forthcoming articles

The following articles are a selection of those recently accepted for publication in Acta Crystallographica Section D: Structural Biology.

See also Forthcoming articles in all IUCr journals.

Accepted 12 April 2018

From deep TLS validation to ensembles of atomic models built from elemental motions. II. Analysis of TLS refinement results by explicit interpretation

The values of anisotropic atomic displacement parameters (ADP) that correspond to concerted motions can be obtained from refined TLS matrices analytically or numerically. A difference between the ADP obtained using these two methods can be used to assess results of TLS refinement.

Accepted 10 April 2018

MR-REX: molecular replacement by cooperative conformational search and occupancy optimization on low-accuracy protein models

A new algorithm, MR-REX, has been developed to perform a molecular-replacement search through replica-exchange Monte Carlo simulations. The algorithm enables cooperative rotation and translation searches and simultaneous clash and occupancy optimization, and improves the success rate of molecular replacement on low-accuracy structure models.

Accepted 10 April 2018

Structure of the flavocytochrome c sulfide de­hydrogenase associated with the copper-binding protein CopC from the haloalkaliphilic sulfur-oxidizing bacterium Thioalkalivibrio paradoxus ARh1

The structure of monohaem flavocytochrome c sulfide dehydrogenase co-purified and co-crystallized with the copper-binding protein CopC was solved and refined to 2.6 Å resolution.

Accepted 2 April 2018

Orthorhombic lysozyme crystallization at acidic pH values driven by phosphate binding

Structures of orthorhombic crystals of lysozyme at pH 4.5 show that the binding of phosphate ion produces long-range conformational changes and that low humidity produces a displacement of the fifth α-helix towards the active-site cavity. The interaction of some anions must be considered when analysing experiments with lysozyme at acidic pH values.

Accepted 27 March 2018

Cryoprotectant-free high-pressure freezing 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 freezing of a relatively larger protein single crystal and the proton polarization of a protein poly crystalline state were demonstrated as preliminary experiments.

Accepted 27 March 2018

Biological small-angle neutron scattering: recent results and development

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

Accepted 27 March 2018

Structural insight into industrially relevant glucoamylases: flexible positions of starch-binding domains

Three industrially relevant glucoamylase structures have been determined, revealing how the starch-binding module can adopt different orientations relative to the catalytic domain.

Accepted 23 March 2018

Domain swap in the C-terminal ubiquitin-like domain of human doublecortin

A large domain swap encompassing half of the molecule is observed in the crystal structure of the C-terminal domain of human doublecortin. Combined with ultracentrifugation data, the domain swap suggests a mechanism by which doublecortin may cooperatively bind and bundle microtubule fibres.

Accepted 22 March 2018

The actions of volatile anesthetics: a new perspective

Recent work applying neutron and X-ray scattering to elucidate molecular mechanisms of volatile anesthetics is reviewed

Accepted 22 March 2018

Determining the Amphipol distribution within membrane-protein fibre samples using small-angle neutron scattering

Using the unique ability of small angle neutron scattering to resolve a hydrogen rich surfactant from a deuterated membrane protein, we reveal the results of removing free surfactant from the equilibrium.

Accepted 21 March 2018

Automated map sharpening by maximization of detail and connectivity

A procedure for optimizing the sharpening of a map based on maximizing the level of detail and connectivity of the map has been developed and applied to 361 pairs of deposited cryo-EM maps and associated models.

Accepted 19 March 2018

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

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

Accepted 19 March 2018

KAMO: towards automated data processing for microcrystals

An automated data-processing pipeline for protein microcrystals is presented. The processing of multiple small-wedge data sets was made dramatically easier by this pipeline.

Accepted 3 March 2018

Multi-position data collection and dynamic beam sizing: recent improvements to the automatic data-collection algorithms on MASSIF-1

Significant improvements to the sample-location, characterization and data-collection algorithms on the autonomous ESRF beamline MASSIF-1 are described. The workflows now include dynamic beam-diameter adjustment and multi-position and multi-crystal data collections.

Accepted 28 February 2018

Microfocus diffraction from different regions of a protein crystal: structural variations and unit-cell polymorphism

Microfocus X-ray data collection from 18 non-overlapping regions of a single protein crystal revealed unit-cell non-isomorphism and subtle protein dynamics across the crystal specimen.

Accepted 28 February 2018

Crystal structure of pyrrolizidine alkaloid N-oxygenase from the grasshopper Zonocerus variegatus

The high-resolution crystal structure of a Z. variegatus flavin-dependent monooxygenase is reported at 1.6 Å resolution together with kinetic studies of structure-based protein variants in order to investigate significant differences in enzyme activity between isoforms.

Accepted 27 February 2018

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.

Accepted 26 February 2018

Apurinic/apyrimidic endonuclease 1 processing of apurinic/apyrimidic sites with 5′ mismatches

Mismatch conformations are dynamic and vary depending on the environment, including restraints imposed by DNA-binding proteins such as apurinic/apyrimidic 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.

Accepted 26 February 2018

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.

Accepted 22 February 2018

Density and electron density of aqueous cryoprotectant solutions at cryogenic temperatures for optimized cryoprotection and diffraction contrast

The densities of aqueous solutions of eight common cryoprotectants were measured at T = 77 K and were used to determine electron densities at T = 77 K and thermal contractions on cooling from room temperature. The results provide a quantitative basis for choosing cryoprotectants to optimize outcomes in cryocrystallography, cryo-SAXS, cryogenic temperature X-ray imaging and vitrification-based biological cryopreservation.

Accepted 20 February 2018

Determination of Patterson group symmetry from sparse multi-crystal data sets in the presence of an indexing ambiguity

A method is presented to simultaneously resolve the crystal symmetry and indexing ambiguity from sparse data sets.

Accepted 19 February 2018

Bacteroides thetaiotaomicron generates diverse α-mannosidase activities through subtle evolution of a distal substrate-binding motif

Analysing two sequence-related bacterial glycoside hydrolase family 92 mannosidases with distinct functions, a structural basis for their varied specificities is revealed.

Accepted 19 February 2018

Structural rearrangements occurring upon cofactor binding in the Mycobacterium smegmatis β-keto­acyl-acyl carrier protein reductase MabA

High-resolution crystal structures of closed and open conformations of Mycobacterium smegmatis MabA are reported.

Accepted 26 January 2018

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.

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