4D49

Crystal structure of computationally designed armadillo repeat proteins for modular peptide recognition.

4D49 の概要

• エントリーDOI: 10.2210/pdb4d49/pdb
• 関連するPDBエントリー: 4D4E
• 分子名称: ARMADILLO REPEAT PROTEIN ARM00027, POLY ARG DECAPEPTIDE, ARGININE, ... (4 entities in total)
• 機能のキーワード: de novo protein-peptide complex, de novo protein/peptide
• 由来する生物種: SYNTHETIC CONSTRUCT; 詳細
• タンパク質・核酸の鎖数: 8
• 化学式量合計: 110114.39

構造登録者

Reichen, C.,Forzani, C.,Zhou, T.,Parmeggiani, F.,Fleishman, S.J.,Mittl, P.R.E.,Madhurantakam, C.,Honegger, A.,Ewald, C.,Zerbe, O.,Baker, D.,Caflisch, A.,Pluckthun, A. (登録日: 2014-10-27, 公開日: 2016-01-13, 最終更新日: 2024-05-01)

主引用文献

Reichen, C.,Forzani, C.,Zhou, T.,Parmeggiani, F.,Fleishman, S.J.,Mittl, P.R.E.,Madhurantakam, C.,Honegger, A.,Ewald, C.,Zerbe, O.,Baker, D.,Caflisch, A.,Pluckthun, A.
Computationally Designed Armadillo Repeat Proteins for Modular Peptide Recognition.
J.Mol.Biol., 428:4467-, 2016

PubMed Abstract: Armadillo repeat proteins (ArmRPs) recognize their target peptide in extended conformation and bind, in a first approximation, two residues per repeat. Thus, they may form the basis for building a modular system, in which each repeat is complementary to a piece of the target peptide. Accordingly, preselected repeats could be assembled into specific binding proteins on demand and thereby avoid the traditional generation of every new binding molecule by an independent selection from a library. Stacked armadillo repeats, each consisting of 42 aa arranged in three α-helices, build an elongated superhelical structure. Here, we analyzed the curvature variations in natural ArmRPs and identified a repeat pair from yeast importin-α as having the optimal curvature geometry that is complementary to a peptide over its whole length. We employed a symmetric in silico design to obtain a uniform sequence for a stackable repeat while maintaining the desired curvature geometry. Computationally designed ArmRPs (dArmRPs) had to be stabilized by mutations to remove regions of higher flexibility, which were identified by molecular dynamics simulations in explicit solvent. Using an N-capping repeat from the consensus-design approach, two different crystal structures of dArmRP were determined. Although the experimental structures of dArmRP deviated from the designed curvature, the insertion of the most conserved binding pockets of natural ArmRPs onto the surface of dArmRPs resulted in binders against the expected peptide with low nanomolar affinities, similar to the binders from the consensus-design series.

PubMed: 27664438
DOI: 10.1016/J.JMB.2016.09.012

実験手法

X-RAY DIFFRACTION (2.09 Å)