Molecular Dynamics Study on Protein and it's Water Structure at High Pressure
| Autor: | Chong Chul Chai, Mu Shik Jhon |
|---|---|
| Rok vydání: | 2000 |
| Předmět: |
Hydrogen
Chemistry Hydrogen bond General Chemical Engineering Thermodynamics chemistry.chemical_element Equations of motion General Chemistry Condensed Matter Physics Accessible surface area Langevin equation Crystallography Molecular dynamics Modeling and Simulation Radius of gyration Molecule General Materials Science Information Systems |
| Zdroj: | Molecular Simulation. 23:257-274 |
| ISSN: | 1029-0435 0892-7022 |
| DOI: | 10.1080/08927020008025372 |
| Popis: | We have performed NPT molecular dynamics simulations (Langevin Piston Method) on two types of solvated proteins-‘denaturation-unfavorable’ protein (insulin) and ‘denaturation-favorable protein’ (ribonuclease A) at high pressure (from 1 bar up to 20 kbar). The method is based on the extended system formalism introduced by Andersen, where the deterministic equations of motion for the piston degree of freedom are replaced by Langevin equation. We report the structural changes of proteins (ribonuclease A and insulin) and water molecules through radius of gyration, solvent accessible surface area, hydrogen bond pattern, and the topology of water clusters connected by the hydrogen bonded circular network. The solvent accessibility of ribonuclease A is mainly decreased by hydrophilic residues rather than hydrophobic residues under high pressure. From the results of hydrogen bond analysis, we have found that α-helix is more stable than β-sheet under high pressure. In addition, from the analysis of the wa... |
| Databáze: | OpenAIRE |
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