Dynamic design: manipulation of millisecond timescale motions on the energy landscape of cyclophilin A.
Dynamic design: manipulation of millisecond timescale motions on the energy landscape of cyclophilin A.
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DOI：
10.1039/c9sc04696h
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发表时间：
2020-01-15
期刊：
影响因子：
8.4
通讯作者：
Michel J
中科院分区：
文献类型：
--
作者：
Juárez-Jiménez J;Gupta AA;Karunanithy G;Mey ASJS;Georgiou C;Ioannidis H;De Simone A;Barlow PN;Hulme AN;Walkinshaw MD;Baldwin AJ;Michel J
蛋白质需要在许多构象之间相互转换才能发挥作用，其中许多构象是瞬时形成的，并且数量稀疏。特别是当这些状态的寿命接近毫秒时间尺度时，识别相关结构和它们相互转换的机制仍然是一个巨大的挑战。在这里，我们介绍了加速 MD (aMD) 模拟和马尔可夫状态建模 (MSM) 的新颖组合，以探索这些“兴奋”构象状态。将其应用于高度动态的蛋白质 CypA（一种参与免疫反应并与 HIV 感染相关的蛋白质），我们确定了五种主要的构象状态以及它们相互转换的原子机制。合理的设计策略预测突变体 D66A 应该稳定次要构象并显着改变动力学，而类似的突变体 H70A 应该使景观基本保持不变。这些预测通过 CPMG 和 R1ρ 溶液态 NMR 测量得到证实。通过在计算机中有效地探索功能相关但具有毫秒寿命的稀疏构象，我们的 aMD/MSM 方法对于蛋白质工程和药物发现的动态蛋白质自由能景观的设计具有巨大的前景。使用分子模拟来设计亲环蛋白 A 酶中的大规模环运动，并使用 NMR 和生物物理方法来验证模型。
Proteins need to interconvert between many conformations in order to function, many of which are formed transiently, and sparsely populated. Particularly when the lifetimes of these states approach the millisecond timescale, identifying the relevant structures and the mechanism by which they interconvert remains a tremendous challenge. Here we introduce a novel combination of accelerated MD (aMD) simulations and Markov state modelling (MSM) to explore these ‘excited’ conformational states. Applying this to the highly dynamic protein CypA, a protein involved in immune response and associated with HIV infection, we identify five principally populated conformational states and the atomistic mechanism by which they interconvert. A rational design strategy predicted that the mutant D66A should stabilise the minor conformations and substantially alter the dynamics, whereas the similar mutant H70A should leave the landscape broadly unchanged. These predictions are confirmed using CPMG and R1ρ solution state NMR measurements. By efficiently exploring functionally relevant, but sparsely populated conformations with millisecond lifetimes in silico, our aMD/MSM method has tremendous promise for the design of dynamic protein free energy landscapes for both protein engineering and drug discovery. Molecular simulations were used to design large scale loop motions in the enzyme cyclophilin A and NMR and biophysical methods were employed to validate the models.
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影响因子：
6.8
作者：
Grant BJ;Gorfe AA;McCammon JA
通讯作者：
McCammon JA
影响因子：
16.6
作者：
Ahmed-Belkacem, Abdelhakim;Colliandre, Lionel;Ahnou, Nazim;Nevers, Quentin;Gelin, Muriel;Bessin, Yannick;Brillet, Rozenn;Cala, Olivier;Douguet, Dominique;Bourguet, William;Krimm, Isabelle;Pawlotsky, Jean-Michel;Guichou, Jean-Francois
通讯作者：
Guichou, Jean-Francois
影响因子：
3.3
作者：
Bartels, C;Karplus, M
通讯作者：
Karplus, M
影响因子：
64.8
作者：
Eisenmesser, EZ;Millet, O;Kern, D
通讯作者：
Kern, D
影响因子：
7.3
作者：
Guichou, JF;Viaud, J;Chavanieu, A
通讯作者：
Chavanieu, A