Self-assembly of bitopic membrane protein M2 of influenza A

• Main Authors: Guan-Wei Li, 李冠緯
• Other Authors: Wolfgang B. Fischer
• Format: Others
• Language: en_US
• Published: 2016
• Online Access: http://ndltd.ncl.edu.tw/handle/13847684437632686457

碩士 === 國立陽明大學 === 生醫光電研究所 === 104 === Ion channels are pore-forming proteins in charge of permeability of specific ions on lipid bilayer by electrochemical gradients. They exist not only in every cellular membrane but in most of viruses and reveal the key part in how cells and viruses work. To investigate how ion channel proteins interact with each other from the aspect of biophysics, there is a program built for helping the user to generate the whole energy profile. This program of ion channel assembly (PICA) has 5 degrees of freedom (DOFs), namely, D, θ r, θ t, N and h, in order to describe each of the ion channel structures. PICA screens every point of DOF in the range the user is setting. Unlike other existing docking program or software that they search space all around the target proteins for proper conformation, PICA only search the space around the side surface of trans-membrane domain (TMD) of protein to find the its possible pore structure. Thus, it is more like a 2 dimensional search method rather than 3 dimensional search algorithm like other programs for globular proteins. The situation of PICA is different from those of the others tools. PICA is built under the assumption that pore-forming proteins are assembled on lipid bilayer of endoplasmic reticulum; that also is, these pore-forming proteins don’t need to be tilted at big angles and is assembled together under the lipid environment whose dielectric constant is nearly 2. An important feature of PICA is that the displacement of the structure includes the Cα atoms and sidechain. It turns out that the Root-Mean-Square Deviation (RMSD) values of top 10 structures are large; however, all of top 10 structures form proper orientation of residues to function as channels. In this research, I also performed other docking software and programs to assemble M2 proton channel of influenza A virus. These software and programs are Molecular Operating Environment (MOE), Sam, M-ZDOCK and Rosetta. In order to see how well it is on predicting pore structures of membrane proteins, RMSD comparison of backbones between original structure and prediction is applied. I also checked the top 10 prediction structures which these software and programs provided to user. Most of these prediction results failed to reproduce the actual structure of the M2 proton channel, and even though RMSD values of some of the predictions are small enough that they seem promising. In the case of M2 proton channel, the pore structure of the M2 channel must have four His and four Trp positioned inside the pore region in order to be proton conducting. The His of channel function as a pH sensor and the Trp forms the ion gate of the channel3. Most of the prediction results of existing software and programs have presented incorrect orientation of His and Trp. The final comparison tells the users that PICA provided ten proper structures to the user, and Sam provided the two, and M-ZDOCK provided the one and both MOE and Rosetta failed to provide any proper structures on the docking of M2 proton channel of influenza A virus.