Conformation and aggregation of M13 coat protein studied by molecular dynamics.
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.
Sanders
J C
JC
Department of Molecular Physics, Agricultural University, HA Wageningen, Netherlands.
van Nuland
N A
NA
Edholm
O
O
Hemminga
M A
MA
D000595:Amino Acid Sequence; D002213:Capsid / Q000737:chemistry*; D036022:Capsid Proteins; D008565:Membrane Proteins / Q000737:chemistry*; D008969:Molecular Sequence Data; D011487:Protein Conformation
D036022:Capsid Proteins; D008565:Membrane Proteins; C025668:coat protein, Bacteriophage M13