title: Additive CHARMM force field for naturally occurring modified ribonucleotides.
abstract: More than 100 naturally occurring modified nucleotides have been found in RNA molecules, in particular in tRNAs. We have determined molecular mechanics force field parameters compatible with the CHARMM36 all-atom additive force field for all these modifications using the CHARMM force field parametrization strategy. Emphasis was placed on fine tuning of the partial atomic charges and torsion angle parameters. Quantum mechanics calculations on model compounds provided the initial set of target data, and extensive molecular dynamics simulations of nucleotides and oligonucleotides in aqueous solutions were used for further refinement against experimental data. The presented parameters will allow for computational studies of a wide range of RNAs containing modified nucleotides, including the ribosome and transfer RNAs.
authors: Department of Biosciences and Nutrition, Karolinska Institutet, HUDDINGE, SE-141 83, Sweden.
authors: You
authors: Y
authors: Xu
authors: Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, Maryland, 21201.|Department of Analytical Chemistry and Pharmaceutical Technology (FABI), Center for Pharmaceutical Research (CePhaR), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, Brussels, B-1090, Belgium.
authors: Kenno
authors: K
authors: Vanommeslaeghe
authors: Department of Biology, Ecole Polytechnique, Laboratoire De Biochimie (CNRS UMR7654), Palaiseau, F-91128, France.
authors: Alexey
authors: A
authors: Aleksandrov
authors: Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, Maryland, 21201.
authors: Alexander D
authors: AD
authors: MacKerell
authors: Department of Biosciences and Nutrition, Karolinska Institutet, HUDDINGE, SE-141 83, Sweden.
authors: Lennart
authors: L
authors: Nilsson
mesh_terms: D015394:Molecular Structure; D011789:Quantum Theory; D012313:RNA / Q000737:chemistry*; D012265:Ribonucleotides / Q000737:chemistry*
chemical_list: D012265:Ribonucleotides; D012313:RNA
keywords: RNA; empirical force field; molecular dynamics; nucleic acids; oligonucleotide; transfer RNA