2bza: Difference between revisions

Revision as of 21:00, 3 May 2008

BOVINE PANCREAS BETA-TRYPSIN IN COMPLEX WITH BENZYLAMINE

OverviewOverview

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 StructureAbout this Structure

2BZA is a Single protein structure of sequence from Bos taurus. Full crystallographic information is available from OCA.

ReferenceReference

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 Sat May 3 21:00:26 2008

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

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 [[Image:2bza.gif|left|200px]]
- {{Structure
+<!--
-|PDB= 2bza |SIZE=350|CAPTION= <scene name='initialview01'>2bza</scene>, resolution 1.90&Aring;
+The line below this paragraph, containing "STRUCTURE_2bza", creates the "Structure Box" on the page.
-|SITE=
+You may change the PDB parameter (which sets the PDB file loaded into the applet)
-|LIGAND= <scene name='pdbligand=ABN:BENZYLAMINE'>ABN</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>
+or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Trypsin Trypsin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.4 3.4.21.4] </span>
+or leave the SCENE parameter empty for the default display.
-|GENE=
+-->
-|DOMAIN=
+{{STRUCTURE_2bza|  PDB=2bza  |  SCENE=  }}
-|RELATEDENTRY=
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2bza FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bza OCA], [http://www.ebi.ac.uk/pdbsum/2bza PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2bza RCSB]</span>
-}}
 '''BOVINE PANCREAS BETA-TRYPSIN IN COMPLEX WITH BENZYLAMINE'''
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 [[Category: Shah, S S.]]
 [[Category: Stroupe, C.]]
-[[Category: hydrolase (serine proteinase)]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 21:00:26 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:14:00 2008''