Conformation and aggregation of M13 coat protein studied by molecular dynamics
| Autor: | N. A. J. Van Nuland, J.C. Sanders, Olle Edholm, Marcus A. Hemminga |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 1991 |
| Předmět: |
Protein Conformation
Dimer Molecular Sequence Data Beta sheet Biophysics Protein aggregation Biochemistry Root mean square chemistry.chemical_compound Molecular dynamics Capsid Amino Acid Sequence Lipid bilayer Protein secondary structure β-Sheet Molecular dynamics simulations Organic Chemistry Membrane Proteins M13 coat protein Crystallography Monomer Biofysica chemistry Capsid Proteins α-Helix |
| Zdroj: | Biophysical Chemistry, 41, 193-202 Biophysical Chemistry 41 (1991) |
| ISSN: | 0301-4622 |
| DOI: | 10.1016/0301-4622(91)80019-n |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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