Conformational flexibility of voltage gated dihydropyridine sensitive calcium channel in hydrated DMPC bilayer.

We have built a model for Ca2+ channel using amino acid sequence from S3 helix of the fourth internal repeat of alpha 1 subunit of dihydropyridine sensitive calcium channel from rabbit skeletal muscle, on the basis of X-ray crystallographic data on four helix bundle. The assembling of the geometry of the pore was achieved using a sixteen residues peptide fragment from short SSI/II loop (residues 1010-1025) which had F1013 and E1014 residues, considered to be important for the drug induced activity of the channel. This had hairpin bend between F1013 to W1016. The drug 2,6-dimethyl 3,5-dicarbomethoxy-4 (2-nitrobenzyl) 1,4 dihydropyridine (DHP) (nifedipine), which is a calcium channel inhibitor used in the treatment of cardiovascular diseases, was introduced, interacting with these two residues via Ca2+ ion. Two more Ca2+ ions were introduced in the pore. The model was incorporated in the bilayer of 36 dimyristoyl phosphatidyl choline (DMPC) molecules with 1201 water molecules and simulated for 200 picoseconds (ps) after equilibration for 120 ps. We also simulated the channel model in vacuum and in aqueous environment for comparison. The latter was unstable after 120 ps. The geometric parameters of the pore are analysed by MOLMOL, PCURVE 3.1 and a special program ANHELIX developed by us. Stability of the pore dimensions during simulations is discussed in this paper.

500 picosecond molecular dynamics simulation of amphiphilic polypeptide Ac(LKKL)4 NHEt with 1,2 di-mysristoyl-sn-glycero-3-phosphorylcholine (DMPC) molecules.

Molecular dynamics (MD) simulation of the interaction between amphiphilic polypeptide Ac(LKKL)4NHEt and 4 DMPC (1,2 di-mysristoyl-sn-glycero-3-phosphorylcholine) molecules has been carried out at 310 K for 500 picoseconds (ps) using AMBER 4.0. Interaction energy and a number of conformational parameters are calculated for the subaveraged coordinates, using P-CURVES 3.1 and our MD trajectory analysis program ANALMD. No significant change in DMPC headgroup conformation was observed. However, the mobility of P atoms was found to be restricted. The chains were quite flexible and their flexibility increased towards the ends. They interacted amongst themselves. The polypeptide remained predominantly in alpha-helical conformation. Leu1 and Lys2 at the N terminus and Leu13 to Leu16 at C terminus assumed non helical conformation and were quite flexible. Average interaction energy between the polypeptide and DMPC molecules was found to be -151.828 kcal*mol-1. The main contributory factor was electrostatic interaction of Lys NH3+ groups with the DMPC phosphates. On an average one Lys chain interacted with 1.5 DMPC molecules. Central region of the polypeptide had better contact with DMPC molecules. A model for the fusogenic properties of the polypeptide is presented on the basis of MD results.

200 picosecond molecular dynamics simulation of interaction of nifedipine with 1-2 dimyristoyl phosphatidylcholine membrane.

Interaction of calcium channel antagonist nifedipine (Nif) with 1-2 dimyristoyl phosphatidylcholine (DMPC) membrane has been studied using molecular dynamics approach. The simulations for one molecule of nifedipine with four DMPC molecules were carried out for 200 pico seconds (ps) using AMBER (Assisted Model Building with Energy Refinement) 3.0 adopted to CYBER 180/930 computer and changes in the structural parameters of DMPC were compared with those for DMPC monolayer (a matrix of nine molecules) optimized separately. Dynamics simulations for the latter had been carried for 40 ps. Our results show that the drug molecule (Nif) penetrates a discrete depth within the phospholipid matrix causing hydrocarbon chains of lipid molecules to swing that makes enough room for the receptor adjacent to the drug molecule.