccination studies. Superior in vivo CD8+ T cell responses have been reported following vaccination with long peptides compared with minimal peptides, which was attributed to selective uptake and cross-presentation by professional antigen-presenting cells. Furthermore, to generate antigen-specific T cell lines for adoptive immunotherapy or to measure antigen-specific T cell responses, protein-spanning pools of overlapping long synthetic peptides can be used to simultaneously activate CD8+ and CD4+ T cells in peripheral blood mononuclear cells (PBMC) ex vivo. Although exogenous antigen is predominantly presented in MHC class II, it has been suggested that cross-presentation of long peptides in MHC class I can occur. However, the mechanism of cross-presentation of exogenous long peptides in MHC class I is not clear. Various models for cross-presentation have been described following uptake of soluble antigen in endosomes, among which antigen transport over the endosomal membrane followed by the classical proteasome- and TAP-dependent route, and entrance of MHC class I in the recycling endocytic MHC class II pathway where peptidase-trimmed exogenous antigens can exchange with peptides in the MHC class I molecules, resulting in TAP- and proteasome-independent cross-presentation. To improve the design of peptides for the in vivo or ex vivo activation of CD8+ T cells we investigated the mechanism and efficiency of cross-presentation of long peptides. We observed that antigen-presenting cells in peripheral blood, in particular monocytes, loaded with 15-mer peptides, 31-mer peptides or full length protein containing the NLV epitope were able to very efficiently induce IFNg production by cytomegalovirus (CMV) pp65 NLV-specific T cells. Specific T cells were most efficiently activated by N-terminally extended variants of the minimal epitope, while the use of C-terminally extended variants resulted in a 10-fold reduction of activation efficiency. Purification of these antigens by high performance liquid chromatography (HPLC) followed by mass spectrometry demonstrated that activation was not caused by contamination with the minimal epitope sequence. Also CD8+ T cells specific for other CMV and minor histocompatibility antigen (mHag) epitopes were activated by monocytes loaded with 15-mer or 20-mer peptides. Again N-terminally extended variants of minimal epitopes very efficiently induced activation, while the use of C-terminally variants or full length protein resulted in highly variable efficiency of activation, ranging from 10-fold reduction to complete absence of activation. Interestingly, TAP-deficient T2 cells loaded with CMV pp65 NLV antigens also efficiently activated NLV-specific T cells, indicating that the route of presentation was TAP-independent. Addition of lactacystin during loading of monocytes with CMV pp65 NLV 15-mer did not affect activation of specific T cells, suggesting that cross-presentation was proteasome-independent. Addition of primaquine reduced activation of specific T cells by the NLV 15-mer peptide, but not by the minimal NLV 9-mer peptide, suggesting that cross-presentation was dependent on endosomal recycling. To compare cross-presentation with presentation of endogenously synthesized antigen, TAP-competent T1 and TAP-deficient T2 cells were retrovirally transduced with the CMV pp65 gene. CMV pp65-specific T cells were activated by CMV pp65 transduced T1 but not T2 cells, indicating that endogenously synthesized CMV pp65 required processing and presentation by the classical proteasome- and TAP-dependent route. These data suggest that long synthetic peptides can be processed by peptidases in endocytic compartments and presented by recycling MHC class I molecules. Not all immunogenic epitopes that have been selected in vivo for efficient processing and presentation by the classical pathway may be presented efficiently by cross-presentation. As the efficiency of cross-presentation of long synthetic peptides may depend on the sequence of the C-terminal extension, a rational design of peptides is crucial for efficient activation of CD8+ T cells in approaches of vaccination, adoptive transfer and immune monitoring.
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Utz, U., S. Koenig, J. E. Coligan, and W. E. Biddison. "Presentation of three different viral peptides, HTLV-1 Tax, HCMV gB, and influenza virus M1, is determined by common structural features of the HLA-A2.1 molecule." Journal of Immunology 149, no. 1 (July 1, 1992): 214–21. http://dx.doi.org/10.4049/jimmunol.149.1.214.

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Abstract To determine whether similar or dissimilar molecular features of class I molecules are involved in the presentation of structurally distinct peptides, we have investigated the influence of different pockets of the HLA-A2.1 molecule on the presentation of three different viral peptides. HTLV-I Tax peptide 12-19, HCMV gB 619-628, and influenza M1 58-66 are minimal peptides that induce HLA-A2.1-restricted noncross-reactive CTL. A detailed analysis of the structural features of HLA-A2.1 that are involved in peptide presentation was undertaken using a panel of 11 HLA-A2 mutants with single amino acid substitutions within pockets present in the peptide binding site. Nine of the 11 mutants affected presentation of each of the three peptides, whereas the other two mutants had negative effects on presentation of only two of these viral peptides. These results indicate that common structural features in HLA-A2 determine the binding of different peptides, and help to provide a plausible explanation for how structurally diverse peptides bind to HLA-A2.
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Fremont, Daved H., Shaodong Dai, Herbert Chiang, Frances Crawford, Philippa Marrack, and John Kappler. "Structural Basis of Cytochrome c Presentation by IEk." Journal of Experimental Medicine 195, no. 8 (April 15, 2002): 1043–52. http://dx.doi.org/10.1084/jem.20011971.

