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Journal articles on the topic 'Peptide binding'

Author: Grafiati

Published: 4 June 2021

Last updated: 6 September 2023

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1

New, Roger R. C., Tam T. T. Bui, and Michal Bogus. "Binding Interactions of Peptide Aptamers." Molecules 25, no. 24 (2020): 6055. http://dx.doi.org/10.3390/molecules25246055.

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Peptide aptamers are short amino acid chains that are capable of binding specifically to ligands in the same way as their much larger counterparts, antibodies. Ligands of therapeutic interest that can be targeted are other peptide chains or loops located on the surface of protein receptors (e.g., GCPR), which take part in cell-to-cell communications either directly or via the intermediary of hormones or signalling molecules. To confer on aptamers the same sort of conformational rigidity that characterises an antibody binding site, aptamers are often constructed in the form of cyclic peptides,

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2

Smith, K. D., B. E. Mace, A. Valenzuela, et al. "Probing HLA-B7 conformational shifts induced by peptide-binding groove mutations and bound peptide with anti-HLA monoclonal antibodies." Journal of Immunology 157, no. 6 (1996): 2470–78. http://dx.doi.org/10.4049/jimmunol.157.6.2470.

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Abstract To determine the influence of peptide-binding groove residues and MHC-bound peptide on HLA-B7 conformation, we investigated the binding sites of nine locus- or allele-specific mAbs using a panel of 82 HLA-B7 variants. The functional mAb epitopes encircle the HLA-B7 peptide-binding groove. Three mAbs are affected by mutations at solvent-accessible peptide-binding groove mutations. Mutations in peptide-binding groove residues 45, 63, and 150 affect multiple nonoverlapping mAb epitopes, probably by interaction with other MHC residues or bound peptide. However, 18 of 24 peptide-binding gr

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3

Nguyen, Andrea T., Christopher Szeto, and Stephanie Gras. "The pockets guide to HLA class I molecules." Biochemical Society Transactions 49, no. 5 (2021): 2319–31. http://dx.doi.org/10.1042/bst20210410.

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Human leukocyte antigens (HLA) are cell-surface proteins that present peptides to T cells. These peptides are bound within the peptide binding cleft of HLA, and together as a complex, are recognised by T cells using their specialised T cell receptors. Within the cleft, the peptide residue side chains bind into distinct pockets. These pockets ultimately determine the specificity of peptide binding. As HLAs are the most polymorphic molecules in humans, amino acid variants in each binding pocket influences the peptide repertoire that can be presented on the cell surface. Here, we review each of t

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Nijenhuis, M., S. Schmitt, E. A. Armandola, R. Obst, J. Brunner, and G. J. Hämmerling. "Identification of a contact region for peptide on the TAP1 chain of the transporter associated with antigen processing." Journal of Immunology 156, no. 6 (1996): 2186–95. http://dx.doi.org/10.4049/jimmunol.156.6.2186.

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Abstract The transporter associated with Ag processing (TAP) translocates cytosolic peptides into the endoplasmic reticulum for presentation by MHC class 1 molecules. Recently, the actual peptide translocation step has been suggested to be preceded by binding of the peptide to TAP. In this study, we investigated the peptide binding site of TAP and its relevance for peptide selection by cross-linking of translocatable peptides. Our data demonstrate, first, that for a TAP heterodimer containing the rat TAPu allelic product, which selects peptides on basis of their C terminus, the translocation e

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5

Wang, P., G. Gyllner, and S. Kvist. "Selection and binding of peptides to human transporters associated with antigen processing and rat cim-a and -b." Journal of Immunology 157, no. 1 (1996): 213–20. http://dx.doi.org/10.4049/jimmunol.157.1.213.

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Abstract Cytotoxic T lymphocytes recognize antigenic peptides presented by MHC class I molecules. The peptides are generated in the cytosol by proteasomes, and probably also other proteases, and are then translocated into the endoplasmic reticulum (ER) lumen. The transporters associated with Ag processing (TAP) are key molecules for transporting peptides from the cytosol to the lumen of the ER. Using semipermeabilized cells, TAP-dependent peptide translocation was demonstrated, and the selectivity of peptide translocation was based on the carboxyl-terminal amino acid of peptides. We have exami

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6

Tussey, L. G., M. Matsui, S. Rowland-Jones, R. Warburton, J. A. Frelinger, and A. McMichael. "Analysis of mutant HLA-A2 molecules. Differential effects on peptide binding and CTL recognition." Journal of Immunology 152, no. 3 (1994): 1213–21. http://dx.doi.org/10.4049/jimmunol.152.3.1213.

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Abstract Previous studies have identified several residues lining the groove of the HLA-A2.1 molecule that are critical for Ag presentation. However, it is not clear whether these residues are critical for binding of the peptide epitope per se or for determining the appropriate conformation of bound peptide. To distinguish between these possibilities, mutations at eight of these residues have been tested for their effects on the ability of the molecule to bind and present two known peptide epitopes--one derived from the influenza A matrix protein, the other from HIV pol. With only one exceptio

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7

McNicholl, J. M., W. C. Whitworth, F. Oftung, et al. "Structural requirements of peptide and MHC for DR(alpha, beta 1*0401)-restricted T cell antigen recognition." Journal of Immunology 155, no. 4 (1995): 1951–63. http://dx.doi.org/10.4049/jimmunol.155.4.1951.

