De Novo Design of a Highly Stable Ovoid TIM Barrel: Unlocking Pocket Shape towards Functional Design.

Q2 Agricultural and Biological Sciences
生物设计研究(英文) Pub Date : 2022-10-10 eCollection Date: 2022-01-01 DOI:10.34133/2022/9842315
Alexander E Chu, Daniel Fernandez, Jingjia Liu, Raphael R Eguchi, Po-Ssu Huang
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引用次数: 0

Abstract

The ability to finely control the structure of protein folds is an important prerequisite to functional protein design. The TIM barrel fold is an important target for these efforts as it is highly enriched for diverse functions in nature. Although a TIM barrel protein has been designed de novo, the ability to finely alter the curvature of the central beta barrel and the overall architecture of the fold remains elusive, limiting its utility for functional design. Here, we report the de novo design of a TIM barrel with ovoid (twofold) symmetry, drawing inspiration from natural beta and TIM barrels with ovoid curvature. We use an autoregressive backbone sampling strategy to implement our hypothesis for elongated barrel curvature, followed by an iterative enrichment sequence design protocol to obtain sequences which yield a high proportion of successfully folding designs. Designed sequences are highly stable and fold to the designed barrel curvature as determined by a 2.1 Å resolution crystal structure. The designs show robustness to drastic mutations, retaining high melting temperatures even when multiple charged residues are buried in the hydrophobic core or when the hydrophobic core is ablated to alanine. As a scaffold with a greater capacity for hosting diverse hydrogen bonding networks and installation of binding pockets or active sites, the ovoid TIM barrel represents a major step towards the de novo design of functional TIM barrels.

Abstract Image

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高稳定性卵形TIM枪管的De Novo设计:解锁口袋形状,实现功能设计。
精细控制蛋白质折叠结构的能力是功能蛋白质设计的重要前提。TIM桶褶是这些工作的一个重要目标,因为它在自然界中具有丰富的多样功能。尽管TIM桶蛋白是从头设计的,但精细改变中心β桶曲率和折叠整体结构的能力仍然难以捉摸,限制了其在功能设计中的实用性。在这里,我们报道了具有卵形(双重)对称性的TIM桶的从头设计,灵感来自于具有卵形曲率的天然β和TIM桶。我们使用自回归主干采样策略来实现我们对细长桶曲率的假设,然后使用迭代富集序列设计协议来获得高比例成功折叠设计的序列。设计序列高度稳定,可折叠至2.1 Å分辨率晶体结构。该设计显示出对剧烈突变的鲁棒性,即使当多个带电荷的残基埋在疏水核中或疏水核被消融为丙氨酸时,也能保持高的熔融温度。作为一种具有更大容量容纳各种氢键网络和安装结合口袋或活性位点的支架,卵形TIM桶代表着功能性TIM桶从头设计的重要一步。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
CiteScore
3.90
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0.00%
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审稿时长
12 weeks
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