1ce5
From Proteopedia
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BOVINE PANCREAS BETA-TRYPSIN IN COMPLEX WITH BENZAMIDINE
Overview
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.
About this Structure
1CE5 is a Single protein structure of sequence from Bos taurus with CA, CL, SO4 and BEN as ligands. Active as Trypsin, with EC number 3.4.21.4 Full crystallographic information is available from OCA.
Reference
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 JM, Shah SA, Mares-Guia M, Brunger AT, Proteins. 1999 Dec 1;37(4):641-53. PMID:10651279
Page seeded by OCA on Tue Nov 20 12:22:37 2007
Categories: Bos taurus | Single protein | Trypsin | Brunger, A.T. | Ferreira-Da-Silva, J.M.S. | Mares-Guia, M. | Ota, N. | Shah, S.S. | Stroupe, C. | BEN | CA | CL | SO4 | Hydrolase (serine proteinase)
