5YY4

Crystal structure of the scFv antibody 4B08 with sulfated epitope peptide

5YY4 の概要

• エントリーDOI: 10.2210/pdb5yy4/pdb
• 分子名称: scFv 4B08, C-C chemokine receptor type 5, SULFATE ION, ... (5 entities in total)
• 機能のキーワード: antibody, biomolecular recognition, md simulations, thermodynamics, immune system
• 由来する生物種: Mus musculus; 詳細
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 28394.64

構造登録者

Caaveiro, J.M.M.,Miyanabe, K.,Tsumoto, K. (登録日: 2017-12-07, 公開日: 2018-07-18, 最終更新日: 2024-10-16)

主引用文献

Miyanabe, K.,Yamashita, T.,Abe, Y.,Akiba, H.,Takamatsu, Y.,Nakakido, M.,Hamakubo, T.,Ueda, T.,Caaveiro, J.M.M.,Tsumoto, K.
Tyrosine Sulfation Restricts the Conformational Ensemble of a Flexible Peptide, Strengthening the Binding Affinity for an Antibody
Biochemistry, 57:4177-4185, 2018

PubMed Abstract: Protein tyrosine sulfation (PTS) is a post-translational modification regulating numerous biological events. PTS generally occurs at flexible regions of proteins, enhancing intermolecular interactions between proteins. Because of the high flexibility associated with the regions where PTS is generally encountered, an atomic-level understanding has been difficult to achieve by X-ray crystallography or nuclear magnetic resonance techniques. In this study, we focused on the conformational behavior of a flexible sulfated peptide and its interaction with an antibody. Molecular dynamics simulations and thermodynamic analysis indicated that PTS reduced the main-chain fluctuations upon the appearance of sulfate-mediated intramolecular H-bonds. Collectively, our data suggested that one of the mechanisms by which PTS may enhance protein-protein interactions consists of the limitation of conformational dynamics in the unbound state, thus reducing the loss of entropy upon binding and boosting the affinity for its partner.

PubMed: 29936828
DOI: 10.1021/acs.biochem.8b00592

実験手法

X-RAY DIFFRACTION (1.59 Å)