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Roderick MacKinnon received an undergraduate degree from Brandeis University, a medical degree from Tufts University, and training in Internal Medicine at Beth Israel Hospital, Harvard Medical School. He then began his scientific career studying the biophysics of potassium channels at Brandeis University from 1986-1989. He joined the faculty at Harvard Medical School as Assistant Professor of Physiology (1989), Associate Professor of Neurobiology (1992) and Professor of Neurobiology (1995).

During this period he and his laboratory characterized potassium channels - their subunit stoichiometry, pore-lining amino acids, and components of their gates - through biochemical and functional analysis. He then moved to Rockefeller University in 1996 where his laboratory has provided the first atomic descriptions of ion selective membrane channels. He is currently professor in the laboratory of Molecular Neurobiology and Biophysics at Rockefeller University and Investigator of the Howard Hughes Medical Institute. In 2003 he shared the Nobel Prize in Chemistry with Peter Agre for his structural and mechanistic studies of ion channels.