title: Development of Site-Specific Mg(2+)-RNA Force Field Parameters: A Dream or Reality? Guidelines from Combined Molecular Dynamics and Quantum Mechanics Simulations.
abstract: The vital contribution of Mg2+ions to RNA biology is challenging to dissect at the experimental level. This calls for the integrative support of atomistic simulations, which at the classical level are plagued by limited accuracy. Indeed, force fields intrinsically neglect nontrivial electronic effects that Mg2+exerts on its surrounding ligands in varying RNA coordination environments. Here, we present a combined computational study based on classical molecular dynamics (MD) and Density Functional Theory (DFT) calculations, aimed at characterizing (i) the performance of five Mg2+force field (FF) models in RNA systems and (ii) how charge transfer and polarization affect the binding of Mg2+ions in different coordination motifs. As a result, a total of ∼2.5 μs MD simulations (100/200 ns for each run) for two prototypical Mg2+-dependent ribozymes showed remarkable differences in terms of populations of inner-sphere coordination site types. Most importantly, complementary DFT calculations unveiled that differences in charge transfer and polarization among recurrent Mg2+-RNA coordination motifs are surprisingly small. In particular, the charge of the Mg2+ions substantially remains constant through different coordination sites, suggesting that the common philosophy of developing site-specific Mg2+ion parameters is not in line with the physical origin of the Mg2+-RNA MD simulations inaccuracies. Overall, this study constitutes a guideline for an adept use of current Mg2+models and provides novel insights for the rational development of next-generation Mg2+FFs to be employed for atomistic simulations of RNA.
authors.affiliation: International School for Advanced Studies (SISSA) , Trieste, Italy.
authors.forename: Lorenzo
authors.identifier: 0000-0003-3581-1148
authors.initials: L
authors.lastname: Casalino
authors.affiliation: Laboratory of Computational Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne , CH-1015 Lausanne, Switzerland.
authors.forename: Giulia
authors.identifier: 0000-0003-1404-8737
authors.initials: G
authors.lastname: Palermo
authors.affiliation: International School for Advanced Studies (SISSA) , Trieste, Italy.|Università degli Studi di Trieste , Trieste, Italy.
authors.forename: Nodira
authors.identifier: 0000-0003-3702-3241
authors.initials: N
authors.lastname: Abdurakhmonova
authors.affiliation: Laboratory of Computational Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne , CH-1015 Lausanne, Switzerland.
authors.forename: Ursula
authors.initials: U
authors.lastname: Rothlisberger
authors.affiliation: CNR-IOM-Democritos National Simulation Center c/o SISSA , via Bonomea 265, Trieste, Italy.
authors.forename: Alessandra
authors.initials: A
authors.lastname: Magistrato
mesh_terms: D007477:Ions / Q000737:chemistry; D008024:Ligands; D008274:Magnesium / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D011789:Quantum Theory; D012313:RNA / Q000737:chemistry*; D016337:RNA, Catalytic / Q000737:chemistry; D014867:Water / Q000737:chemistry
chemical_list: D007477:Ions; D008024:Ligands; D016337:RNA, Catalytic; D014867:Water; D012313:RNA; D008274:Magnesium