Ligand binding calculated

Grubmiiller et al., 1996] Grubmiiller, H., Heymann, B., and Tavan, P. Ligand binding and molecular mechanics calculation of the streptavidin-biotin rupture force. Science. 271 (1996) 997-999... 

We have previously calculated conformational free energy differences for a well-suited model system, the catalytic subunit of cAMP-dependent protein kinase (cAPK), which is the best characterized member of the protein kinase family. It has been crystallized in three different conformations and our main focus was on how ligand binding shifts the equilibrium among these ([Helms and McCammon 1997]). As an example using state-of-the-art computational techniques, we summarize the main conclusions of this study and discuss a variety of methods that may be used to extend this study into the dynamic regime of protein domain motion. 

FIGURE 8.14 Simulation for 5,000 theoretical ligands with calculated efficacy (Equation 8.11) and affinity (Equation 8.10). It can be seen that efficacy and affinity are correlated suggesting that all ligands that have been shown to bind to a receptor should be extensively tested for possible efficacy effects on the receptor directly, through agonist-effects on the receptor or changes in constitutive behavior of the receptor itself. Redrawn from [15]. 

Csilibrsition. Quantitative binding analysis requires knowing the concentration of FLPEP, which can be determined for a stock solution of FLPEP by absorption spectroscopy. The quenching by the antibody is essentially quantitative, and the relative amounts of free and bound ligand are calculated from the relative fluorescence intensity. 

Reddy MR, Erion MD, Agarwal A. Free energy calculations Use and limitations in predicting ligand binding affinities. In Lipkowitz KB, Boyd DB, editors. Reviews in Computational Chemistry, Vol. 16. New York Wiley-VCH, 2000. p. 217-304. 

Simonson, T. Archontis, G. Karplus, M., Continuum treatment of long-range interactions in free energy calculations. Application to protein-ligand binding, J. Phys. Chem. B 1997, 101, 8349-8362... 

To illustrate these methods, we consider the main biological problems that have motivated their development. The problems that have received the most attention are the receptor-ligand binding problem [12-16] and the calculation of proton binding affinities (pKa shifts) [17-20], The methods described can also be applied to many related problems, such as redox protein behavior, protein-protein association, protein folding, or membrane insertion. 

Woo, H.J. Roux, B., Calculation of absolute protein ligand binding free energy from computer simulations, Proc. Natl Acad. Sci. USA 2005,102, 6825-6830... 

Sham, Y.Y. Shao, Z.T. Tao, H. Warshel, A., Examining methods for calculations of binding free energies LRA, LIE and PDLD/S-LRA calculations of ligand binding to an HIV protease, Proteins 2000, 39, 393-407... 

As shown in Figure 6, the solvent molecules tend to be ordered around the molecules and when the protein and the ligand bind, several of these molecules are liberated and become disordered (entropic effect). Therefore, upon complex formation water molecules are released, receptor and ligand lose degrees of freedom and the interaction between the ligand and the receptor is calculated. 

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