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Preview: Forthcoming article in Acta Crystallographica Section D: Biological Crystallography

Forthcoming article in Acta Crystallographica Section D Structural Biology



Acta Crystallographica Section D: Structural Biology welcomes the submission of articles covering any aspect of structural biology, with a particular emphasis on the structures of biological macromolecules and the methods used to determine them. Reports o



 



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.



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.



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.



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.



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.



Predicting data quality in biological X-ray solution scattering
First-principles signal-to-noise calculations for BioSAXS are 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.



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.



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



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.



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.



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.



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.



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.



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.



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/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.



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.



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.



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.



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 M. smegmatis MabA are reported.



ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps
ISOLDE is an interactive molecular-dynamics environment for rebuilding models against experimental cryo-EM or crystallographic maps. Analysis of its results reinforces the need for great care when validating models built into low-resolution data.



Microtubule architecture in vitro and in cells revealed by cryo-electron tomography
Electron microscopy is a key methodology for studying microtubule structure and organization. Here, the results of cryo-electron tomography experiments on in vitro-polymerized microtubules and comparisons with microtubule ultrastructure in cells are described.



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.