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首页> 外文期刊>Journal of Molecular Biology >Computationally Designed Armadillo Repeat Proteins for Modular Peptide Recognition
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Computationally Designed Armadillo Repeat Proteins for Modular Peptide Recognition

机译：计算设计的犰狳重复蛋白，用于模块化肽段识别。

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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 as arranged in three a-helices, build an elongated superhelical structure. Here, we analyzed the curvature variations in natural ArmRPs and identified a repeat pair from yeast importin-a 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. (C) 2016 Elsevier Ltd. All rights reserved.
机译：犰狳重复蛋白（ArmRP）以扩展的构象识别其靶肽，并以第一个近似值结合每个重复序列两个残基。因此，它们可以构成构建模块化系统的基础，其中每个重复序列与一段靶肽互补。因此，可以根据需要将预选的重复序列组装成特异性结合蛋白，从而通过从文库中进行独立选择避免了每个新结合分子的传统产生。堆叠的犰狳重复序列（每个包含42个，排列成三个a螺旋）构成细长的超螺旋结构。在这里，我们分析了天然ArmRP中的曲率变化，并确定了来自酵母importin-a的重复对，该重复对具有最佳的曲率几何形状，可在肽的全长上互补。我们采用了对称的计算机设计，以在保持所需曲率几何形状的同时获得可堆叠重复序列的均匀序列。计算设计的ArmRP（dArmRP）必须通过突变来稳定，以去除具有较高柔韧性的区域，这通过在显式溶剂中进行的分子动力学模拟来确定。使用来自共有设计方法的N帽重复序列，确定了dArmRP的两个不同晶体结构。尽管dArmRP的实验结构偏离了设计曲率，但将天然ArmRP最保守的结合口袋插入dArmRP的表面仍导致了与纳摩尔亲和力较低的预期肽的结合剂，类似于共识设计系列的结合剂。 （C）2016 Elsevier Ltd.保留所有权利。

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