forthcoming articles in Acta Crystallographica Section D

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

See also Forthcoming articles in all IUCr journals.

Accepted 15 December 2014

Two way street - complementary methods

I. Tews and J. Cooper

Synopsis: An introduction to the 2014 CCP4 Study Weekend.

Accepted 10 December 2014

Interaction of the amyloid precursor protein-like protein 1 (APLP1) E2 domain with heparan sulfate involves two distinct binding modes

S. O. Dahms, M. C. Mayer, D. Roeser, G. Multhaup and M. E. Than

Synopsis: Two X-ray structures of APLP1-E2 with and without heparin dodecasaccharide are presented, revealing two distinct binding modes of the protein to heparan sulfate. The data give a mechanistic explanation how APP like proteins bind to heparan sulfates and how they specifically recognize non-reducing structures of heparan sulfates.

Accepted 9 December 2014

Three-dimensional structures of Plasmodium falciparum spermidine synthase with bound inhibitors suggest new strategies for drug design

J. Sprenger, B. Svensson, J. Hålander, J. Carey, L. Persson and S. Al-Karadaghi

Accepted 8 December 2014

BioSAXS Sample Changer: a robotic sample changer for rapid and reliable high-throughput X-ray solution scattering experiments

A. Round, F. Felisaz, L. Fodinger, A. Gobbo, J. Huet, C. Villard, C. E. Blanchet, P. Pernot, S. McSweeney, M. Roessle, D. I. Svergun and F. Cipriani

Synopsis: A robotic sample changer for solution X-ray scattering experiments optimized for speed and to use the minimum amount of material has been developed. This system is now in routine use at three high-brilliance European synchrotron sites, each capable of several hundred measurements per day.

Accepted 8 December 2014

Structural and functional analysis of Hikeshi, a new nuclear transport receptor of Hsp70

J. Song, S. Kose, A. Watanabe, S.-Y. Son, S. Choi, H. Hong, E. Yamashita, I. Y. Park, N. Imamoto and S. J. Lee

Synopsis: The crystal structure and functions of Hikeshi, a nuclear transport receptor of Hsp70s, are described.

Accepted 8 December 2014

Structural analysis of DNA binding by C.Csp231I, a novel class of R-M controller proteins regulating gene expression

M. B. Shevtsov, S. D. Streeter, S.-J. Thresh, A. Swiderska, J. E. McGeehan and G. G. Kneale

Accepted 5 December 2014

In pursuit of an accurate spatial and temporal model of biomolecules at the atomistic level: a perspective on computer simulation

A. Gray, O. G. Harlen, S. A. Harris, S. Khalid, Y. M. Leung, R. Lonsdale, A. J. Mulholland, A. R. Pearson, D. J. Read and R. A. Richardson

Synopsis: The current computational techniques available for biomolecular simulation are described, and the successes and limitations of each with reference to the experimental biophysical methods that they complement are presented.

Accepted 5 December 2014

Catalytically distinct states captured in a crystal lattice: the substrate-bound and scavenger states of acylamino­acyl peptidase and their implications for functionality

D. K. Menyhárd, Z. Orgován, Z. Szeltner, I. Szamosi and V. Harmat

Synopsis: A mechanism of oligopeptidases for their dual function is decoupling substrate binding and catalytic activity. Crystal structures of A. pernix aclyaminoacyl peptidase/covalent inhibitor complex provide insights into the role of substrates in this mechanism.

Accepted 4 December 2014

Structure calculation, refinement and validation using CcpNmr Analysis

S. P. Skinner, B. T. Goult, R. H. Fogh, W. Boucher, T. J. Stevens, E. D. Laue and G. W. Vuister

Synopsis: This report describes the working of the program CcpNmr Analysis for both NMR chemical shift assignment and structure determination of biological macromolecules.

Accepted 4 December 2014

The structure of apo ArnA features an unexpected central binding pocket and provides an explanation for enzymatic cooperativity

U. Fischer, S. Hertlein and C. Grimm

Synopsis: The crystal structure of apo ArnA features an unexpected central binding pocket and explains the strong cooperative effect seen in the dehydrogenase activity of ArnA.

