Change of the unbinding mechanism upon a mutation: A molecular dynamics study of an antibody-hapten complex
Change of the unbinding mechanism upon a mutation: A molecular dynamics study of an antibody-hapten complex
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DOI：
10.1110/ps.041280705
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发表时间：
2005-10-01
期刊：
影响因子：
8
通讯作者：
Paci, E
中科院分区：
文献类型：
--
作者：
Curcio, R;Caflisch, A;Paci, E
我们研究强制解结合的荧光素从野生型（WT）和突变体[H（H58）A]的单链可变片段（scFv）抗荧光素抗体FITC-E2的分子动力学模拟使用各种拉技术。需要大量的长时间模拟来获得统计学上有意义的结果，因为野生型和H（H58）A突变体的解结合都是通过多个途径发生的，通常具有亚稳态中间体。对于野生型，解结合过程中的限速步骤对应于特定中间体的非天然相互作用特征的破坏。H（H58）A突变不利于该中间体的出现。在野生型的广泛平衡模拟中观察到半抗原在没有拉力的情况下部分解结合的两个事件，并且它们的分析表明，强制解结合和自发解结合沿着沿着类似的途径进行。在模拟中观察到的不同的解结合机制表明了两种抗体之间实验解离速率差异的可能原因。我们预测的突变，预计调制的发生未结合的中间体。对于两个这样的新突变体[H（H58）A和S（H52）A]，我们的预测通过额外的模拟在计算机上得到验证。Honegger等人在本期的随附论文中报告了FITC-E2与荧光素衍生物的X射线结构，该衍生物被用作本文所述工作的起始构象。
We study forced unbinding of fluorescein from the wild type (WT) and a mutant [H(H58)A] of the single-chain variable-fragment (scFv) anti-fluorescein antibody FITC-E2 by molecular dynamics simulations using various pulling techniques. A large number of long simulations were needed to obtain statistically meaningful results as both the wild type and the H(H58)A mutant unbinding occurs through multiple pathways, often with metastable intermediates. For the wild type, the rate-limiting step in the unbinding process corresponds to the breaking of the non-native interactions characteristic of a specific intermediate. The H(H58)A mutation disfavors the occurrence of this intermediate. Two events where the hapten partially unbinds in the absence of pulling force are observed in extensive equilibrium simulations of the wild type, and their analysis indicates that forced unbinding and spontaneous unbinding proceed along similar pathways. The different unbinding mechanisms observed in the simulations suggest a possible reason for the difference in the experimental off-rate between the two antibodies. We predict mutations that are expected to modulate the occurrence of the unbinding intermediate. For two such new mutants [H(H58)A and S(H52)A], our predictions are validated in silico by additional simulations. The accompanying paper in this issue by Honegger et al. reports the X-ray structure of FITC-E2 with a derivative of fluorescein, which was used as the starting conformation for the work presented here.