Neutron Crystallography Shows How Drugs Bind to Enzymes


X-ray crystallography is commonly used to determine how the atoms comprising a biological macromolecule are arranged. However, it has one serious limitation: it cannot observe directly where all of the hydrogen atoms are located, because they scatter x-rays very weakly (or in the case of H+, not at all). This underscores a major weakness of x-ray crystallography since an enzyme’s behavior usually depends on the arrangement of hydrogen atoms around its active site. In contrast, neutron crystallography can reveal the position of hydrogen atoms since they scatter neutrons as strongly as the other atoms found in proteins (i.e., C, N, O, and S). A recent study used neutron crystallography to show how carbonic anhydrase (HCA), an enzyme found in all life forms, binds acetazolamide (AZM), a carbonic anhydrase inhibitor drug clinically used to treat disorders ranging from glaucoma to epilepsy to altitude sickness. Experiments at the Protein Crystallography Station at Los Alamos National Laboratory (LANL) identified the hydrogen atoms at the binding site. The results clearly show the ionization state of AZM and how drug binding displaces key active site water molecules in HCA. It also revealed the hydrogen bonding interactions between the drug and the enzyme and showed the role of certain water molecules in drug binding. The experiments demonstrate that neutron beams provide crucial and specific information that will assist in applications such as structure-based drug design. The research was carried out by scientists at LANL and the University of Florida.


Fisher, S. Z., M. Aggarwal, A. Y. Kovalevsky, D. N. Silverman, and R. McKenna. 2012. “Neutron Diffraction of Acetazolamide-Bound Human Carbonic Anhydrase II Reveals Atomic Details of Drug Binding,” Journal of the American Chemical Society 134(36), 14726-729.  DOI: 10.1021/ja3068098.