alexa Molecular conformations in a phospholipid bilayer extracted from dipolar couplings: a computer simulation study.
Bioinformatics & Systems Biology

Bioinformatics & Systems Biology

Journal of Computer Science & Systems Biology

Author(s): Thaning J, Hgberg CJ, Stevensson B, Lyubartsev AP, Maliniak A

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Abstract This paper describes an analysis of NMR dipolar couplings in a bilayer formed by dimyristoylphosphatidylcholine (DMPC). The couplings are calculated from a trajectory generated in a molecular dynamics (MD) simulation based on a realistic atom-atom interaction potential. The analysis is carried out employing a recently developed approach that focuses on the construction of the conformational distribution function. This approach is a combination of two models, the additive potential (AP) model and the maximum entropy (ME) method, and is therefore called APME. In contrast to the AP model, the APME procedure does not require an intuition-based choice of the functional form of the torsional potential and is, unlike the ME method, applicable to weakly ordered systems. The conformational distribution function for the glycerol moiety of the DMPC molecule derived from the APME analysis of the dipolar couplings is in reasonable agreement with the "true" distributions calculated from the trajectory. Analyses of dipolar couplings derived from MD trajectories can, in general, serve as guidelines for experimental investigations of bilayers and other complex biological systems. This article was published in J Phys Chem B and referenced in Journal of Computer Science & Systems Biology

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