PMID- 34937342
OWN - NLM
STAT- MEDLINE
DCOM- 20220228
LR  - 20220228
IS  - 1535-3907 (Electronic)
IS  - 1535-3893 (Linking)
VI  - 21
IP  - 1
DP  - 2022 Jan 7
TI  - Abundance, Betweenness Centrality, Hydrophobicity, and Isoelectric Points Are 
      Relevant Factors in the Processing of Parental Proteins of the HLA Class II 
      Ligandome.
PG  - 164-171
LID - 10.1021/acs.jproteome.1c00662 [doi]
AB  - Adaptive cellular and humoral immune responses to infectious agents require 
      previous recognition of pathogenic peptides bound to human leukocyte antigen 
      (HLA) class II molecules exposed on the surface of the professional 
      antigen-presenting cells. Knowledge of how these peptide ligands are generated is 
      essential to understand the basis for CD4(+) T-cell-mediated immunity and 
      tolerance. In this study, a high-throughput mass spectrometry analysis was used 
      to identify more than 16,000 cell peptides bound to several HLA-DR and -DP class 
      II molecules isolated from large amounts of uninfected and virus-infected human 
      cells (ProteomeXchange accession: PXD028006). The analysis of the 1808 parental 
      proteins containing HLA class II ligands revealed that these cell proteins were 
      more acidic, abundant, and highly connected but less hydrophilic than 
      non-parental proteomes. Therefore, the percentage of acidic residues was 
      increased and hydroxyl and polar residues were decreased in the parental proteins 
      for the HLA class II ligandomes versus the non-parental proteomes. This 
      definition of the properties shared by parental proteins that constitute the 
      source of the HLA class II ligandomes can serve as the basis for the development 
      of bioinformatics tools to predict proteins that are most likely recognized by 
      the immune system through the CD4(+) helper T lymphocytes in both autoimmunity 
      and infection.
FAU - Lorente, Elena
AU  - Lorente E
AD  - Unidad de Presentacion y Regulacion Inmunes, Instituto de Salud Carlos III, 
      Majadahonda, 28220 Madrid, Spain.
FAU - Martin-Galiano, Antonio J
AU  - Martin-Galiano AJ
AD  - Unidad de Infecciones Intrahospitalarias, Instituto de Salud Carlos III, 
      Majadahonda, 28220 Madrid, Spain.
FAU - Kadosh, Dganit Melamed
AU  - Kadosh DM
AD  - Department of Biology, Technion-Israel Institute of Technology, 32000 Haifa, 
      Israel.
FAU - Barriga, Alejandro
AU  - Barriga A
AD  - Unidad de Presentacion y Regulacion Inmunes, Instituto de Salud Carlos III, 
      Majadahonda, 28220 Madrid, Spain.
FAU - Garcia-Arriaza, Juan
AU  - Garcia-Arriaza J
AD  - Department of Molecular and Cellular Biology, Centro Nacional de Biotecnologia, 
      Consejo Superior de Investigaciones Cientificas (CSIC), 28049 Madrid, Spain.
FAU - Mir, Carmen
AU  - Mir C
AD  - Unidad de Presentacion y Regulacion Inmunes, Instituto de Salud Carlos III, 
      Majadahonda, 28220 Madrid, Spain.
FAU - Esteban, Mariano
AU  - Esteban M
AD  - Department of Molecular and Cellular Biology, Centro Nacional de Biotecnologia, 
      Consejo Superior de Investigaciones Cientificas (CSIC), 28049 Madrid, Spain.
FAU - Admon, Arie
AU  - Admon A
AUID- ORCID: 0000-0003-0504-3950
AD  - Department of Biology, Technion-Israel Institute of Technology, 32000 Haifa, 
      Israel.
FAU - Lopez, Daniel
AU  - Lopez D
AUID- ORCID: 0000-0003-0268-5878
AD  - Unidad de Presentacion y Regulacion Inmunes, Instituto de Salud Carlos III, 
      Majadahonda, 28220 Madrid, Spain.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20211222
PL  - United States
TA  - J Proteome Res
JT  - Journal of proteome research
JID - 101128775
RN  - 0 (HLA Antigens)
RN  - 0 (HLA-DR Antigens)
SB  - IM
MH  - CD4-Positive T-Lymphocytes
MH  - *HLA Antigens/genetics/metabolism
MH  - *HLA-DR Antigens
MH  - Humans
MH  - Hydrophobic and Hydrophilic Interactions
MH  - Isoelectric Point
MH  - Parents
OTO - NOTNLM
OT  - HLA
OT  - antigen presentation
OT  - ligand
OT  - mass spectrometry
EDAT- 2021/12/24 06:00
MHDA- 2022/03/01 06:00
CRDT- 2021/12/23 05:20
PHST- 2021/12/24 06:00 [pubmed]
PHST- 2022/03/01 06:00 [medline]
PHST- 2021/12/23 05:20 [entrez]
AID - 10.1021/acs.jproteome.1c00662 [doi]
PST - ppublish
SO  - J Proteome Res. 2022 Jan 7;21(1):164-171. doi: 10.1021/acs.jproteome.1c00662. 
      Epub 2021 Dec 22.