Güner Yılmaz Ö Zeynep, Doruker Pemra, Kurkcuoglu Ozge
Department of Chemical Engineering, Istanbul Technical University, Istanbul 34467, Turkey.
Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, United States.
J Chem Inf Model. 2025 Aug 11;65(15):8137-8157. doi: 10.1021/acs.jcim.5c00431. Epub 2025 Jul 23.
This study presents a computationally efficient approach to generate plausible protein conformers for ensemble docking to enable evaluations of interactions between ligand and protein for ranking the docked ligands according to their binding affinities. Two binding regions of triose phosphate isomerase (TIM), its catalytic site with DHAP ( TIM), and its dimer interface with 3PG (TIM) involving flexible loops were investigated as case studies. The binding sites of the apo and holo forms were modeled at the atomistic scale (high resolution) while the remaining structure was coarse-grained (low resolution) leading to a mixed-resolution description of the protein. The slowest three normal modes related to the functional dynamics of TIM were obtained using the Anisotropic Network Model and employed to derive 36 conformers of the truncated high-resolution regions by assessing six deformation parameters in both directions of the harmonic motions. Through energy minimization and docking calculations in Glide, optimal extents of deformation were identified. The docked truncated structures were then subjected to independent molecular dynamics (MD) simulations to confirm the interactions of the ligands in the binding sites. To prevent the disintegration of the truncated structure, different buffer zones and harmonic restraints were assessed to finally decide on four distinct zones with restraints of 0, 25, 35, and 50 kcal/mol·Å. Each conformer underwent 900 ns-long simulations across three replicates reaching a total simulation time of 15.2 μs. Binding free energy calculations were conducted using the MM-GBSA approach using the first 50, first 100, first 200, and 300 ns intervals, which pointed out that 100 ns-long simulations were sufficient to estimate the binding affinities for TIM. Results consistently indicated comparable binding energies between the intact and truncated TIM structures underscoring the approach's reliability, where the truncated conformers also offered varying binding site geometries yielding favorable interactions. Comparative docking at the dimer interface of TIM further highlighted species-specific binding dynamics, affirming the methodology's applicability for diverse biological questions and establishing a computationally efficient approach to estimate binding free energy values even for supramolecular assemblages.
本研究提出了一种计算效率高的方法，用于生成合理的蛋白质构象异构体以进行整体对接，从而能够评估配体与蛋白质之间的相互作用，以便根据对接配体的结合亲和力对其进行排序。作为案例研究，研究了磷酸丙糖异构酶（TIM）的两个结合区域，即其与二羟丙酮磷酸（DHAP）的催化位点（TIM）以及其与3-磷酸甘油（3PG）的二聚体界面（TIM），这些区域涉及柔性环。在原子尺度（高分辨率）上对无配体和有配体形式的结合位点进行建模，而其余结构则进行粗粒化（低分辨率），从而得到蛋白质的混合分辨率描述。使用各向异性网络模型获得与TIM功能动力学相关的最慢的三个正常模式，并通过评估谐波运动两个方向上的六个变形参数，用于推导截短的高分辨率区域的36个构象异构体。通过在Glide中进行能量最小化和对接计算，确定了最佳变形程度。然后对对接的截短结构进行独立的分子动力学（MD）模拟，以确认配体在结合位点的相互作用。为了防止截短结构解体，评估了不同的缓冲区和谐波约束，最终确定了四个不同的区域，约束分别为0、25、35和50千卡/摩尔·埃。每个构象异构体在三个重复实验中进行了900纳秒长的模拟，总模拟时间达到15.2微秒。使用MM-GBSA方法在第一个50纳秒、第一个100纳秒、第一个200纳秒和300纳秒的时间间隔内进行结合自由能计算，结果表明100纳秒长的模拟足以估计TIM的结合亲和力。结果一致表明完整和截短的TIM结构之间的结合能具有可比性，强调了该方法的可靠性，其中截短的构象异构体也提供了不同的结合位点几何形状，产生了有利的相互作用。在TIM二聚体界面处的比较对接进一步突出了物种特异性的结合动力学，证实了该方法对各种生物学问题的适用性，并建立了一种计算效率高的方法来估计结合自由能值，即使对于超分子组装体也是如此。
