Abstract
Molecular dynamics (MD) simulations have been performed on a series of mutants of the 20 amino acid peptide Betanova in order to critically assess the ability of MD simulations to reproduce the folding and stability of small β-sheet-forming peptides on currently accessible time-scales. Simulations were performed in both water and in 40% methanol solution, using an explicit solvent model. The simulations suggest that all mutants adopt a wide range of conformations in solution, that the structures are highly flexible, and that stabilization of compact structures is due to a delicate balance of hydrophobic and polar side-chain interactions. Simulations longer than 100 ns, although not sufficient for a complete thermodynamic and kinetic description of the system, sample an ensemble of compact conformations characterized by the loss of ordered β-sheet secondary structure. This suggests that no significant free energy barrier separates the different conformations available.
Original language | English (US) |
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Pages (from-to) | 734-746 |
Number of pages | 13 |
Journal | Proteins: Structure, Function and Genetics |
Volume | 57 |
Issue number | 4 |
DOIs | |
State | Published - Dec 1 2004 |
Externally published | Yes |
All Science Journal Classification (ASJC) codes
- Structural Biology
- Biochemistry
- Molecular Biology