Paper Citing NAMD - Abstract
Hsin, Jen; Gumbart, James; Trabuco, Leonardo G.; Villa, Elizabeth; Qian, Pu; Hunter, C. Neil; Schulten, Klaus
Protein-Induced Membrane Curvature Investigated through Molecular Dynamics Flexible Fitting
BIOPHYSICAL JOURNAL, 97:321-329, JUL 8 2009
In the photosynthetic purple bacterium Rhodobacter (Rba.) sphaeroides, light is absorbed by membrane-bound light-harvesting (LH) proteins LH1 and LH2. LH1 directly surrounds the reaction center (RC) and, together with PufX, forms a dimeric (RC-LH1-PufX)(2) protein complex. In LH2-deficient Rba. sphaeroides mutants, RC-LH1-PufX dimers aggregate into tubular vesicles with a radius of similar to 250-550 angstrom, making RC-LH1-PufX one of the few integral membrane proteins known to actively induce membrane curvature. Recently, a three-dimensional electron microscopy density map showed that the Rba. sphaeroides RC-LH1-PufX dimer exhibits a prominent bend at its dimerizing interface. To investigate the curvature properties of this highly bent protein, we employed molecular dynamics simulations to fit an all-atom structural model of the RC-LH1-PufX dimer within the electron microscopy density map. The simulations reveal how the dinner produces a membrane with high local curvature, even though the location of PufX cannot yet be determined uniquely. The resulting membrane curvature agrees well with the size of RC-LH1-PufX tubular vesicles, and demonstrates how the local curvature properties of the RC-LH1-PufX dinner propagate to form the observed long-range organization of the Rba. sphaeroides tubular vesicles.
