Abstract
Thermodynamic integration (TI) molecular dynamics (MD) simulations for the binding of a pair of a reference (“ref”) ligand and an analogous (“analog”) ligand to either tagged (with six extra residues at the N-terminus) or untagged p38 kinase proteins were carried out in order to probe how the binding affinity is influenced by the presence or absence of the peptide tag in p38 kinase. This possible effect of protein length on the binding affinity of a ligand—which is seldom addressed in the literature—is important because, even when two labs claim to have performed experiments with the same protein, they may actually have studied variants of the same protein with different lengths because they applied different protein expression conditions/procedures. Thus, if we wanted to compare ligand binding affinities measured in the two labs, it would be necessary to account for any variation in ligand binding affinity with protein length. The pair of ligand–p38 kinase complexes examined in this work (pdb codes: 3d7z and 3lhj, respectively) were ideal for investigating this effect. The experimentally determined binding energy for the ref ligand with the untagged p38 kinase was −10.9 kcal mol−1, while that for the analog ligand with the tagged p38 kinase was −11.9 kcal mol−1. The present TI-MD simulation of the mutation of the ref ligand into the analog ligand while the ligand is bound to the untagged p38 kinase predicted that the binding affinity of the analog ligand is 2.0 kcal mol−1 greater than that of the ref ligand. A similar simulation also indicated that the same was true for ligand binding to the tagged protein, but in this case the binding affinity for the analog ligand is 2.5 kcal mol−1 larger than that for the ref ligand. These results therefore suggest that the presence of the peptide tag on p38 kinase increased the difference in the binding energies of the ligands by a small amount of 0.5 kcal mol−1. This result supports the assumption that the presence of a peptide tag has only a minor effect on ΔG values. The error bars in the computed ΔG values were then estimated via confidence interval analysis and a time autocorrelation function for the quantity dV/dλ. The estimated correlation time was ~0.5 ps and the error bar in the ΔG values estimated using nanosecond-scale simulations was ±0.3 kcal mol−1 at a confidence level of 95%. These predicted results can be verified in future experiments and should prove useful in subsequent similar studies.
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Acknowledgments
We would like to thank Drs. Ross Walker, Joseph Kaus, and Jason Swails for helpful discussions on using the pmemd module of Amber14. Financial support from the Ministry of Science and Technology is acknowledged, as well as the huge computing resources provided by the National Center for High-Performance Computing to facilitate this research. We also thank the NTNU English clinic service.
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Highlights
• We performed TI-MD simulations involving the mutation of a reference ligand to an analogous ligand while the ligand is bound to either untagged or tagged p38 kinase in order to compare the predicted ΔΔG values for the complexes containing untagged and tagged p38 kinases.
• The ΔΔG predicted for the complex with tagged p38 kinase was slightly (0.5 kcal mol−1) lower than that for the complex with untagged p38 kinase, supporting the assumption that the presence of a peptide tag has only a minor effect on ΔG values.
• A procedure that was used to estimate the error bar in the predicted (via simulation) ΔG values via the calculated time autocorrelation function for the quantity dV/dλ is described. This error bar was estimated as ±0.3 kcal mol−1.
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Sun, YC., Hsu, WC., Hsu, CJ. et al. Investigation of differences in the binding affinities of two analogous ligands for untagged and tagged p38 kinase using thermodynamic integration MD simulation. J Mol Model 21, 283 (2015). https://doi.org/10.1007/s00894-015-2825-8
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DOI: https://doi.org/10.1007/s00894-015-2825-8