PMID- 36003074 OWN - NLM STAT- PubMed-not-MEDLINE LR - 20240214 IS - 2752-6542 (Electronic) IS - 2752-6542 (Linking) VI - 1 IP - 3 DP - 2022 Jul TI - Charge-based interactions through peptide position 4 drive diversity of antigen presentation by human leukocyte antigen class I molecules. PG - pgac124 LID - 10.1093/pnasnexus/pgac124 [doi] LID - pgac124 AB - Human leukocyte antigen class I (HLA-I) molecules bind and present peptides at the cell surface to facilitate the induction of appropriate CD8+ T cell-mediated immune responses to pathogen- and self-derived proteins. The HLA-I peptide-binding cleft contains dominant anchor sites in the B and F pockets that interact primarily with amino acids at peptide position 2 and the C-terminus, respectively. Nonpocket peptide-HLA interactions also contribute to peptide binding and stability, but these secondary interactions are thought to be unique to individual HLA allotypes or to specific peptide antigens. Here, we show that two positively charged residues located near the top of peptide-binding cleft facilitate interactions with negatively charged residues at position 4 of presented peptides, which occur at elevated frequencies across most HLA-I allotypes. Loss of these interactions was shown to impair HLA-I/peptide binding and complex stability, as demonstrated by both in vitro and in silico experiments. Furthermore, mutation of these Arginine-65 (R65) and/or Lysine-66 (K66) residues in HLA-A*02:01 and A*24:02 significantly reduced HLA-I cell surface expression while also reducing the diversity of the presented peptide repertoire by up to 5-fold. The impact of the R65 mutation demonstrates that nonpocket HLA-I/peptide interactions can constitute anchor motifs that exert an unexpectedly broad influence on HLA-I-mediated antigen presentation. These findings provide fundamental insights into peptide antigen binding that could broadly inform epitope discovery in the context of viral vaccine development and cancer immunotherapy. CI - (c) The Author(s) 2022. Published by Oxford University Press on behalf of the National Academy of Sciences. FAU - Jackson, Kyle R AU - Jackson KR AD - University of Texas MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA. FAU - Antunes, Dinler A AU - Antunes DA AD - Department of Biology and Biochemistry, University of Houston, Houston, TX, USA. FAU - Talukder, Amjad H AU - Talukder AH AD - Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA. FAU - Maleki, Ariana R AU - Maleki AR AD - Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA. FAU - Amagai, Kano AU - Amagai K AD - Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA. FAU - Salmon, Avery AU - Salmon A AD - University of Texas MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA. FAU - Katailiha, Arjun S AU - Katailiha AS AD - Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA. FAU - Chiu, Yulun AU - Chiu Y AD - Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA. FAU - Fasoulis, Romanos AU - Fasoulis R AD - Department of Computer Science, Rice University, Houston, TX, USA. FAU - Rigo, Mauricio Menegatti AU - Rigo MM AD - Department of Computer Science, Rice University, Houston, TX, USA. FAU - Abella, Jayvee R AU - Abella JR AUID- ORCID: 0000-0002-8574-1144 AD - Department of Computer Science, Rice University, Houston, TX, USA. FAU - Melendez, Brenda D AU - Melendez BD AD - University of Texas MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA. FAU - Li, Fenge AU - Li F AD - Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA. FAU - Sun, Yimo AU - Sun Y AD - University of Texas MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA. FAU - Sonnemann, Heather M AU - Sonnemann HM AD - University of Texas MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA. FAU - Belousov, Vladislav AU - Belousov V AD - BostonGene Corporation, Waltham, MA, USA. FAU - Frenkel, Felix AU - Frenkel F AD - BostonGene Corporation, Waltham, MA, USA. FAU - Justesen, Sune AU - Justesen S AD - Immunitrack Aps, Copenhagen, Denmark. FAU - Makaju, Aman AU - Makaju A AD - ThermoFisher Scientific, San Jose, CA, USA. FAU - Liu, Yang AU - Liu Y AD - ThermoFisher Scientific, San Jose, CA, USA. FAU - Horn, David AU - Horn D AD - ThermoFisher Scientific, San Jose, CA, USA. FAU - Lopez-Ferrer, Daniel AU - Lopez-Ferrer D AD - ThermoFisher Scientific, San Jose, CA, USA. FAU - Huhmer, Andreas F AU - Huhmer AF AD - ThermoFisher Scientific, San Jose, CA, USA. FAU - Hwu, Patrick AU - Hwu P AD - Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA. FAU - Roszik, Jason AU - Roszik J AUID- ORCID: 0000-0002-4561-6170 AD - Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA. FAU - Hawke, David AU - Hawke D AUID- ORCID: 0000-0002-6102-7843 AD - Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX, USA. FAU - Kavraki, Lydia E AU - Kavraki LE AD - Department of Computer Science, Rice University, Houston, TX, USA. FAU - Lizee, Gregory AU - Lizee G AUID- ORCID: 0000-0003-4449-7461 AD - Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA. LA - eng GR - R21 CA209941/CA/NCI NIH HHS/United States GR - U01 CA258512/CA/NCI NIH HHS/United States PT - Journal Article DEP - 20220727 PL - England TA - PNAS Nexus JT - PNAS nexus JID - 9918367777906676 PMC - PMC9391200 OTO - NOTNLM OT - computational modeling OT - human leukocyte antigen (HLA) OT - mass spectrometry OT - molecular dynamics OT - peptide antigen presentation EDAT- 2022/08/26 06:00 MHDA- 2022/08/26 06:01 PMCR- 2022/07/27 CRDT- 2022/08/25 02:14 PHST- 2022/01/20 00:00 [received] PHST- 2022/07/20 00:00 [accepted] PHST- 2022/08/25 02:14 [entrez] PHST- 2022/08/26 06:00 [pubmed] PHST- 2022/08/26 06:01 [medline] PHST- 2022/07/27 00:00 [pmc-release] AID - pgac124 [pii] AID - 10.1093/pnasnexus/pgac124 [doi] PST - epublish SO - PNAS Nexus. 2022 Jul 27;1(3):pgac124. doi: 10.1093/pnasnexus/pgac124. eCollection 2022 Jul.