Molecular Dynamics III 4038-Pos Board B766 All-Atom Simulation and Continuum Elastic Theory of Gramicidin a in Binary Component Lipid Bilayers Andrew H. Beaven 1 , Alexander J. Sodt 2 , Denise V. Greathouse 3 , Roger E. Koeppe II, 3 , Richard W. Pastor 2 , Olaf S. Andersen 4 , Wonpil Im 5 . 1 Chemistry, The University of Kansas, Lawrence, KS, USA, 2 Laboratory of Computational Biology, NHLBI, NIH, Bethesda, MD, USA, 3 Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, USA, 4 Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA, 5 Molecular Biosciences and Center for Bioinformatics, The University of Kansas, Lawrence, KS, USA. The linear gramicidins are a group of peptides with alternating L and D chirality that fold into b-helices. The prototypical gramicidin is [Val 1 ] grami- cidin A (gA), which has been extensively studied using electrophysiology, spectroscopy, and molecular dynamics simulations. gA channels form by transmembrane dimerization and have been used to examine the interactions between membrane proteins and their host bilayer. This study focuses on gA channels in lipid bilayers composed of two phosphatidylcholines with different acyl chain lengths. The bilayers were formed from equimolar mixtures of DC 16:1 PCþDC 24:1 PC or DC 18:1 PCþDC 22:1 PC mixture, as well as pure DC 20:1 PC, all of which have the same average tail length. These gA-bilayer systems were simulated for 3.5 ms to explore the characteristics and energetics of lateral lipid redistribution around a protein. The simulations indicate: i) the overall bilayer thickness profile adjacent to the channel is similar in the three systems tested; ii) in the DC 16:1 PCþDC 24:1 PC mixture, the shorter DC 16:1 PC is enriched by nearly a factor of two in the first lipid shell around the channel; iii) thickness matching is dominant, even when the disparity between lengths is large; and iv) the acyl chains adopt non-native conformations in order to match achieve hydrophobic matching between the gA dimer and the bilayer core. In contrast to the results in the DC 16:1 PCþDC 24:1 PC mixture, enrich- ment in the DC 18:1 PCþDC 22:1 PC mixture is statistically insignificant. The pref- erence for the better matching lipid (DC 16:1 PC) near the channel in the DC 16:1 PCþDC 24:1 PC mixture can be explained by a continuum model that accounts for the energetic penalty associated with compressing the longer lipid (DC 24:1 PC) to match the channel’s hydrophobic length. 4039-Pos Board B767 Molecular Modeling of Paclitaxel Interacting with Membranes Myungshim Kang, Sharon Loverde. Chemistry, City University of New York, College of Staten Island, Staten Island, NY, USA. Cell membranes define a confined space for the cell and form an essential bar- rier from the surrounding environments. They also provide active/passive transport systems for some essential nutrients and small molecules. But it is unclear how most of hydrophobic drugs such as paclitaxel penetrate through the cell membranes. Paclitaxel has been shown to aggregate both in hydro- philic and hydrophobic environments. Additionally it has been suggested to contribute to pore formation in the membrane. Here we investigated interactions between paclitaxel and a model cell membrane of 1-palmitoyl- 2-oleoyl-sn-glycero-3-phosphocholine (POPC) using molecular dynamics simulations. The change of free energy across the bilayer interface calculated by adaptive biasing force method showed good agreement with experimental data. We performed 300ns long simulations of POPC membranes with randomly inserted drugs up to 0.1 mole fraction. We compared the results with a separate set of simulations where the drugs were initially inserted at lat- tice points with a single orientation. Interestingly, the main baccatinic core and the three more hydrophobic phenyl rings showed different preferential posi- tioning in the membrane along the z-axis. This was consistent with the rotation and orientation of the drug. The clustering of the drug molecules in the mem- brane, order parameters of lipid tails, and water penetration along with the drug clusters were analyzed. Modeling the transport of hydrophobic drugs into the cell through computational investigations will provide insights of the drug delivery process at a molecular level. 4040-Pos Board B768 Mechanism of Cx26-G45E Deafness Mutant Dysregulation Explored by Molecular Dynamics Simulations Michael Purdy 1 , Mark Yeager 1,2 . 