AMBER force field parameters for the naturally occurring modified nucleosides in RNA
AMBER force field parameters for the naturally occurring modified nucleosides in RNA
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DOI：
10.1021/ct600329w
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发表时间：
2007-07-01
影响因子：
5.5
通讯作者：
SantaLucia, John, Jr.
中科院分区：
文献类型：
--
作者：
Aduri, Raviprasad;Psciuk, Brian T.;SantaLucia, John, Jr.
经典分子动力学（MD）模拟可用于表征生物大分子的结构和动力学，最终导致生物功能的阐明。AMBER力场被广泛使用，对于所有常见的氨基酸和核苷酸都有明确的键长、键角、部分电荷和货车范德华参数，但对于核酸和蛋白质中发现的许多修饰，它缺乏参数。目前已知有107种天然存在的修饰在RNA稳定性、折叠和其他功能中发挥重要作用。修饰的核苷酸存在于几乎所有的转运RNA、大小亚基的核糖体RNA以及许多其他功能性RNA中。我们为目前已知存在于RNA中的107种修饰核苷酸开发了力场参数。用于推导修饰的核苷酸参数的方法与用于开发Cornell等人力场的方法一致。这些参数将改善AMBER的功能，以便现在可以容易地对具有转录后修饰的不同RNA进行模拟。
Classical molecular dynamics (MD) simulations are useful for characterizing the structure and dynamics of biological macromolecules, ultimately, resulting in elucidation of biological function. The AMBER force field is widely used and has well-defined bond length, bond angle, partial charge, and van der Waals parameters for all the common amino acids and nucleotides, but it lacks parameters for many of the modifications found in nucleic acids and proteins. Presently there are 107 known naturally occurring modifications that play important roles in RNA stability, folding, and other functions. Modified nucleotides are found in almost all transfer RNAs, ribosomal RNAs of both the small and large subunits, and in many other functional RNAs. We developed force field parameters for the 107 modified nucleotides currently known to be present in RNA. The methodology used for deriving the modified nucleotide parameters is consistent with the methods used to develop the Cornell et al. force field. These parameters will improve the functionality of AMBER so that simulations can now be readily performed on diverse RNAs having post-transcriptional modifications.