Non-Boltzmann thermodynamic integration (NBTI) for macromolecular systems: relative free energy of binding of trypsin to benzamidine and benzylamine.Ota, N., Stroupe, C., Ferreira-da-Silva, J.M., Shah, S.A., Mares-Guia, M., Brunger, A.T.
(1999) Proteins 37: 641-653
- PubMed: 10651279
- Primary Citation of Related Structures:  1CE5
- PubMed Abstract:
- The Geometry of the Reactive Site and of the Peptide Groups in Trypsin, Trypsinogen and its Complexes with Inhibitors
Marquart, M.,Walter, J.,Deisenhofer, J.,Bode, W.,Huber, R.
(1983) Acta Crystallogr.,Sect.B 39: 480
- Crystal Structure of Bovine Beta-Trypsin at 1.5 A Resolution in a Crystal Form with Low Molecular Packing Density. Active Site Geometry, Ion Pairs and Solvent Structure
Bartunik, J.D.,Summers, L.J.,Bartsch, H.H.
(1989) J.Mol.Biol. 210: 813
The relative free energies of binding of trypsin to two amine inhibitors, benzamidine (BZD) and benzylamine (BZA), were calculated using non-Boltzmann thermodynamic integration (NBTI). Comparison of the simulations with the crystal structures of both ...
The relative free energies of binding of trypsin to two amine inhibitors, benzamidine (BZD) and benzylamine (BZA), were calculated using non-Boltzmann thermodynamic integration (NBTI). Comparison of the simulations with the crystal structures of both complexes, trypsin-BZD and trypsin-BZA, shows that NBTI simulations better sample conformational space relative to thermodynamic integration (TI) simulations. The relative binding free energy calculated using NBTI was much closer to the experimentally determined value than that obtained using TI. The error in the TI simulation was found to be primarily due to incorrect sampling of BZA's conformation in the binding pocket. In contrast, NBTI produces a smooth mutation from BZD to BZA using a surrogate potential, resulting in a much closer agreement between the inhibitors' conformations and the omit electron density maps. This superior agreement between experiment and simulation, of both relative binding free energy differences and conformational sampling, demonstrates NBTI's usefulness for free energy calculations in macromolecular simulations.
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA.