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Partial peptide dissociation and binding groove plasticity in two major histocompatibility complex class I alleles - differences between alleles versus force field and sampling effects
Ruhr Univ Bochum, Theoret Chem, Bochum, Germany.
Theoretical Chemistry, Ruhr University Bochum, Bochum, Germany.
2022 (English)In: RSC Advances, E-ISSN 2046-2069, Vol. 12, no 46, p. 29908-29914Article in journal (Refereed) Published
Abstract [en]

Major histocompatibility complex class I (MHC I) reports a cell's health status by presenting antigenic peptides inside its binding groove. However, MHC I binding grooves can differ largely in their plasticity, from binding grooves that are conformationally stable by themselves to those that require a high-affinity peptide to be bound to attain conformational stability. These latter MHC I alleles are dependent on the C-terminus of the peptide that stabilizes the F-pocket region of their binding grooves. It has remained unclear to what extent a peptide-MHC I complex (pMHC I) can tolerate the (intermittent) partial dissociation of high-affinity peptides, especially of the peptide's N-terminus. Using bias exchange umbrella sampling (BEUS), a technique to achieve enhanced sampling in molecular dynamics (MD) simulations, we obtained the free-energy profiles of the N-terminal dissociation of a respective high-affinity peptide from HLA-B*35:01 and HLA-B*44:02, two alleles on opposite ends of the scale regarding binding groove plasticity. The potential of mean force (PMF) for HLA-B*35:01 was calculated for two different sets of starting structures and is compared with a PMF obtained previously with a different force field to disentangle allele differences from force field and sampling effects. For both alleles, the free-energy profiles indicate that the peptide N-terminus dissociates in a substantial fraction of the pMHC I, suggesting that their crystal structures with fully bound peptides only partially capture the dynamic conformational ensemble of pMHC I in solution, and thus in the cell.

Place, publisher, year, edition, pages
Royal Society of Chemistry (RSC) , 2022. Vol. 12, no 46, p. 29908-29914
National Category
Biophysics
Identifiers
URN: urn:nbn:se:kth:diva-321015DOI: 10.1039/d2ra05324aISI: 000869861200001PubMedID: 36321080Scopus ID: 2-s2.0-85141924230OAI: oai:DiVA.org:kth-321015DiVA, id: diva2:1708438
Note

QC 20221104

Available from: 2022-11-04 Created: 2022-11-04 Last updated: 2023-09-25Bibliographically approved

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Wingbermühle, Sebastian

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