Atomistic structure and dynamics of the human MHC-I peptide-loading complex Olivier Fisettea , Gunnar F. Schroder¨ b,c,d, and Lars V. Schafer¨ a,1 aTheoretical Chemistry, Ruhr University Bochum, D-44780 Bochum, Germany; bInstitute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Julich,¨ D-52425 Julich,¨ Germany; cJulich¨ Centre for Structural Biology (JuStruct), Forschungszentrum Julich,¨ D-52425 Julich,¨ Germany; and dPhysics Department, Heinrich-Heine-Universitat¨ Dusseldorf,¨ D-40225 Dusseldorf,¨ Germany Edited by Peter Cresswell, Yale University, New Haven, CT, and approved July 14, 2020 (received for review March 9, 2020) The major histocompatibility complex class-I (MHC-I) peptide- sive achievement. However, such a low-resolution structure loading complex (PLC) is a cornerstone of the human adaptive does not provide the atomic-level picture of the PLC required immune system, being responsible for processing antigens that to fully elucidate its inner workings. A static, averaged pic- allow killer T cells to distinguish between healthy and com- ture like the one provided by cryo-EM does not inform us promised cells. Based on a recent low-resolution cryo-electron about the many dynamic events that take place in the com- microscopy (cryo-EM) structure of this large membrane-bound plex, such as assembly, the roles of the various components protein complex, we report an atomistic model of the PLC in the formation of a stable complex, the recruitment of sub- and study its conformational dynamics on the multimicrosec- optimally loaded MHC-I, the process of peptide selection, or ond time scale using all-atom molecular dynamics (MD) simu- the release of antigen-loaded MHC-I. Understanding these lations in an explicit lipid bilayer and water environment (1.6 events is crucial to human health since they can be hindered million atoms in total). The PLC has a layered structure, with by immune evasion mechanisms (18, 19), rendering the PLC two editing modules forming a flexible protein belt surround- inoperative. ing a stable, catalytically active core. Tapasin plays a central Here, we present the structure and conformational dynam- role in the PLC, stabilizing the MHC-I binding groove in a ics of the PLC at the atomic level. We integrated the cryo-EM conformation reminiscent of antigen-loaded MHC-I. The MHC- density of the complex with high-resolution structural informa- I–linked glycan steers a tapasin loop involved in peptide edit- tion on individual PLC components to obtain an atomistic model ing toward the binding groove. Tapasin conformational dynam- (Fig. 2). This atomic structure was embedded into a solvated BIOPHYSICS AND COMPUTATIONAL BIOLOGY ics are also affected by calreticulin through a conformational lipid bilayer and subjected to all-atom molecular dynamics (MD) selection mechanism that facilitates MHC-I recruitment into the simulations, in which the motions of the complex unfold on the complex. microsecond time scale. We also simulated alternative models of the PLC where individual domains, subunits, or even large parts immunity j MHC-I j peptide-loading complex j of the complex were removed and compared protein dynam- molecular dynamics simulations j protein dynamics ics in these truncated systems to what we observed in the full complex. This computational structural biology approach pin- points the origin of dynamic events and relates them to biological o protect us against cancer and intracellular pathogens, the functions. Thuman adaptive immune system relies on a signaling mech- Our results highlight the central role of the two tapasin (Tsn) anism whereby antigens are exposed at the surface of cells by subunits in the PLC. Tsn and MHC-I form a rigid core sur- major histocompatibility complex class-I (MHC-I) proteins for rounded by a flexible belt of accessory proteins, and the dual recognition by killer T cells (1–3). These antigens are, for the most part, short peptides (8 to 12 amino acids) resulting from Significance the degradation of intracellular proteins. Peptides exposed at the cell surface by MHC-I therefore mirror cellular contents: The major histocompatibility complex class-I (MHC-I) peptide- In healthy cells, only peptides from the “self” are exposed; in loading complex (PLC) translocates cytosolic degradation cells compromised by a virus or cancer-causing mutation, both products to the endoplasmic reticulum to load antigenic pep- self and “nonself” peptides, either viral or mutated, are exposed. tides onto MHC-I molecules. Stable peptide–MHC-I complexes + Patrolling CD8 T lymphocytes detect tainted cells by scanning are presented at the cell surface to mirror cellular contents the peptide–MHC-I (pMHC-I) complexes via T cell receptors for patrolling T cells, which