Frequency-Selective Anharmonic Mode Analysis of Thermally Excited Vibrations in Proteins
Frequency-Selective Anharmonic Mode Analysis of Thermally Excited Vibrations in Proteins
复制标题
蛋白质热激发振动的频率选择性非简谐振动模式分析
DOI：
10.1021/acs.jctc.2c01309
复制
发表时间：
2023
影响因子：
5.5
通讯作者：
Heyden, Matthias
中科院分区：
文献类型：
--
作者：
Sauer, Michael A.;Heyden, Matthias
远红外频率的低频分子振动在室温下被热激发。因此，热波动不仅限于势能表面上局部最小值附近，并且非简谐特性也不能被忽略。后者与具有多种构象的分子尤其相关，例如蛋白质和其他生物分子。然而，迄今为止，用于分析分子振动的现有理论和计算框架受到谐波或准谐波近似的限制，这些近似不适合描述非谐波低频振动。在这里，我们引入了基于时间相关形式主义的分子振动的完全非调和分析，消除了对谐波或准谐波近似的需要。我们使用小蛋白质的分子动力学模拟来证明，与谐波和准谐波正常模式相比，这种新方法可以正确识别与任何给定频率下的分子振动相关的集体自由度。这使我们能够明确地表征远红外光谱中低频振动的非谐波特征。
Low-frequency molecular vibrations at far-infrared frequencies are thermally excited at room temperature. As a consequence, thermal fluctuations are not limited to the immediate vicinity of local minima on the potential energy surface, and anharmonic properties cannot be ignored. The latter is particularly relevant in molecules with multiple conformations, such as proteins and other biomolecules. However, existing theoretical and computational frameworks for the analysis of molecular vibrations have so far been limited by harmonic or quasi-harmonic approximations, which are ill-suited to describe anharmonic low-frequency vibrations. Here, we introduce a fully anharmonic analysis of molecular vibrations based on a time correlation formalism that eliminates the need for harmonic or quasi-harmonic approximations. We use molecular dynamics simulations of a small protein to demonstrate that this new approach, in contrast to harmonic and quasi-harmonic normal modes, correctly identifies the collective degrees of freedom associated with molecular vibrations at any given frequency. This allows us to unambiguously characterize the anharmonic character of low-frequency vibrations in the far-infrared spectrum.