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Structure of the virus capsid protein VP1 of enterovirus 71 predicted by some homology modeling and molecular docking studies
Journal of computational chemistry, 2006-10, Vol.27 (13), p.1556-1570
Ke, Yi-Yu
Chen, Yun-Chu
Lin, Thy-Hou
2006
Volltextzugriff (PDF)
Details
Autor(en) / Beteiligte
Ke, Yi-Yu
Chen, Yun-Chu
Lin, Thy-Hou
Titel
Structure of the virus capsid protein VP1 of enterovirus 71 predicted by some homology modeling and molecular docking studies
Ist Teil von
Journal of computational chemistry, 2006-10, Vol.27 (13), p.1556-1570
Ort / Verlag
Hoboken: Wiley Subscription Services, Inc., A Wiley Company
Erscheinungsjahr
2006
Quelle
MEDLINE
Beschreibungen/Notizen
The homology modeling technique has been used to construct the structure of enterovirus 71 (EV 71) capsid protein VP1. The protein is consisted of 297 amino acid residues and treated as the target. The amino acid sequence identity between the target protein and sequences of template proteins 1EAH, 1PIV, and 1D4M searched from NCBI protein BLAST and WorkBench protein tools were 38, 37, and 36%, respectively. Based on these template structures, the protein model was constructed by using the InsightII/Homology program. The protein model was briefly refined by energy minimization and molecular dynamics (MD) simulation steps. The protein model was validated using some web available servers such as ERRAT, PROCHECK, PROVE, and PROSA2003. However, an inconsistency between the docking scores and the measured activity was observed for a series of EV 71 VP1 inhibitors synthesized by Shia et al. (J Med Chem 2002, 45, 1644) and docked into the binding pocket of the protein model using the DOCK 4.0.2 program. The protein model with an EV 71 VP1 inhibitor docked and engulfed was then refined further by some MD simulation steps in the presence of water molecules. The docking scores obtained for these inhibitors after such a MD refinement were well correlated with the activities. The structure–activity relationships for the ligand–protein model system was also analyzed using the GRID‐VOLSURF programs and the corresponding noncrossvalidated and crossvalidated (by leave‐one‐out) r2 and q2 were 0.99 and 0.61, respectively. The hydrophobic nature of the binding pocket of the protein model was also examined using the GRID21 program. The possibility of improving the potency of the current series of EV 71 VP1 inhibitors was discussed based on all the studies presented. © 2006 Wiley Periodicals, Inc. J Comput Chem 27: 1556–1570, 2006
Sprache
Englisch
Identifikatoren
ISSN: 0192-8651
eISSN: 1096-987X
DOI: 10.1002/jcc.20460
Titel-ID: cdi_proquest_miscellaneous_68792288
Format
–
Schlagworte
Amino Acid Sequence
,
Amino acids
,
capsid protein
,
Capsid Proteins - chemistry
,
enterovirus
,
Enterovirus - chemistry
,
homology modeling
,
hydrophobic interaction
,
Models, Molecular
,
molecular docking
,
Molecular Sequence Data
,
Molecular structure
,
Protein Conformation
,
Proteins
,
Sequence Homology, Amino Acid
,
Structure-Activity Relationship
,
Viruses
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