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The COOH-terminal peptides of pigeon and moth cytochrome c, bound to mouse IEk, are two of the most thoroughly studied T cell antigens. We have solved the crystal structures of the moth peptide and a weak agonist–antagonist variant of the pigeon peptide bound to IEk. The moth peptide and all other peptides whose structures have been solved bound to IEk, have a lysine filling the p9 pocket of IEk. However, the pigeon peptide has an alanine at p9 shifting the lysine to p10. Rather than kinking to place the lysine in the anchor pocket, the pigeon peptide takes the extended course through the binding groove, which is characteristic of all other peptides bound to major histocompatibility complex (MHC) class II. Thus, unlike MHC class I, in which peptides often kink to place optimally anchoring side chains, MHC class II imposes an extended peptide conformation even at the cost of a highly conserved anchor residue. The substitution of Ser for Thr at p8 in the variant pigeon peptide induces no detectable surface change other than the loss of the side chain methyl group, despite the dramatic change in recognition by T cells. Finally, these structures can be used to interpret the many published mutational studies of these ligands and the T cell receptors that recognize them.
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Hombach, J., H. Pircher, S. Tonegawa, and R. M. Zinkernagel. "Strictly transporter of antigen presentation (TAP)-dependent presentation of an immunodominant cytotoxic T lymphocyte epitope in the signal sequence of a virus protein." Journal of Experimental Medicine 182, no. 5 (November 1, 1995): 1615–19. http://dx.doi.org/10.1084/jem.182.5.1615.

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Peptides presented by major histocompatibility complex (MHC) class I molecules are derived from intracellularly synthesized proteins. Cytosolic proteins are fragmented into peptides, which are subsequently transported via the transporter of antigen presentation (TAP) into the endoplasmic reticulum (ER), where they bind to MHC class I molecules. We have investigated the requirements for MHC class I presentation of the immunodominant gp33 cytotoxic T lymphocyte epitope of the lymphocytic choriomeningitis virus. This epitope is located within the leader peptide of the virus glycoprotein. Such an epitope is expected to be presented in a TAP-independent manner, since it is released into the ER by signal peptidase. Taking advantage of TAP1-/- mice, however, we show both in vitro and in vivo that, after virus infection, the presentation of the gp33 epitope is strictly dependent on a functional TAP heterodimer. The results are discussed with respect to peptide trimming processes in the ER.
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Neisig, A., J. Roelse, A. J. Sijts, F. Ossendorp, M. C. Feltkamp, W. M. Kast, C. J. Melief, and J. J. Neefjes. "Major differences in transporter associated with antigen presentation (TAP)-dependent translocation of MHC class I-presentable peptides and the effect of flanking sequences." Journal of Immunology 154, no. 3 (February 1, 1995): 1273–79. http://dx.doi.org/10.4049/jimmunol.154.3.1273.

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Abstract The MHC-encoded transporter associated with Ag presentation (TAP) translocates peptides from the cytosol to the ER lumen, where association with MHC class I molecules occurs. The MHC class I/peptide complex is subsequently transported to the cell surface for presentation to CD8+T cells. We studied TAP-dependent translocation of defined MHC class I presentable murine peptides by competition for translocation of a radiolabeled model peptide, to address whether efficient peptide presentation by MHC class I molecules is preceded by equal efficient peptide translocation by TAP. Surprisingly, we observed that four immunodominant viral peptides of 16 peptides tested were very inefficiently transported by TAP. Inefficient translocation could be overcome by substitution of a proline residue present at position 3 in the peptides. Furthermore, addition of natural flanking amino acids directly surrounding a poorly transported peptide could considerably improve translocation by TAP. Our data suggest that some peptides are efficiently transported by TAP in their optimal size for MHC class I binding, whereas other peptides are transported as larger peptide fragments that need further trimming in the ER for MHC class I binding.
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Daniel, Soizic, Vladimir Brusic, Sophie Caillat-Zucman, Nicolai Petrovsky, Leonard Harrison, Daniela Riganelli, Francesco Sinigaglia, Fabio Gallazzi, Jürgen Hammer, and Peter M. van Endert. "Relationship Between Peptide Selectivities of Human Transporters Associated with Antigen Processing and HLA Class I Molecules." Journal of Immunology 161, no. 2 (July 15, 1998): 617–24. http://dx.doi.org/10.4049/jimmunol.161.2.617.

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Abstract Efficiency of presentation of a peptide epitope by a MHC class I molecule depends on two parameters: its binding to the MHC molecule and its generation by intracellular Ag processing. In contrast to the former parameter, the mechanisms underlying peptide selection in Ag processing are poorly understood. Peptide translocation by the TAP transporter is required for presentation of most epitopes and may modulate peptide supply to MHC class I molecules. To study the role of human TAP for peptide presentation by individual HLA class I molecules, we generated artificial neural networks capable of predicting the affinity of TAP for random sequence 9-mer peptides. Using neural network-based predictions of TAP affinity, we found that peptides eluted from three different HLA class I molecules had higher TAP affinities than control peptides with equal binding affinities for the same HLA class I molecules, suggesting that human TAP may contribute to epitope selection. In simulated TAP binding experiments with 408 HLA class I binding peptides, HLA class I molecules differed significantly with respect to TAP affinities of their ligands. As a result, some class I molecules, especially HLA-B27, may be particularly efficient in presentation of cytosolic peptides with low concentrations, while most class I molecules may predominantly present abundant cytosolic peptides.
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Mo, X. Y., Paolo Cascio, Kristen Lemerise, Alfred L. Goldberg, and Kenneth Rock. "Distinct Proteolytic Processes Generate the C and N Termini of MHC Class I-Binding Peptides." Journal of Immunology 163, no. 11 (December 1, 1999): 5851–59. http://dx.doi.org/10.4049/jimmunol.163.11.5851.

