5TOF

Room temperature structure of ubiquitin variant u7ub25

5TOF の概要

• エントリーDOI: 10.2210/pdb5tof/pdb
• 関連するPDBエントリー: 5TOG
• 分子名称: Polyubiquitin-B, SULFATE ION (3 entities in total)
• 機能のキーワード: computationally designed ubiquitin, usp7, signaling protein
• 由来する生物種: Homo sapiens (Human)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 8929.12

構造登録者

Biel, J.T.,Thompson, M.C.,Cunningham, C.N.,Corn, J.E.,Fraser, J.S. (登録日: 2016-10-17, 公開日: 2017-05-24, 最終更新日: 2023-10-04)

主引用文献

Biel, J.T.,Thompson, M.C.,Cunningham, C.N.,Corn, J.E.,Fraser, J.S.
Flexibility and Design: Conformational Heterogeneity along the Evolutionary Trajectory of a Redesigned Ubiquitin.
Structure, 25:739-749.e3, 2017

PubMed Abstract: Although protein design has been used to introduce new functions, designed variants generally only function as well as natural proteins after rounds of laboratory evolution. One possibility for this pattern is that designed mutants frequently sample nonfunctional conformations. To test this idea, we exploited advances in multiconformer modeling of room-temperature X-ray data collection on redesigned ubiquitin variants selected for increasing binding affinity to the deubiquitinase USP7. Initial core mutations disrupt natural packing and lead to increased flexibility. Additional, experimentally selected mutations quenched conformational heterogeneity through new stabilizing interactions. Stabilizing interactions, such as cation-pi stacking and ordered waters, which are not included in standard protein design energy functions, can create specific interactions that have long-range effects on flexibility across the protein. Our results suggest that increasing flexibility may be a useful strategy to escape local minima during initial directed evolution and protein design steps when creating new functions.

PubMed: 28416112
DOI: 10.1016/j.str.2017.03.009

実験手法

X-RAY DIFFRACTION (1.12 Å)