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摘要
The hypothetical scanning molecular dynamics (HSMD) method combined with thermodynamic integration (HSMD-TI) has been extended recently for calculating Delta A(0)-the absolute free energy of binding of a ligand to a protein. With HSMD-TI, Delta A(0) is obtained in a new way as a sum of several components, among them is Delta S-ligand-the change in the conformational entropy as the ligand is transferred from the bulk solvent to the active site-this entropy is obtained by a specific reconstruction procedure. This unique aspect of HSMD (which is useful in rational drug design) is in particular important for treating large ligands, where Delta S-ligand might be significant. Technically, one should verify that the results for Delta S-ligand converge-a property that might become more difficult for large ligands; therefore, studying ligands of increasing size would define the range of applicability of HSMD-TI for binding. In this paper, we check the performance of HSMD-TI by applying it to the relatively large ligand FK506 (126 atoms) complexed with the protein FKBP12, where Delta A(0) = 12.8 kcal/mol is known experimentally as well as the crystal structure of the complex. This structure was initially equilibrated by carrying out a 100 ns molecular dynamics trajectory, where the system is modeled by the AMBER force field, TIP3P water, and Particle Mesh Ewald. HSMD-TI calculations were carried out in three conformational regions defined by the intervals [0.2,2], [2,5], and [5,100] ns along the trajectory, where local equilibration of the total energy has been observed; we obtained Delta A(0) = -13.6 +/- 1.1, -16.6 +/- 1.4, and -16.7 +/- 1.4 kcal/mol, respectively indicating the following: (1) The second and third regions belong to the same conformational subspace of the complex, which is different from the [0.2,2] ns subspace. (2) The unsatisfactory result for Delta A(0) obtained in the well equilibrated (hence theoretically preferred) latter regions reflects the nonperfect modeling used, which however (3) has led to the experimental Delta A(0) in the [0.2,2] ns region close to the crystal structure. Keeping the complex near its crystal structure has been a successful approach in the literature. To check this avenue further, we applied harmonic restraints on backbone atoms and obtained unsatisfactory results for Delta A(0), suggesting that implementation of this approach is not straightforward. Converging results for Delta S-ligand were obtained in all regions, where the result Delta S-ligand([0.2,2]) = 7.1 +/- 1.2 kcal/mol is less region dependent than Delta A(0) and is relatively large probably due to the large ligand.
- 出版日期2013-10
