Calculation of absolute protein-ligand binding affinity using path and endpoint approaches.
A comparative analysis is provided of rigorous and approximate methods for calculating absolute binding affinities of two protein-ligand complexes: the FKBP protein bound with small molecules 4-hydroxy-2-butanone and FK506. Our rigorous approach is an umbrella sampling technique where a potential of mean force is determined by pulling the ligand out of the protein active site over several simulation windows. The results of this approach agree well with experimentally observed binding affinities. Also assessed is a commonly used approximate endpoint approach, which separately estimates enthalpy, solvation free energy, and entropy. We show that this endpoint approach has numerous variations, all of which are prone to critical shortcomings. For example, conventional harmonic and quasiharmonic entropy estimation procedures produce disparate results for the relatively simple protein-ligand systems studied in this work.
Lee
Michael S
MS
Department of Cell Biology and Biochemistry, U.S. Army Medical Research Institute of Infectious Diseases, Frederick, Maryland 21702, USA. michael.lee@amedd.army.mil
Olson
Mark A
MA
D001665:Binding Sites; D001703:Biophysics / Q000379:methods*; D002074:Butanones / Q000737:chemistry*; D002352:Carrier Proteins; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D019277:Entropy; D006358:Hot Temperature; D006860:Hydrogen Bonding; D007700:Kinetics; D008024:Ligands; D008958:Models, Molecular; D015394:Molecular Structure; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012997:Solvents; D016559:Tacrolimus / Q000737:chemistry*; D013816:Thermodynamics
C460540:3,4-dihydroxy-2-butanone; D002074:Butanones; D002352:Carrier Proteins; D008024:Ligands; D011506:Proteins; D012997:Solvents; D016559:Tacrolimus