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Abstract Most of the MHC class I peptides presented to the immune system are generated during the course of protein breakdown by the proteasome. However, the precise role of the proteasome, e.g., whether this particle or some other protease generates the carboxyl (C) and amino (N) termini of the presented 8- to 10-residue peptides, is not clear. Here, we show that presentation on Db of ASNENMETM, a peptide from influenza nucleoprotein, and on Kb of FAPGNYPAL, a peptide from Sendai virus nucleoprotein, was blocked by the proteasome inhibitor, lactacystin. Using plasmid minigene constructs encoding oligopeptides of various lengths, we found that presentation of ASNENMETM from C-terminally extended peptides that contain this antigenic peptide plus three or five additional amino acids and presentation of FAPGNYPAL from a peptide containing FAPGNYPAL plus one additional C-terminal residue required the proteasome. In contrast, the proteasome inhibitor did not reduce presentation of cytosolically expressed ASNENMETM or FAPGNYPAL or N-terminally extended versions of these peptides, suggesting involvement of aminopeptidase(s) in trimming these N-extended variants. Accordingly, when the N termini of these 3N-extended peptides were blocked by acetylation, they were resistant to hydrolysis by cellular aminopeptidases and pure leucine aminopeptidase. Moreover, if introduced into the cytosol, Ag presentation of these peptides occurred to a much lesser extent than from their nonacetylated counterparts. Thus, the proteasome is essential for the generation of ASNENMETM and FAPGNYPAL peptides from the full-length nucleoproteins. Although it generates the C termini of these presented peptides, distinct aminopeptidase(s) can trim the N termini of these presented peptides to their proper size.
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Monji, T., and D. Pious. "Exogenously provided peptides fail to complex with intracellular class II molecules for presentation by antigen-presenting cells." Journal of Immunology 158, no. 7 (April 1, 1997): 3155–64. http://dx.doi.org/10.4049/jimmunol.158.7.3155.

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Abstract Exogenously supplied antigenic peptides can bind to and be presented by cell surface class II molecules of APCs without prior processing. However, it has been unclear whether peptide Ags exogenously supplied to APCs can also form complexes with nascent intracellular class II molecules that contribute to Ag presentation. We found that exogenously provided peptide Ags, unlike whole protein Ags, are presented as efficiently by fixed as by unfixed B lymphoblastoid APCs, suggesting that intracellular processes do not contribute to the presentation of exogenously supplied peptides by unfixed APCs. Consistent with this finding, exogenously provided peptides do not bind detectably to nascent intracellular class II molecules. We studied the basis for this failure. First, as compared with whole proteins, exogenously supplied peptides accumulate very poorly intracellularly. Second, peptides are more rapidly exocytosed. The limited ability of APCs to accumulate exogenously supplied peptides intracellularly provides a likely explanation for the failure of these peptides to associate with nascent intracellular class II molecules. Exogenously supplied peptides probably never reach the intracellular vesicles in which peptide loading of class II molecules occurs. These findings have implications for the use of peptides therapeutically to block presentation of autoantigens in autoimmune disease.
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Stryhn, A., L. O. Pedersen, T. Romme, A. C. Olsen, M. H. Nissen, C. J. Thorpe, and S. Buus. "pH dependence of MHC class I-restricted peptide presentation." Journal of Immunology 156, no. 11 (June 1, 1996): 4191–97. http://dx.doi.org/10.4049/jimmunol.156.11.4191.

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Abstract The function of MHC class I molecules is to bind and present antigenic peptides to cytotoxic T cells. Here, we report that class I-restricted peptide presentation is strongly pH dependent. The presentation of some peptides was enhanced at acidic pH, whereas the presentation of others was inhibited. Biochemical peptide-MHC class I binding assays demonstrated that peptide-MHC class I complexes are more stable at neutral pH than at acidic pH. We suggest that acid-dependent peptide dissociation can generate empty class I molecules and that the resulting binding potential can be exploited by a subset of peptide-MHC class I combinations, in some cases leading to considerable peptide exchange. We further speculate that the relative instability of peptide-class I complexes under acidic conditions may affect the outcome of class I-restricted Ag presentation, as less stably associated peptides may dissociate from class I during passage of the acidic trans-Golgi network, and therefore may not be presented. Finally, our results may in part explain how endocytosed proteins can be presented by MHC class I molecules to cytotoxic T cells.
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Dissertations / Theses on the topic "Presentation of peptides"

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Howarth, Mark. "The presentation of suboptimal peptides by MHC Class I." Thesis, University of Oxford, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.398092.

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Springer, Sebastian Hartmut. "The biochemistry of antigen presentation." Thesis, University of Oxford, 1996. http://ora.ox.ac.uk/objects/uuid:34d1afd2-fafc-4732-8e43-e00dcd8460d1.

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This thesis describes studies on the binding of peptides to the murine major histocompatibility complex (MHC) class I molecule H-2Db (Db). The expression of the recombinant soluble Db molecule in Chinese hamster ovary cells and its subsequent purification by nickel affinity chromatography, gel filtration, and preparative native isoelectric focusing are reported. The product is the correct molecule, homogeneous, a dimer of dimers, and free of endogenous peptide. A novel binding assay based on the enhancement of natural tryptophan fluorescence by the binding of peptide is introduced. This assay is used to determine melting curves of the empty and peptide-loaded protein, and to measure association rate constants by stopped-flow fluorescence spectroscopy. Radioligand binding measurements of equilibrium as well as association and dissociation rate constants and their temperature dependence are reported. In agreement with earlier observations, the ratio of association and dissociation rate constants is much larger than the equilibrium association constant. Fluorescence anisotropy decay spectroscopy gives evidence for conformational alterations in the Db molecule upon peptide binding. The data, possible errors and ways to avoid them, and mathematical models of binding are discussed to obtain an overall picture of the binding process.
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Winchester, Christopher Charles. "The roles of Hsp70 proteins in antigen processing and presentation." Thesis, University of Oxford, 1997. http://ora.ox.ac.uk/objects/uuid:567dff45-08ce-43b4-b011-d08afea42f76.

