Molecular Dynamics Simulations of Highly Crowded Amino Acid Solutions: Comparisons of Eight Different Force Field Combinations with Experiment and with Each Other

Abstract

Although it is now commonly accepted that the highly crowded conditions encountered inside biological cells have the potential to significantly alter the thermodynamic properties of biomolecules, it is not known to what extent the thermodynamics of fundamental types of interactions such as salt bridges and hydrophobic interactions are strengthened or weakened by high biomolecular concentrations. As one way of addressing this question we have performed a series of all-atom explicit solvent molecular dynamics (MD) simulations to investigate the effect of increasing solute concentration on the behavior of four types of zwitterionic amino acids in aqueous solution. We have simulated systems containing glycine, valine, phenylalanine or asparagine at concentrations of 50, 100, 200 and 300 mg/ml. Each molecular system has been simulated for 1 μs in order to obtain statistically converged estimates of thermodynamic parameters, and each has been conducted with 8 different force fields and water models; the combined simulation time is 128 μs. The density, viscosity, and dielectric increments of the four amino acids calculated from the simulations have been compared to corresponding experimental measurements. While all of the force fields perform well at reproducing the density increments, discrepancies for the viscosity and dielectric increments raise questions both about the accuracy of the simulation force fields and, in certain cases, the experimental data. We also observe large differences between the various force fields' descriptions of the interaction thermodynamics of salt bridges and, surprisingly, these differences also lead to qualitatively different predictions of their dependences on solute concentration. For the aliphatic interactions of valine sidechains, fewer differences are observed between the force fields, but significant differences are again observed for aromatic interactions of phenylalanine sidechains. Taken together, the results highlight the potential power of using explicit-solvent simulation methods to understand behavior in concentrated systems but also hint at potential difficulties in using these methods to obtain consistent views of behavior in intracellular environments.

Macromolecular crowding studies of amino acids using NMR diffusion measurements and molecular dynamics simulations

“…For example, obstruction is a many-body problem and in general a numerical solution of the obstruction factor is the only practicable approach. MD simulations for these systems can provide valuable information on the solute-solute, solvent-solvent and solute-solvent interactions at the atomic level [37,38,[74][75][76].…”

“…A number of force fields have been developed to study a variety of different systems or properties by computer simulation [77][78][79][80]. These force fields have the same interaction sites of molecules but differ in the Lennard-Jones and Coulombic terms, which give significant differences in calculated properties for the molecules of interest [37,81]. Hence, the choice of force fields plays a crucial role in determining different interactions between molecules for a particular system.…”

“…Hence, the choice of force fields plays a crucial role in determining different interactions between molecules for a particular system. Elcock et al [37] investigated the performance of different force fields on highly crowded amino acid solutions. Note that the effect of different force fields on the simulated diffusion coefficients of water and amino acids also needs to be compared with experimental results.…”

“…Amino acids, being simpler than proteins, are a logical stepping stone toward understanding crowded biological systems. The clustering of amino acids such as glycine has been studied using NMR diffusion experiments and molecular dynamics (MD) simulations as a function of concentration, pH and temperature [22][23][24][34][35][36][37][38]. Hughes et al [23] used a multidisciplinary approach (i.e., NMR diffusion, MD simulations and small-angle neutron scattering) to investigate the crystallization of glycine in aqueous solutions.…”

“…despite the significance of crowding on solution thermodynamics, the molecular level mechanism of crowding including how it influences diffusion remains to be clarified [19,[36][37][38]. The major hindrance to understanding crowding is the lack of a direct comparison of experimental data with theoretical data for the same system [39].…”