Accepted 4 December 2014

X-ray, spectroscopic and normal-mode dynamics of calexcitin: structure-function studies of a neuronal calcium-signalling protein

P. T. Erskine, A. Fokas, C. Muriithi, H. Rehman, L. A. Yates, A. Bowyer, I. S. Findlow, R. Hagan, J. M. Werner, A. J. Miles, B. A. Wallace, S. A. Wells, S. P. Wood and J. B. Cooper

Accepted 3 December 2014

Structural insights into Aspergillus fumigatus lectin specificity: AFL binding sites are functionally non-equivalent

J. Houser, J. Komarek, G. Cioci, A. Varrot, A. Imberty and M. Wimmerova

Synopsis: The interaction between A. fumigatus lectin AFL and biologically relevant oligosaccharides has been examined. The functional data were combined with detailed structures of the protein-saccharide complexes to understand the ligand binding at the atomic level.

Accepted 1 December 2014

Structure of the GH76 [alpha]-mannanase BT2949 from the gut symbiont Bacteroides thetaiotaomicron

A. J. Thompson, F. Cuskin, R. J. Spears, J. Dabin, J. P. Turkenburg, H. J. Gilbert and G. J. Davies

Synopsis: A high-resolution structure of a noncanonical [alpha]-mannanase relevant to human health and nutrition has been solved via heavy-atom phasing of a selenomethionine derivative.

Accepted 1 December 2014

The structure of bradyzoite-specific enolase from Toxoplasma gondii reveals insights into its dual cytoplasmic and nuclear functions

J. Ruan, T. Mouveaux, S. H. Light, G. Minasov, W. F. Anderson, S. Tomavo and H. M. Ngô

Synopsis: The second crystal structure of a parasite protein preferentially enriched in the brain cyst of T. gondii is solved at 2.75 Å resolution. Bradyzoite enolase 1 is reported to have differential functions as a glycolytic enzyme and a transcriptional regulator in bradyzoites.

Accepted 30 November 2014

Room-temperature serial crystallography at synchrotron X-ray sources using slowly flowing free-standing high-viscosity microstreams

S. Botha, K. Nass, T. R. M. Barends, W. Kabsch, B. Latz, F. Dworkowski, L. Foucar, E. Panepucci, M. Wang, R. L. Shoeman, I. Schlichting and R. B. Doak

Synopsis: High-throughput, room-temperature serial crystallography using a slow stream is demonstrated at a synchrotron source. The data quality is sufficiently good to allow de novo phasing.

Accepted 29 November 2014

Protein-RNA affinity of ribosomal protein L1 mutants does not correlate with the number of intermolecular interactions

S. Tishchenko, O. Kostareva, A. Gabdulkhakov, A. Mikhaylina, E. Nikonova, N. Nevskaya, A. Sarskikh, W. Piendl, M. Garber and S. Nikonov

Synopsis: Comparison of the structures of RNA complexes of wild-type and mutant variants of TthL1 and analysis of the kinetics of RNA binding to the protein show that complex formation restores the distorted RNA-binding surface of the mutated protein and that the affinity of the protein for RNA cannot be correlated with the number of intermolecular contacts and hydrogen bonds.

Accepted 27 November 2014

Indexing amyloid peptide diffraction from serial femtosecond crystallography: new algorithms for sparse patterns

A. S. Brewster, M. R. Sawaya, J. Rodriguez, J. Hattne, N. Echols, H. T. McFarlane, D. Cascio, P. D. Adams, D. S. Eisenberg and N. K. Sauter

Synopsis: Special methods are required to interpret sparse diffraction patterns from peptide crystals collected at X-ray free-electron lasers. Bragg spots can be indexed from composite-image powder rings, with crystal orientations then deduced from a very limited number of spot positions.

Accepted 26 November 2014

The structure of the proteinaceous inhibitor PliI from Aeromonas hydrophila in complex with its target lysozyme

S. Leysen, J. M. Van Herreweghe, K. Yoneda, M. Ogata, T. Usui, T. Araki, C. W. Michiels and S. V. Strelkov

Accepted 26 November 2014

Data Exploration Toolkit for serial diffraction experiments

O. B. Zeldin, A. S. Brewster, J. Hattne, M. Uervirojnangkoorn, A. Y. Lyubimov, Q. Zhou, M. Zhao, W. I. Weis, N. K. Sauter and A. T. Brunger

Synopsis: A set of tools allowing experimentalists insight into the variation present within large serial data sets is described.