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Abstract We identified functionally important regions of the DR(alpha, beta 1*0401) peptide binding site and present a model of bound peptide. DR(alpha, beta 1*0401)-restricted T cell recognition and peptide binding of Mycobacterium leprae (ML) peptide 38-50 and overlapping peptides from the 18-kDa heat-shock protein were analyzed. ML38-50 is unusual in its restricted binding pattern, binding to only one of five DR4 subtypes and no other DR molecules tested. Amino acid substitutions were introduced into ML38-50 and the DR(alpha, beta 1*0401) peptide binding site at positions likely to influenc

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8

Choppin, J., F. Martinon, E. Gomard, et al. "Analysis of physical interactions between peptides and HLA molecules and application to the detection of human immunodeficiency virus 1 antigenic peptides." Journal of Experimental Medicine 172, no. 3 (1990): 889–99. http://dx.doi.org/10.1084/jem.172.3.889.

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The physical association of 40 antigenic peptides and purified HLA class I and class II molecules was monitored using a direct peptide binding assay (PBA) in solid phase and an inhibition peptide binding assay (IPBA) in which the competing peptide was present in a soluble phase. We also examined the ability of different peptides to inhibit the lytic activity of human antiviral cytolytic T cells towards cells incubated with the corresponding target peptide. Our results showed that: (a) Binding of a given human T cell-recognized peptide to several HLA class I and class II molecules occurred freq

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9

Kaveri, S. V., C. Y. Kang, and H. Köhler. "Natural mouse and human antibodies bind to a peptide derived from a germline VH chain. Evidence for evolutionary conserved self-binding locus." Journal of Immunology 145, no. 12 (1990): 4207–13. http://dx.doi.org/10.4049/jimmunol.145.12.4207.

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Abstract Murine antibodies derived from the V1 S107/T15 germline structure combined with Vk 22 L chains express the property of self-binding. Previous studies have shown that the self-binding is mediated by the Fab fragment involving structures of the hapten binding site. The molecular locus of self-binding has also been identified by showing that a peptide derived from the CDR2/FR3 region of the V1 S107 H chain inhibits self-binding. We have addressed the question of whether self-binding antibodies interact with peptides that inhibit self-binding. We found that labeled TEPC15 (T15) binds to i

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10

Ojcius, D. M., J. P. Abastado, A. Casrouge, E. Mottez, L. Cabanie, and P. Kourilsky. "Dissociation of the peptide-MHC class I complex limits the binding rate of exogenous peptide." Journal of Immunology 151, no. 11 (1993): 6020–26. http://dx.doi.org/10.4049/jimmunol.151.11.6020.

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Abstract Soluble, single-chain molecules for two MHC class I alleles, H-2Kd and H-2Kb, were used to analyze the kinetics of antigenic peptide binding to MHC. After MHC preloading with radiolabeled or fluorescent peptides, the observed rate of MHC-peptide complex dissociation increased after addition of an excess of unlabeled competitor peptide. Although exogenous peptides conforming to the allele-specific motif were required for the enhanced complex dissociation to occur, the dissociation rate of the complex was independent of exogenous peptide concentration. Similarly, the association rate of

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11

Simon, Ágnes, Csaba Magyar, László Héja, and Julianna Kardos. "Peptide Binding Sites of Connexin Proteins." Chemistry 2, no. 3 (2020): 662–73. http://dx.doi.org/10.3390/chemistry2030042.

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Intercellular gap junction (GJ) contacts formed by the coupling of connexin (Cx) hemichannels (HCs) embedded into the plasma membranes of neighboring cells play significant role in the development, signaling and malfunctions of mammalian tissues. Understanding and targeting GJ functions, however, calls for finding valid Cx subtype-specific inhibitors. We conjecture the lack of information about binding interactions between the GJ interface forming extracellular EL1 and EL2 loops and peptide mimetics designed to specifically inhibit Cx43HC coupling to Cx43GJ. Here, we explore active spots at th

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12

Gaseitsiwe, Simani, Davide Valentini, Raija Ahmed, et al. "Major Histocompatibility Complex Class II Molecule-Human Immunodeficiency Virus Peptide Analysis Using a Microarray Chip." Clinical and Vaccine Immunology 16, no. 4 (2009): 567–73. http://dx.doi.org/10.1128/cvi.00441-08.

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ABSTRACT Identification of major histocompatibility complex (MHC) class II binding peptides is a crucial step in rational vaccine design and immune monitoring. We designed a novel MHC class II molecule-peptide microarray binding assay and evaluated 346 peptides from already identified human immunodeficiency virus (HIV) epitopes and an additional set (n = 206) of 20-mer peptides, overlapping by 15 amino acid residues, from HIV type 1B (HIV-1B) gp160 and Nef as a paradigm. Peptides were attached via the N-terminal part to a linker that covalently binds to the epoxy glass slide. The 552 peptides

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13

VanVolkenburg, M. A., N. D. Griggs, M. A. Jarpe, J. L. Pace, S. W. Russell, and H. M. Johnson. "Binding site on the murine IFN-gamma receptor for IFN-gamma has been identified using the synthetic peptide approach." Journal of Immunology 151, no. 11 (1993): 6206–13. http://dx.doi.org/10.4049/jimmunol.151.11.6206.

