Paper Citing NAMD - Abstract
Sener, M., Hsin, J., Trabuco, L.G., Villa, E., Qian, P., Hunter, C.N., Schulten, K.
Structural model and excitonic properties of the dimeric RC-LH1-Pufx complex from Rhodobacter sphaeroides
CHEMICAL PHYSICS, 357:188-197, FEB 23 2009
The light-harvesting apparatus of the purple bacterial photosynthetic unit consists of a pool of peripheral light-harvesting complexes that transfer excitation energy to a reaction center (RC) via the surrounding pigment-protein complex LH1. Recent electron microscopy and atomic force microscopy studies have revealed that RC-LH1 units of Rhodobacter (Rba.) sphaeroides form membrane-bending dimeric complexes together with the polypeptide PufX. We present a structural model for these RC-LH1-PufX dimeric complexes constructed using the molecular dynamics flexible fitting method based on an EM density map. The arrangement of the LH1 BChls displays a distortion near the proposed location of the PufX poly-peptide. The resulting atomic model for BChl arrays is used to compute the excitonic properties of the dimeric RC-LH1 complex. A comparison is presented between the structural and excitonic features of the S-shaped dimeric BChl array of Rba. sphaeroides and the circular BChl arrangement found in other purple bacteria. (C) 2009 Elsevier B.V. All rights reserved.