Neutron crystallography for the elucidation of enzyme catalysis
Section snippets
Neutron crystallography on structural biology
X-ray crystallography is the technique most commonly used to determine the tertiary structures of biomacromolecules such as proteins and nucleic acids, but it is difficult to observe light elements, especially hydrogen atoms, because the X-ray scattering factors are proportional to the number of electrons (i.e. the atomic number) of an atom. Hydrogen atoms comprise about half of all atoms in proteins and play essential roles in the catalytic reactions of enzymes. X-ray structures determined at
Neutron structural analyses of ascorbate peroxidase
Peroxidases are heme-containing metalloenzymes that catalyze the oxidation of various substrates by reducing hydrogen peroxide (H2O2). Cytochrome c peroxidase (CcP) catalyzes the oxidation of cytochrome c, and ascorbate peroxidase (APX), which is closely related to CcP, oxidizes ascorbate. Peroxidases have in common a catalytic cycle that consists of sequential redox steps involving the formation of two highly oxidized FeIV (ferryl) intermediates (named compound I and compound II) [8]. Two
Neutron structural analyses of the main protease of SARS-CoV-2
The current COVID-19 pandemic is caused by a novel coronavirus known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) [21]. The main protease (Mpro) of SARS-CoV-2 plays an indispensable role in viral replication, making it a promising target for inhibitor (drug) design to prevent SARS-CoV-2 activity [22]. Mpro forms a homodimer, and its overall structure is highly conserved among coronaviruses [23]. Each monomer consists of three domains (domains I–III), and the active site is
Neutron structural analyses of copper-containing nitrite reductase
Copper-containing nitrite reductases (CuNIRs) catalyze a critical step in denitrification, the one-electron reduction of nitrite (NO2−) to nitric oxide (NO), which generates gaseous NO. This reaction breaks down terrestrial fertilizer. CuNIRs form a homotrimer, and each monomer contains one type 1 copper (T1Cu) and one type 2 copper (T2Cu) [33, 34, 35, 36]. The T1Cu site is involved in accepting an electron from physiological electron donor proteins, such as cytochrome c551, and then, the
Conclusion and outlook
The use of neutron crystallography in structural biology remains limited, at least in terms of the number of structure determinations, but enables the direct observation of hydrogen atoms, which is extremely difficult by other methods. Neutron crystallography has been used to elucidate the detailed catalytic reactions of several enzymes by precisely determining protonation states and hydration structures.
Technical developments will make neutron crystallography a more common method in structural
Conflict of interest statement
Nothing declared.
Acknowledgements
The authors are grateful to Drs. Andreas Ostermann, Leighton Coates, and Yohta Fukuda for critical reading and valuable comments.
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