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Abstract We have studied the structural parameters involved in the binding of murine IFN-gamma (MuIFN-gamma) to its receptor. Ten synthetic overlapping peptides corresponding to the extracellular domain of the MuIFN-gamma receptor (MuIFN-gamma R) were synthesized. In direct binding studies, biotinylated MuIFN-gamma bound specifically to receptor peptide (95-120). Further, the NH2-terminal IFN-gamma peptide, MuIFN-gamma (1-39), also specifically bound to receptor peptide (95-120). Binding of both labeled MuIFN-gamma and MuIFN-gamma (1-39) to MuIFN-gamma R peptide (95-120) was inhibited by eithe

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14

Blaszczyk, Maciej, Maciej Pawel Ciemny, Andrzej Kolinski, Mateusz Kurcinski, and Sebastian Kmiecik. "Protein–peptide docking using CABS-dock and contact information." Briefings in Bioinformatics 20, no. 6 (2018): 2299–305. http://dx.doi.org/10.1093/bib/bby080.

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Abstract CABS-dock is a computational method for protein–peptide molecular docking that does not require predefinition of the binding site. The peptide is treated as fully flexible, while the protein backbone undergoes small fluctuations and, optionally, large-scale rearrangements. Here, we present a specific CABS-dock protocol that enhances the docking procedure using fragmentary information about protein–peptide contacts. The contact information is used to narrow down the search for the binding peptide pose to the proximity of the binding site. We used information on a single-chosen and rand

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15

Donatan, Senem, Mehmet Sarikaya, Candan Tamerler, and Mustafa Urgen. "Effect of solid surface charge on the binding behaviour of a metal-binding peptide." Journal of The Royal Society Interface 9, no. 75 (2012): 2688–95. http://dx.doi.org/10.1098/rsif.2012.0060.

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Over the last decade, solid-binding peptides have been increasingly used as molecular building blocks coupling bio- and nanotechnology. Despite considerable research being invested in this field, the effects of many surface-related parameters that define the binding of peptide to solids are still unknown. In the quest to control biological molecules at solid interfaces and, thereby, tailoring the binding characteristics of the peptides, the use of surface charge of the solid surface may probably play an important role, which then can be used as a potential tuning parameter of peptide adsorptio

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16

Chen, Ji-Li, Guillaume Stewart-Jones, Giovanna Bossi, et al. "Structural and kinetic basis for heightened immunogenicity of T cell vaccines." Journal of Experimental Medicine 201, no. 8 (2005): 1243–55. http://dx.doi.org/10.1084/jem.20042323.

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Analogue peptides with enhanced binding affinity to major histocompatibility class (MHC) I molecules are currently being used in cancer patients to elicit stronger T cell responses. However, it remains unclear as to how alterations of anchor residues may affect T cell receptor (TCR) recognition. We correlate functional, thermodynamic, and structural parameters of TCR–peptide–MHC binding and demonstrate the effect of anchor residue modifications of the human histocompatibility leukocyte antigens (HLA)–A2 tumor epitope NY–ESO-1157–165–SLLMWITQC on TCR recognition. The crystal structure of the wi

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17

Shimojo, N., W. L. Maloy, R. W. Anderson, W. E. Biddison, and J. E. Coligan. "Specificity of peptide binding by the HLA-A2.1 molecule." Journal of Immunology 143, no. 9 (1989): 2939–47. http://dx.doi.org/10.4049/jimmunol.143.9.2939.

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Abstract The HLA-A2 molecule contains a putative peptide binding site that is bounded by two alpha-helices and a beta-pleated sheet floor. Previous studies have demonstrated that the influenza virus matrix peptide M1 55-73 can sensitize target cells for lysis by HLA-A2.1-restricted virus-immune CTL and can induce CTL that can lyse virus-infected target cells. To assess the specificity of peptide binding by the HLA-A2.1 molecule, we examined the ability of seven variant M1 peptides to be recognized by a panel of M1 55-73 peptide-specific HLA-A2.1-restricted CTL lines. The results demonstrate th

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18

Zajonc, Dirk M. "Unconventional Peptide Presentation by Classical MHC Class I and Implications for T and NK Cell Activation." International Journal of Molecular Sciences 21, no. 20 (2020): 7561. http://dx.doi.org/10.3390/ijms21207561.

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T cell-mediated immune recognition of peptides is initiated upon binding of the antigen receptor on T cells (TCR) to the peptide-MHC complex. TCRs are typically restricted by a particular MHC allele, while polymorphism within the MHC molecule can affect the spectrum of peptides that are bound and presented to the TCR. Classical MHC Class I molecules have a confined binding groove that restricts the length of the presented peptides to typically 8–11 amino acids. Both N- and C-termini of the peptide are bound within binding pockets, allowing the TCR to dock in a diagonal orientation above the MH

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19

Delgado, Julio, Hernando Escobar, David Crockett, Eduardo Reyes-Vargas, and Peter Jensen. "Analysis of the performance of peptide predicting methods using MHC class I peptide sequencing in the C57BL/6 mouse (78.11)." Journal of Immunology 182, no. 1_Supplement (2009): 78.11. http://dx.doi.org/10.4049/jimmunol.182.supp.78.11.

