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Molecular Dynamics and Spin-Lattice NMR Relaxation in $$\alpha$$- and $$\varepsilon$$-Polylysine
Applied Magnetic Resonance ( IF 1 ) Pub Date : 2020-09-14 , DOI: 10.1007/s00723-020-01260-8
V. V. Bezrodnyi , O. V. Shavykin , S. E. Mikhtaniuk , I. M. Neelov , D. A. Markelov

The NMR relaxation method is widely used in various biomedical applications. Investigation of model homopeptides is an important step for understanding of structure and NMR properties of more complex branched peptides based on lysine monomers, for example, dendrimers, dendrigrafts and dendritic polymer brushes. In this paper, we perform molecular dynamics simulation of two linear lysine peptides with the same number of lysine monomers but with different connection between them through $$\alpha$$ - or $$\varepsilon$$ -peptide bonds. We obtained that the end-to-end distance and radius of gyration are smaller and radial density near the center of mass is essentially larger and decrease faster with radial distance for $$\alpha$$ -lysine peptide than for $$\varepsilon$$ -lysine peptide. Orientational mobility of $$\hbox {CH}_2$$ groups in both peptides could be described by second order orientational autocorrelation function and by spin-lattice NMR relaxation time. We calculated both functions and found that the relaxation of vector in side chains of $$\alpha$$ -lysine peptide is slightly faster in comparison with mobility of $$\hbox {CH}_2$$ groups in main chain of $$\varepsilon$$ -lysine peptide. Thus the big difference between the relaxation rates of these two types of $$\hbox {CH}_2$$ groups in lysine dendrimers obtained recently both in NMR and in simulation is mainly due to dendrimer effect and not due to difference in position (side or main chain) of $$\hbox {CH}_2$$ group in short linear lysine fragments. This result allows to use NMR for discrimination between $$\alpha$$ -lysine and $$\varepsilon$$ -lysine peptides as well as between linear lysine peptides (or their mixtures) and lysine dendrimers.

中文翻译:

$$\alpha$$- 和 $$\varepsilon$$-聚赖氨酸中的分子动力学和自旋晶格核磁共振弛豫

核磁共振弛豫方法广泛用于各种生物医学应用。模型同肽的研究是了解基于赖氨酸单体的更复杂分支肽的结构和 NMR 特性的重要步骤,例如树枝状聚合物、树枝状聚合物和树枝状聚合物刷。在本文中,我们对两个具有相同数量赖氨酸单体但它们之间通过 $$\alpha$$ - 或 $$\varepsilon$$ - 肽键连接不同的线性赖氨酸肽进行分子动力学模拟。我们发现,$$\alpha$$-赖氨酸肽的端到端距离和回转半径更小,质心附近的径向密度基本上更大,并且随着径向距离的增加而减少得比$$\varepsilon$ 快$-赖氨酸肽。两种肽中$$\hbox {CH}_2$$ 基团的取向迁移率可以通过二阶取向自相关函数和自旋晶格核磁共振弛豫时间来描述。我们计算了这两个函数,发现$$\alpha$$-赖氨酸肽侧链中vector的弛豫速度比$$\主链中$$\hbox {CH}_2$$基团的移动性稍快varepsilon$$ -赖氨酸肽。因此,最近在核磁共振和模拟中获得的赖氨酸树枝状聚合物中这两种 $$\hbox {CH}_2$$ 基团的弛豫率之间的巨大差异主要是由于树枝状大分子效应而不是由于位置差异(侧或主链)的 $$\hbox {CH}_2$$ 组在短的线性赖氨酸片段中。
更新日期:2020-09-14
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