8ISN

HLA-A24 in complex with modified 9mer WT1 peptide

8ISN の概要

• エントリーDOI: 10.2210/pdb8isn/pdb
• 分子名称: MHC class I antigen, Beta-2-microglobulin, CYS-TYR-THR-TRP-ASN-GLN-MET-ASN-LEU, ... (6 entities in total)
• 機能のキーワード: immune system
• 由来する生物種: Homo sapiens (human); 詳細
• タンパク質・核酸の鎖数: 6
• 化学式量合計: 96854.83

構造登録者

Bekker, G.J.,Numoto, N.,Kawasaki, M.,Hayashi, T.,Yabuno, S.,Kozono, Y.,Shimizu, T.,Kozono, H.,Ito, N.,Oda, M.,Kamiya, N. (登録日: 2023-03-21, 公開日: 2023-09-13, 最終更新日: 2024-10-23)

主引用文献

Bekker, G.J.,Numoto, N.,Kawasaki, M.,Hayashi, T.,Yabuno, S.,Kozono, Y.,Shimizu, T.,Kozono, H.,Ito, N.,Oda, M.,Kamiya, N.
Elucidation of binding mechanism, affinity, and complex structure between mWT1 tumor-associated antigen peptide and HLA-A*24:02.
Protein Sci., 32:e4775-e4775, 2023

PubMed Abstract: We have applied our advanced computational and experimental methodologies to investigate the complex structure and binding mechanism of a modified Wilms' Tumor 1 (mWT1) protein epitope to the understudied Asian-dominant allele HLA-A*24:02 (HLA-A24) in aqueous solution. We have applied our developed multicanonical molecular dynamics (McMD)-based dynamic docking method to analyze the binding pathway and mechanism, which we verified by comparing the highest probability structures from simulation with our experimentally solved x-ray crystal structure. Subsequent path sampling MD simulations elucidated the atomic details of the binding process and indicated that first an encounter complex is formed between the N-terminal's positive charge of the 9-residue mWT1 fragment peptide and a cluster of negative residues on the surface of HLA-A24, with the major histocompatibility complex (MHC) molecule preferring a predominantly closed conformation. The peptide first binds to this closed MHC conformation, forming an encounter complex, after which the binding site opens due to increased entropy of the binding site, allowing the peptide to bind to form the native complex structure. Further sequence and structure analyses also suggest that although the peptide loading complex would help with stabilizing the MHC molecule, the binding depends in a large part on the intrinsic affinity between the MHC molecule and the antigen peptide. Finally, our computational tools and analyses can be of great benefit to study the binding mechanism of different MHC types to their antigens, where it could also be useful in the development of higher affinity variant peptides and for personalized medicine.

PubMed: 37661929
DOI: 10.1002/pro.4775

実験手法

X-RAY DIFFRACTION (2.48 Å)