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Abstract MHC class I peptide-binding motifs can defined by sequencing of peptides naturally bound to MHC class I molecules. More recently MHC class I-peptide binding motifs have be defined on the basis of quantitative MHC-peptide binding assays in vitro using peptide libraries. The information on peptide binding motifs obtained using binding assays have been useful to develop numerous bioinformatics-based tools to predict the binding of peptides to MHC class I molecules. To date few studies have analyzed the performance of these bioinformatics tools to predict peptides determined by sequencing

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20

Hörig, Heidi, Aideen C. M. Young, Nicholas J. Papadopoulos, Teresa P. DiLorenzo, and Stanley G. Nathenson. "Binding of Longer Peptides to the H-2Kb Heterodimer Is Restricted to Peptides Extended at Their C Terminus: Refinement of the Inherent MHC Class I Peptide Binding Criteria." Journal of Immunology 163, no. 8 (1999): 4434–41. http://dx.doi.org/10.4049/jimmunol.163.8.4434.

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Abstract MHC class I molecules usually bind short peptides of 8–10 amino acids, and binding is dependent on allele-specific anchor residues. However, in a number of cellular systems, class I molecules have been found containing peptides longer than the canonical size. To understand the structural requirements for MHC binding of longer peptides, we used an in vitro class I MHC folding assay to examine peptide variants of the antigenic VSV 8 mer core peptide containing length extensions at either their N or C terminus. This approach allowed us to determine the ability of each peptide to producti

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21

Nikcevich, K. M., D. Kopielski, and A. Finnegan. "Interference with the binding of a naturally processed peptide to class II alters the immunodominance of T cell epitopes in vivo." Journal of Immunology 153, no. 3 (1994): 1015–26. http://dx.doi.org/10.4049/jimmunol.153.3.1015.

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Abstract T lymphocytes elicited in response to an immunizing Ag usually recognize only one or a few immunodominant peptides. The mechanisms governing this process are poorly understood. This study examines the consequences of peptide competition on immunodominance. Immunization of B10.A mice with the native Staphylococcus aureus nuclease protein primes T cells to the dominant 86-100 peptide presented in association with I-Ek class II molecules. To render the 86-100 peptide incapable of binding to the class II molecule, single amino acid substitutions were introduced in the native Staphylococcu

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22

Boone, Kyle, Aya Kirahm Cloyd, Emina Derakovic, Paulette Spencer, and Candan Tamerler. "Designing Collagen-Binding Peptide with Enhanced Properties Using Hydropathic Free Energy Predictions." Applied Sciences 13, no. 5 (2023): 3342. http://dx.doi.org/10.3390/app13053342.

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Collagen is fundamental to a vast diversity of health functions and potential therapeutics. Short peptides targeting collagen are attractive for designing modular systems for site-specific delivery of bioactive agents. Characterization of peptide–protein binding involves a larger number of potential interactions that require screening methods to target physiological conditions. We build a hydropathy-based free energy estimation tool which allows quick evaluation of peptides binding to collagen. Previous studies showed that pH plays a significant role in collagen structure and stability. Our de

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23

Tabaczewski, P., E. Chiang, M. Henson, and I. Stroynowski. "Alternative peptide binding motifs of Qa-2 class Ib molecules define rules for binding of self and nonself peptides." Journal of Immunology 159, no. 6 (1997): 2771–81. http://dx.doi.org/10.4049/jimmunol.159.6.2771.

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Abstract Studies of naturally processed peptides eluted from membrane-bound and soluble isoforms of murine class Ib Qa-2 molecules determined several features of these ligands, such as the conserved nonameric length and the preferred usage of specific residues at four to six of nine peptide positions. The structural information derived from these studies proved insufficient to distinguish between two interpretations: 1) that Qa-2 are peptide receptors of higher stringency than ordinary class I molecules, and 2) that Qa-2 molecules, like classical class I Ags, bind diverse arrays of peptides. W

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Ting, Yi Tian, Paul W. R. Harris, Gaelle Batot, Margaret A. Brimble, Edward N. Baker, and Paul G. Young. "Peptide binding to a bacterial signal peptidase visualized by peptide tethering and carrier-driven crystallization." IUCrJ 3, no. 1 (2016): 10–19. http://dx.doi.org/10.1107/s2052252515019971.

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Bacterial type I signal peptidases (SPases) are membrane-anchored serine proteases that process the signal peptides of proteins exported via the Sec and Tat secretion systems. Despite their crucial importance for bacterial virulence and their attractiveness as drug targets, only one such enzyme, LepB from Escherichia coli, has been structurally characterized, and the transient nature of peptide binding has stymied attempts to directly visualize SPase–substrate complexes. Here, the crystal structure of SpsB, the type I signal peptidase from the Gram-positive pathogen Staphylococcus aureus, is r

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25

Schönbach, C., M. Ibe, H. Shiga, et al. "Fine tuning of peptide binding to HLA-B*3501 molecules by nonanchor residues." Journal of Immunology 154, no. 11 (1995): 5951–58. http://dx.doi.org/10.4049/jimmunol.154.11.5951.

