The automated docking program AutoDock was used to dock nine phosphatidic acids (PAs), six phosphatidylcholines, five phosphatidylethanolamines, four phosphatidylglycerols, one phosphatidylinositol and two phosphatidylserines, which have two identical saturated fatty acid residues with an even numbers of carbon atoms, onto the active site of Streptomyces sp. PMF phospholipase D (PLD). Two PAs with one double bond on the fatty acid chain linked to the C2 of the glycerol residue were also docked. In general, binding energies become progressively more negative as fatty acid residues become longer. When these residues are of sufficient length, one is coiled against a hydrophobic cliff in a well that also holds the glycerol and phosphate residues and the head group, while the other generally is bound by a hydrophobic surface outside the well. Phosphatidylcholines have the only head group that is firmly bound by the active site, giving a possible structural explanation for the low selectivity of Streptomyces PLD for other phospholipid substrates.

Automated docking methodology as a means to study protein-ligand complexes Kinetic measurements of hydrolysis and transphosphatidylation CHAPTER 3: COMPUTATIONAL TECHNIQUES Ligand construction Constructing the enzyme Docking calculations Calculation of electrostatic surface potentials Analysis of the docking results CHAPTER 4: RESULTS Docking small molecule phospholipid mimetics Docking the full phospholipids 21 CHAPTER 5: CONCLUSIONS APPENDIX 3

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