2bza

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{{STRUCTURE_2bza| PDB=2bza | SCENE= }}
{{STRUCTURE_2bza| PDB=2bza | SCENE= }}
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'''BOVINE PANCREAS BETA-TRYPSIN IN COMPLEX WITH BENZYLAMINE'''
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===BOVINE PANCREAS BETA-TRYPSIN IN COMPLEX WITH BENZYLAMINE===
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==Overview==
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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.
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{{ABSTRACT_PUBMED_10651279}}
==About this Structure==
==About this Structure==
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[[Category: Shah, S S.]]
[[Category: Shah, S S.]]
[[Category: Stroupe, C.]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 21:00:26 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 04:48:13 2008''

Revision as of 01:48, 28 July 2008

Image:2bza.png

Template:STRUCTURE 2bza

BOVINE PANCREAS BETA-TRYPSIN IN COMPLEX WITH BENZYLAMINE

Template:ABSTRACT PUBMED 10651279

About this Structure

2BZA is a Single protein structure of sequence from Bos taurus. 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

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