Reorientations of aromatic amino acids and their side chain models: anisotropy measurements and molecular dynamics simulations.
Reorientations of aromatic amino acids and their side chain models: anisotropy measurements and molecular dynamics simulations.
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芳香族氨基酸及其侧链模型的重新取向：各向异性测量和分子动力学模拟。
DOI：
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发表时间：
2010
影响因子：
2.9
通讯作者：
G. Jas
中科院分区：
文献类型：
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作者：
K. Kuczera;J. Unruh;Carey K. Johnson;G. Jas
本文研究了三种芳香氨基酸在水溶液中的重定向动力学及其侧链模型。实验中，对阻断色氨酸、酪氨酸和苯丙氨酸以及模型化合物对甲酚和3-甲基吲哚进行了皮秒时间分辨率的各向异性衰减测量。计算上，采用分子动力学方法模拟了苯、甲苯、苯酚、对甲酚、吲哚和3-甲基吲哚三种芳香残基及其侧链模型在显式水中的旋转扩散。我们的模拟使用了CHARMM蛋白力场和相关的TIP3P水模型，往往低估了旋转相关时间。然而，模拟对重新定向运动产生了一些有趣的定性见解，补充了实验测量。取代基和温度对母体化合物取向的影响在计算上得到了很好的再现。此外，模拟结果表明，大多数化合物具有强烈的各向异性取向，构象动力学和旋转扩散之间存在时间尺度的分离。与连续流体动力学模型的比较表明，我们可以认为被阻断的氨基酸在黏着边界条件下运动，而大多数模型化合物的动力学处于黏着和滑动之间。我们对阻断氨基酸的系统处理，从母体化合物（苯、苯酚和吲哚）开始，为理解更复杂的肽系统的各向异性衰减信号提供了基础。
We present a study of reorientation dynamics of the three aromatic amino acids and their side chain models in aqueous solution. Experimentally, anisotropy decay measurements with picosecond time resolution were performed for blocked tryptophan, tyrosine, and phenyalanine and model compounds p-cresol and 3-methylindole. Computationally, rotational diffusion was modeled by molecular dynamics simulations for the three aromatic residues and their side chain models: benzene, toluene, phenol, p-cresol, indole, and 3-methylindole in explicit water. Our simulations used the CHARMM protein force field and associated TIP3P water model and tend to underestimate the rotational correlation times. However, the simulations yield several interesting qualitative insights into reorientational motions that complement the experimental measurements. The effects of substituent and temperature on reorientations of the parent compounds are well reproduced computationally. Additionally, simulations indicate strongly anisotropic reorientations for most of the studied compounds and a separation of time scales between conformational dynamics and rotational diffusion. Comparison with continuum hydrodynamic models suggests that we may consider that the blocked amino acids move under stick boundary conditions, while the dynamics for most of the model compounds falls between stick and slip conditions. Our systematic treatment of blocked amino acids, starting from the parent compounds (benzene, phenol, and indole) provides a baseline for understanding the anisotropy decay signals of more complicated peptide systems.