Fully quantum mechanical energy optimization for protein-ligand structure
Copyright 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1431-1437, 2004
| Veröffentlicht in: | Journal of computational chemistry. - 1984. - 25(2004), 12 vom: 05. Sept., Seite 1431-7 |
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| Weitere Verfasser: | , |
| Format: | Aufsatz |
| Sprache: | English |
| Veröffentlicht: |
2004
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| Zugriff auf das übergeordnete Werk: | Journal of computational chemistry |
| Schlagworte: | Journal Article Carrier Proteins Fatty Acid-Binding Proteins Ligands Propionates Proteins propionic acid JHU490RVYR |
| Zusammenfassung: | Copyright 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1431-1437, 2004 We present a quantum mechanical approach to study protein-ligand binding structure with application to a Adipocyte lipid-binding protein complexed with Propanoic Acid. The present approach employs a recently develop molecular fractionation with a conjugate caps (MFCC) method to compute protein-ligand interaction energy and performs energy optimization using the quasi-Newton method. The MFCC method enables us to compute fully quantum mechanical ab initio protein-ligand interaction energy and its gradients that are used in energy minimization. This quantum optimization approach is applied to study the Adipocyte lipid-binding protein complexed with Propanoic Acid system, a complex system consisting of a 2057-atom protein and a 10-atom ligand. The MFCC calculation is carried out at the Hartree-Fock level with a 3-21G basis set. The quantum optimized structure of this complex is in good agreement with the experimental crystal structure. The quantum energy calculation is implemented in a parallel program that dramatically speeds up the MFCC calculation for the protein-ligand system. Similarly good agreement between MFCC optimized structure and the experimental structure is also obtained for the streptavidin-biotin complex. Due to heavy computational cost, the quantum energy minimization is carried out in a six-dimensional space that corresponds to the rigid-body protein-ligand interaction |
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| Beschreibung: | Date Completed 29.04.2005 Date Revised 24.11.2016 published: Print Citation Status MEDLINE |
| ISSN: | 1096-987X |