Molecular dynamics simulation of hepatitis C virus IRES IIId domain: structural behavior, electrostatic and energetic analysis

The dynamic behavior of the HCV IRES IIId domain is analyzed by means of a 2.6-ns molecular dynamics simulation, starting from an NMR structure. The simulation is carried out in explicit water with Na+ counterions, and particle-mesh Ewald summation is used for the electrostatic interactions. In this...

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Veröffentlicht in:	Journal of molecular modeling 2004-02, Vol.10 (1), p.60-68
Hauptverfasser:	Golebiowski, Jérôme, Antonczak, Serge, Di-Giorgio, Audrey, Condom, Roger, Cabrol-Bass, Daniel
Format:	Artikel
Sprache:	eng
Schlagworte:	Amino Acid Motifs Base Sequence Binding Sites Carbohydrates - chemistry Computer Simulation Crystallography, X-Ray Guanine - chemistry Hepacivirus - metabolism Hydrogen Bonding Ions Magnetic Resonance Spectroscopy - methods Models, Chemical Models, Molecular Models, Statistical Molecular Conformation Nucleic Acid Conformation Protein Binding Protein Conformation Protein Structure, Tertiary Ribosomes - chemistry RNA, Viral Sodium - chemistry Static Electricity Water - chemistry
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