5J7D

Computationally Designed Thioredoxin dF106

5J7D の概要

• エントリーDOI: 10.2210/pdb5j7d/pdb
• 分子名称: Designed Thioredoxin dF106, COPPER (II) ION (3 entities in total)
• 機能のキーワード: thioredoxin, computational design, rosetta, oxidoreductase, de novo protein
• 由来する生物種: synthetic construct
• タンパク質・核酸の鎖数: 8
• 化学式量合計: 104671.51

構造登録者

Horowitz, S.,Johansen, N.,Olsen, J.G.,Winther, J.R. (登録日: 2016-04-06, 公開日: 2016-10-05, 最終更新日: 2024-01-10)

主引用文献

Johansson, K.E.,Johansen, N.T.,Christensen, S.,Horowitz, S.,Bardwell, J.C.,Olsen, J.G.,Willemoes, M.,Lindorff-Larsen, K.,Ferkinghoff-Borg, J.,Hamelryck, T.,Winther, J.R.
Computational Redesign of Thioredoxin Is Hypersensitive toward Minor Conformational Changes in the Backbone Template.
J.Mol.Biol., 428:4361-4377, 2016

PubMed Abstract: Despite the development of powerful computational tools, the full-sequence design of proteins still remains a challenging task. To investigate the limits and capabilities of computational tools, we conducted a study of the ability of the program Rosetta to predict sequences that recreate the authentic fold of thioredoxin. Focusing on the influence of conformational details in the template structures, we based our study on 8 experimentally determined template structures and generated 120 designs from each. For experimental evaluation, we chose six sequences from each of the eight templates by objective criteria. The 48 selected sequences were evaluated based on their progressive ability to (1) produce soluble protein in Escherichia coli and (2) yield stable monomeric protein, and (3) on the ability of the stable, soluble proteins to adopt the target fold. Of the 48 designs, we were able to synthesize 32, 20 of which resulted in soluble protein. Of these, only two were sufficiently stable to be purified. An X-ray crystal structure was solved for one of the designs, revealing a close resemblance to the target structure. We found a significant difference among the eight template structures to realize the above three criteria despite their high structural similarity. Thus, in order to improve the success rate of computational full-sequence design methods, we recommend that multiple template structures are used. Furthermore, this study shows that special care should be taken when optimizing the geometry of a structure prior to computational design when using a method that is based on rigid conformations.

PubMed: 27659562
DOI: 10.1016/j.jmb.2016.09.013

実験手法

X-RAY DIFFRACTION (2.4 Å)