Interaction of the disordered Yersinia effector protein YopE with its cognate chaperone SycE.
We describe an efficient approach to model the binding interaction of the disordered effector protein to its cognate chaperone in the type III secretion system (T3SS). Starting from de novo models, we generated ensembles of unfolded conformations of the Yersinia effector YopE using REMD simulations and docked them to the chaperone SycE using a multistep protein docking strategy. The predicted YopE/SycE complex was in good agreement with the experimental structure. The ability of our computational protocol to mimic the structural transition upon chaperone binding opens up the possibility of studying the underlying specificity of chaperone/effector interactions and devising strategies for interfering with T3SS transport.
Hu
Xin
X
Biotechnology HPC Software Applications Institute, Telemedicine and Advanced Technology Research Center, US Army Medical Research and Materiel Command, Fort Detrick, Maryland 21702, USA.
Lee
Michael S
MS
Wallqvist
Anders
A
D000465:Algorithms; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D001665:Binding Sites; D003198:Computer Simulation; D008958:Models, Molecular; D018832:Molecular Chaperones / Q000378:metabolism*; D011485:Protein Binding; D011487:Protein Conformation; D017510:Protein Folding; D015534:Trans-Activators / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*
D001426:Bacterial Proteins; D018832:Molecular Chaperones; C081269:SycE protein, Yersinia; D015534:Trans-Activators