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The ability of members of the hsp70 family to bind to peptides in vivo and in vitro suggests that they may be involved in the processing of antigens for binding to Major Histocompatibility (MHC) class I and/or class n molecules. The aims of this thesis have been to provide evidence for the involvement of hsp70s in antigen processing and to characterise the binding of peptides by hspTOs by structural and functional studies. Firstly, the peptide-binding domains of two hsp70s, hsp70hom and PBP74, were expressed in isolation from the rest of the molecule for structure determination. Both of these hsp70s were implicated in antigen processing: hsp70hom in the class I pathway, due to its cytoplasmic localisation and constitutive expression, and the presence of its gene in the MHC; and PBP74 in the class n pathway because published work indicated that it was localised to endosomes and that antibodies against it inhibited antigen processing. The expression and purification of both peptide-binding domains was very successful, and one dimensional NMR experiments indicated that they were folded. However, it was not possible to determine their structures by NMR spectroscopy or X-ray crystallography because they aggregated in solution at high concentrations. Instead, the structure of the C-terminal region of hsp70hom, which includes its peptidebinding domain, was modelled based on the known structure of the equivalent portion of dnaK, the hsp70 of E.coli. The structure of hsp70hom is predicted to be very similar to that of dnaK, and modelling studies suggest that it is likely to bind peptides in a closely related fashion. The modelling of complexes between hsp70hom and two peptides suggest that the peptide-binding groove is very versatile, accounting for the broad peptide-binding specificity of hsp70s. The interactions of hsp70hom and PB74 with peptides were investigated using plate binding assays and isothermattitration calorimetry. A biotinylated peptide bound to the peptide-binding domain of hsp70hom, immobilised in plastic wells, with a Kd of <25 μM, which is within the range of Kds reported for other hsp70-peptide complexes (0.1-100 μM). In solution, isothermal titration calorimetry showed that the binding of peptides to the peptide-binding domains of hsp70hom and PBP74 was likely to be entropically rather than enthalpically driven, and, therefore, the interactions involved are likely to be predominantly hydrophobic. Secondly, PBP74, an hsp70 thought to be involved in the class II antigen processing pathway in endosomes, was localised by immunofluorescence microscopy. It was shown to be a mitochondrial protein, and is, therefore, unlikely to be involved in antigen processing. The presence of other members of the hsp70 family in lysosomes purified from a B cell line by Percoll density gradient centrifugation was investigated using antibodies that reacted with many Afferent members of the hsp70 family. No hsp70s were detected in these late endocytic compartments, even after heat shock or serum starvation. However, the presence of an hsp70 in endosomes, or of a member of this family not detected by the antibodies used, in lysosomes, cannot be ruled out. A third approach investigated the induction of the three hsp70 genes found in the MHC by four cytokines. The hsp70-l and hsp70-2 genes are induced at the mRNA level by IFN-γ and IL- 1, while TNF induces hsp70-2 alone. This data supports a role for the heat-inducible hsp70 in MHC class I antigen processing, as it appears to be coregulated with known members of this antigen processing pathway. The expression of hsp70hom was unaffected by any of the four cytokines examined. In addition, the mitochondrial hsp70 (which is not encoded in the MHC) appears to be induced by IFN-γ at the protein level. The research presented in this thesis provides a greater understanding of the peptide-binding properties of two hsp70s. Further work is necessary to show conclusively whether any of the hsp70s is involved in antigen processing.
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Farfán, Arribas Diego José. "On the Source of Peptides for Major Histocompatibility Class I Antigen Presentation: A Dissertation." eScholarship@UMMS, 2012. https://escholarship.umassmed.edu/gsbs_diss/589.

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Peptides generated from cellular protein degradation via the ubiquitin-proteasome pathway are presented on MHC class I as a means for the immune system to monitor polypeptides being synthesized by cells. For CD8 + T cells to prevent the spread of an incipient infection, it appears essential they should be able to sense foreign polypeptides being synthesized as soon as possible. A prompt detection of viral proteins is of great importance for the success of an adaptive immune response. Defective ribosomal products (DRiPs) have been postulated as a preferential source which would allow for a rapid presentation of peptides derived from the degradation of all newly synthesized proteins. Although this hypothesis is intellectually appealing there is lack of experimental data supporting a mechanism that would prioritize presentation from DRiPs. In this dissertation I describe a series of experiments that probe the DRiPs hypothesis by assessing the contribution to class I presentation of model epitopes derived from DRiPs or from functional proteins. The results show that even at the early stages after mRNA synthesis DRiPs do not account for a significant fraction of the class I presented peptides. These observations suggest that the currently widespread model whereby a mechanism exists which selectively allows for DRiPs to preferentially contribute to class I antigen presentation, is incorrect. Rather, properly folded functional proteins can significantly contribute to class I antigen presentation as they are normally turned over by the ubiquitin-proteasome pathway.
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Lenz, Laurel L. "Presentation of formylated bacterial peptides to cytotoxic T cells by an MHC class Ib molecule /." Thesis, Connect to this title online; UW restricted, 1998. http://hdl.handle.net/1773/8339.