1 Molecular Physiology & Biological Physics, University of Virginia School of Medicine, Charlottesville, VA, USA, 2 Cardiovascular Medicine, University of Virginia Health System, Charlottesville, VA, USA. To explore the mechanism by which Ca 2þ blocks ionic conductance during tis- sue injury, we recently solved the X-ray crystal structures of the Cx26 gap junction channel with and without bound Ca 2þ . The two structures were nearly identical, ruling out a large-scale steric mechanism for channel block. Also, the pore diameter was ~15 A ˚ , sufficient for the passage of hydrated ions. The sites for Ca 2þ coordination reside at the interface between adjacent subunits, near the entrance to the extracellular gap. Ca 2þ binding occurs by local conformational shifts of Ca 2þ -chelating residues. Molecular dynamics simulations and electrostatic calculations suggest that Ca 2þ induces an electro- static barrier to the passage of cations. We used MD simulations to explore the mechanism of channelopathy in the G45E mutant. The simulations suggest that the additional acidic side-chain at each of the channel-lining Ca 2þ binding sites is unable to contribute to Ca 2þ coordination. We propose that the additional negative charge contributed by the glutamate carboxylate disrupts normal Ca 2þ -dependent electrostatic regulation of Cx26 ion selectivity and permeability. 4041-Pos Board B769 Drug Extrusion Process of Mate Multidrug Efflux Transporter Revealed by Molecular Dynamics Simulations Wataru Nishima 1,2 , Yoshiki Tanaka 3 , Ryuichiro Ishitani 4 , Osamu Nureki 4 , Yuji Sugita 1,2 . 1 Theoretical Molecular Science Laboratory, RIKEN, Wako, Japan, 2 iTHES, RIKEN, Wako, Japan, 3 The Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan, 4 Department of Biophysics and Biochemistry, The University of Tokyo, Tokyo, Japan. MATE (the Multidrug And Toxic compound Extrusion) is one of the five multi- drug efflux transporter super-families. It is featured as primary secondary active transporter and comprises of 12 trans-membrane helices. The first and last six transmembrane helices (TMs) form N-lobe and C-lobe domains, showing a two-fold rotational symmetry. It is considered that the drug release/capture related motions are characterized by switching of inward/outward-facing con- formations (rocker-switch model). Recently, multiple structures of the MATE from P.furiosus (PfMATE), has been determined by X-ray crystallography in outward-facing conformation. Two distinct structures ‘Straight’ and ‘Bent’ are characterized by conforma- tions of TM1. Furthermore, PfMATE is shown to be H þ driven antiporter, sug- gesting that D41 and D184 in N-lobe are involved as important proton pathway. It is also interesting that MATE has the hydrophobic surface of inner cavity, since other multidrug transporters exhibit hydrophilic. The sharply opened interface to the lipid molecules suggests the possibilities that the lipid mole- cules intensively interact with the inside of the cavity. To further elucidate the drug release mechanism in outward facing stage, we adopted several promising simulation methods, continuum electrostatic anal- ysis to predict protonation states, a number of independent all-atom Molecular Dynamics (MD) simulations by changing conditions (initial conformations, protonations, lipid positions, etc.) for dynamics and interactions, and quantum mechanics calculation for drug forcefield development. Our results suggest that D41 is protonated in Straight, while D41 and D184 are both protonated in Bent. Furthermore, we successfully observed multiple drug release events in some conditions of MD simulations. In the poster presentation, we will report and discuss the dynamics and interactions of PfMATE revealed by different condi- tions of MDs. We will also discuss the insights of the drug release mechanism of PfMATE obtained by the simulations. 4042-Pos Board B770 Exploring the Elastic Properties of Bilayer Membranes using Molecular Dynamics Simulations Gilles Pieffet 1,2 , Alonso Botero 2 , Gu¨ nther H. Peters 3 , Manu Forero-Shelton 2 , Chad Leidy 2 . 1 Physics, Universidad Antonio Narin˜o, Bogota´, Colombia, 2 Physics, Universidad de los Andes, Bogota´, Colombia, 3 Chemistry, Technical University of Denmark, Bogota´, Denmark. Local membrane deformation has been implicated in regulating a variety of cellular processes, such as ion channel function and vesicle fusion. In this work, we show how molecular dynamic simulations can be used alone or in conjunction with the continuum elastic model to estimate membrane elastic properties. Detail analysis allowed us to divide the energetic cost associated with the partial or complete extraction of a DOPE lipid from a POPC bilayer into two main contributions: a) the elastic deformation of the membrane, involving displacement of neighboring lipids, and b) the solvation energy associated to the exposure of the acyl chains to the water phase. Membrane elastic deformation was observed in molecular detail, and structural informa- tion from the simulations was used with the continuum elastic model to estimate an effective membrane spring constant independently from the energy parameters of the simulations. The membrane spring constant was also calculated from the potential of mean force and a good agreement was Wednesday, February 19, 2014 801a