Browsing Theses and Dissertations, Electronic (ETDs) by Author "Abdullah, Zafirah Liyana"
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ItemSTUDYING TRYPTOPHAN FLUORESCENCE TO DETERMINE MEMBRANE BURIAL: ATOMIC DETAIL INSIGHT FROM UNBIASED MOLECULAR DYNAMICS SIMULATIONS(Johns Hopkins University, 2017-05-04) Abdullah, Zafirah Liyana; ULMSCHNEIDER, MARTIN BMembrane-protein interactions play an important role in a wide variety of biological processes. These interactions are fundamental, as the interactions between peptides and lipids are the driving force for the mechanisms of numerous membrane-mediated cellular processes. Tryptophan (Trp) fluorescence measurement is an analytical tool to measure protein and peptide interactions with lipid membranes. Particularly, it is used to determine the depth of membrane burial of peptides containing an indole side chain in protein structures. Indole groups are solvent-sensitive fluorophores, and therefore, the location of tryptophan residues in proteins can be observed via their emission spectra. While the degree of solvation of the Trp side chain in phospholipid membranes can be determined with high accuracy using the fluorescent spectra of successive lipid titrations, the atomic detail configurations of the buried states remain unknown. This study quantitatively compares the burial of Trp in vitro via fluorescence measurement and in silico via molecular dynamics (MD) simulations. Fluorescence measurements of acetylated Trp containing penta-peptides WLRLL showed binding in both simulations and fluorescence measurements. However, the pentapeptide WARAA showed no partitioning using fluorescence, while atomistic trajectories showed that the penta-peptide bind strongly to the interface of the model membrane, 1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC). This suggests that there might be an error in MD simulations force fields, and further improvement especially of the water model may be needed to achieve a precisely and accurately capture the biological processes.