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Thomas, Lawrence James. "Proteolytic Cleavages of Molecules Involved in Antigen Processing and Presentation: A Thesis." eScholarship@UMMS, 1989. https://escholarship.umassmed.edu/gsbs_diss/97.

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The overall goal of my thesis research was to understand better the mechanisms that control antigen processing and presentation by class II MHC molecules. Towards this goal I investigated ways in which the physical structure and post-translational modifications of the class II MHC alpha and beta chains and associated molecules might serve to regulate antigen processing and presentation. Specifically, I investigated (1) a hypothesis that Ii might aid binding of foreign antigenic peptides to the class II MHC foreign antigen binding site (desetope), and the application of this hypothesis to the prediction of class II-presented peptides; (2) the proteolytic cleavage of Ii to p25; (3) the proteolytic cleavage of the class II MHC alpha and beta chains, and (4) the phosphorylation of Iiand the alpha and beta chains. In exploring the hypothesis that amphipathic alpha helical peptides digested from foreign antigen, bind to the class II MHC desetope, to be presented to T cell receptors, we found such an extended, amphipathic helix in Ii (Phe146-Val164). A hypothesis was developed that this amphipathic alpha helix of Ii bound to the desetope of class II MHC molecules, and remained there from time of synthesis until catalyzing the charging of the desetope with a foreign peptide. This region of Iicould then be considered to be the prototypic T cell-presented peptide and the "strip-of-helix" algorithm was developed to search the sequences of proteins for similar amphipathic alpha helices. Such peptides might bind to the class II MHC desetope and have a high probability to be presented to the T cell. The strip-of-helix algorithm calculated the mean hydrophobicity (from Kyte-Doolittle values; Kyte and Doolittle, 1982) of sets of amino acids in axial strips down sides of helices for 3 to 6 turns, at positions n, n+4, n+7, n+11, n+14, and n+18. Peptides correlating well with T cell responsiveness had: (1) 12 to 19 amino acids (4-6 turns of an alpha helix), (2) a strip with highly hydrophobic residues, (3) adjacent, moderately hydrophilic strips, and (4) no prolines to break the helix. This algorithm predicted 10 of 12 T cell-presented peptides in 7 well-studied proteins. In a study of the post-translational modifications of Ii, an early proteolytic pathway of the destruction of Ii, resulting in the generation of p25, was described. This 25,000 dalton protein, seen in immunoprecipitates with antibodies to class II MHC molecules or to Ii, was shown to be a C-termina1 fragment of a high mannose form of Ii. The evidence for this conclusion includes the following results. [35S]methionine-1abe1ed Ii and associated molecules were immunoprecipitated, denatured, resolubi1ized and subjected to a second immunoprecipitation with various antibodies. Two antisera to C-termina1 peptides of Ii (183-193 and 192-211), but not an antiserum to an N-termina1 peptide (12-28), immunoprecipitated p25. A monoclonal antibody (mAb) to Ii immunoprecipitated [35S]methionine-1abe1ed p25 but not [35S]cysteine-1abe1ed p25, consistent with the loss of a portion of Ii containing the only cysteine in Ii, Cys28. [35S]methionine pulse-chase labeling demonstrated the maximal appearance of p25 at 20-40 min chase times. p25 molecules were reduced to about 10.5 kD by treatment with endoglycosidases F and H. p25 was, therefore, generated from a high mannose form of Ii in the ER or cis-Golgi. This finding could either implicate that site for class II MHC desetope charging with foreign peptides or reflect a mechanism for degradation of "excess" Ii molecules in the ER. Digestion of class II MHC antigen-Ii complexes with various proteases yielded fragments, migrating at and near p25 in 2-D electrophoretic gels, which were relatively resistant to further digestion. This observation was consistent with the presence of relatively protease-resistant secondary structures (domains) and a relatively protease-sensitive (IgG hinge-like) region in Iinear its insertion into the membrane. In a study of the post-translational modifications of the class II MHC alpha and beta chains, well conserved pairs of basic amino acids in the sequences of these molecules were observed. It was hypothesized these could be sites for proteolytic cleavage, as precedented in other systems (i.e.proinsulin processing). These potential cleavage sites fall in significant locations with respect to the deduced structure of the class II MHC desetope, supporting the hypothesis that these cleavages might either aid or destroy antigen presenting functions. To test this hypothesis we looked for remnant polypeptides of the alpha and beta chains. Polypeptides were observed in gels of immunoprecipitated class II MHC complexes. To identify if such polypeptides were derived from the alpha and beta chains, immunoblotting to electrotransferred polypeptides was attempted, with antisera made to synthesized peptides that mimicked eight regions of the alpha and beta chains. These antisera were produced and characterized by dot blotting, ELISA, western blotting, and immunoprecipitation of native and denatured material. One antiserum, to an alpha chain peptide (77-88), blotted to a polypeptide immunoprecipitated by anti-class II MHC antiserum. This observation supported the hypothesis that the alpha and beta chains undergo proteolytic cleavages, possibly in the control of antigen presentation. It was also demonstrated that Ii and the alpha and beta chains can be phosphorylated under varying culture conditions, but this project was not pursued.
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Parshotam, L. E. "Dynamic modelling of the processing of peptides for presentation on major histocompatibility complex class I proteins." Thesis, University College London (University of London), 2017. http://discovery.ucl.ac.uk/1559176/.