protect against viral infections and induce their apoptosis. and cancer-causing mutations by inducing apoptosis in cells Most peptide sequences have little or no immunogenic value. that expose nonself peptides. Due to its size and dynamic Triaging the vast pool of cytosolic degradation products to find nature, the atomic-level details of the PLC remained unknown. the few peptides that have a high affinity for MHC-I requires We built an all-atom model of the human MHC-I PLC by a sophisticated machinery, the peptide-loading complex (PLC) combining the recent 9.9-A˚ resolution cryo-EM density with (Fig. 1) (4, 5). Anchored to the endoplasmic reticulum (ER) microsecond molecular dynamics simulations in a membrane membrane, this large macromolecular assembly integrates sev- and water environment (1.6 million atoms). The results pro- eral MHC-I antigen-processing functions into a single molecular vide unprecedented insights into the molecular underpinnings machine: antigen transport to the ER, MHC-I stabilization dur- of our adaptive immune response. ing the loading process, and catalytic selection of high-affinity antigenic peptides (or peptide editing). Author contributions: O.F. and L.V.S. designed research; O.F. performed research; O.F., The molecular structure of the PLC was only recently resolved G.F.S., and L.V.S. analyzed data; and O.F. and L.V.S. wrote the paper.y by single-particle cryo-electron microscopy (cryo-EM) (5). The The authors declare no competing interest.y map resolution obtained for the full PLC in this study was This article is a PNAS Direct Submission.y only 9.9 A,˚ which could be improved to 5.8 A˚ by focusing Published under the PNAS license.y on a single module of the PLC (Fig. 1). In light of the large 1 To whom correspondence may be addressed. Email: Lars.Schaefer@ruhr-uni- size of the complex and the transient nature of the interac- bochum.de.y tions between its components, this study represents an impres- First published August 11, 2020. www.pnas.org/cgi/doi/10.1073/pnas.2004445117 PNAS j August 25, 2020 j vol. 117 j no. 34 j 20597–20606 Downloaded by guest on October 1, 2021 Fig. 1. Structural overview of the MHC-I PLC. The PLC can be divided into three parts, ER-luminal, TM, and cytosolic. The ER-luminal part consists of two editing modules, M1 and M2, each of which contains one Tsn, ERp57, Crt, and MHC-I. MHC-I proteins (1–3, 6, 7) are heterodimers formed of a variable α heavy chain (αHC) and an invariant, light β2 microglobulin (β2m). αHC comprises three soluble domains, two of which, α1 and α2, form the peptide-binding groove (PBG). MHC-Is have an N-linked branched glycan that reflects their loading status: A terminal glucose allows recognition and binding by Crt and acts as a signal that MHC-I should be recruited to the PLC for peptide editing; antigen-loaded MHC-Is that exit the ER are deglucosylated. Newly synthesized “empty” MHC-I proteins (eMHC-I) are unstable; in the PLC, Tsn acts as an MHC-I chaperone. Tsn (8–10) is the central component of the editing modules. It has two ER-luminal domains: N-terminal TN and C-terminal TC. M1 and M2 are organized around a pseudosymmetry axis at the interface between the two Tsns. Tsn forms a complex with MHC-I and accelerates the off rate of low-affinity MHC-I–bound peptides to perform peptide editing (9, 11–13). Tsn is also disulfide bonded to ERp57 (14), a four-domain protein playing a structural role. Crt (15, 16) consists of three soluble domains, a globular lectin domain with a binding site for the monoglucosylated branch of the N-linked MHC-I glycan, a flexible P domain that extends over the PBG and contacts ERp57, and a calcium-sensing C domain with an extended α-helix that contacts Tsn. The transporter associated with antigen processing (TAP) (17) is the main component of both the TM and cytosolic parts of the PLC. TAP shuttles peptides from the cytosol to the ER, providing the PLC with its substrate for antigen processing. TAP is a heterodimer of TAP-1 and TAP-2, each of which has an N-terminal four-helix TM domain, TMD0, that provides a docking site for the TM helix of Tsn. A TM helix also anchors MHC-I to the ER membrane. editing modules formed by Tsn are essential for global com- Results and Discussion plex stability. MHC-I binding-groove width is modulated by the ERp57 and Crt Form a Flexible Belt around Tsn•MHC-I. To study environment of the PLC. The MHC-I N-linked glycan modulates the structural dynamics of the human PLC at the atomic level, the conformational dynamics of a solvent-exposed Tsn loop puta- all-atom MD simulations of the entire PLC, embedded in a lipid tively involved in peptide editing [called the “scoop loop” (20) by bilayer and solvated by water and ions (Fig. 2), were carried out. some authors].