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A comprehensive mutational scan of the TAPBPR scoop loop defines a region of the sequence-activity landscape for class I MHC interactions

ABSTRACT: A comprehensive mutational scan of the TAPBPR scoop loop defines a region of the sequence-activity landscape for class I MHC interactions

PROVIDER: PRJNA486132 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7695720_1.fastq.gz	Fastqsanger.gz
	SRR7695720_2.fastq.gz	Fastqsanger.gz
	SRR7695711_1.fastq.gz	Fastqsanger.gz
	SRR7695711_2.fastq.gz	Fastqsanger.gz
	SRR7695721_1.fastq.gz	Fastqsanger.gz

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A comprehensive mutational scan of the TAPBPR scoop loop defines a region of the sequence-activity landscape for class I MHC interactions

2019-10-31 | GSE118568 | GEO

A deep mutational scan of the MHC class I-specific chaperone tapasin

Project description:A deep mutational scan of the MHC class I-specific chaperone tapasin

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A deep mutational scan of the MHC class I-specific chaperone tapasin

Project description:Tapasin acts as the principal MHC-I-specific chaperone for facilitating folding and antigenic peptide loading of nascent MHC class I substrates in the cell. In cells where tapasin has been knocked out, the processing and surface trafficking of the human MHC-I allele HLA-A2 is substantially reduced. Over-expression of tapasin rescues HLA-A2 surface expression. Using this assay as the basis for a fluorescence-based selection, tapasin was deep mutationally scanned at 108 positions in the core, at the interface with MHC-I, and on the ‘backside’ distal from where MHC-I binds. Critical residues of tapasin for rescue of HLA-A2 processing map to sites that contact the underside of the MHC-I alpha-2 domain, to the surface contacting the MHC-1 beta2m and alpha-3 domains, and to the base of a protruding loop that rests above the peptide-binding groove (but not to the tip of the loop itself).

2020-10-09 | GSE159247 | GEO

A deep mutational scan of the MHC class I-specific chaperone TAPBPR for sites important for peptide editing

Project description:A deep mutational scan of the MHC class I-specific chaperone TAPBPR for sites important for peptide editing

| PRJNA905819 | ENA

A deep mutational scan of the MHC class I-specific chaperone TAPBPR for sites important for peptide editing

Project description:TAP-binding protein-related (TAPBPR) is an endoplasmic reticulum-resident chaperone that facilitates class I MHC (MHC-I) processing and peptide loading. TAPBPR has (1) chaperone function to stabilize misfolded or partially folded nascent MHC-I substrates, and (2) editing function, in which it catalyzes the exchange of low affinity for high affinity antigenic peptides in the MHC-I peptide-binding groove. TAPBPR-TM is a chimera of the TAPBPR ectodomain and a canonical TM domain, which escapes the endoplasmic reticulum to reach the cell surface. We reasoned that at the cell surface, TAPBPR-TM is more likely to interact with folded MHC-I and thus surface interactions will be more representative of editing function. When tapasin, a homolog of TAPBPR and the main MHC-I-specific chaperone, is knocked out, surface trafficking of HLA-A2 (a human MHC-I allele) is severely diminished, but surface HLA-A2 levels are rescued by over-expression of TAPBPR-TM. Using this assay as the foundation for a fluorescence-based selection, we deep mutationally scanned 104 positions on TAPBPR-TM to identify sites critical for engaging folded MHC-I.

2023-03-09 | GSE218828 | GEO

Deep mutational scan of a drug efflux pump reveals its structure-function landscape

Project description:Deep mutational scan of a drug efflux pump reveals its structure-function landscape

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Critical residues within the TAPBPR scoop loop for HLA-A2 binding and peptide loading are determined by deep mutational scanning

Project description:The loading of high affinity peptides onto nascent class I MHC (MHC-I) molecules is facilitated by chaperones, including the class I-specific chaperone TAP-binding protein-related (TAPBPR). TAPBPR features a loop (amino acids 24-35) that projects towards the empty MHC-I peptide binding groove and rests above the F pocket. The 24-35 loop is much shorter in the closely related homologue tapasin, and therefore may be partly responsible for the unique antigen editing properties of TAPBPR. Previously we reported a deep mutational scan of human TAPBPR focused on the 24-35 loop, and determined the relative effects of single amino acid mutations on binding and peptide-mediated release of the murine H2-Dd MHC-I allomorph. Here, we extend our studies to determine the mutational landscape of the 24-35 loop when TAPBPR binds a human MHC-I allomorph, HLA-A*02:01. The data highlights how TAPBPR affinity can be increased or decreased for different MHC-I allomorphs by tuning the electrostatic complementarity of the 24-35 loop for surfaces on the rim of the peptide-binding groove. By changing the selection pressure from HLA-A2 binding to HLA-A2 loading and processing, we find that TAPBPR is reasonably tolerant of mutations in the 24-35 loop for efficient peptide-MHC-I processing and surface trafficking.

2019-09-01 | GSE126206 | GEO

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Project description:Sequencing and annotation of equine MHC class II region

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MHC class I and MHC class II reporter mice enable analysis of immune oligodendroglia in mouse models of multiple sclerosis

Project description:Oligodendrocytes and their progenitors upregulate MHC pathways in response to inflammation, but the frequency of this phenotypic change is unknown and the features of these immune oligodendroglia are poorly defined. We generated MHC class I and II transgenic reporter mice to define their dynamics in response to inflammatory demyelination, providing a means to monitor MHC activation in diverse cell types in living mice and define their roles in aging, injury and disease.

2022-09-23 | GSE213739 | GEO

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