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 |
|---|---|
| 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 |
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All Science Journal Classification (ASJC) codes
- Genetics
- Structural Biology
- Biochemistry
Cite this
Characterization of the conformational space of a triple-stranded β-sheet forming peptide with molecular dynamics simulations. / Soto, Patricia; Colombo, Giorgio.
In: Proteins: Structure, Function and Genetics, Vol. 57, No. 4, 01.12.2004, p. 734-746.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Characterization of the conformational space of a triple-stranded β-sheet forming peptide with molecular dynamics simulations
AU - Soto, Patricia
AU - Colombo, Giorgio
PY - 2004/12/1
Y1 - 2004/12/1
N2 - 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.
AB - 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.
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U2 - 10.1002/prot.20236
DO - 10.1002/prot.20236
M3 - Article
VL - 57
SP - 734
EP - 746
JO - Proteins: Structure, Function and Genetics
JF - Proteins: Structure, Function and Genetics
SN - 0887-3585
IS - 4
ER -