Biological Sciences Collegiate Division, University of Chicago, Chicago, IL 60637, USA.
Department of Chemical and Materials Engineering, University of Alberta, Alberta, T6G 1H9 Canada.
Sci Rep. 2017 Feb 8;7:41671. doi: 10.1038/srep41671.
Molecular dynamics simulations of ubiquitin in water/glycerol solutions are used to test the suggestion by Karplus and coworkers that proteins in their biologically active state should exhibit a dynamics similar to 'surface-melted' inorganic nanoparticles (NPs). Motivated by recent studies indicating that surface-melted inorganic NPs are in a 'glassy' state that is an intermediate dynamical state between a solid and liquid, we probe the validity and significance of this proposed analogy. In particular, atomistic simulations of ubiquitin in solution based on CHARMM36 force field and pre-melted Ni NPs (Voter-Chen Embedded Atom Method potential) indicate a common dynamic heterogeneity, along with other features of glass-forming (GF) liquids such as collective atomic motion in the form of string-like atomic displacements, potential energy fluctuations and particle displacements with long range correlations ('colored' or 'pink' noise), and particle displacement events having a power law scaling in magnitude, as found in earthquakes. On the other hand, we find the dynamics of ubiquitin to be even more like a polycrystalline material in which the α-helix and β-sheet regions of the protein are similar to crystal grains so that the string-like collective atomic motion is concentrated in regions between the α-helix and β-sheet domains.
采用水/甘油溶液中泛素的分子动力学模拟来检验 Karplus 及其同事的观点，即具有生物活性的蛋白质应表现出类似于“表面熔化”的无机纳米颗粒 (NPs) 的动力学。受最近的研究表明表面熔化的无机 NPs 处于“玻璃态”，这是介于固体和液体之间的中间动力学状态的启发，我们探讨了这种类比的有效性和重要性。具体来说，基于 CHARMM36 力场和预熔化 Ni NPs（Voter-Chen 嵌入原子法势）的溶液中泛素的原子模拟表明存在共同的动态异质性，以及玻璃形成 (GF) 液体的其他特征，如以串状原子位移形式的集体原子运动、势能波动和具有长程相关性的粒子位移（“有色”或“粉红”噪声），以及在地震中发现的具有幂律标度的粒子位移事件。另一方面，我们发现泛素的动力学甚至更像多晶材料，其中蛋白质的α-螺旋和β-折叠区域类似于晶体颗粒，因此串状集体原子运动集中在α-螺旋和β-折叠区域之间。