Accepted 25 November 2014

Exploring the speed and performance of molecular replacement with AMPLE using QUARK ab initio protein models

R. M. Keegan, J. Bibby, J. Thomas, D. Xu, Y. Zhang, O. Mayans, M. D. Winn and D. J. Rigden

Synopsis: Two ab initio modelling programs solve complementary sets of targets, enhancing the success of AMPLE with small proteins.

Accepted 23 November 2014

The structure of SAV1646 from Staphylococcus aureus belongs to a new `ribosome-associated' subfamily of bacterial proteins

Y. N. Chirgadze, T. E. Clarke, V. Romanov, G. Kisselman, J. Wu-Brown, M. Soloveychik, T. S. Y. Chan, R. D. Gordon, K. P. Battaile, E. F. Pai and N. Y. Chirgadze

Accepted 21 November 2014

Jacalin-carbohydrate interactions: distortion of the ligand molecule as a determinant of affinity

K. V. Abhinav, K. Sharma, C. P. Swaminathan, A. Surolia and M. Vijayan

Synopsis: Using the crystal structures of complexes of jacalin with [alpha]- and [beta]-galactosides, supplemented by thermodynamic data, it has been demonstrated that the low affinity of the lectin for [beta]-galactosides is caused by the distortion of the ligand and not by unfavourable protein-ligand interactions.

Accepted 20 November 2014

Efficient calculation of diffracted intensities in the case of nonstationary scattering by biological macromolecules under XFEL pulses

V. Y. Lunin, A. N. Grum-Grzhimailo, E. V. Gryzlova, D. O. Sinitsyn, T. E. Petrova, N. L. Lunina, N. K. Balabaev, K. B. Tereshkina, A. S. Stepanov and Y. F. Krupyanskii

Synopsis: Algorithms are proposed which enable the calculation of the time-accumulated diffraction intensities for a biological macromolecule with time-dependent atomic scattering factors at a computational cost comparable with that for the conventional time-independent case.

Accepted 20 November 2014

A fragmentation and reassembly method for ab initio phasing

R. Shrestha and K. Y. J. Zhang

Synopsis: Low-accuracy de novo models can be used successfully for ab initio phasing by the reassembly of molecular-replacement solutions of individual fragments derived from these de novo models.

Accepted 20 November 2014

Structural insights into the efficient CO2-reducing activity of an NAD-dependent formate de­hydrogenase from Thiobacillus sp. KNK65MA

H. Choe, J. M. Ha, J. C. Joo, H. Kim, H.-J. Yoon, S. Kim, S. H. Son, R. M. Gengan, S. T. Jeon, R. Chang, K. D. Jung, Y. H. Kim and H. H. Lee

Synopsis: Structural and functional studies of an NAD-dependent formate dehydrogenase from Thiobacillus sp. KNK65MA (TsFDH) revealed that TsFDH is an efficient CO2-reducing biocatalyst.

Accepted 19 November 2014

Structural and biochemical analyses of the Streptococcus pneumoniae L,D-carboxypeptidase DacB

J. Zhang, Y.-H. Yang, Y.-L. Jiang, C.-Z. Zhou and Y. Chen

Synopsis: The structure of L,D-carboxypeptidase DacB from S. pneumoniae provides novel insights into substrate recognition and catalysis in the metallopeptidase M15B subfamily.

Accepted 18 November 2014

A national facility for biological cryo-electron microscopy

H. R. Saibil, K. Grünewald and D. I. Stuart

Synopsis: This review provides a brief update on the use of cryo-electron microscopy for integrated structural biology, along with an overview of the plans for the UK national facility for electron microscopy being built at the Diamond synchrotron.

Accepted 17 November 2014

Ligand-bound structures of 3-de­oxy-D-manno-octulosonate 8-phosphate phosphatase from Moraxella catarrhalis reveals a water channel connecting the active site for the second step of catalysis

S. Dhindwal, P. Priyadarshini, D. N. Patil, S. Tapas, P. Kumar, S. Tomar and P. Kumar

Synopsis: The crystal structure of KdsC from M. catarhallis reveals an intersubunit water tunnel proposed to provide water molecule at the active site for catalysis.

Accepted 17 November 2014

Analysis of the HindIII-catalyzed reaction by time-resolved crystallography

T. Kawamura, T. Kobayashi and N. Watanabe

Synopsis: A time-resolved study using the freeze-trap method elucidates the mechanism of the DNA-cleaving reaction of HindIII.

