All-atom structures and calcium binding sites of the bacterial photosynthetic LH1-RC core complex from Thermochromatium tepidum.
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 α and β polypeptides from this particular LH1 complex and the related bacterial LH templates to design the LH1 torus composed of 16 αβ 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 Ca(2+) 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 Ca(2+) trapping sites can be responsible for attractive interaction of neighboring αβ subunits of LH1 with relevance to stability of the calcium-bound LH1-RC complex.
Department of Chemistry, M.V. Lomonosov Moscow State University, Leninskie Gory 1/3, Moscow, 119991, Russian Federation.
Maria G
MG
Khrenova
Alexander V
AV
Nemukhin
Bella L
BL
Grigorenko
Peng
P
Wang
Jian-Ping
JP
Zhang
D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism; D001429:Bacteriochlorophylls / Q000737:chemistry / Q000378:metabolism; D001665:Binding Sites; D002122:Calcium Chloride / Q000737:chemistry* / Q000378:metabolism; D002338:Carotenoids / Q000737:chemistry / Q000378:metabolism; D002841:Chromatiaceae / Q000737:chemistry* / Q000145:classification / Q000378:metabolism; D045342:Light-Harvesting Protein Complexes / Q000737:chemistry* / Q000378:metabolism; D008051:Lipid Bilayers; D056004:Molecular Dynamics Simulation; D010788:Photosynthesis; D011485:Protein Binding; D011487:Protein Conformation; D055503:Protein Multimerization; D055550:Protein Stability; D013329:Structure-Activity Relationship; D014867:Water / Q000737:chemistry
D001426:Bacterial Proteins; D001429:Bacteriochlorophylls; D045342:Light-Harvesting Protein Complexes; D008051:Lipid Bilayers; D014867:Water; D002338:Carotenoids; D002122:Calcium Chloride