Molecular Recognition: An Example from Ligand Binding to Proteins
To illustrate the use of free energy simulations for increasing our understanding of molecular recognition, alchemical molecular dynamics simulations are performed to evaluate the interactions involved in determining the difference in the free energy of binding of the tyrosine substrate between the wild type of tyrosyl-tRNAsynthetase (TyrRS) from Bacillus stearothermophilus and the mutant Tyr 169 → Phe. The Tyr 169 hydroxyl group interacts with the ammonium group of the substrate in a manner corresponding to that found in other amino acid binding proteins (e.g., the Asp receptor of the chemotactic bacterium Salmonella typhimurium (Milburn et al., 1991) and class I major histocompatibility complex molecules (Madden et al., 1992)). The calculated free energy change due to the Tyr 169 → Phe mutation is 3.4 kcal/mol (the statistical error is ±0.5 kcaVmol) in satisfactory agreement with the experimental value of 3 ± 0.5 kcal/mole. By use of thermodynamic integration, the contribution of the different terms to the free energy change are estimated. It is found that there are large protein contributions to the alchemical free energy difference of the bound and free enzyme but that they cancel in the overall result. Due to this cancellation, the essential interactions contributing to the free energy change are those between the OH group of Tyr 169 and water in the free enzyme and those between the OH group of Tyr 169 and the ammonium group of the substrate in the bound system. The results support simple models based on a balance of hydrogen bonding interactions (Jencks, 1969; Hine, 1972; Fersht, 1988).
KeywordsFree Energy Free Energy Change Free Enzyme Ammonium Group Potential Energy Function
Unable to display preview. Download preview PDF.
- Berkowitz, M., Karim, O. A., McCammon, J. A., & Rossky, P. J. (1984) J. Am. Chem. Soc. 105, 577.Google Scholar
- Blow, D.M. & Brick, P. (1985) Biological Macromolecules and Assemblies: Nucleic Acids and Interactive Proteins (Jurnak, F. & McPherson, A., Eds.) Vol. 2. pp 442–469 ( Wiley, New York ).Google Scholar
- Dang, L.X., Merz K.M. & Kollman P.A. (1989). Free Energy Calculations on Protein Stability: Thr-157→ Val-157 Mutation of T4 Lysozyme, J. Am. Chem. Soc. 111, 8505–8508. Fersht, A.R. (1988). Relationships Between Apparent Binding Energies Measured in Site-Directed Mutagenesis Experiments and Energetics of Binding and Catalysis, Biochemistry 27 1577–1580.Google Scholar
- Fersht, A.R., Leatherbarrow, R.J. & Wells, T.N.C. (1986). Binding energy and catalysis: A lesson from protein engineering of the tyrosyl-t RNA synthetase, TIBS 11, 321–325.Google Scholar
- Jencks, W.P. (1969). Catalysis & Enzymology ( McGraw Hill, New York).Google Scholar
- Reiher, W. (1985). Theoretical Studies of Hydrogen Bonding. Ph.D. thesis, Chemistry (Harvard University) (available from University Microfilms).Google Scholar
- Simonson, T., & Brünger, A. (1992) Biochemistry 31, 8661–8674. In this paper it is correctly pointed out that the decomposition is path-dependent although the example given to demonstrate this is not correct.Google Scholar
- Straatsma, T.P. & McCammon, J.A. (1992). Computational Alchemy, Ann. Rev. Phys. Chem. 407–435.Google Scholar
- Tidor, B. (1990). Molecular modeling of contributions to free energy changes:applications to proteins Thesis, Harvard University.Google Scholar