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Abstract The prerequisites of peptide HLA-B*3501 interactions have been revisited by quantitative peptide binding assays with 190 chemically synthesized peptide possessing two anchor residues corresponding to the HLA-B*3501 peptide motif and a statistical residue-position analysis of binding and nonbinding peptides. According to the peptide motif of HLA-B*3501, aliphatic hydrophobic (Leu, Ile, and Met) or aromatic residues (Tyr and Phe) specify the main anchor at the C terminus, and position 2 renders an auxiliary anchor for proline. The importance of these residues was confirmed as a minimum

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26

Sim, Malcolm John Wyness, Stacy A. Malaker, Ayesha Khan, et al. "Canonical and cross-reactive binding of NK cell inhibitory receptors to HLA-C allotypes is dictated by peptides bound to HLA-C." Journal of Immunology 198, no. 1_Supplement (2017): 222.25. http://dx.doi.org/10.4049/jimmunol.198.supp.222.25.

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Abstract Human NK cell activity is regulated by killer-cell Ig-like receptors (KIR) that bind HLA class I. Combinations of KIR and HLA genotypes are associated with disease, including susceptibility to viral infection and disorders of pregnancy. KIR2DL1 binds group C2 HLA-C (Lys80), while KIR2DL2/3 bind group C1 HLA-C (Asn80). The goal of this study was to determine how the endogenous HLA-C peptide repertoire influences specific binding of inhibitory KIR to HLA-C allotypes. HLA-C*05:01 (C2) and HLA-C*08:02 (C1) have identical sequences apart from the key KIR specificity determining residues at

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Hoerter, John A. H., Joanna Brzostek, Maxim N. Artyomov, et al. "Coreceptor affinity for MHC defines peptide specificity requirements for TCR interaction with coagonist peptide–MHC." Journal of Experimental Medicine 210, no. 9 (2013): 1807–21. http://dx.doi.org/10.1084/jem.20122528.

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Recent work has demonstrated that nonstimulatory endogenous peptides can enhance T cell recognition of antigen, but MHCI- and MHCII-restricted systems have generated very different results. MHCII-restricted TCRs need to interact with the nonstimulatory peptide–MHC (pMHC), showing peptide specificity for activation enhancers or coagonists. In contrast, the MHCI-restricted cells studied to date show no such peptide specificity for coagonists, suggesting that CD8 binding to noncognate MHCI is more important. Here we show how this dichotomy can be resolved by varying CD8 and TCR binding to agonist

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28

Jiang, H., F. A. Robey, and H. Gewurz. "Localization of sites through which C-reactive protein binds and activates complement to residues 14-26 and 76-92 of the human C1q A chain." Journal of Experimental Medicine 175, no. 5 (1992): 1373–79. http://dx.doi.org/10.1084/jem.175.5.1373.

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Studies were initiated to localize the C-reactive protein (CRP) binding site on the collagen-like region (CLR) of C1q. CRP bound preferentially to the A chain of reduced C1q, in contrast to aggregated immunoglobulin G (Agg-IgG), which reacted preferentially with the C chain. A group of C1q A chain peptides, including peptides identical to residues 81-97, 76-92, and 14-26, respectively, were synthesized from predicted binding regions. Peptide 76-92 contained two proximal lysine groups, and peptide 14-26 contained four proximal arginine groups. CRP-trimers and CRP-ligand complexes did not bind t

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Kim, Ellen J., Kannan Natarajan, Lisa F. Boyd, Jiansheng Jiang, Michael G. Mage, and David H. Margulies. "Peptide editing and MHC binding mechanisms of Tapasin and TAP binding protein related, TAPBPR." Journal of Immunology 202, no. 1_Supplement (2019): 177.15. http://dx.doi.org/10.4049/jimmunol.202.supp.177.15.

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Abstract Cell surface major histocompatibility complex class I (MHC-I) molecules play a crucial role in immunity to microbes and tumors by presenting intracellular peptides for recognition by CD8+ T cells. Since the repertoire of bound peptides is crucial to MHC-I stability as well as to T cell and NK cell recognition, the molecular mechanism by which peptides are selectively loaded onto MHC-I molecules is of considerable interest. A key role is played by the well-characterized chaperone tapasin as indicated by reduced cell surface MHC-I levels and altered peptide repertoires in tapasin defici

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Detmers, Frank J. M., Frank C. Lanfermeijer, and Bert Poolman. "Peptides and ATP binding cassette peptide transporters." Research in Microbiology 152, no. 3-4 (2001): 245–58. http://dx.doi.org/10.1016/s0923-2508(01)01196-2.

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Zhang, Zhiwen, Weiguang Zhu, and Thomas Kodadek. "Selection and application of peptide-binding peptides." Nature Biotechnology 18, no. 1 (2000): 71–74. http://dx.doi.org/10.1038/71951.

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Harig, Sabine, Mathias Witzens, Angela M. Krackhardt, et al. "Induction of cytotoxic T-cell responses against immunoglobulin V region–derived peptides modified at human leukocyte antigen–A2 binding residues." Blood 98, no. 10 (2001): 2999–3005. http://dx.doi.org/10.1182/blood.v98.10.2999.

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Abstract Cytotoxic T-lymphocyte (CTL) responses can be generated against peptides derived from the immunoglobulin (Ig) V region in some but not all patients. The main reason for this appears to be the low peptide-binding affinity of Ig-derived peptides to major histocompatibility complex (MHC) class I molecules and their resulting low immunogenicity. This might be improved by conservative amino acid modifications at the MHC-binding residues of the peptides (heteroclitic peptides). In this study, it was found that in 18 Ig-derived peptides, that heteroclitic peptides from the Ig gene with impro

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Nag, B., D. Passmore, S. V. Deshpande, and B. R. Clark. "In vitro maximum binding of antigenic peptides to murine MHC class II molecules does not always take place at the acidic pH of the in vivo endosomal compartment." Journal of Immunology 148, no. 2 (1992): 369–72. http://dx.doi.org/10.4049/jimmunol.148.2.369.

