甘氨酸三肽和六肽的构象变化
Conformational changes in glycine tri- and hexapeptide
摘要：
本文研究了由三个和六个氨基酸组成的甘氨酸链的势能面。对于这些分子，我们已经计算了势能面作为一个函数的Ramachandran角φ和psi，这是广泛用于表征的多肽链。这些特定的自由度对于表征蛋白质折叠过程是必不可少的。计算是在基于密度泛函理论的从头算理论框架内进行的，考虑了体系中所有的电子。我们已经确定了稳定的构象，并计算了它们之间的转换的能量障碍。使用热力学方法，我们估计了这些构象之间的特征转换的时间。我们的计算结果进行了比较，与其他理论方法和蛋白质数据库中提取的实验数据。这种比较表明，在计算的势能面上的最突出的最小值与天然蛋白质中出现的甘氨酸链的实验测量的角度phi和psi的合理对应。我们还研究了多肽链的二级结构对势能景观形成的影响。这种分析已经进行了6个氨基酸的链的片和螺旋构象。
英文摘要：
We have investigated the potential energy surfaces for glycine chains consisting of three and six amino acids. For these molecules we have calculated potential energy surfaces as a function of the Ramachandran angles phi and psi, which are widely used for the characterization of the polypeptide chains. These particular degrees of freedom are essential for the characterization of proteins folding process. Calculations have been carried out within ab initio theoretical framework based on the density functional theory and accounting for all the electrons in the system. We have determined stable conformations and calculated the energy barriers for transitions between them. Using a thermodynamic approach, we have estimated the times of the characteristic transitions between these conformations. The results of our calculations have been compared with those obtained by other theoretical methods and with the available experimental data extracted from the Protein Data Base. This comparison demonstrates a reasonable correspondence of the most prominent minima on the calculated potential energy surfaces to the experimentally measured angles phi and psi for the glycine chains appearing in native proteins. We have also investigated the influence of the secondary structure of polypeptide chains on the formation of the potential energy landscape. This analysis has been performed for the sheet and the helix conformations of chains of six amino acids.
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