Comparison of a GB solvation method with explicit solvent simulations: potentials of mean force and conformational preferences of alanine dipeptide and 1,2-dichloroethane

Article Abstract:

A study was conducted to determine the potential of mean force in aqueous solution for rotation around two backbone dihedrals of the alanine dipeptide in explicit water. The mean force was also obtained in the continuum approximation by numerical integration of the self-energies and generalized Born equation. In addition, the potential for rotation around the C-C bond in the gas and liquid phases was also analyzed.

Alanine, Dielectrics, Dielectric materials

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Free energy surface of the helical peptide Y (MEARA)6

Article Abstract:

A series of molecular dynamics simulations with an implicit solvation model that allowed sampling of a total of more than 4 mu s is used to study the folding of the helical peptide Y(MEARA)6. The folding mechanism and free energy surface presented are found to be in agreement with previous theoretical models and experimental data on different helical sequences.

Science & research, Molecular dynamics

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Thermodynamics and kinetics of folding of two model peptides investigated by molecular dynamics simulations

Article Abstract:

Molecular dynamics simulations of two model peptides were undertaken in order to quantitatively assess the thermodynamics and kinetics of folding. The sequence of events for unfolding is the inverse of the one for folding.

Protein folding

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