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Abstract Presentation of Ag to the T cell requires binding of specific peptide fragments of the Ag to MHC II molecules. The ability of a peptide to bind to MHC class II appears to be pH dependent. Recent reports indicate that the binding of peptide to MHC class II molecules takes place primarily within an endosomal compartment of the cell at around pH 5. In this study, we have explored the in vitro pH dependence of peptide binding to different haplotypes of murine MHC class II molecules. The binding of peptides to MHC II was analyzed and quantitated by silica gel TLC, using radiolabeled peptid

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DiBrino, M., T. Tsuchida, R. V. Turner, K. C. Parker, J. E. Coligan, and W. E. Biddison. "HLA-A1 and HLA-A3 T cell epitopes derived from influenza virus proteins predicted from peptide binding motifs." Journal of Immunology 151, no. 11 (1993): 5930–35. http://dx.doi.org/10.4049/jimmunol.151.11.5930.

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Abstract The potential value of peptide binding motifs of HLA class I molecules for the prediction of viral epitopes presented to T cells has been analyzed for two common HLA alleles. CTL generated against type A influenza virus recognize peptide epitopes derived from the nucleoprotein (NP) and basic polymerase 1 presented by HLA-A1, and epitopes derived from NP presented by HLA-A3. Distinct peptide binding motifs with characteristic anchor residues were previously identified for each of these class I molecules based on the sequences of endogenous peptides: for HLA-A1, position 3 = Asp or Glu

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Chicz, R. M., D. F. Graziano, M. Trucco, J. L. Strominger, and J. C. Gorga. "HLA-DP2: self peptide sequences and binding properties." Journal of Immunology 159, no. 10 (1997): 4935–42. http://dx.doi.org/10.4049/jimmunol.159.10.4935.

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Abstract Although self peptides bound to HLA-DQ and, especially, HLA-DR allotypes have been described in some detail, few ligands that bind to HLA-DP have been identified. Toward this aim, naturally processed peptides were isolated from immunoaffinity-purified HLA-DP2 molecules expressed in cultured B lymphocytes. The size distribution of the peptide repertoire is generally similar to those reported for self peptides bound to HLA-DR and HLA-DQ molecules. Twelve peptides representing individual sequences including two nested sets were sequenced by mass spectrometry and/or N-terminal Edman analy

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Parker, K. C., M. DiBrino, L. Hull, and J. E. Coligan. "The beta 2-microglobulin dissociation rate is an accurate measure of the stability of MHC class I heterotrimers and depends on which peptide is bound." Journal of Immunology 149, no. 6 (1992): 1896–904. http://dx.doi.org/10.4049/jimmunol.149.6.1896.

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Abstract Stable, recombinant, water-soluble complexes of HLA-A2 and HLA-B27 were reconstituted from 125I-labeled beta 2-microglobulin (beta 2m), a synthetic peptide, and HLA H chain fragments expressed as inclusion bodies in the Escherichia coli cytoplasm. Using this system, we were able to show: 1) the t1/2 of beta 2m dissociation from HLA complexes at 37 degrees C varied from approximately 40 h to less than 1 h, depending on the peptide employed for reconstitution. Peptide length and composition were found to be critical factors in determining the beta 2m dissociation rate. Endogenous peptid

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Robinson, R. A., and D. R. Lee. "Studies of tum- peptide analogs define an alternative anchor that can be utilized by Ld ligands lacking the consensus P2 anchor." Journal of Immunology 156, no. 11 (1996): 4266–73. http://dx.doi.org/10.4049/jimmunol.156.11.4266.

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Abstract To determine how peptides that lack a consensus binding motif interact with class I molecules, we have studied the binding of the tumor-associated tum- P91A 14-22 (tum-) peptide to Ld. Previously, a proline at position 2 (P2) and a hydrophobic residue at P9 had been defined as anchors for Ld ligands. However, the tum- peptide lacks the P2 proline anchor. To compare how peptides with and without the P2 proline anchor bind to Ld, we analyzed the binding of monosubstituted analogues of the murine cytomegalovirus (MCMV) pp89 168-176 and the tum- peptides to Ld. As expected, the binding of

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Collins, Edward J., Bruce L. Booth, and Vincenzo Cerundolo. "Extensive Alanine Substitutions Increase Binding Affinity of an Influenza Nucleoprotein Peptide to HLA-Aw68 and Do Not Abrogate Peptide-Specific CTL Recognition." Journal of Immunology 162, no. 1 (1999): 331–37. http://dx.doi.org/10.4049/jimmunol.162.1.331.

