1. THE DYNAMIC STUDY OF LYOTROPIC LIQUID CRYSTALLS USING THE MOLECULAR DYNAMICS SIMULATION METHOD ** А.А.Shahinyan, * L.H.Arsenyan, ** A.H.Poghosyan, ** ** P.K.Hakobyan artsha@sci.am * Institute of Applied Problems of Physics NAS RA ** The International Scientific-Educational Center of the NAS RA

2. SUBJECT OF SIMULATION The concentrated water solutions of Lamelles of biological and commercial amphiphilic compounds are investigated, including: а) Molecular Dynamics study of structure of transmembrane protein allocated in the Lamellas of biological origin. b) Molecular Dynamics study of phase transition from coagel in Lammelar Liquid crystaline phase.

3. Computational Details For the system construction was created Molecules of amphiphilic compounds using Hyperchem (Hypercube Inc.) software. By random rotation and translation of each SPDS molecule, using MDesigner program package (developed by us), was received lamella consisting of 512 amphiphilic molecules. The Langevin dynamics with 5ps -1 damping coefficient was used for constant temperature control. Constant pressure was controlled by using the Langevin piston Nose Hoover method. System energy minimization and simulation run were done in presence of 512 amphiphilic molecules and 8887 water molecules, with 1 fs timestep, using GROMACS software code with CHARMM27 all-atom force field on parallel Linux cluster.

4. Computational Details (continuation) The force field parameters of molecules were generated using Dundee PRODRG server. 500 ns (0.5) overall parallel Molecular Dynamics (MD) run in ensemble was done, correspondingly 300ns for T=300K, 100ns for T=323K and 100ns for T=323K The parallel MD simulation was performed on ArmGrid sites (http://www.grid.am ) using 48 processors.http://www.grid.am

5. Object of study: Computer research of Lamellar phase. In this direction the following problems are solved: Building of computer model of all molecules and the system as a whole Choice of a force field and tools of experiment Simulation Obtain and the analysis of the data

6. RESULTS AND DISCUSSION Lamellar phase of Lyotropic Liquid Crystal with Lamellа of biological origin: Human Red Blood Cell (Erythrocite) Membrane

7. The fragment of Human Red Blood Cell (Erythrocite) Membrane

8. Proportion of phospholipids and cholesterol in the model of asymmetric erythrocyte membrane (Lamella). NameAcyl Chain Concentrati on in outer layer of membrane (%) Concentratio n in Inner layer of membrae (%) Average Consistence, (%) Chem. Symbol Sphingomyelin 24:0–14:019.8 %2.3 % 21.8 % LSM Sphingomyelin16:0-14:020.6 %2.3 %HSM Phosphaditylseri ne 18:0- 20:4w6 0 %9.9 % 10.3 SAPS Phosphaditylseri ne 18:0- 22:6w3 0 %10.8 %SDPS Phosphadityletha nol amine 18:0-20:43.3 %18.3 %11.7SAPE Phosphaditylchol ine 16:0-18:114,9 %7.6 % 22.6 POPC Phosphaditylchol ine 18:0-18:115,7 %7.6 %SOPC Cholesterol24,1 %22,9 %23,5 %Chol

9. Lignoceroyl Sphingomyelin /24:0–14:0 Hexadecanoyl Sphingomyelin / 16:0-14:0 1-stearoyl-2-arachidonoyl-sn-glycero-3-phosphaditylSerine /18:0-20:4 1-stearoyl-2-docosahexaenoyl-sn-glycero-3-phosphaditylSerine/18:0-22:6 1-stearoyl-2-oleoyl-sn-glycero-3-phosphocholine /18:0 - 18:1

10. 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine /16:0-18:1 1-stearoyl-2-arachidonoyl-sn-glycero-3-phosphoethanolamine /18:0-20:4 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine /16:0-18:1

11. Thermodynamic equilibrium model of erythrocyte membrane with protein molecule

13. Dynamics of Protein and Water Molecule in Lamella. Animation

15. The map of contacts of aminoacid residuals of α and β helixes of Glicophorin A in Lamella (asymmetric membrane of Erythrocyte)

17. Dynamics of change of distances between aminoacid residuals of α and β helixes of Glicophorin A in Lamella (asymmetric membrane of Erythrocyte) Leu75 - Ile76 Gly79 - Val80 Gly80 - Gly83 Leu75 - Ile76 Gly79 - Val80 Gly80 - Gly83

20. Behavior of Protein molecule in Lamella. Animation

21. Behavior of Cholesterol Molecules in Lamella (Animation)

22. Roughness of Lamella Surface Surface roughness of the lamella represents the amount of vertical displacement of the molecules on the surface, described by the function: Z(r) and Z(r+R) are z-cordinates of the phosphorous atoms of phospholipid molecules on the surface of lamella.

23. Surface Roughness function of Lamella and Snapshot of Phospholipids Phosphorus atoms ordering after 80 ns MD simulation

24. The Roughness of Lamella Surface at the random moment of Computer experiment

25. Lamellar phase of commercial Surfactant`s Lyotropic Liquid Crystal : Sodium Pentadecylsulphonate – C 15 H 31 SO 3 Na (SPDS)

26. Lyotropic Systems Phase Diagram

27. SPDS(512)/water(8887) system 500ns MD run

28. Main tasks – investigation of structural parameters: Interlayer spacing Average area per SPDS molecule headgroup on the surface of Lamella Lamella thickness SPDS alkyl chains orientation Water-PDS interactions

29. Interlayer spacing dependence on temperature

30. Average area per SPDS molecule headgroup dependence on temperature

31. Average lamella thickness dependence on temperature

32. SPDS molecules alkyl tails orientation order parameter

33. Radial distribution function of water oxygens from SPDS headgroup sulphur atoms

34. SPDS molecules average length dependence on temperature

35. Lamella two monolayers average interpenetration dependence on temperature

36. All developed models are available in database of MDesigner

37. Тhank you