AMBER force field parameters for the naturally occurring modified nucleosides in RNA

被引:155
作者
Aduri, Raviprasad [1 ]
Psciuk, Brian T. [1 ]
Saro, Pirro [1 ]
Taniga, Hariprakash [1 ]
Schlegel, H. Bernhard [1 ]
SantaLucia, John, Jr. [1 ]
机构
[1] Wayne State Univ, Dept Chem, Detroit, MI 48202 USA
关键词
D O I
10.1021/ct600329w
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 ; 081704 ;
摘要
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.
引用
收藏
页码:1464 / 1475
页数:12
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