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Antigen presentation is broadly implicated in disease and represents an important target for prophylactic and therapeutic treatments. A better understanding of the components of this system is fundamental to our understanding of disease path- ways and to treatment design. This thesis focuses on modelling the processing of peptides by enzymes in the cytosol and in the endoplasmic reticulum (ER) in the context of major histocompatibility complex class I (MHC) antigen presentation, and expounds upon current knowledge of the mechanistic details and specificity of both the proteasome and the endoplasmic reticulum aminopeptidase-1 (ERAP1). We use nonlinear ordinary differential equations to model the biochemical reaction pathways of amino-terminal peptide trimming by ERAP1 and distinguish parameter dependencies of two prevailing theories for the mechanism of ERAP1 trimming us- ing algebraic and numerical analysis. Importantly, we show that ERAP1 has a role in peptide optimisation when MHC acts as a template, but not when it trims free peptide using an internal molecular ruler. We present testable hypotheses that may elucidate the dominant trimming mechanism used by ERAP1 in vivo, which has been the subject of debate for more than 25 years. We show that all ERAP1 trimming mechanism hypotheses are able to predict the qualitative distribution of cell surface presentation of SIINFEKL derived from amino-terminally extended precursors. Notably, we find that the molecular ruler trimming mechanism is more robust than the MHC-as-template mechanism. Finally, we use neural networks to predict carboxyl-terminal cleavage by the proteasome, and demonstrate that we are able to distinguish between cleavage and non-cleavage sites on an unseen set of known peptide epitopes. Overall, this thesis contributes a more thorough quantitative and mechanistic understanding of the generation of peptides presented on MHC class I molecules.
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Eccleston, Ruth Charlotte. "A mechanistic model predicting cell surface presentation of peptides by MHC class I proteins, considering peptide competition, viral intracellular kinetics and host genotype factors." Thesis, University College London (University of London), 2017. http://discovery.ucl.ac.uk/10038760/.

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Major histocompatability complex class I (MHC-I) proteins present short fragments of pathogenic or cancerous proteins (peptides) on the surface of infected cells for recognition by T lymphocytes which are stimulated upon recognition of foreign peptides. Due to the diversity of peptide sequences and the sequence-specificity of MHC-I alleles, being able to determine which peptides will be presented by which MHC-I alleles and in what proportion could be important for the development of vaccines and treatments based on the presented peptiodome. Machine learning tools, trained on experimental data, are widely used to predict immunogenic peptides. However they are unable to account for the impact the intracellular kinetics of the pathogenic or cancerous protein which will greatly influence the resultant peptidome. Here we describe a mechanistic model of peptide presentation, validated against experimental data, which accounts for intracellular peptide concentration, and can predict the relative cell surface presentation of competing peptides with varying affinities for MHC-I proteins. We demonstrate how combining this mechanistic model with the intracellular kinetics of HIV proteins can provide insight in to the experimentally reported immunogenicity of the viral protein Gag, and show how such a model can be used to predict the most abundant viral peptides presented on the cell surface. Similarly, we predict the HeLa cell peptidome and demonstrate how a simple metric can be used to approximate the abundance of a peptide based solely on protein synthesis and degradation, peptide-MHC affinity and proteasomal cleavage.
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McMurtrey, Curtis Paul. "Human leukocyte antigen class I presentation and immune recognition of West Nile virus peptide epitopes." Oklahoma City : [s.n.], 2009.

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Schirmacher, Anastasiya. "Modification of transmembrane peptides to probe SNARE-induced membrane fusion and cross-presentation of membrane-buried epitopes." Doctoral thesis, Niedersächsische Staats- und Universitätsbibliothek Göttingen, 2020. http://hdl.handle.net/21.11130/00-1735-0000-0005-1576-F.

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Books on the topic "Presentation of peptides"

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Z, Atassi M., and Abbott Laboratories, eds. Immunobiology of proteins and peptides IV: T-cell recognition and antigen presentation. New York: Plenum Press, 1987.

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F, Lüscher Thomas, ed. The endothelium in cardiovascular disease: Pathophysiology, clinical presentation, and pharmacotherapy. Berlin: Springer, 1995.

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Atassi, M. Zouhair, and Howard L. Bachrach. Immunobiology of Proteins and Peptides IV: T-Cell Recognition and Antigen Presentation. Springer London, Limited, 2012.

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Atassi, M. Zouhair. Immunobiology of Proteins and Peptides Iv: T-Cell Recognition And Antigen Presentation. Springer, 2012.

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Lüscher, Thomas F. Endothelium in Cardiovascular Disease: Pathophysiology, Clinical Presentation and Pharmacotherapy. Springer London, Limited, 2011.

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Luscher, Thomas F. The Endothelium in Cardiovascular Disease: Pathophysiology, Clinical Presentation and Pharmacotherapy. Springer-Verlag Telos, 1995.

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Luscher, Thomas F. The Endothelium in Cardiovascular Disease: Pathophysiology, Clinical Presentation, and Pharmacology. Springer-Verlag, 1995.

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Levy, David. Presentation and early clinical course. Oxford University Press, 2016. http://dx.doi.org/10.1093/med/9780198766452.003.0002.

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The clinical importance of taking care with diagnostic terms for Type 1 diabetes and the need to avoid obsolete and confusing names. Clinical features at presentation of Type 1 diabetes, and features that differentiate it from later-onset autoimmune diabetes (LADA). The persistently high rate of presentation in diabetic ketoacidosis and its likely neuropsychiatric consequences. Key features of complex cases of DKA and current management strategies. The controversy over which subcutaneous insulin regimens to use after resolution of DKA. Definitions of and factors associated with partial remission (‘honeymoon’). Establishing good glycaemic control shortly after diagnosis probably preserves C-peptide levels.
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van der Vlag, Johan, and Jo H. M. Berden. The patient with systemic lupus erythematosus. Edited by Giuseppe Remuzzi. Oxford University Press, 2015. http://dx.doi.org/10.1093/med/9780199592548.003.0161.

