Conformation and aggregation of M13 coat protein studied by molecular dynamics.

TitleConformation and aggregation of M13 coat protein studied by molecular dynamics.
Publication TypeJournal Article
Year of Publication1991
AuthorsSanders, J. C., N. A. J. van Nuland, O. Edholm, and M. A. Hemminga
JournalBiophys Chem
Volume41
Issue2
Pagination193-202
Date Published1991 Nov
ISSN0301-4622
KeywordsAmino Acid Sequence, Capsid, Capsid Proteins, Membrane Proteins, Molecular Sequence Data, Protein Conformation
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.

Alternate JournalBiophys. Chem.
PubMed ID1773012