Paper Citing NAMD - Abstract
Madsen, Jesper J.; Linderoth, Lars; Subramanian, Arun K.; Andresen, Thomas L.; Peters, Gunther H.
Secretory Phospholipase A(2) Activity toward Diverse Substrates
JOURNAL OF PHYSICAL CHEMISTRY B, 115:6853-6861, JUN 2 2011
We have studied secretory phospholipase A(2)-IIA (sPLA(2)) activity toward different phospholipid analogues by performing biophysical 1 characterizations and molecular dynamics simulations. The phospholipids were natural substrates, triple alkyl phospholipids, a prodrug anticancer etherlipid, and an inverted ester. The latter were included to study head group-enzyme interactions. Our simulation results show that the lipids are optimally placed into the binding cleft and that water molecules can freely reach the active site through a well-defined pathway; both are indicative that these substrates are efficiently hydrolyzed, which is in good agreement with our experimental data. The phospholipid analogue with three alkyl side chains forms aggregates of different shapes with no well-defined sizes due to its cone-shape structure. Phosphatidylglycerol and phosphatidylcholine head groups interact with specific charged residues, but relatively large fluctuations are observed, suggesting that these interactions are not necessarily important for stabilizing substrate binding to the enzyme.
