1ce5

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{{STRUCTURE_1ce5| PDB=1ce5 | SCENE= }}
{{STRUCTURE_1ce5| PDB=1ce5 | SCENE= }}
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'''BOVINE PANCREAS BETA-TRYPSIN IN COMPLEX WITH BENZAMIDINE'''
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===BOVINE PANCREAS BETA-TRYPSIN IN COMPLEX WITH BENZAMIDINE===
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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.]]
[[Category: Stroupe, C.]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 12:37:50 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 20:37:09 2008''

Revision as of 17:37, 30 June 2008

Image:1ce5.png

Template:STRUCTURE 1ce5

BOVINE PANCREAS BETA-TRYPSIN IN COMPLEX WITH BENZAMIDINE

Template:ABSTRACT PUBMED 10651279

About this Structure

1CE5 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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