| Popis: |
The power of the current computer clusters allows us to study relatively large biomolecular systems by theoretical computational methods, such as widely used classical molecular dynamics (MD) simulations, at atomic level on the time scale of tens of nanoseconds. The limiting factor for classical MD simulations on most of the physiologically relevant systems is the lack of available force field (FF) parameters. Three biomolecular systems were studied in this thesis, namely membrane protein photosystem II (PSII), green bacteria antennas called chlorosomes and flavoprotein WrbA from E. coli, and all of them contain molecules or molecular fragments for which no FF parameters are available. Therefore, development of new FF parameters for all non-protein molecules was performed by applying quantum-mechanics (QM) methods. Once all FF parameters were available, MD simulations were applied. The computational studies were based on the conditions from wet experiments performed earlier by our research group. For the first time, proposed light-induced conformational changes of the reaction center (RC) of PSII and subsequent changes in arrangement of PSII RC pigments, were confirmed and described at atomic level by series of MD simulations over 20 ns. Optical spectra calculated on equilibrated MD model of PSII RC were in better agreement with experimental analogues when compared with earlier calculations on static model of PSII RC taken from crystal structure. Successful application of classical mechanics, QM and advanced optical spectra calculations on PSII represents one of a few existing computational studies on similar membrane pigment-protein systems. In the case of chlorosomes, equilibrated molecular lamellar models were constructed and critical structural parameters were elucidated by series of MD simulations over 30 ns. The presented models are the first lamellar models of chlorosomes at such scale so far. The equilibrated MD models of flavoprotein WrbA based on recent crystal structure provides starting point for further theoretical studies aimed to elucidate structural details of proposed ping-pong mechanism. |
