Department of Chemical Engineering, Indian Institute of Technology Delhi, Hauz Khas, Delhi 110016, India.
J Chem Theory Comput. 2022 May 10;18(5):3268-3283. doi: 10.1021/acs.jctc.1c01243. Epub 2022 Apr 28.
While extremely important for relating the protein structure to its biological function, determination of the protein conformational transition pathway upon ligand binding is made difficult due to the transient nature of intermediates, a large and rugged conformational space, and coupling between protein dynamics and ligand-protein interactions. Existing methods that rely on prior knowledge of the bound (holo) state structure are restrictive. A second concern relates to the correspondence of intermediates obtained to the metastable states on the apo → holo transition pathway. Here, we have taken the protein apo structure and ligand-binding site as only inputs and combined an elastic network model (ENM) representation of the protein Hamiltonian with linear response theory (LRT) for protein-ligand interactions to identify the set of slow normal modes of protein vibrations that have a high overlap with the direction of the protein conformational change. The structural displacement along the chosen direction was performed using excited normal modes molecular dynamics (MDeNM) simulations rather than by the direct use of LRT. Herein, the MDeNM excitation velocity was optimized on-the-fly on the basis of its coupling to protein dynamics and ligand-protein interactions. Thus, a determined set of structures was validated against crystallographic and simulation data on four protein-ligand systems, namely, adenylate kinase-di(adenosine-5')pentaphosphate, ribose binding protein-β-d-ribopyranose, DNA β-glucosyltransferase-uridine-5'-diphosphate, and G-protein α subunit-guanosine-5'-triphosphate, which present important differences in protein conformational heterogeneity, ligand binding mechanism, viz. induced-fit or conformational selection, extent, and nonlinearity in protein conformational changes upon ligand binding, and presence of allosteric effects. The obtained set of intermediates was used as an input to path metadynamics simulations to obtain the free energy profile for the apo → holo transition.
虽然确定蛋白质构象转变途径对于将蛋白质结构与其生物功能相关联非常重要，但由于中间产物的瞬态性质、大而崎岖的构象空间以及蛋白质动力学与配体-蛋白质相互作用之间的耦合，使得这一任务变得困难。现有的方法依赖于结合（全）态结构的先验知识，因此具有一定的局限性。第二个关注点涉及到获得的中间产物与apo→holo 转变途径上的亚稳态之间的对应关系。在这里，我们仅将蛋白质的apo 结构和配体结合位点作为输入，并将蛋白质哈密顿量的弹性网络模型（ENM）表示与线性响应理论（LRT）结合，以确定一组与蛋白质构象变化方向具有高重叠的慢蛋白质振动正则模态。在所选择的方向上的结构位移是通过激发正常模式分子动力学（MDeNM）模拟而不是直接使用 LRT 来完成的。在此，MDeNM 激发速度是根据其与蛋白质动力学和配体-蛋白质相互作用的耦合在飞行中进行优化的。因此，一组确定的结构是针对四个蛋白质-配体系统（即腺苷酸激酶-二（腺苷-5'）五磷酸、核糖结合蛋白-β-D-核糖吡喃糖、DNA β-葡萄糖基转移酶-尿苷-5'-二磷酸和 G 蛋白α亚基-鸟苷-5'-三磷酸）的晶体学和模拟数据进行验证的，这些系统在蛋白质构象异质性、配体结合机制（即诱导契合或构象选择）、程度和非线性、配体结合时蛋白质构象变化以及变构效应的存在等方面存在重要差异。获得的一组中间产物被用作输入到路径元动力学模拟中，以获得 apo→holo 转变的自由能分布。
