Mechanism of helix nucleation and propagation: Microscopic view from microsecond time scale MD simulations

Article Abstract:

Microsecond time scale molecular dynamics simulations of the 13-residue peptide RN-24 were carried out to investigate the mechanism of helix nucleation and propagation. It is concluded that beta-turn and 3(super 10)-helix play an important role in helix nucleation, and the conversion from beta-turn to alpha-is the most commonly observed nucleation mechanism, with ~60% probability, and involves bifurcated hydrogen bonds.

Protein folding, Nucleation, Nucleation (Chemistry)

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Molecular dynamics simulation of a polyunsaturated lipid bilayer susceptible to lipid peroxidation

Article Abstract:

The molecular dynamics (MD) simulations using Gromacs are applied to obtain a bilayer consisting of 1-palmitoyl-2-linoleyl-snglycero-3-phosphatidylcholine (PLPC). The MD simulations of the polyunsaturated lipid bilayer provide the structural properties of the system and show that the unsaturation induces disorder and affects the physical properties of the membrane.

Chemistry, Physical and theoretical, Physical chemistry, Lipid membranes, Lipid peroxidation

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Interactions of a transmembrane helix and a membrane: comparative simulations of bacteriorhodopsin helix A

Article Abstract:

Molecular dynamics are used to simulate helix A of bacteriorhodopsin, both in isolation and as part of the complete protein. A study on these systems revealed that octane is good alternative to lipid bilayer membranes, because it will provide fast equilibrium, increased sampling, and decreased computational cost.

Membrane proteins, Chemical properties

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