Conference proceeding
Trypsin-Ligand Binding Free Energy Calculation with AMOEBA
Conference proceedings (IEEE Engineering in Medicine and Biology Society. Conf.), Vol.1, pp.2328-2331
2009
DOI: 10.1109/IEMBS.2009.5335108
PMCID: PMC2819397
PMID: 19965178
Abstract
The binding free energies of several benzamidine-like inhibitors to trypsin were examined using a polarizable potential. All the computed binding free energies are in good agreement with the experimental data. From free energy decomposition, electrostatic interaction was found to be the driving force for the binding. Structural analysis shows that the ligands form hydrogen bonds with residues and water molecules nearby in a competitive fashion. The dependence of binding free energy on molecular dipole moment and polarizability was also studied. While the binding free energy is independent on the dipole moment, it shows a negative correlation with the polarizability.
Details
- Title: Subtitle
- Trypsin-Ligand Binding Free Energy Calculation with AMOEBA
- Creators
- Yue Shi - Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, 78712 USADian Jiao - Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, 78712 USAMichael J Schnieders - Department of Chemistry, Stanford University School of Medicine, Stanford, CA 94305Pengyu Ren - Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, 78712 USA
- Resource Type
- Conference proceeding
- Publication Details
- Conference proceedings (IEEE Engineering in Medicine and Biology Society. Conf.), Vol.1, pp.2328-2331
- DOI
- 10.1109/IEMBS.2009.5335108
- PMID
- 19965178
- PMCID
- PMC2819397
- NLM abbreviation
- Conf Proc IEEE Eng Med Biol Soc
- eISBN
- 9781424432967; 1424432960
- ISSN
- 1557-170X
- eISSN
- 1558-4615
- Language
- English
- Date published
- 2009
- Academic Unit
- Roy J. Carver Department of Biomedical Engineering; Biochemistry and Molecular Biology
- Record Identifier
- 9984024421502771
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