Exploration of the forbidden regions of the Ramachandran plot (ϕ-ψ) with QTAIM,Physical Chemistry Chemical Physics

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Exploration of the forbidden regions of the Ramachandran plot (ϕ-ψ) with QTAIM
Physical Chemistry Chemical Physics ( IF 2.9 ) Pub Date : 2017-09-11 00:00:00 , DOI: 10.1039/c7cp05124g
Roya Momen _{1,

2,

3,

4,

5} , Alireza Azizi _{1,

2,

3,

4,

5} , Lingling Wang _{1,

2,

3,

4,

5} , Yang Ping _{1,

2,

3,

4,

5} , Tianlv Xu _{1,

2,

3,

4,

5} , Steven R. Kirk _{1,

2,

3,

4,

5} , Wenxuan Li _{6,

7,

8,

9} , Sergei Manzhos _{6,

7,

8,

9} , Samantha Jenkins _{1,

2,

3,

4,

5}

Affiliation

A new QTAIM interpretation of the Ramachandran plot is formulated from the most and least facile eigenvectors of the second-derivative matrix of the electron density with a set of 29 magainin-2 peptide conformers. The presence of QTAIM eigenvectors associated with the most and least preferred directions of electronic charge density explained the role of hydrogen bonding, H⋯H contacts and the glycine amino acid monomer in peptide folding. The highest degree of occupation of the QTAIM interpreted Ramachandran plot was found for the glycine amino acid monomer compared with the remaining backbone peptide bonds. The mobility of the QTAIM eigenvectors of the glycine amino acid monomer was higher than for the other amino acids and was comparable to that of the hydrogen bonding, explaining the flexibility of the magainin-2 backbone. We experimented with a variety of hybrid QTAIM–Ramachandran plots to highlight and explain why the glycine amino acid monomer largely occupies the ‘forbidden’ region on the Ramachandran plot. In addition, the new hybrid QTAIM–Ramachandran plots contained recognizable regions that can be associated with concepts familiar from the conventional Ramachandran plot whilst retaining the character of the QTAIM most and least preferred regions.

中文翻译：

用QTAIM探索Ramachandran图（ϕ-ψ）的禁区。

Qachim对Ramachandran图的新解释是根据具有29个magainin-2肽构象体的电子密度二阶导数矩阵的最不易变的本征向量制定的。与电子电荷密度的最佳方向最不相关的QTAIM特征向量的存在解释了氢键，H⋯H接触和甘氨酸氨基酸单体在肽折叠中的作用。与剩余的骨架肽键相比，发现甘氨酸氨基酸单体的QTAIM解释的Ramachandran图具有最高的占领度。甘氨酸氨基酸单体的QTAIM特征向量的迁移率高于其他氨基酸，并且与氢键相当，说明了magainin-2主链的柔性。我们对各种QTAIM-Ramachandran混合图进行了试验，以突出显示和解释为什么甘氨酸氨基酸单体在Ramachandran图上主要占据“禁止”区域。此外，新的QTAIM-Ramachandran混合图包含可识别的区域，这些区域可与传统Ramachandran图熟悉的概念相关联，同时保留了QTAIM最受偏爱的区域的特征。

更新日期：2017-09-25

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