Gattin Zrinka, Schwartz Julian, Mathad Raveendra I, Jaun Bernhard, van Gunsteren Wilfred F
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zürich, Switzerland.
Chemistry. 2009 Jun 22;15(26):6389-98. doi: 10.1002/chem.200802523.
A proper description of the conformational equilibrium of polypeptides or proteins is essential for a correct description of their function. The conformational ensembles from 16 molecular dynamic simulations of two beta- heptapeptides were used to interpret the primary NMR data, which were also compared to a set of NMR model structures (see graphic).One of the most used spectroscopic techniques for resolving the structure of a biomolecule, such as a protein or peptide, is NMR spectroscopy. Because only NMR signal intensities and frequencies are measured in the experiment, a conformational interpretation of the primary data, that is, measured data, is not straightforward, especially for flexible molecules. It is hampered by the occurrence of conformational and/or time-averaging, by insufficient number of experimental data and by insufficient accuracy of experimental data. All three problematic aspects of structure refinement based on NMR nuclear Overhauser effect (NOE) intensities and (3)J coupling data are illustrated by using two beta-heptapeptides in methanol as an example. We have performed 16 molecular dynamics (MD) simulations between 20 to 100 ns in length of unrestrained and NOE distance-restrained cases (instantaneous and time-averaged) of two beta-heptapeptides with a central beta-HAla(alpha-OH) amino acid in methanol at two different temperatures using two different GROMOS force-field parameter sets, 45 A3 and 53 A6. The created conformational ensembles were used to interpret the primary NMR data on these molecules. They also were compared to a set of NMR model structures derived by single-structure refinement in vacuo by using standard techniques. It is shown that the conformational interpretation of measured experimental data can be significantly improved by using unrestrained, instantaneous and time-averaged restrained MD simulations of the peptides by using a thermodynamically calibrated force field and by explicitly including solvent degrees of freedom.
对多肽或蛋白质的构象平衡进行恰当描述对于正确阐释其功能至关重要。通过对两个β - 七肽进行16次分子动力学模拟得到的构象系综用于解释主要的核磁共振数据，这些数据还与一组核磁共振模型结构进行了比较（见图）。核磁共振光谱法是解析生物分子（如蛋白质或肽）结构时最常用的光谱技术之一。由于在实验中仅测量核磁共振信号强度和频率，对原始数据（即测量数据）进行构象解释并非易事，尤其是对于柔性分子。这受到构象和/或时间平均的影响、实验数据数量不足以及实验数据准确性不足的阻碍。以甲醇中的两个β - 七肽为例，说明了基于核磁共振核Overhauser效应（NOE）强度和（3）J耦合数据进行结构优化时的所有这三个问题。我们在两种不同温度下，使用两种不同的GROMOS力场参数集（45 A3和53 A6），对甲醇中含有中心β - HAla(α - OH)氨基酸的两个β - 七肽进行了长度在20至100纳秒之间的16次无约束和NOE距离约束（瞬时和时间平均）的分子动力学（MD）模拟。所创建的构象系综用于解释这些分子的主要核磁共振数据。它们还与通过使用标准技术在真空中进行单结构优化得到的一组核磁共振模型结构进行了比较。结果表明，通过使用经过热力学校准的力场并明确纳入溶剂自由度，对肽进行无约束、瞬时和时间平均约束的MD模拟，可以显著改善对实测实验数据的构象解释。
