Examination of possible structural constraints of MHC‐binding peptides by assessment of their native structure within their source proteins
Identifieur interne : 001393 ( Istex/Curation ); précédent : 001392; suivant : 001394Examination of possible structural constraints of MHC‐binding peptides by assessment of their native structure within their source proteins
Auteurs : Ora Schueler-Furman [Israël, États-Unis] ; Yael Altuvia [Israël] ; Hanah Margalit [Israël]Source :
- Proteins: Structure, Function, and Bioinformatics [ 0887-3585 ] ; 2001-10-01.
English descriptors
- Teeft :
- Additional examples, Anchor position, Antigenic, Antigenic peptides, Binding groove, Binding nonamers, Binding peptides, Biol, Chicken ovalbumin, Conceivable hypothesis, Conformation, Conformation space, Constraint, Crystal structure, Crystal structures, Cterminal anchor position, Data sets, Different conformations, Different environments, Different protein environments, Direct implications, Groove, Hanah margalit, Higher limit, Highest fraction, Histocompatibility, Identical subsequences, Israeli cancer research foundation, Largest difference, Major histocompatibility, Matrix protein, Mhcbinding peptides, Molecular genetics, Native conformation, Native conformations, Native peptide conformations, Native peptides, Native protein, Native source protein, Native source proteins, Native structure, Native structures, Nature struct biol, Nonameric peptides, Nonamers, Other peptide positions, Overall conformation space, Pairwise rmsc, Peptide, Peptide conformations, Peptide motifs, Peptide sequences, Peptide structures, Peptide termini, Proc natl acad, Protein data bank, Random conformations, Random peptides, Random sets, Rmsc, Same length, Secondary structure, Secondary structure types, Secondary structures, Short subsequences, Solution structure, Source protein, Source proteins, Standard deviation, Statistical analysis, Strand conformation, Structural constraints, Structural diversity, Structural preferences, Subsequence, Terminal distances, Unique structure, Wide range.
Abstract
Antigenic peptides bind to major histocompatibility complex (MHC) molecules as a prerequisite for their presentation to T cells. In this study, we investigate possible structural preferences of MHC‐binding peptides by examining the conformation space defined by the structures of these peptides within their native source proteins. Comparison of the conformation space of the native structures of MHC‐binding nonamers and a corresponding conformation space defined by a random set of nonamers showed no significant difference. This suggests that the environment of the MHC binding groove has evolved to bind peptides with essentially any “structural background.” A slight tendency for an extended β‐conformation at positions 8 and 9 was observed for the set of native structures. We suggest that such a preference may facilitate the binding of the C‐terminal anchor position of processed peptides into the corresponding specificity pocket. MHC‐binding peptides represent examples of short subsequences that are present in two different structural environments: within their native protein and within the MHC binding groove. Comparison of the native and of the bound structure of the peptides showed that peptides up to 14 residues long may adopt different conformations within different protein environments. This has direct implications for structure prediction algorithms. Proteins 2001;45:47–54. © 2001 Wiley‐Liss, Inc.
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DOI: 10.1002/prot.1122
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In this study, we investigate possible structural preferences of MHC‐binding peptides by examining the conformation space defined by the structures of these peptides within their native source proteins. Comparison of the conformation space of the native structures of MHC‐binding nonamers and a corresponding conformation space defined by a random set of nonamers showed no significant difference. This suggests that the environment of the MHC binding groove has evolved to bind peptides with essentially any “structural background.” A slight tendency for an extended β‐conformation at positions 8 and 9 was observed for the set of native structures. We suggest that such a preference may facilitate the binding of the C‐terminal anchor position of processed peptides into the corresponding specificity pocket. MHC‐binding peptides represent examples of short subsequences that are present in two different structural environments: within their native protein and within the MHC binding groove. Comparison of the native and of the bound structure of the peptides showed that peptides up to 14 residues long may adopt different conformations within different protein environments. This has direct implications for structure prediction algorithms. Proteins 2001;45:47–54. © 2001 Wiley‐Liss, Inc.</div></front></TEI></record>Pour manipuler ce document sous Unix (Dilib)
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