Significantly, their insights arose not just from meticulous biochemical studies, but also from using sophisticated simulation techniques to perform "chemistry in the computer."
In a paper published Nov. 24, 2005 online in the journal Biochemistry, members of the interdisciplinary collaboration described how they discovered the probable orientation required for a Cdc25B phosphatase enzyme to "dock" with and activate a cyclin-dependent kinase protein complex that also functions as an enzyme, known as Cdk2-pTpY--CycA. The work was funded by the National Institutes of Health.
Detailed study of such docking is important because uncontrolled overreaction of the Cdc25 family of enzymes has been associated with the development of various cancers. Anti-cancer drugs that jam the enzyme, preventing its docking with the kinase, could halt cell over proliferation to treat such cancers. However, developing such drugs has been hampered by lack of detailed understanding of how the Cdc25s fit with their associated kinases.
"To me this is the culmination of my six years here at Duke," said Johannes Rudolph, the Duke assistant professor of chemistry and biochemistry who led the research. "It's very exciting. I think it's a really hard problem."
A successful docking between the two enzymes not only requires the "active sites" -- where chemical reactions occur --on the phosphatase and the kinase to link precisely, Rudolph said. The two molecules' component parts, or "residues," must also orient in a tongue-and-groove fit at a few other special places, which the researchers dubbed 'hot spots," on the irr