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Systemic lupus erythematosus (SLE) is a systemic autoimmune disease with various clinical manifestations. The hallmark of SLE is the presence of antibodies against nuclear constituents, such as double-stranded (ds)DNA, histones, and nucleosomes. Local deposition of antinuclear antibodies in complex with nuclear autoantigens induces serious inflammatory conditions that can affect several tissues and organs, including the kidney.The levels of antinucleosome and anti-dsDNA antibodies seem to correlate with glomerulonephritis and these autoantibodies can often be detected years before the patient is diagnosed with SLE. Apoptotic debris is present in the extracellular matrix and circulation of patients with SLE due to an aberrant process of apoptosis and/or insufficient clearance of apoptotic cells and apoptotic debris. The non-cleared apoptotic debris in patients with SLE may lead to activation of both the innate (myeloid and plasmacytoid dendritic cells) and adaptive (T and B cells) immune system. In addition to the activation by apoptotic debris and immune complexes, the immune system in SLE may be deregulated at the level of (a) presentation of self-peptides by antigen-presenting cells, (b) selection processes for both B and T cells, and (c) regulatory processes of B- and T-cell responses. Lupus nephritis may be classified in different classes based on histological findings in renal biopsies. The chromatin-containing immune complexes deposit in the capillary filter, most likely due to the interaction of chromatin with the polysaccharide heparan sulphate. A decreased renal expression of the endonuclease DNaseI further contributes to the glomerular persistence of chromatin and the development of glomerulonephritis.Current treatment of lupus nephritis is not specific and aims to reduce the inflammatory response with general immunosuppressive therapies. However, research has revealed novel potential therapeutic candidates at the level of dendritic cells, B cells, and T cells.
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Book chapters on the topic "Presentation of peptides"

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Wittmann, Valentin, and Sonja Seeberger. "Spatial Screening of Lectin Ligands. Cyclic Peptides as Scaffolds for Multivalent Presentation of Carbohydrates." In Peptides: The Wave of the Future, 174–76. Dordrecht: Springer Netherlands, 2001. http://dx.doi.org/10.1007/978-94-010-0464-0_78.

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Pierce, Susan K., Ellen K. Lakey, Emanuel Margoliash, Lori A. Smolenski, and Lisa A. Casten. "The Presentation of Processed, Ia Restricted, T Cell Antigenic Peptides on Antigen Presenting Cell Surfaces." In H-2 Antigens, 485–92. Boston, MA: Springer US, 1987. http://dx.doi.org/10.1007/978-1-4757-0764-9_48.

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Janeway, C. A., P. Preston-Hurlburt, B. Al-Ramadi, J. Rothbard, D. B. Murphy, E. P. Reich, and A. Y. Rudensky. "Rules for the Presentation of Peptides by Class II Molecules of the Major Histocompatibility Complex." In Progress in Immunology Vol. VIII, 181–88. Berlin, Heidelberg: Springer Berlin Heidelberg, 1993. http://dx.doi.org/10.1007/978-3-642-51479-1_24.

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Forquet, Frédérique, Ursula Danilczyk, Ying Lang, and Terry L. Delovitch. "Interactions between Peptides and Major Histocompatibility Complex Molecules during Antigen Processing and Presentation (Part 1 of 2)." In Chemical Immunology and Allergy, 63–75. Basel: KARGER, 1993. http://dx.doi.org/10.1159/000319181.

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Forquet, Frédérique, Ursula Danilczyk, Ying Lang, and Terry L. Delovitch. "Interactions between Peptides and Major Histocompatibility Complex Molecules during Antigen Processing and Presentation (Part 2 of 2)." In Chemical Immunology and Allergy, 76–87. Basel: KARGER, 1993. http://dx.doi.org/10.1159/000319182.

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Momburg, Frank, Günter J. Hämmerling, and Jacques J. Neefjes. "TAP Peptide Transporters and Antigen Presentation." In MHC Molecules: Expression, Assembly and Function, 35–63. Boston, MA: Springer US, 1996. http://dx.doi.org/10.1007/978-1-4684-6462-7_3.

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Haug, Markus, Günther E. Dannecker, and Ursula Holzer. "Impact of HSP-Chaperoned Peptides on the MHC Class II-Dependent Presentation and Activation of CD4+ T Cells in Regard of Allo- and Autoantigens." In Heat Shock Proteins: Potent Mediators of Inflammation and Immunity, 275–88. Dordrecht: Springer Netherlands, 2007. http://dx.doi.org/10.1007/978-1-4020-5585-0_17.

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van Bleek, Grada M., and Stanley G. Nathenson. "Peptide Presentation by Major Histocompatibility Class I Molecules." In Chemical Immunology and Allergy, 1–17. Basel: KARGER, 1993. http://dx.doi.org/10.1159/000319173.

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Jung, Günther. "Peptide presentation by major histocompatibility complex-class I and in vivo induction of cytotoxic T-lymphocytes." In Peptide Chemistry 1992, 627–31. Dordrecht: Springer Netherlands, 1993. http://dx.doi.org/10.1007/978-94-011-1474-5_180.

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Compagnone, Mirco, and Doriana Fruci. "Peptide Trimming for MHC Class I Presentation by Endoplasmic Reticulum Aminopeptidases." In Antigen Processing, 45–57. New York, NY: Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-9450-2_4.

