Molecular dynamics of a respiratory protein fragment in phospholipid monomolecular films

Gupta, Santosh K. (Santosh Kumar) (2009) Molecular dynamics of a respiratory protein fragment in phospholipid monomolecular films. Masters thesis, Memorial University of Newfoundland.

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Abstract

Molecular dynamics simulations of the fragment Mini-B of Surfactant Protein B were carried out in the NVT ensemble for simulation times ranging from 20 ns to 80 ns. These simulations were performed in DPPC:POPG monolayers and POPG monolayers at different cross-sectional areas per lipid, varying the initial depth and orientation of the peptide. Analysis was carried out to determine what depth the peptide can attain in the monolayers towards the end of the simulations. Secondary structure of the peptide was also examined, and it was found that in the majority of cases both alpha helices remained alpha helical to a reasonable degree in the monolayers. The tilt angles of the alpha helices of Mini-B in the DPPC:POPG monolayers seemed to show relatively small deviations from those of the corresponding structure determined in SDS micelles by NMR, provided that the peptide was placed at a low enough depth. A study was also performed to determine the effect of sodium ions on the interaction between the cationic Arginine and Lysine residues of Mini-B and the anionic phosphate headgroups of POPG.

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