Evaluating the strengths of salt bridges in the CutA1 protein using molecular dynamic simulations: a comparison of...

Ion-ion interactions (salt bridges) between favorable pairs of charged residues are important for the conformational stability of proteins. Molecular dynamic (MD) simulations are useful for elucidating the interactions among charged residues fluctuating in solution. However, the quality of MD results depends strongly on the force fields used. In this study, we compared the strengths of salt bridges among force fields by performing MD simulations using the CutA1 protein (trimer) from the hyperthermophile Pyrococcus horikoshii (PhCutA1), which has an unusually large proportion of charged residues. The force fields Chemistry at HARvard Macromolecular Mechanics (Charmm)27, Assisted Model Building and Energy Refinement (Amber)99sb, Amber14sb, GROningen Molecular Simulation (Gromos)43a1, and Gromos53a6 were used in combination with two different water models, tip3p (for Charmm27, Amber99sb, and Amber14sb) and simple point charge/extended (for Amber99sb, Gromos43a1, and Gromos53a6), yielding a total of six combinations. The RMSDs of all Cα atoms of PhCutA1 were similar among force fields, except for Charmm27, during 400-ns MD simulations at 300 K; however, the radius of gyration (R_g ) was greater for Amber99sb and shorter for Gromos43a1. The average strengths of salt bridges for each positively charged residue did not differ greatly among force fields, but the strengths at specific sites within the structure depended sensitively on the force field used. In the case of the Gromos group, positively charged residues could engage in favorable interactions with many more charged residues than in the other force fields, especially in loop regions; consequently, the apparent strength at each site was lower.