Structure-based design of a T-cell receptor leads to nearly 100-fold improvement in binding affinity for pepMHC
Structure-based design of a T-cell receptor leads to nearly 100-fold improvement in binding affinity for pepMHC
复制标题
DOI：
10.1002/prot.22203
复制
发表时间：
2009-03-01
影响因子：
2.9
通讯作者：
Weng, Zhiping
中科院分区：
文献类型：
--
作者：
Haidar, Jaafar N.;Pierce, Brian;Weng, Zhiping
T细胞受体（TCR）是识别抗原呈递细胞表面主要组织相容性复合体（MHC）结合的外源蛋白的多肽的蛋白质。这种相互作用使T细胞能够启动细胞介导的免疫应答，以终止在其MHC上展示外源肽的细胞。天然存在的TCR对肽-MHC（pepMHC）复合物具有高特异性但低亲和力。这阻止了溶解的TCR用于诊断和治疗病毒感染或癌症的用途。近年来已经报道了通过随机文库和体外选择来增强几种TCR的结合亲和力的努力。然而，还没有报道通过基于结构的设计来增强亲和力的努力，这允许更多地控制和理解改进的机制。在这里，我们已经将基于结构的设计应用于人TCR以改善其pepMHC结合。我们的设计方法基于预测、测试和基于新数据生成更多预测的迭代步骤而发展。最终的设计函数，命名为ZAFFI，有一个相关性为0.77和平均误差为0.35千卡/摩尔的结合自由能的26个点突变，我们测量的表面等离子体共振（SPR）的系统。应用我们开发的过滤器来去除非结合预测，这种相关性增加到0.85，平均误差降低到0.3千卡/摩尔。使用该算法，我们预测并测试了几个改善结合的点突变，其中一个点突变提供了超过六倍的结合改善。然后将改善结合的点突变中的四个组合以得到比野生型TCR强99倍地结合pepMHC的突变TCR。
T-cell receptors (TCRs) are proteins that recognize peptides from foreign proteins bound to the major histocompatibility complex (MHC) on the surface of in antigen-presenting cell. This interaction enables the T cells to initiate a cell-mediated immune response to terminate cells displaying the foreign peptide on their MHC. Naturally occurring TCRs have high specificity but low affinity toward the peptide-MHC (pepMHC) complex. This prevents the usage of solubilized TCRs for diagnosis and treatment of viral infections or cancers. Efforts to enhance the binding affinity of several TCRs have been reported in recent years, through randomized libraries and in vitro selection. However, there have been no reported efforts to enhance the affinity via structure-based design, which allows more control and understanding of the mechanism of improvement. Here, we have applied structure-based design to a human TCR to improve its pepMHC binding. Our design method evolved based on iterative steps of prediction, testing, and generating more predictions based on the new data. The final design function, named ZAFFI, has a correlation of 0.77 and average error of 0.35 kcal/mol with the binding free energies of 26 point mutations for this system that we measured by surface plasmon resonance (SPR). Applying the filter that we developed to remove nonbinding predictions, this correlation increases to 0.85, and the average error decreases to 0.3 kcal/mol. Using this algorithm, we predicted and tested several point mutations that improved binding, with one giving over sixfold binding improvement. Four of the point mutations that improved binding were then combined to give a mutant TCR that binds the pepMHC 99 times more strongly than the wild-type TCR.