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Abstract Class I MHC molecules bind peptides in the endoplasmic reticulum and present them at the cell surface to circulating CD8+ T cells for analysis. We have examined binding of peptides and stabilization of HLA-Aw68 class I molecules using synthetic peptide variants of an influenza virus nucleoprotein peptide, NP91-99 (KTGGPIYKR). We have demonstrated that insertion of increasing numbers of alanines in the center of the peptide (between P and I), to increase a natural bulging out of the peptide-binding cleft, results in a large decrease in thermal stability. Although there is a great decre

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Mauerer, Katja, Gullu Gorgun, David Zahrieh, and John G. Gribben. "Successful Generation of Cytotoxic T-Cells That Kill CLL Cells Using Heteroclitic Peptides Is Independent of the Native Peptide Binding Affinity to HLA-A*0201." Blood 106, no. 11 (2005): 54. http://dx.doi.org/10.1182/blood.v106.11.54.54.

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Abstract Targeting immunoglobulin (Ig) framework region (FR) derived peptides offers the advantage of a less patient specific immunotherapeutic strategy in B-cell malignancies. A major limitation of this method is the generally low immunogenicity and low binding affinity of these peptides to MHC class I and class II molecules. Heteroclitic peptide modifications can increase immunogenicity of low binding peptides while leaving T-cell recognition residues intact, and improve ability to generate cytotoxic T cells lines (CTL). It is not known whether such CTLs can still kill tumor cells that expre

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Hammer, J., E. Bono, F. Gallazzi, C. Belunis, Z. Nagy, and F. Sinigaglia. "Precise prediction of major histocompatibility complex class II-peptide interaction based on peptide side chain scanning." Journal of Experimental Medicine 180, no. 6 (1994): 2353–58. http://dx.doi.org/10.1084/jem.180.6.2353.

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We describe here a new method for predicting class II major histocompatibility complex-binding peptides, based on the preferences observed in a systematic series of peptide binding experiments where each position in a "minimal" peptide was replaced individually by every amino acid. The DRB1*0401 peptide binding preferences were determined and incorporated into a computer program that looks through sequences for potential epitopes and assigns each a score. These scores correlate well with previously determined T cell epitopes of foreign antigens and endogenous peptides from self proteins. Our f

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Mohri, Hiroshi, та Takao Ohkubo. "Effects of Hybrid Peptide Analogs to Receptor Recognition Domains on α- and γ-Chains of Human Fibrinogen on Fibrinogen Binding to Platelets". Thrombosis and Haemostasis 69, № 05 (1993): 490–95. http://dx.doi.org/10.1055/s-0038-1651639.

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SummaryWe synthesized a series of hybrid peptides that correspond to the γ-chain dodecapeptide (400-411), variable numbers of glycine residues, and the RGDS peptide [Y-HHLGGAK-QAGDV(G) n RGDS] to investigate the relationship of these receptor recognition domains of fibrinogen to platelet membrane glycoprotein IIb/IIIa. The tetrapeptide RGDS, the GRGDSPA peptide and the dodecapeptide inhibited binding of fibrinogen to GPIIb/IIIa by 50% (IC50) at concentrations of 17 ± 1.6 μM, 15 ± 2.1 μM, and 87 ± 6.8 μM, respectively. The inhibitory effect of hybrid peptides increased as the number of glycine

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Negroni, Maria, and Lawrence Stern. "Unexpected side reaction of lysine and arginine side chains preceding a photocleavable group in MHC-II UV-cleavable peptides. (P5028)." Journal of Immunology 190, no. 1_Supplement (2013): 41.15. http://dx.doi.org/10.4049/jimmunol.190.supp.41.15.

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Abstract MHC class II molecules (MHCII) present peptides to CD4+ T cells, and HLA-DM (DM) catalyzes peptide exchange favoring binding of high affinity peptides. The effects of DM on peptide association and dissociation kinetics are not yet clear. In the absence of peptide, DR1 (a MHCII) is in equilibrium between inactive and active conformations. In order to understand the kinetics of this process and how it is affected by DM, we wanted to generate DR1 in the active conformation using a peptide carrying the photocleavable 3-amino-3-(2-nitrophenyl)-propionic acid residue, an approach previously

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He, S., S. Tsang, J. North, N. Chohan, R. B. Sim, and K. Whaley. "Epitope mapping of C1 inhibitor autoantibodies from patients with acquired C1 inhibitor deficiency." Journal of Immunology 156, no. 5 (1996): 2009–13. http://dx.doi.org/10.4049/jimmunol.156.5.2009.

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Abstract We report six patients with acquired C1 inhibitor (C1-inh) deficiency associated with serum C1-inh autoantibodies and circulating cleaved (96 kDa), functionally inactive C1-inh. In three patients, all of whom had IgG-kappa paraproteins in their sera, the Abs were IgG-kappa. In the remaining three patients, the Abs were IgM (2 kappa, 1 lambda). These data suggest that all the Abs were monoclonal. The autoantibodies recognized two synthetic peptides (peptides 2 and 3), which spanned the reactive center of C1-inh. Binding to peptide 3 (residues 448-459) was greater than to peptide 2 (res

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Schwaminger, S. P., S. A. Blank-Shim, I. Scheifele, P. Fraga-García, and S. Berensmeier. "Peptide binding to metal oxide nanoparticles." Faraday Discussions 204 (2017): 233–50. http://dx.doi.org/10.1039/c7fd00105c.

