微管稳定剂调控β微管蛋白 M 环构象的分子动力学机制

Molecular dynamics mechanisms of microtubule stabilizers in regulating M-loop conformation of β-tubulin

摘要

微管稳定剂通过结合β微管蛋白引发构象变化,抑制肿瘤增殖,但其分子调控机制及多分子协同作用对稳定性的影响尚不明确。基于分子动力学模拟,构建β微管蛋白单体、紫杉醇、紫杉醇-莱利霉素双配体及多紫杉醇复合体系,通过均方根偏差(RMSD)、结合自由能(MM/PBSA)及差异接触网络分析,系统解析药物对蛋白构象的调控机制。RMSD 分析表明,小分子的结合使β微管蛋白的构象稳定性显著提高,其 RMSD 值降低并稳定在0.35~0.40 nm 范围内。进一步的残基接触分析显示,紫杉醇增强了结构域1与 M 环、结构域2之间的相互作用。结合自由能计算揭示疏水作用与氢键为关键驱动力,其中多紫杉醇体系结合能最低(-478.83 kJ/mol),表明多价配体策略可显著提升药物效能。动态网络分析证实小分子通过增强 M 环与α6、α7、β10等群落的连通性削弱其自身相互作用,诱导 M 环形成稳定的α螺旋构象,最终形成全局稳定化构象。研究从原子尺度揭示了微管稳定剂诱导 M 环动态重构的网络机制,为开发抗癌药物提供了分子层面的理论支撑。

Abstract

Microtubule stabilizers inhibit tumor proliferation by binding to β-tubulin and inducing conformational changes. However, their molecular regulatory mechanisms and the impact of multi-molecular synergistic effects on stability remain unclear. Based on molecular dynamics simulations, this study constructed β-tubulin monomer, paclitaxel, paclitaxel-laulimalide dual-ligand, and multi-paclitaxel complex systems. Through root mean square deviation (RMSD), binding free energy (MM/PBSA), and differential contact network analyses, the regulatory mechanisms of drugs on protein conformation are systematically investigated. The RMSD analysis indicated that the binding of the small molecule significantly increased the conformational stability of β-tubulin, with the RMSD value decreasing and stabilizing within the range of 0.35-0.40 nm. Further residue contact analysis revealed that paclitaxel enhanced the interactions between domain 1 and the M-loop, as well as residues in domain 2. Binding free energy calculations identified hydrophobic interactions and hydrogen bonds as key driving forces, with the multi-paclitaxel system exhibiting the lowest binding energy (-478.83 kJ/mol), indicating that the multivalent ligand strategy substantially enhances drug efficacy. Dynamic network analysis confirms that small molecules weaken intrinsic interactions by enhancing connectivity between the M-loop and α6, α7, β10 communities, inducing the M-loop to adopt a stable α-helical conformation, ultimately forming a globally stabilized conformation. This study atomistically elucidates the network mechanism of microtubule stabilizer-induced dynamic remodeling of the M-loop, providing molecular-level theoretical support for developing anticancer drugs.

关键词

β微管蛋白 / 紫杉醇 / 莱利霉素 / 分子动力学模拟 / 结合机制 / 相互作用网络

Key words

β-tubulin / paclitaxel / laulimalide / molecular dynamics simulation / binding mechanism / interaction network

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基金资助

中国博士后科学基金(62305205)