First time at Proteopedia? Click on the green links: they change the 3D image. Click and drag the molecules. Proteopedia is a 3D, interactive encyclopedia of proteins, RNA, DNA and other molecules. With a free user account, you can edit pages in Proteopedia. Visit the Main Page to learn more.
2bza
From Proteopedia
| 2bza, resolution 1.90Å () | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Ligands: | , , , | ||||||||
| Activity: | Trypsin, with EC number 3.4.21.4 | ||||||||
| |||||||||
| |||||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||
BOVINE PANCREAS BETA-TRYPSIN IN COMPLEX WITH BENZYLAMINE
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.
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
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
About this Structure
2BZA is a 1 chain structure of sequence from Bos taurus. Full crystallographic information is available from OCA.
Reference
- Ota N, Stroupe C, Ferreira-da-Silva JM, Shah SA, Mares-Guia M, Brunger AT. Non-Boltzmann thermodynamic integration (NBTI) for macromolecular systems: relative free energy of binding of trypsin to benzamidine and benzylamine. Proteins. 1999 Dec 1;37(4):641-53. PMID:10651279
Page seeded by OCA on Tue Feb 17 00:23:53 2009
