Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations

Abstract

Alkali (Li+, Na+, K+, Rb+, and Cs+) and halide (F−, Cl−, Br−, and I−) ions play an important role in many biological phenomena, roles that range from stabilization of biomolecular structure, to influence on biomolecular dynamics, to key physiological influence on homeostasis and signaling. To properly model ionic interaction and stability in atomistic simulations of biomolecular structure, dynamics, folding, catalysis, and function, an accurate model or representation of the monovalent ions is critically necessary. A good model needs to simultaneously reproduce many properties of ions, including their structure, dynamics, solvation, and moreover both the interactions of these ions with each other in the crystal and in solution and the interactions of ions with other molecules. At present, the best force fields for biomolecules employ a simple additive, nonpolarizable, and pairwise potential for atomic interaction. In this work, we describe our efforts to build better models of the monovalent ions within the pairwise Coulombic and 6-12 Lennard-Jones framework, where the models are tuned to balance crystal and solution properties in Ewald simulations with specific choices of well-known water models. Although it has been clearly demonstrated that truly accurate treatments of ions will require inclusion of nonadditivity and polarizability (particularly with the anions) and ultimately even a quantum mechanical treatment, our goal was to simply push the limits of the additive treatments to see if a balanced model could be created. The applied methodology is general and can be extended to other ions and to polarizable force-field models. Our starting point centered on observations from long simulations of biomolecules in salt solution with the AMBER force fields where salt crystals formed well below their solubility limit. The likely cause of the artifact in the AMBER parameters relates to the naive mixing of the Smith and Dang chloride parameters with AMBER-adapted Åqvist cation parameters. To provide a more appropriate balance, we reoptimized the parameters of the Lennard-Jones potential for the ions and specific choices of water models. To validate and optimize the parameters, we calculated hydration free energies of the solvated ions and also lattice energies (LE) and lattice constants (LC) of alkali halide salt crystals. This is the first effort that systematically scans across the Lennard-Jones space (well depth and radius) while balancing ion properties like LE and LC across all pair combinations of the alkali ions and halide ions. The optimization across the entire monovalent series avoids systematic deviations. The ion parameters developed, optimized, and characterized were targeted for use with some of the most commonly used rigid and nonpolarizable water models, specifically TIP3P, TIP4PEW, and SPC/E. In addition to well reproducing the solution and crystal properties, the new ion parameters well reproduce binding energies of the ions to water and the radii of the first hydration shells.

Free Energy Landscape of GAGA and UUCG RNA Tetraloops

“…The systems described in Table 1 were solvated in a truncated dodecahedral box with TIP3P 22 water molecules and neutralized by adding Na + counterions. 23 RNA was modeled using the Amber99 force field 24 with parmbsc0 25 and χ OL3 corrections. 9 We will refer to this combination of force field corrections as Amberχ OL3 in the remainder of this paper.…”

Long-Range Conformational Transition of a Photoswitchable Allosteric Protein: Molecular Dynamics Simulation Study

“…The protein was described using the Amber99sb * -ILDN [53][54][55] force field, the water by the TIP3P 56 model, and the ions with the model of Ref. 57 To obtain the force field parameters for the azobenzene photoswitch and the attached cysteine side chains, the structure of the switch and the side chains in the cis and the trans conformation was optimized on the B3LYP/6-31G* level using the GAUSSIAN g09 program suite. 58 For both minimized structures the electrostatic potential was computed using the Hartree Fock method and the 6-31G* basis set.…”

The pathway to GTPase activation of elongation factor SelB on the ribosome

“…Parameters for potassium and chloride ions were taken from ref. 85 and for modified nucleotides from Aduri et al 86 . Atom types for selenocysteine were obtained with ANTECHAMBER 87 and partial charges were determined using DFT-B3LYP with a 6-31/G* basis set.…”