Accepted 17 November 2014

Insight into cofactor recognition in arylamine N-acetyltransferase enzymes: structure of Mesorhizobium loti arylamine N-acetyltransferase in complex with coenzyme A

X. Xu, I. Li de la Sierra-Gallay, X. Kubiak, R. Duval, A. F. Chaffotte, J.-M. Dupret, A. Haouz and F. Rodrigues-Lima

Accepted 15 November 2014

Crystallization of lysozyme with (R)-, (S)- and (RS)-2-methyl-2,4-pentanediol

M. Stauber, J. Jakoncic, J. Berger, J. M. Karp, A. Axelbaum, D. Sastow, S. V. Buldyrev, B. J. Hrnjez and N. Asherie

Synopsis: Crystallization of lysozyme with (R)-2-methyl-2,4-pentanediol produces more ordered crystals and a higher resolution protein structure than crystallization with (S)-2-methyl-2,4-pentanediol. The results suggest that chiral interactions with chiral additives are important in protein crystal formation.

Accepted 15 November 2014

Structure of [gamma]-conglutin: insight into the quaternary structure of 7S basic globulins from legumes

J. Czubinski, J. Barciszewski, M. Gilski, K. Szpotkowski, J. Debski, E. Lampart-Szczapa and M. Jaskolski

Synopsis: The crystal structure of the 45 kDa [gamma]-conglutin from lupin seeds was determined at 2 Å resolution, showing that in contrast to the tetrameric structure of another 7S basic globulin from a legume plant (soybean), it forms a ring-like hexamer.

Accepted 14 November 2014

Biochemical and structural investigation of two paralogous glycoside hydrolases from Zobellia galactanivorans: novel insights into the evolution, dimerization plasticity and catalytic mechanism of the GH117 family

E. Ficko-Blean, D. Duffieux, É. Rebuffet, R. Larocque, A. Groisillier, G. Michel and M. Czjzek

Synopsis: Structural, functional and phylogenetic analyses reveal enzyme diversity within family 117 glycoside hydrolases, which remove terminal [alpha]-1,3-linked 3,6-anhydro-L-galactose from neoagaro-oligosaccharides produced by [beta]-agarases. A product complex with the unique [beta]-3,6-anhydro-L-galactose provides strong crystallographic evidence for an inverting mechanism in this family of enzymes.

Accepted 12 November 2014

The design and structural characterization of a synthetic pentatricopeptide repeat protein

B. S. Gully, K. R. Shah, M. Lee, K. Shearston, N. M. Smith, A. Sadowska, A. J. Blythe, K. Bernath-Levin, W. A. Stanley, I. D. Small and C. S. Bond

Accepted 11 November 2014

Structures of lactate de­hydrogenase A (LDHA) in apo, ternary and inhibitor-bound forms

S. Kolappan, D. L. Shen, R. Mosi, J. Sun, E. J. McEachern, D. J. Vocadlo and L. Craig

Synopsis: X-ray crystal structures of LDHA in complex with two quinoline-based inhibitors show the inhibitors bound to a site overlapping the NADH-binding site. Apo, oxalate/NADH-bound and oxalate/kanamycin-bound LDHA structures are also reported.

Accepted 7 November 2014

Structural and biochemical characterization of the laminarinase ZgLamCGH16 from Zobellia galactanivorans suggests preferred recognition of branched laminarin

A. Labourel, M. Jam, L. Legentil, B. Sylla, J.-H. Hehemann, V. Ferrières, M. Czjzek and G. Michel

Synopsis: The storage polysaccharide of brown algae is laminarin, a [beta]-1,3-glucan with occasional [beta]-1,6 branches. The catalytic module of the [beta]-glucanase ZgLamC from the marine bacterium Z. galactanivorans has been characterized. Notably, the structure of an inactive mutant of ZgLamC in complex with a thio-[beta]-glucan analogue suggests specific recognition of the branched domains of laminarin.

Accepted 1 October 2014

Tools for macromolecular model building and refinement into electron cryo-microscopy reconstructions

A. Brown, F. Long, R. A. Nicholls, J. Toots, P. Emsley and G. Murshudov

Synopsis: A description is given of new tools to facilitate model building and refinement into electron cryo-microscopy reconstructions.

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