title: AMBER Force Field Parameters for the Naturally Occurring Modified Nucleosides in RNA.
abstract: 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.
authors.affiliation: Department of Chemistry, Wayne State University, Detroit, Michigan 48202.
authors.forename: Raviprasad
authors.initials: R
authors.lastname: Aduri
authors.affiliation: Department of Chemistry, Wayne State University, Detroit, Michigan 48202.
authors.forename: Brian T
authors.initials: BT
authors.lastname: Psciuk
authors.affiliation: Department of Chemistry, Wayne State University, Detroit, Michigan 48202.
authors.forename: Pirro
authors.initials: P
authors.lastname: Saro
authors.affiliation: Department of Chemistry, Wayne State University, Detroit, Michigan 48202.
authors.forename: Hariprakash
authors.initials: H
authors.lastname: Taniga
authors.affiliation: Department of Chemistry, Wayne State University, Detroit, Michigan 48202.
authors.forename: H Bernhard
authors.initials: HB
authors.lastname: Schlegel
authors.affiliation: Department of Chemistry, Wayne State University, Detroit, Michigan 48202.
authors.forename: John
authors.initials: J
authors.lastname: SantaLucia