Additive CHARMM force field for naturally occurring modified ribonucleotides.

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TitleAdditive CHARMM force field for naturally occurring modified ribonucleotides.
Publication TypeJournal Article
Year of Publication2016
AuthorsXu, Y, Vanommeslaeghe, K, Aleksandrov, A, Mackerell, AD, Nilsson, L
JournalJ Comput Chem
Volume37
Issue10
Pagination896-912
Date Published2016 Apr 15
ISSN1096-987X
KeywordsMolecular Structure, Quantum Theory, Ribonucleotides, RNA
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.

DOI10.1002/jcc.24307
Alternate JournalJ Comput Chem
PubMed ID26841080
PubMed Central IDPMC4801715
Grant ListR01 GM051501 / GM / NIGMS NIH HHS / United States
GM051501 / GM / NIGMS NIH HHS / United States
GM070855 / GM / NIGMS NIH HHS / United States