Tilt and azimuthal angles of a transmembrane peptide: a comparison between molecular dynamics calculations and solid-state NMR data of sarcolipin in lipid membranes.
We report molecular dynamics simulations in the explicit membrane environment of a small membrane-embedded protein, sarcolipin, which regulates the sarcoplasmic reticulum Ca-ATPase activity in both cardiac and skeletal muscle. In its monomeric form, we found that sarcolipin adopts a helical conformation, with a computed average tilt angle of 28 +/- 6 degrees and azymuthal angles of 66 +/- 22 degrees, in reasonable accord with angles determined experimentally (23 +/- 2 degrees and 50 +/- 4 degrees, respectively) using solid-state NMR with separated-local-field experiments. The effects of time and spatial averaging on both (15)N chemical shift anisotropy and (1)H/(15)N dipolar couplings have been analyzed using short-time averages of fast amide out-of-plane motions and following principal component dynamic trajectories. We found that it is possible to reproduce the regular oscillatory patterns observed for the anisotropic NMR parameters (i.e., PISA wheels) employing average amide vectors. This work highlights the role of molecular dynamics simulations as a tool for the analysis and interpretation of solid-state NMR data.
Shi
Lei
L
Department of Chemistry, University of Minnesota, Minneapolis, Minnesota, USA.
Cembran
Alessandro
A
Gao
Jiali
J
Veglia
Gianluigi
G
D000465:Algorithms; D016880:Anisotropy; D003198:Computer Simulation; D008051:Lipid Bilayers / Q000737:chemistry*; D008958:Models, Molecular; D009038:Motion; D009124:Muscle Proteins / Q000737:chemistry* / Q000378:metabolism*; D009587:Nitrogen Isotopes; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods; D010713:Phosphatidylcholines / Q000378:metabolism; D025341:Principal Component Analysis; D011487:Protein Conformation; D011510:Proteolipids / Q000737:chemistry* / Q000378:metabolism*; D014316:Tritium; D014867:Water / Q000378:metabolism
D008051:Lipid Bilayers; D009124:Muscle Proteins; D009587:Nitrogen Isotopes; D010713:Phosphatidylcholines; D011510:Proteolipids; D014867:Water; D014316:Tritium; C077258:sarcolipin; C017251:1,2-oleoylphosphatidylcholine