Calculation of Relative Binding Free Energy in the Water-Filled Active Site of Oligopeptide-Binding Protein A
AbstractThe periplasmic oligopeptide binding protein A (OppA) represents a well-known example of water-mediated protein-ligand interactions. Here, we perform free-energy calculations for three different ligands binding to OppA, using a thermodynamic integration approach. The tripeptide ligands share a high structural similarity (all have the sequence KXK), but their experimentally-determined binding free energies differ remarkably. Thermodynamic cycles were constructed for the ligands, and simulations conducted in the bound and (freely solvated) unbound states. In the unbound state, it was observed that the difference in conformational freedom between alanine and glycine leads to a surprisingly slow convergence, despite their chemical similarity. This could be overcome by increasing the softness parameter during alchemical transformations. Discrepancies remained in the bound state however, when comparing independent simulations of the three ligands. These difficulties could be traced to a slow relaxation of the water network within the active site. Fluctuations in the number of water molecules residing in the binding cavity occur mostly on a timescale larger than the simulation time along the alchemical path. After extensive simulations, relative binding free energies that were converged to within thermal noise could be obtained, which agree well with available experimental data. View Full-Text
- Supplementary File 1:
Supplementary (PDF, 1044 KB)
Scifeed alert for new publicationsNever miss any articles matching your research from any publisher
- Get alerts for new papers matching your research
- Find out the new papers from selected authors
- Updated daily for 49'000+ journals and 6000+ publishers
- Define your Scifeed now
Maurer, M.; de Beer, S.B.A.; Oostenbrink, C. Calculation of Relative Binding Free Energy in the Water-Filled Active Site of Oligopeptide-Binding Protein A. Molecules 2016, 21, 499.
Maurer M, de Beer SBA, Oostenbrink C. Calculation of Relative Binding Free Energy in the Water-Filled Active Site of Oligopeptide-Binding Protein A. Molecules. 2016; 21(4):499.Chicago/Turabian Style
Maurer, Manuela; de Beer, Stephanie B.A.; Oostenbrink, Chris. 2016. "Calculation of Relative Binding Free Energy in the Water-Filled Active Site of Oligopeptide-Binding Protein A." Molecules 21, no. 4: 499.
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.