Paper Citing NAMD - Abstract
Khrenova, Maria G.; Nemukhin, Alexander V.; Grigorenko, Bella L.; Wang, Peng; Zhang, Jian-Ping
All-atom structures and calcium binding sites of the bacterial photosynthetic LH1-RC core complex from Thermochromatium tepidum
JOURNAL OF MOLECULAR MODELING, 20 Art. No. 2287, JUN 2014
Computationally derived structures of the photosynthetic core complex composed of the light-harvesting (LH) system LH1 and the reaction center (RC) from a thermophilic purple sulfur bacterium Thermochromatium tepidum are reported providing first models of the LH1 system at atomic resolution. We used the known primary structure of alpha and beta polypeptides from this particular LH1 complex and the related bacterial LH templates to design the LH1 torus composed of 16 alpha beta subunits trapping bacteriochlorophyll (BChl-a) dimers and carotenoid molecules. The macromolecule of RC was placed in the center of the ring and the LH1-RC complex was inserted inside the lipid bilayer to simulate the membrane environment. Since thermal stability of the LH1-RC complex is linked to Ca2+ binding by the complex, location of trapping sites of calcium ions in the LH1 polypeptides is examined by using molecular dynamics simulations of the entire system solvated in water with CaCl2 molecules in the system. The newly predicted Ca2+ trapping sites can be responsible for attractive interaction of neighboring alpha beta subunits of LH1 with relevance to stability of the calcium-bound LH1-RC complex.