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Magnetic metal oxide nanoparticles demonstrate great applicability in several fields such as biotechnology, medicine and catalysis. A stable, magnetic and low-cost material, nanoscale magnetite, is an interesting adsorbent for protein purification. Downstream processing can account for up to 80% of the total production costs in biotechnological production. As such, the development of new innovative separation methods can be regarded as highly profitable. While short peptide sequences can be used as specific affinity tags for functionalised adsorber surfaces, they need expensive affinity ligand

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Lin, Wen-Wei, Yu-Jen Wang, Cheng-Wen Ko, Tain-Lu Cheng, and Yeng-Tseng Wang. "Cyclic Peptide Inhibitors of the Tsg101 UEV Protein Interactions Refined through Global Docking and Gaussian Accelerated Molecular Dynamics Simulations." Polymers 12, no. 10 (2020): 2235. http://dx.doi.org/10.3390/polym12102235.

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Tsg101 UEV domain proteins are potential targets for virus infection therapy, especially for HIV and Ebola viruses. Peptides are key in curbing virus transmission, and cyclic peptides have a greater survival time than their linear peptides. To date, the accurate prediction of cyclic peptide-protein receptors binding conformations still is challenging because of high peptide flexibility. Here, a useful approach combined the global peptide docking, Gaussian accelerated molecular dynamics (GaMD), two-dimensional (2D) potential of mean force (PMF), normal molecular dynamics (cMD), and solvated int

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Sims, Kurtis L., and Anthony B. Schryvers. "Peptide-Peptide Interactions between Human Transferrin and Transferrin-Binding Protein B from Moraxellacatarrhalis." Journal of Bacteriology 185, no. 8 (2003): 2603–10. http://dx.doi.org/10.1128/jb.185.8.2603-2610.2003.

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ABSTRACT Transferrin-binding protein B (TbpB) is one component of a bipartite receptor in several gram-negative bacterial species that binds host transferrin and mediates the uptake of iron for growth. Transferrin and TbpB are both bilobed proteins, and the interaction between these proteins seems to involve similar lobe-lobe interactions. Synthetic overlapping peptide libraries representing the N lobe of TbpB from Moraxella catarrhalis were prepared and probed with labeled human transferrin. Transferrin-binding peptides were localized to six different regions of the TbpB N lobe, and reciproca

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Tompkins, S. M., J. C. Moore, and P. E. Jensen. "An insulin peptide that binds an alternative site in class II major histocompatibility complex." Journal of Experimental Medicine 183, no. 3 (1996): 857–66. http://dx.doi.org/10.1084/jem.183.3.857.

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We report that a peptide from the B chain of insulin, B(10-30), binds with high affinity to multiple class II proteins, including IAb,d,k, IEd,k, and DR1. The ability of B(10-30) to inhibit the binding of other peptide antigens to class II does not correlate with its affinity for class II. B(10-30) only weakly inhibits the binding of antigenic peptides. Conversely, peptides with high affinity for the peptide-binding groove of various class II proteins do not inhibit B(10-30) binding. The rate of association of B(10-30) with class II is unusually rapid, approaching saturation in 1-2 h compared

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Sette, A., S. Southwood, J. Miller, and E. Appella. "Binding of major histocompatibility complex class II to the invariant chain-derived peptide, CLIP, is regulated by allelic polymorphism in class II." Journal of Experimental Medicine 181, no. 2 (1995): 677–83. http://dx.doi.org/10.1084/jem.181.2.677.

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Major histocompatibility complex class II-associated invariant chain (Ii) provides several important functions that regulate class II expression and function. One of these is the ability to inhibit class II peptide loading early in biosynthesis. This allows for efficient class II folding and egress from the endoplasmic reticulum, and protects the class II peptide binding site from loading with peptides before entry into endosomal compartments. The ability of Ii to interact with class II and interfere with peptide loading has been mapped to Ii exon 3, which encodes amino acids 82-107. This same

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Chen, Y., J. Sidney, S. Southwood, et al. "Naturally processed peptides longer than nine amino acid residues bind to the class I MHC molecule HLA-A2.1 with high affinity and in different conformations." Journal of Immunology 152, no. 6 (1994): 2874–81. http://dx.doi.org/10.4049/jimmunol.152.6.2874.

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Abstract An equilibrium binding assay was used to directly measure the relative affinities of naturally processed 9-mer, 10-mer, and 12-mer peptides for the human class I MHC molecule HLA-A2.1. The peptides exhibited a range of affinities with IC50 values of 11 to 214 nM. The mode of interaction between these peptides and HLA-A2.1 was examined using peptides in which Asp had been substituted for suspected anchor residues. Regardless of length, the previously identified Leu at position 2 relative to the amino terminus was critical for peptide binding. While the carboxyl terminal residue was als

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Liu, Yang, Xia-hui Ouyang, Zhi-Xiong Xiao, Le Zhang, and Yang Cao. "A Review on the Methods of Peptide-MHC Binding Prediction." Current Bioinformatics 15, no. 8 (2021): 878–88. http://dx.doi.org/10.2174/1574893615999200429122801.

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Background: T lymphocyte achieves an immune response by recognizing antigen peptides (also known as T cell epitopes) through major histocompatibility complex (MHC) molecules. The immunogenicity of T cell epitopes depends on their source and stability in combination with MHC molecules. The binding of the peptide to MHC is the most selective step, so predicting the binding affinity of the peptide to MHC is the principal step in predicting T cell epitopes. The identification of epitopes is of great significance in the research of vaccine design and T cell immune response. Objective: The tradition

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