Insight Derived from Molecular Dynamics Simulations into Molecular Motions, Thermodynamics and Kinetics of HIV-1 gp120

Although the crystal structures of the HIV-1 gp120 core bound and pre-bound by CD4 are known, the details of dynamics involved in conformational equilibrium and transition in relation to gp120 function have remained elusive. The homology models of gp120 comprising the N- and C-termini and loops V3 and V4 in the CD4-bound and CD4-unbound states were built and subjected to molecular dynamics (MD) simulations to investigate the differences in dynamic properties and molecular motions between them. The results indicate that the CD4-bound gp120 adopted a more compact and stable conformation than the unbound form during simulations. For both the unbound and bound gp120, the large concerted motions derived from essential dynamics (ED) analyses can influence the size/shape of the ligand-binding channel/cavity of gp120 and, therefore, were related to its functional properties. The differences in motion direction between certain structural components of these two forms of gp120 were related to the conformational interconversion between them. The free energy calculations based on the metadynamics simulations reveal a more rugged and complex free energy landscape (FEL) for the unbound than for the bound gp120, implying that gp120 has a richer conformational diversity in the unbound form. The estimated free energy difference of ∼−6.0 kJ/mol between the global minimum free energy states of the unbound and bound gp120 indicates that gp120 can transform spontaneously from the unbound to bound states, revealing that the bound state represents a high-probability “ground state” for gp120 and explaining why the unbound state resists crystallization. Our results provide insight into the dynamics-and-function relationship of gp120, and facilitate understandings of the thermodynamics, kinetics and conformational control mechanism of HIV-1 gp120.

尽管目前已知CD4结合与预结合状态下的HIV-1 gp120核心晶体结构，但与gp120功能相关的构象平衡与转变过程的动力学细节仍不明晰。本研究构建了CD4结合与未结合状态下、包含N端、C端以及V3、V4环的gp120同源建模模型，并通过分子动力学（MD）模拟探究二者在动力学特性与分子运动模式上的差异。模拟结果显示，相较于未结合状态的gp120，CD4结合状态的gp120在模拟过程中呈现出更为紧凑且稳定的构象。无论是未结合还是结合状态的gp120，通过本质动力学（ED）分析得到的大型协同运动均可影响gp120配体结合通道/空腔的尺寸与形态，因此与该蛋白的功能特性密切相关。两种状态下gp120特定结构组分的运动方向差异，与二者间的构象互变存在关联。基于元动力学模拟的自由能计算结果表明，未结合状态gp120的自由能景观（FEL）相较于结合状态更为崎岖且复杂，这意味着未结合状态的gp120具有更为丰富的构象多样性。未结合与结合状态gp120的全局最低自由能态之间的自由能差约为−6.0 kJ/mol，这表明gp120可自发地从未结合状态转变为结合状态，说明结合状态是gp120的高概率“基态”，同时也解释了为何未结合状态的gp120难以结晶。本研究结果为揭示gp120的动力学-功能关系提供了新的见解，同时有助于进一步理解HIV-1 gp120的热力学、动力学及构象调控机制。