F pocket flexibility influences the tapasin dependence of two differentially disease‐associated MHC Class I proteins

Abstract

The human MHC class I protein HLA-B*27:05 is statistically associated with ankylosing spondylitis, unlike HLA-B*27:09, which differs in a single amino acid in the F pocket of the peptide-binding groove. To understand how this unique amino acid difference leads to a different behavior of the proteins in the cell, we have investigated the conformational stability of both proteins using a combination of in silico and experimental approaches. Here, we show that the binding site of B*27:05 is conformationally disordered in the absence of peptide due to a charge repulsion at the bottom of the F pocket. In agreement with this, B*27:05 requires the chaperone protein tapasin to a greater extent than the conformationally stable B*27:09 in order to remain structured and to bind peptide. Taken together, our data demonstrate a method to predict tapasin dependence and physiological behavior from the sequence and crystal structure of a particular class I allotype.Keywords: Ankylosing spondylitis r HLA-B27 r Major histocompatibility complex r Molecular dynamics r Natively unstructured proteins r Protein folding r Simulations Additional supporting information may be found in the online version of this article at the publisher's web-site Introduction MHC class I molecules are heterotrimeric proteins that transport antigenic peptides to the cell surface and present them to cytotoxic T cells. They consist of the transmembrane heavy chain (HC), the noncovalently associated light chain beta-2 microglobulin (β 2 m), and an antigenic peptide of eight to ten amino acids. The Correspondence: Prof. Sebastian Springer e-mail: s.springer@jacobs-university.de extracellular part of the heavy chain comprises the α 1 , α 2 , and α 3 domains. The α 1 and α 2 domains form the peptide-binding groove, a superdomain that consists of an antiparallel beta sheet surmounted by two alpha helices, between which the peptide binds [1,2].In the cell, peptide binding to class I is a multistep process within the ER. It involves the peptide-loading complex, which consists of the peptide transporter associated with antigen processing (TAP) that transports peptides from the cytosol into the ER lumen [3] and several chaperone proteins such as tapasin, which binds both to the class I molecule and TAP [4,5].C 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim www.eji-journal.eu Eur. J. Immunol. 2015. 45: 1248-1257 Molecular immunology 1249The sequence of peptides that can bind to class I is determined by interactions with the amino acid side chains of the peptide-binding groove. The high sequence polymorphism of the peptide-binding groove in human class I molecules (human leukocyte antigens, HLA-A, -B, and -C) means that different allotypes bind different peptides; thus, individual HLA allotypes-such as HLA-B27-support-specific immune responses and are statistically associated with disease [6,7]. Among the subtypes of HLA-B27 [8,9], HLA-B*27:05 (B*27:05) shows a very strong statistical association with spondyloarthropathies such as ankylosing spondylitis (AS), in contr...

MHC class II complexes sample intermediate states along the peptide exchange pathway

“…The above presented concept of the relevance of the conformational landscape of a ‘receptor' molecule on downstream pathways might not only be applicable to the closely related tapasin-catalysed peptide loading of MHC class I molecules42434445 but is also known to other biological systems: The energy landscape of G-protein coupled receptors that strongly impacts activation pathways has been shown to depend on the individual receptor/ligand complex46 and as shown in this study, ligands might not act on the crystallizable ground states but on low-populated excited states47. For example, an order-to-disorder transition of two helical segments in the rhodopsin effector Gαi1 has been postulated and mutations that affect the thermodynamic stability of this region were shown to have a large effect on GDP release48.…”

Major Histocompatibility Complex (MHC) Class I and MHC Class II Proteins: Conformational Plasticity in Antigen Presentation

“…In contrast, increasing experimental and computational evidence of wild type (WT) and mutant MHC complexes over the past years incontestably revealed that changes in conformational dynamics in MHC proteins have to accompany peptide loading and exchange (22, 40–46). …”

“…In such simulations, peptide-free class I protein is modeled from the crystal structure by deleting the atoms of the bound peptide. In the absence of peptide, an increased conformational flexibility of the F pocket region was observed for several allelic variants (HLA-A*02:01, HLA-B*44:02, HLA-B*44:05, HLA-B*27:05, HLA-B*27:09, H-2D b , and H-2K b ) (9, 15, 21, 22, 69–71). Longer simulations of chicken and human class I allotypes showed increased global motion in the peptide-free form when compared to the peptide-bound proteins (72, 73).…”

“…In the PLC, tapasin is a protein that catalyzes, together with other chaperones, the loading of high-affinity peptides derived from proteolysis of endogenously expressed proteins (Figure 1C, left panel) (17, 18). In the absence of tapasin, some class I allotypes (such as HLA-B*44:02) are retained in the ER (tapasin-dependent), whereas other class I proteins (tapasin-independent, such as HLA-B*44:05 and HLA-B*27:09) can bind peptides and travel to the cell surface (19–22). There is no crystal structure of the MHC class I/tapasin complex, but several structural models and mutational studies suggested that tapasin binds two regions in the HC of MHC class I, a loop in the α 3 domain (residues 222–229), and a region of the α 2 domain (residues 128–137) adjacent to the F-pocket (Figure 1B) (18, 21, 23–29).…”

The interplay between HLA-B27 and ERAP1/ERAP2 aminopeptidases: from anti-viral protection to spondyloarthritis

“…These data can also be interpreted on the basis of recent biophysical and computational analyses. Indeed, several studies have described an enhanced degree of flexibility and disorder of B*2705 and B*2704 peptide-binding cleft in comparison to that of B*2706 and B*2709 alleles [45][46][47]. This would influence the tapasin dependence, the folding dynamics and the stability of HLA-peptide complexes overall [46].…”