Free-Energy-Based Protein Design: Re-Engineering Cellular Retinoic Acid Binding Protein II Assisted by the Moveable-Type Approach.
Free-Energy-Based Protein Design: Re-Engineering Cellular Retinoic Acid Binding Protein II Assisted by the Moveable-Type Approach.
复制标题
基于自由能的蛋白质设计：在可移动型方法的辅助下重新设计细胞视黄酸结合蛋白 II。
DOI：
10.1021/jacs.7b10368
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发表时间：
2018
影响因子：
15
通讯作者：
MerzJr,KennethM
中科院分区：
文献类型：
--
作者：
Zhong,HaizhenA;Santos,ElizabethM;Vasileiou,Chrysoula;Zheng,Zheng;Geiger,JamesH;Borhan,Babak;MerzJr,KennethM
如何通过改变氨基酸残基组成来微调小分子与受体结合的自由能是蛋白质工程中的一个关键问题。事实上，这个问题的最终解决方案--化学精度(±1千卡/摩尔)--将在蛋白质设计中产生深远而广泛的应用。已经开发了许多工具来解决这个问题，使用基于知识的模型来进行更密集的基于分子动力学模拟的自由能计算，但是虽然已经取得了一些成功，但在总体精度和方法速度方面仍有改进的空间。在这里，我们报告了一种快速的、基于知识的可动型(MT)方法来估计受蛋白质中小分子结合位点突变影响的结合的绝对和相对自由能。我们使用维甲酸与细胞维甲酸结合蛋白II(CRABPII)系统的突变数据来回顾验证我们的方法，然后做出经过实验证实的前瞻性预测。我们方法的整体表现得到了它成功识别出维甲酸与CRABPII系统的高甚至亚纳米摩尔结合亲和力的突变体的支持。
How to fine-tune the binding free energy of a small-molecule to a receptor site by altering the amino acid residue composition is a key question in protein engineering. Indeed, the ultimate solution to this problem, to chemical accuracy (±1 kcal/mol), will result in profound and wide-ranging applications in protein design. Numerous tools have been developed to address this question using knowledge-based models to more computationally intensive molecular dynamics simulations-based free energy calculations, but while some success has been achieved there remains room for improvement in terms of overall accuracy and in the speed of the methodology. Here we report a fast, knowledge-based movable-type (MT)-based approach to estimate the absolute and relative free energy of binding as influenced by mutations in a small-molecule binding site in a protein. We retrospectively validate our approach using mutagenesis data for retinoic acid binding to the Cellular Retinoic Acid Binding Protein II (CRABPII) system and then make prospective predictions that are borne out experimentally. The overall performance of our approach is supported by its success in identifying mutants that show high or even sub-nano-molar binding affinities of retinoic acid to the CRABPII system.