Tilt and azimuthal angles of a transmembrane peptide: A comparison between molecular dynamics calculations and solid-state NMR data of sarcolipin in lipid membranes

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Abstract

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° and azymuthal angles of 66 ± 22°, in reasonable accord with angles determined experimentally (23 ± 2° and 50 ± 4°, respectively) using solid-state NMR with separated-local-field experiments. The effects of time and spatial averaging on both 15N chemical shift anisotropy and 1H/15N 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.

Original languageEnglish (US)
Pages (from-to)3648-3662
Number of pages15
JournalBiophysical journal
Volume96
Issue number9
DOIs
StatePublished - 2009

Bibliographical note

Funding Information:
This work was supported by National Institutes of Health grants GM64742, GM072701, and HL080081 to G.V. and GM46736 to J.G.

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