Modeling a spin-labeled fusion peptide in a membrane: implications for the interpretation of EPR experiments.
Site-directed spin-labeling and electron paramagnetic resonance are powerful tools for studying structure and conformational dynamics of proteins, especially in membranes. The position of the spin label is used as an indicator of the position of the site to which it is attached. The interpretation of these experiments is based on the assumptions that the spin label does not affect the peptide configuration and that it has a fixed orientation and distance with respect to the protein backbone. Here, the validity of these assumptions is examined through implicit membrane molecular dynamics simulations of the influenza hemagglutinin fusion peptide that has been labeled with methanethiosulfonate spin label. We find that the methanethiosulfonate spin label can occasionally induce peptide orientations that differ from those adopted by the wild-type peptide. Furthermore, the spin-label resides, on average, several Angstroms deeper in the membrane than the corresponding backbone C(alpha)-atom even at sites pointing toward the solvent. The nitroxide spin label exhibits flexibility and adopts various configurations depending on the surrounding residues.
Sammalkorpi
Maria
M
Mechanical and Aerospace Engineering, Princeton University, Princeton, New Jersey, USA.
Lazaridis
Themis
T
D000595:Amino Acid Sequence; D002244:Carbon / Q000737:chemistry; D004578:Electron Spin Resonance Spectroscopy / Q000379:methods*; D019267:Hemagglutinin Glycoproteins, Influenza Virus / Q000737:chemistry; D007700:Kinetics; D008956:Models, Chemical; D008958:Models, Molecular; D008968:Molecular Conformation; D008969:Molecular Sequence Data; D009154:Mutation; D009569:Nitric Oxide / Q000737:chemistry; D010455:Peptides / Q000737:chemistry; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D013113:Spin Labels
D019267:Hemagglutinin Glycoproteins, Influenza Virus; D010455:Peptides; D013113:Spin Labels; D009569:Nitric Oxide; D002244:Carbon