Reliable Oligonucleotide Conformational Ensemble Generation in Explicit Solvent for Force Field Assessment Using Reservoir Replica Exchange Molecular Dynamics Simulations

Abstract

Molecular dynamics force field development and assessment requires a reliable means for obtaining a well-converged conformational ensemble of a molecule in both a time-efficient and cost-effective manner. This remains a challenge for RNA because its rugged energy landscape results in slow conformational sampling and accurate results typically require explicit solvent which increases computational cost. To address this, we performed both traditional and modified replica exchange molecular dynamics simulations on a test system (alanine dipeptide) and an RNA tetramer known to populate A-form-like conformations in solution (single-stranded rGACC). A key focus is on providing the means to demonstrate that convergence is obtained, for example by investigating replica RMSD profiles and/or detailed ensemble analysis through clustering. We found that traditional replica exchange simulations still require prohibitive time and resource expenditures, even when using GPU accelerated hardware, and our results are not well converged even at 2 microseconds of simulation time per replica. In contrast, a modified version of replica exchange, reservoir replica exchange in explicit solvent, showed much better convergence and proved to be both a cost-effective and reliable alternative to the traditional approach. We expect this method will be attractive for future research that requires quantitative conformational analysis from explicitly solvated simulations.

Small Details Matter: The 2′-Hydroxyl as a Conformational Switch in RNA

“…They include the following: (i) standard simulations in hairpin and kissing loop RNA motives ; (ii) potentials of mean force (PMF) of the  rotation at the dinucleotide (rCpC) level using umbrella sampling (US) with an 18° interval grid of the κ torsional space (500 ps equilibration and 2.5 ns of averaging per window); and (iii) Hamiltonian-replica exchange molecular dynamics (H-REMD) to evaluate the conformational landscape of two small RNA tetranucleotides (rGACC and rCCCC) for which experimental structural data in solution are available. 19,20 All calculations were performed using the parm99 force field 21,22 supplemented with the bsc0 23 and chiOL3 24,25 modifications for RNA; some control simulations were performed with a local experimental RNA version of the parmbsc1 forcefield. 26 Electroneutrality was achieved by adding K + and extra K + Cl -to generate a 150 mM concentration (taking Dang's parameters [27][28][29] to represent ions).…”

“…A representative structure of the first peak is indicated with a dotted arrow and corresponds to the unique conformation observed in NMR. 19 (E) RMSD distribution calculated using the backbone atoms of all residues in a RNA hairpin (PDBID: 2KOC) from two unbiased 1µs long MD simulations using parmbsc0chiOL3 (black line) or parmbsc0chiOL3KappavdW (red line). (F) Same as in (E) but for the region containing the loop plus the first stem base pair.…”

“…A-form portion of the H. marismortui ribosome crystal structure (PDBID: 3G6E, residues 164 2623-2626), following the same approach as Henriksen et al 19 rCCCC initial structure was 165 generated in a random conformation using NAB. The RNA molecule in each system was 166 modelled using parmbsc0chiOL3, solvated using the TIP3P model 10 NVT.…”

Highly sampled tetranucleotide and tetraloop motifs enable evaluation of common RNA force fields

“…A step in the right direction has been the application of enhanced sampling methods which have been used to identify problems and validate updates to force field parameter sets (Mlýnský et al 2010;Chen and García 2013;Nguyen et al 2014). Widely applied among enhanced sampling methodologies are replica exchange molecular dynamics (REMD) simulations, which have become a common way to evaluate conformational ensembles of RNA (Sorin et al 2002;Vaiana and Sanbonmatsu 2009;Chen and García 2013;Henriksen et al 2013;Kührová et al 2013;Bergonzo et al 2014;Roe et al 2014). In REMD, several independent simulations are run at different temperatures or Hamiltonians (referred to as T-REMD and H-REMD, respectively), and exchanges are attempted between them at specific intervals (Hansmann 1997;Sugita and Okamoto 1999).…”

Structural fidelity and NMR relaxation analysis in a prototype RNA hairpin

“…Both X-ray and NMR show that the formation of hairpin fold leads the adoption of noncanonical backbone conformations and base-pairings. For these reasons, certain RNA hairpins have received recently considerable attention in both molecular dynamics (MD) studies (Banas et al 2010;Deng and Cieplak 2010;DePaul et al 2010;Zuo et al 2010;Chen and Garcia 2013;Henriksen et al 2013;Kührová et al 2013) that drove AMBER and CHARMM force-field modifications (Cheatham and Case 2013) as well as in RNA three dimensional structure prediction studies (Das 2011).…”