Generalized fundamental measure theory for atomistic modeling of macromolecular crowding.
Macromolecular crowding inside cells affects the thermodynamic and kinetic properties of proteins. The scaled particle theory (SPT) has played an important role toward establishing a qualitative picture for the effects of crowding. However, SPT-based modeling lacks molecular details. Molecular dynamics simulations overcome this limitation, but at great computational cost. Here, we present a theoretical method for modeling crowding at the atomic level. The method makes it possible to achieve exhaustive conformational sampling in modeling crowding effects and to tackle challenges posed by large protein oligomers and by complex mixtures of crowders.
Qin
Sanbo
S
Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA.
Zhou
Huan-Xiang
HX
D003198:Computer Simulation; D008956:Models, Chemical; D008958:Models, Molecular; D046912:Multiprotein Complexes / Q000737:chemistry* / Q000648:ultrastructure*; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000648:ultrastructure*; D011789:Quantum Theory
D046912:Multiprotein Complexes; D011506:Proteins