Investigation of Dynamic Structure of Protein Encountering Complex with Paramagnetic NMR

Abstract

Proteins recognize partner proteins and take function through short-range interaction at a small interface area. Therefore, protein and its partner form a series of encounter complex ensembles on the pathway to simplify conformational searching and facilitate protein-protein association. The encounter complex is hard to detect by traditional structural-biology methods due to its short life and low population. This paper chose histidine phosphate carrier protein (HPr) and enzyme II (EIIAGlc) complex as the research target, combining paramagnetic relaxation enhancement (PRE) with molecular dynamics simulation to characterize the encounter complex structure and dynamics. We found that the HPr first formed encounter complexes with EIIAGlc in three directions, and then compelled the formation of the specific complex. The methods utilized in this paper can visualize the encounter complex ensembles, and help understand the mechanism of bio-molecule interaction and protein function pathway in cell.

Keywords

• nuclear magnetic resonance (nmr)
• encounter complex
• molecular dynamics simulation
• sugar phosphotransferase system