Diffraction structural biology – introductory overview

An introductory overview to the articles on diffraction structural biology in this special issue of the journal.

Biological small-angle neutron scattering: recent results and development

Small-angle neutron scattering (SANS) provides structural information on biological macromolecules in solution that is perfectly complementary to the information obtained using other structural biology techniques, including crystallography, nuclear magnetic resonance and electron microscopy. Compared with its sister technique small-angle X-ray scattering, SANS allows specific and individual information to be obtained on subunits within important heterogeneous biological assemblies such as multiprotein or protein–RNA/DNA complexes as well as solubilized membrane proteins.

Predicting data quality in biological X-ray solution scattering

First-principles signal-to-noise calculations for BioSAXS have been developed and applied to evaluate the impact of energy, source brightness, window scattering and other variables on the ability to detect and distinguish protein conformational changes.

Phosphoramidon inhibits the integral membrane protein zinc metalloprotease ZMPSTE24

The interaction between the integral membrane protein zinc metalloprotease ZMPSTE24 and the natural product broad-specificity zinc metalloprotease peptidic inhibitor phosphoramidon has been characterized functionally and structurally. The functional results demonstrate the sensitivity of ZMPSTE24 to phosphoramidon in a manner consistent with competitive inhibition, as in soluble zinc metalloproteases, and that the overall mode of binding of phosphoramidon to ZMPSTE24 and soluble zinc metalloproteases, especially gluzincins, is conserved.

The crystal structure of Proteus vulgaris tryptophan indole-lyase complexed with oxindolyl-L-alanine: implications for the reaction mechanism

The structure of tryptophan indole-lyase with a bound inhibitor, oxindolyl-L-alanine, was determined. The structure provides new insights into the reaction mechanism of the enzyme.

Apurinic/apyrimidinic (AP) endonuclease 1 processing of AP sites with 5′ mismatches

Mismatch conformations are dynamic and vary depending on the environment, including restraints imposed by DNA-binding proteins such as apurinic/apyrimidinic endonuclease 1 (APE1), a key DNA-repair enzyme. Here, both key insights revealed by X-ray crystallography of APE1 bound to mismatch-containing substrates and the specific challenges associated with elucidating base-pairing properties based on implied protonation states and X-ray crystallographic data alone are highlighted.

Crystallographic study of dioxygen chemistry in a copper-containing nitrite reductase from Geobacillus thermodenitrificans

A structure of a copper-containing nitrite reductase from Geobacillus thermodenitrificans (GtNIR) was determined using an anaerobically manipulated crystal. Furthermore, a peroxide-bound structure of GtNIR was determined.

IMAGINE: neutrons reveal enzyme chemistry

The capabilities of the IMAGINE neutron protein diffractometer at the Oak Ridge National Laboratory High Flux Isotope Reactor and highlights of the first five years of the scientific program are reviewed.

Cryoprotectant-free high-pressure cooling and dynamic nuclear polarization for more sensitive detection of hydrogen in neutron protein crystallography

To improve the sensitivity of hydrogen detection using neutrons, high-pressure cooling of a relatively large protein single crystal and proton polarization of a protein polycrystalline state have been demonstrated as preliminary experiments.

The rise of neutron cryo-crystallography

The application of the cryogenic data-collection environments used in protein X-ray crystallography to neutron protein crystallography is discussed.

Evaluation of models determined by neutron diffraction and proposed improvements to their validation and deposition

Models of crystal structures determined by neutron diffraction and deposited in the Protein Data Bank to date were analysed. The lessons learned from this data-mining effort are summarized and suggestions for improvements to the deposition and validation of neutron models are outlined.