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Conference papers on the topic "Presentation of peptides"

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Tian, Fei, Fan Yang, and Junfeng Liang. "Lab-on-fiber optofluidic platform for in-situ study of therapeutic peptides and bacterial response (Rising Researcher Presentation) (Conference Presentation)." In Smart Biomedical and Physiological Sensor Technology XIV, edited by Brian M. Cullum, Eric S. McLamore, and Douglas Kiehl. SPIE, 2017. http://dx.doi.org/10.1117/12.2262923.

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Jiang, Yang, Jing Chen, Danielle K. Turgeon, Joel H. Rubenstein, Thomas D. Wang, and Eric J. Seibel. "Quantification of multiplexed fluorescence peptides in human esophagus for early cancer detection (Conference Presentation)." In Endoscopic Microscopy XIV, edited by Melissa J. Suter, Guillermo J. Tearney, and Thomas D. Wang. SPIE, 2019. http://dx.doi.org/10.1117/12.2511815.

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Long, S. Randolph, and Chih-Cong Chou. "Laser Desorption/Ionization Mass Spectrometry of Biological Materials." In Laser Applications to Chemical Analysis. Washington, D.C.: Optica Publishing Group, 1992. http://dx.doi.org/10.1364/laca.1992.pd5.

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The detection, identification, and analysis of biological materials in "real time" is of significant current interest in a number of fields. As with chemical materials, mass spectrometry holds great promise for such applications. We are presently engaged in a study of approaches to mass spectrometric analysis of biological materials, utilizing laser desorption/vaporization/ionization in conjunction with Fourier transform mass spectrometry. In this presentation, we focus on laser desorption/ionization applied to peptides. Although laser desorption can generate mass spectra with reasonably abundant molecular ion for relatively small peptides in the pure state, use of matrix-enhanced desorption techniques facilitates greatly the generation of molecular ion, We demonstrate this using examples of 248 nm laser desorption mass spectra of polypeptides. The nature of the substrate from which ions are desorbed is found also to be an important factor in the desorption/fragmentation processes through a study of a range of metallic supports. Thermal conductivity of the substrate appears to be the key parameter.
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Taylor, Phillip. "Computational design of collagen-like-peptides (CLP) for desired CLP triple helix melting transition and assembled structure." In Proposed for presentation at the 2022 CINT Annual User Conference held September 20-22, 2022 in Albuquerque , NM. US DOE, 2022. http://dx.doi.org/10.2172/2004798.

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Chan, Warren C. W. "Elucidating the Interactions of Nanomaterials With Biological Systems." In ASME 2010 First Global Congress on NanoEngineering for Medicine and Biology. ASMEDC, 2010. http://dx.doi.org/10.1115/nemb2010-13377.

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Nanotechnology is a rapidly growing research fields with many applications in biology and medicine. At a heart of nanotechnology research is engineered nanostructures, which possess distinct optical, electronic, and magnetic properties based on their size, shape, and chemical composition. Researchers can now design their surface chemistry with small bi-functional organic molecules or amphiphillic polymers so that they are biocompatible and can be coated with bio-recognition molecules such as antibodies, aptamers, and peptides. Nanoparticles are used as a platform for drug delivery, as a physical trigger for controlling drug release, as a contrast agent for quantifying biological molecules. Thus, the applications of engineered nanostructures are diverse. In this presentation, an overview of the field of nanomedicine is described with an emphasis on results obtained from studying the in vivo interactions of nanostructures as it pertains to their applications in cancer.
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Vicente, M. Graca H. "EGFR-targeted photosensitizer-peptide conjugates (Conference Presentation)." In 17th International Photodynamic Association World Congress, edited by Tayyaba Hasan. SPIE, 2019. http://dx.doi.org/10.1117/12.2528197.

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Hochbaum, Allon. "Bioinspired design of conductive peptide nanofibers (Conference Presentation)." In Organic and Hybrid Sensors and Bioelectronics XI, edited by Ruth Shinar, Ioannis Kymissis, Luisa Torsi, and Emil J. List-Kratochvil. SPIE, 2018. http://dx.doi.org/10.1117/12.2322688.

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Ashkenasy, Nurit. "Peptide based supramolecular materials for transient electronics (Conference Presentation)." In Organic and Hybrid Sensors and Bioelectronics XV, edited by Ruth Shinar, Ioannis Kymissis, and Emil J. List-Kratochvil. SPIE, 2022. http://dx.doi.org/10.1117/12.2633402.

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Borum, Raina, Matthew N. Creyer, Yu-Ci Chang, and Jesse V. Jokerst. "Self-assembled peptide-dye nanoparticles for targeted photoacoustic tumor imaging (Conference Presentation)." In Reporters, Markers, Dyes, Nanoparticles, and Molecular Probes for Biomedical Applications XIV, edited by Ramesh Raghavachari and Mikhail Y. Berezin. SPIE, 2023. http://dx.doi.org/10.1117/12.2650751.

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Zhang, Zhihong, Lisen Lu, Yuan Qian, Sha Qiao, and Qingming Luo. "Targeting delivery of nanovaccine/nanoimmunomudulator based on peptide-lipid nanoparticle for immunotherapy in vivo (Conference Presentation)." In Biophotonics and Immune Responses XIV, edited by Wei R. Chen. SPIE, 2019. http://dx.doi.org/10.1117/12.2507601.

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Reports on the topic "Presentation of peptides"

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Waqas, Muhammad Talha. Leveraging Machine Learning to Predict Peptide Presentation by MHC Proteins: A Comprehensive Research Analysis. ResearchHub Technologies, Inc., April 2024. http://dx.doi.org/10.55277/researchhub.nic100aw.

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