| Abstract [eng] |
Bacteriorhodopsin is a protein responsible for proton transfer across cell membrane. To activate this function (proton transfer) light energy is required. Bacteriorhodopsin was discovered 40 years ago in organism named Halobacterium salinarum. In bacteriorhodopsin active center there is retinal molecule. Its configuration changes (from all-trans to 13-cis, 15-anti) allow proton transfer process to occur. There are a lot of methods used for bacteriorhodopsin modeling. The most popular methods are DFT (density functional theory) and ADMP (ab-initio molecular dynamics). A lot of studies use those methods, because they are pretty fast and accurate. Because of that, we used these methods in this work. In nature retinal 13-cis, 15-anti configuration is very stable, and its duration is more than 1 ps (we can see it from bacteriorhodopsin photocycle). But molecular dynamics calculations show, that its duration is around 30 fs. There is a big difference between the theoretical calculations and observations. This work main objective is to evaluate stability of retinal 13-cis, 15-anti configuration. |
