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Conformation and aggregation of M13 coat protein studied by molecular dynamics
J C Sanders1, N A van Nuland, O Edholm
1Department of Molecular Physics, Agricultural University, HA Wageningen, Netherlands.
Abstract:
Molecular dynamics (MD) simulations are performed on M13 coat protein, a small membrane protein for which both alpha- and beta-structures have been suggested. The simulations are started from initial conformations that are either monomers or dimers of alpha-helices or U-shaped beta-sheets. The lipid bilayer is represented by a hydrophobic potential. The results are analyzed in terms of stability, energy and secondary structure. The U-shaped beta-structure changes from a planar to a twisted form with larger twist for the monomer than the dimer. The beta-sheet is much more flexible than the alpha-helix as monitored by the root mean square (rms) fluctuations of the C alpha atoms. A comparison of the energies after 100 ps MD simulation shows that of the monomers, the alpha-helix has the lowest energy. The energy difference between alpha- and beta-structures decreases from 266 kJ/mol to 148 kJ/mol, when going from monomers to dimers. It is expected that this difference will decrease with higher aggregation numbers.
Insights
Molecular dynamics simulations reveal that M13 coat protein
Area of Science:
- Biophysics
- Computational Biology
- Protein Structure
Background:
- M13 coat protein, a small membrane protein, exhibits proposed alpha-helical and beta-sheet structures.
- Understanding its conformational dynamics is crucial for membrane protein research.
Purpose of the Study:
- To investigate the stability and structural dynamics of M13 coat protein using molecular dynamics simulations.
- To compare the behavior of alpha-helical and beta-sheet conformations in a lipid bilayer environment.
Main Methods:
- Molecular dynamics (MD) simulations were conducted on M13 coat protein monomers and dimers.
- Simulations utilized initial alpha-helical and U-shaped beta-sheet conformations within a hydrophobic potential representing a lipid bilayer.
- Analysis focused on stability, energy, and secondary structure changes, including root mean square (RMS) fluctuations.
Main Results:
- Beta-sheets exhibited greater flexibility than alpha-helices, indicated by C-alpha atom RMS fluctuations.
- The U-shaped beta-structure transitioned to a twisted form, with monomeric forms showing greater twisting than dimeric forms.
- Monomeric alpha-helices demonstrated lower energy compared to beta-structures after 100 ps of simulation.
Conclusions:
- The energy difference between alpha-helical and beta-sheet structures of M13 coat protein diminishes with increased aggregation.
- These findings provide insights into the conformational preferences and stability of M13 coat protein in membrane environments.