EFFECTS OF LYSO-LIPIDS ON MSCL ACTIVATION STUDIED BY MOLECULAR DYNAMICS SIMULATION

• Main Author: Aditama, Reza
• Format: Theses
• Language: Indonesia
• Subjects: Kimia
• Online Access: https://digilib.itb.ac.id/gdl/view/35477
• Institution: Institut Teknologi Bandung

Mechanosensitive (MS) Channel is a protein that is very interesting to be studied. This protein is a membrane protein that has the ability to sense mechanical changes in membrane lipids and then turn it into chemical signals to perform the reaction against such action. Inside the cell, this protein functions as a safey-valve which can reduce the turgor pressure when there is a lot of water in the cell by releasing it so that cells can be protected from lysis. Mechanosensitive channels of large conductance (MscL) is one type of MS that has been well-known structure. It has been previously shown in vitro that the addition of lyso-lipids into the vesicle unilamelar solution can trigger an activation of MscL. But the reason why this phenomenon can be occured is not known clearly. Several hypotheses have been proposed to explain the activation phenomena. The most acceptable hypothesis, however, is the existence of the intrinsic membrane curvature caused by the presence of lyso-lipids that is believed by many scientist as the trigger for the activation of the MscL protein. Therefore, the purpose of this study was to mimic the experiments with in silico approaches to understand the phenomenon of MscL activation by lyso-lipids at the atomic level. The method used in this study were divided into three phases namely system preparation, system simulation, and analysis of simulation results. In this study MscL was embedded into several bilayer of DPPC- (lyso-PPC) systems. The system is made into three models, namely MscL without modification in the membrane bilayer, symmetrical and asymmetrical membrane bilayers. Molecular dynamics simulations were performed using the MARTINI coarse-grained model and each simulation is run for 300 ns. Unlike the all-atomic simulations, coarse-grained is highly efficient to relieve the burden on the simulation calculations in order to achieve a longer simulation time than the all-atomic simulations. In addition, we also performed simulations for the structure of the gain of function mutant V21D in addition to wild-type MscL. The simulation results on the structure of Mscl wild-type was still unable to explain the role of lyso-lipids to MscL activation. Most of the simulation results did not show any activation of MscL even some simulations showed the damage of the membrane bilayer because of the stability of the membrane bilayer to be lower in the presence of lyso-lipids. From the Mscl wild-type simulations, we obtained only two active structures, ie the system without modification and the system of asymmetrical membran bilayer, when we applied the voltage of about 63 mN/ps. These results can not give an explanation on the effect of lyso-lipids activation, therefore, we also perform simulations using V21D mutant that has been known in previous studies to have lower activation voltage compared with the wild-type. V21D simulations provide significant differences at membrane tension of 40 mN/ps, where the system without modification did not have activation, while the membrane asymmetry was succesfully activated. The structure of active MscL mutants has a channel diameter of 1.22 nm. It was smaller than the experimental results that can reach a diameter of 2.5 nm. This significant difference is caused by the difference in the activation time in which the simulation was performed in much shorter time (order of nanoseconds) compared with the experiment that reached the order of milliseconds. From the results of trajectory analysis, it is known that the process of activation for the MscL wild-type and mutant followed the iris-like mechanism, where initial small opening was occurred first, and then followed by the opening of the greater channel. The simulation results are also consistent with previous experiments which showed that the lyso-lipids can reduce the tension threshold for activation of MscL (from ~77 mN/ps to 40 mN/ps). From the simulation results shown also that the curvature in the bilayer is not required for activation of MscL.