Mapping ligand movement
Contrary to the common presentation of a ligand binding to a protein, the two molecules do not remain static and subtle
ZURICH—Contrary to the common presentation of a ligand binding to a protein, the two molecules do not remain static and subtle but rapid movements between the two can translate to significant changes in binding characteristics. Recently, researchers at the University of Zurich, University of Ulm, and University of Illinois at Urbana-Champaign used IR exchange spectroscopy to try to capture subpicosecond motions.
As they reported in PNAS, the researchers looked at the light-induced migration of carbon monoxide molecules between its binding site on myoglobin (Mb) and the protein's heme group. Using transient 2D-IR exchange spectroscopy (T2D-IR-EXSY), they noted distinct CO spectra indicative of CO bound to either of two positions on the heme (A1, A3).
Following a brief laser pulse, however, the heme:CO peaks diminished to be replaced by Mb:CO peaks in a matter of picoseconds. The latter peaks suggested the CO molecules bound to any of three positions on Mb (B0, B1, B2). The researchers then found that they could even determine correlations in the migration behavior from distinct A-state positions to the B-state positions, which they confirmed with another spectroscopic method.
According to the researchers, the method should be "well applicable to other light-induced processes", making it a useful tool in our efforts to understand protein-ligand interactions.