Paper Citing NAMD - Abstract
Hsin, Jen; Chipot, Christophe; Schulten, Klaus
A Glycophorin A-Like Framework for the Dimerization of Photosynthetic Core Complexes
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 131:17096-+, DEC 2 2009
The core complex in photosynthetic bacteria plays a central role in photosynthesis. This molecular assembly is composed of two protein complexes, viz., the light-harvesting complex I (LH1), which absorbs sunlight by means of the protein-bound bacteriochlorophylls, and the reaction center (RC), which uses the light-excitation energy absorbed by the LH complexes to produce a transmembrane (TM) charge gradient, subsequently employed for energy conversion. In Rhodobacter (Rba.) sphaeroides, the core complex contains, in addition, two copies of the single TM alpha-helix protein, PufX, and forms a (RC-LH1-PUfX)(2) dimer. To this date, no high-resotution structure has been reported for the entire core complex. In particular, the location of Puff within the (RC-LH1-PufX)(2) dimer is still the subject of much debate. Here, one of the proposed locations for Puff, requiring its dimerization, is examined. The Puff-dimer model on the basis of the glycophorin A (GpA) dimer was constructed, and its robustness was probed through a series of molecular dynamics (MID) simulations. The free-energy change due to the replacement of Gly35 by valine was also determined to assess whether this mutation is responsible for distinct Puff oligomerization states in different Rba. species. The present study shows that Puff helices form a stable GpA-like dimer with a helix-helix crossing angle that could constitute the molecular basis of the reported highly bent and V-shaped structure of the Rba. sphaeroides core complex dimer.
