AZURIN INSERTION DYNAMIC IN MEMBRANE LIPID USING COARSE-GRAINED MODELING OPTIMIZATION

• Main Author: Fitrasari, Dian
• Format: Dissertations
• Language: Indonesia
• Online Access: https://digilib.itb.ac.id/gdl/view/80733
• Institution: Institut Teknologi Bandung

Protein-lipid modeling and simulation are currently developing very rapidly to understand detailed interactions in a physical system. One of the interesting proteins is Azurin, which is the result of secondary metabolism from the bacteria Pseudomonas aeruginosa and is also related to the development of therapy using azurin to inhibit the spread of cancer cells and cause apoptosis. The dynamics of azurin penetration through the plasma membrane are still not well understood experimentally due to the short reaction time. Molecular dynamics is one method that can explain this phenomenon with long relaxation times. In this research, to shorten computing time, we use the Coarse Grained model and, more specifically, the MARTINI-CG (Coarse-Grained) model. The MARTINI-CG model, apart from shortening computing time, can also simplify calculations. Dynamics analysis using the CG model can still describe the physical properties of complex systems. One is that we examine the scaling relationship by varying the window separation and electrostatic parameters. Rescaling the electrostatic interaction by a factor of 0.04 produces a free energy value of -140.80 kcal/mol; after optimization of the separation window, the free energy value becomes -71.80 kcal/mol. This value is closer to the experimental results. The explanation is that this scaling is needed because the MARTINI-CG model essentially has a greater density than the allatom (AA) model. This affects the downscaling of electrostatic interactions in the MARTINI-CG model. Furthermore, in the azurin-lipid raft system, free energy calculations were analyzed on two models. The first model of azurin is on the surface with initial conditions of azurin on the surface of the lipid raft ?Gforward=- 35.422 kcal/mol. The azurin condition when the lipid raft undergoes a curvature change ?Gforward=-65.30 kcal/mol. Model II with initial conditions azurin is in a lipid raft ?Gforward = -1.85 kcal/mol. The condition of azurin in the transition state (fission intermediate) ?Gforward =-8.94 kcal/mol. The state of azurin in the final state (fission) ?Gforward=14.11 kcal/mol. The three free energy values illustrate that the phase change of the curvature of the azurin lipid raft is a spontaneous reaction. Furthermore, we carried out an analysis using the MIUS-WHAM (Multiple Independent Umbrella Sampling-Weighted Histogram Analysis Method) to describe the FEL (Free Energy Landspace) during the process. FEL analysis of changes in curvature when azurin is on the surface of lipid rafts (Model I). FEL is a function of the COM distance between azurin and lipid rafts over 4 ns. The selected distance is in the range of 25-30 Å. The equilibrium point is at a COM distance of 25.75 Å. At a COM distance of 26.92 Å the free energy begins to increase reaching 6.11 kcal/mol which indicates the energy required during this process. In Model II, azurin is in lipid rafts, the equilibrium state value is around 25Å, which shows the phase change in curvature. At a center of mass distance of 31Å, the bond free energy begins to increase to the range of 152 kcal/mol, indicating that this process requires energy to occur. The energy value tends to converge at an energy of 150 kcal/mol. Based on this analysis, it is found that the equilibrium state value is around 6.88Å, which shows the process of configuration change. At a center of mass distance of 14.46Å, when azurin starts to make holes in the membrane, the free energy is 29.47 kcal/mol which indicates that this process requires energy to occur. An energy value of 29.47 kcal/mol was observed in the fission intermediate phase in this study. This was confirmed by previous research where the energy value increased in this phase.