Defining the interface between the C-terminal fragment of alpha-transducin and photoactivated rhodopsin.
A novel combination of experimental data and extensive computational modeling was used to explore probable protein-protein interactions between photoactivated rhodopsin (R*) and experimentally determined R*-bound structures of the C-terminal fragment of alpha-transducin (Gt(alpha)(340-350)) and its analogs. Rather than using one set of loop structures derived from the dark-adapted rhodopsin state, R* was modeled in this study using various energetically feasible sets of intracellular loop (IC loop) conformations proposed previously in another study. The R*-bound conformation of Gt(alpha)(340-350) and several analogs were modeled using experimental transferred nuclear Overhauser effect data derived upon binding R*. Gt(alpha)(340-350) and its analogs were docked to various conformations of the intracellular loops, followed by optimization of side-chain spatial positions in both R* and Gt(alpha)(340-350) to obtain low-energy complexes. Finally, the structures of each complex were subjected to energy minimization using the OPLS/GBSA force field. The resulting residue-residue contacts at the interface between R* and Gt(alpha)(340-350) were validated by comparison with available experimental data, primarily from mutational studies. Computational modeling performed for Gt(alpha)(340-350) and its analogs when bound to R* revealed a consensus of general residue-residue interactions, necessary for efficient complex formation between R* and its Gt(alpha) recognition motif.
Taylor
Christina M
CM
Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, USA.
Nikiforovich
Gregory V
GV
Marshall
Garland R
GR
D001665:Binding Sites; D003198:Computer Simulation; D008027:Light; D008956:Models, Chemical; D008958:Models, Molecular; D010777:Photochemistry / Q000379:methods*; D011485:Protein Binding; D011487:Protein Conformation; D012243:Rhodopsin / Q000737:chemistry* / Q000528:radiation effects / Q000648:ultrastructure*; D015293:Transducin / Q000737:chemistry* / Q000648:ultrastructure*
D012243:Rhodopsin; D015293:Transducin