Fully quantum mechanical energy optimization for protein-ligand structure

Copyright 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1431-1437, 2004

Bibliographische Detailangaben
Veröffentlicht in:Journal of computational chemistry. - 1984. - 25(2004), 12 vom: 05. Sept., Seite 1431-7
1. Verfasser: Xiang, Yun (VerfasserIn)
Weitere Verfasser: Zhang, Da W, Zhang, John Z H
Format: Aufsatz
Sprache:English
Veröffentlicht: 2004
Zugriff auf das übergeordnete Werk:Journal of computational chemistry
Schlagworte:Journal Article Carrier Proteins Fatty Acid-Binding Proteins Ligands Propionates Proteins propionic acid JHU490RVYR
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245 1 0 |a Fully quantum mechanical energy optimization for protein-ligand structure 
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520 |a Copyright 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1431-1437, 2004 
520 |a 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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650 7 |a Carrier Proteins  |2 NLM 
650 7 |a Fatty Acid-Binding Proteins  |2 NLM 
650 7 |a Ligands  |2 NLM 
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650 7 |a Proteins  |2 NLM 
650 7 |a propionic acid  |2 NLM 
650 7 |a JHU490RVYR  |2 NLM 
700 1 |a Zhang, Da W  |e verfasserin  |4 aut 
700 1 |a Zhang, John Z H  |e verfasserin  |4 aut 
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