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Roderick MacKinnon (born 19 February 1956) is a professor of Molecular Neurobiology and Biophysics at Rockefeller University who won the Nobel Prize in Chemistry together with Peter Agre in 2003 for his work on the structure and operation of ion channels.

MacKinnon was born in Burlington, Massachusetts and initially attended the University of Massachusetts Boston. MacKinnon then transferred to Brandeis University after one year, and there he received a bachelor's degree in biochemistry in 1978, studying calcium transport through the cell membrane for his honors thesis in Christopher Miller's laboratory. It was also at Brandeis where MacKinnon met his future wife and working-colleague Alice Lee.

After receiving his degree from Brandeis, MacKinnon entered medical school at Tufts University. He got his M.D. in 1982 and received training in Internal Medicine at Beth Israel Hospital in Boston. He did not feel satisfied enough with the medical profession, so in 1986 he returned to Christopher Miller's laboratory at Brandeis for postdoctoral studies.

In 1989 he was appointed assistant professor at Harvard University where he studied the interaction of the potassium channel with a specific toxin derived from scorpion venom, acquainting himself with methods of protein purification and X-ray crystallography. In 1996 he moved to Rockefeller University as a professor and head of the Laboratory of Molecular Neurobiology and Biophysics where he started to work on the structure of the potassium channel. These channels are of particular importance to the nervous system and the heart and enable potassium ions to cross the cell membrane.

Potassium channels demonstrate a seemingly counterintuitive activity: they permit the passage of potassium ions, whereas they do not allow the passage of the much smaller sodium ions. Before MacKinnon's work, the detailed molecular architecture of potassium channels and the exact means by which they conduct ions remained speculative. In 1998, despite barriers to the structural study of integral membrane proteins that had thwarted most attempts for decades, MacKinnon and colleagues determined the three-dimensional molecular structure of a potassium channel from bacteria utilizing X-ray crystallography. With this structure and other biochemical experiments, MacKinnon and colleagues were able to explain the exact mechanism by which potassium channel selectivity occurs.

His prize-winning research was conducted primarily at the Cornell High Energy Synchrotron Source (CHESS) of Cornell University, and at the National Synchrotron Light Source (NSLS) of Brookhaven National Laboratory.