Towards a structural biology work bench

The trends to investigate larger complexes and more transient phenomena pose some challenges to software developers.

On the usefulness of ion-mobility mass spectrometry and SAXS data in scoring docking decoys

In this research, the usefulness of low-resolution shape data for scoring docking decoys is explored. Within this context, a new scoring function is introduced that combines the regular HADDOCK score with either small-angle X-ray scattering or collision cross-section data.

On the development of three new tools for organizing and sharing information in three-dimensional electron microscopy

This work describes three developments promoting integrative biology, standardization and workflow processing, namely PeppeR, the EMX initiative and Scipion.

OpenStructure: an integrated software framework for computational structural biology

Current developments in the computational structural biology framework OpenStructure are presented.

The role of structural bioinformatics resources in the era of integrative structural biology

The integration of structural data on atomistic to cellular scales with genetic, taxonomic and functional information is discussed. The challenges to the PDB and EMDB archives and some pertinent developments at PDBe to address these are discussed.

The structure of cardiac troponin C regulatory domain with bound Cd²⁺ reveals a closed conformation and unique ion coordination

A 1.4 Å resolution crystal structure of wild-type human cardiac troponin C regulatory domain (cNTnC) in complex with Cd²⁺ is compared with structures of other EF-hand containing proteins that have been cocrystallized with Cd²⁺. Structures of cNTnC with disease-related mutations L29Q and NIQD (D2N/V28I/L29Q/G30G) are also determined.

Structural and functional characterization of HP0377, a thioredoxin-fold protein from Helicobacter pylori

The results of structural and functional characterizations of H. pylori HP0377, a thioredoxin-fold protein, are reported. HP0377 can reduce apocytochrome c₅₅₃ (HP1227) and forms a covalent complex with a putative L,D-transpeptidase (HP0518) via a disulfide bond, suggesting that HP0377 may serve multiple functions as a reductase in H. pylori.

Mechanism for controlling the monomer–dimer conversion of SARS coronavirus main protease

The crystal structure of the dimeric R298A mutant of SARS-CoV M^pro offers insights into the molecular mechanism controlling monomer–dimer conversion during the process of M^pro maturation.

Atomic resolution structures of the c-Src SH3 domain in complex with two high-affinity peptides from classes I and II

The first crystallographic structures of the c-Src SH3 domain in complex with two different high-affinity peptides have been solved at atomic resolution.

The 1.6 Å resolution structure of a FRET-optimized Cerulean fluorescent protein

The high resolution X-ray structure of the cyan fluorescent protein mCerulean3 demonstrates that different combinations of correlated residue substitutions can provide near optimum quantum yield values for fluorescence.

The structure of the caspase recruitment domain of BinCARD reveals that all three cysteines can be oxidized

The mitochondrial localization of BinCARD and the susceptibility to oxidation of all three of its cysteines suggest the possibility of a role in redox regulation.

Structural analysis of malaria-parasite lysyl-tRNA synthetase provides a platform for drug development

Crystal structure of malaria parasite lysyl tRNA synthetase provides basis for drug development.

AutoDrug: fully automated macromolecular crystallography workflows for fragment-based drug discovery

New software has been developed for automating the experimental and data-processing stages of fragment-based drug discovery at a macromolecular crystallography beamline. A new workflow-automation framework orchestrates beamline-control and data-analysis software while organizing results from multiple samples.

Structural basis of L-phosphoserine binding to Bacillus alcalophilus phosphoserine aminotransferase

The structures of Bacillus alcalophilus phosphoserine aminotransferase in the presence or absence of L-phosphoserine were determined at 1.5 and 1.6 Å resolution, respectively. Structural comparison revealed local conformational changes and the formation of a tight phosphate-binding site upon L-phosphoserine binding.

Inhibition of a type III secretion system by the deletion of a short loop in one of its membrane proteins

Crystal structures of the cytoplasmic domain of FlhB from S. typhimurium and A. aeolicus were solved at 2.45 and 2.55 Å resolution, respectively. The deletion of a short loop in the cytoplasmic domain of Salmonella FlhB completely abolishes secretion by the type III secretion system. A molecular-dynamics simulation shows that the deletion of the loop affects the flexibility of a linker between the transmembrane and cytoplasmic domains of FlhB.

Structure of a complete four-domain chitinase from Moritella marina, a marine psychrophilic bacterium

Chitinase from a cold-adapted bacterium has been examined in the unliganded form and in complexes with the reaction intermediate and the reaction product. The structure, which consists of four linearly arranged domains, has been examined for features responsible for the activity, specificity and adaptation to low temperatures of the enzyme.

The structures of Arabidopsis Deg5 and Deg8 reveal new insights into HtrA proteases

The crystal structures of Arabidopsis Deg5 and Deg8 have been determined to resolutions of 2.6 and 2.0 Å, respectively, revealing novel structural features of HtrA proteases.

Anomalous signal from S atoms in protein crystallographic data from an X-ray free-electron laser

Analysis of serial femtosecond crystallographic data measured using the SACLA free-electron laser at RIKEN Harima shows the weak anomalous signal from naturally occurring S atoms in a protein.

Towards protein-crystal centering using second-harmonic generation (SHG) microscopy

The potential of second-harmonic generation (SHG) microscopy for automated crystal centering to guide synchrotron X-­ray diffraction of protein crystals has been explored.

Imaging protein three-dimensional nanocrystals with cryo-EM

Electron imaging of three-dimensional protein nanocrystals using a Titan Krios electron microscope and a Falcon direct electron detector revealed structural details at higher than 3 Å resolution. Image processing with IMAGIC (cryo-EM single-particle analysis software) could improve the data to beyond 2 Å resolution.

Effects of cryoprotectants on the structure and thermostability of the human carbonic anhydrase II–acetazolamide complex

Here, a case study of the effects of cryoprotectants on the kinetics of carbonic anhydrase II (CA II) and its inhibition by the clinically used inhibitor acetazolamide (AZM) is presented.

Structures of Enterovirus 71 3C proteinase (strain E2004104-TW-CDC) and its complex with rupintrivir

The crystal structures of Enterovirus 71 3C proteinase and its complex with rupintrivir are reported.

On optimal placement of molecules in the unit cell

Standard ways for the placement of molecules in the unit cell are proposed.

The structure of the SBP-Tag–streptavidin complex reveals a novel helical scaffold bridging binding pockets on separate subunits

The structure of the SBP-Tag–streptavidin complex reveals a novel mode of peptide recognition in which a single peptide binds simultaneously to biotin-binding pockets from adjacent subunits of streptavidin. The molecular details of peptide recognition suggest how the SBP-Tag can be further modified to become an even more useful tag for a wider range of biotechnological applications.

Structural analysis of coniferyl alcohol 9-O-methyltransferase from Linum nodiflorum reveals a novel active-site environment

The de novo structure of coniferyl alcohol 9-O-methyltransferase and ITC measurements suggest a novel binding mode and reaction mechanism in plant small-molecule O-methyltransferases.

Camel and bovine chymosin: the relationship between their structures and cheese-making properties

Analysis of the crystal structures of the two milk-clotting enzymes bovine and camel chymosin has revealed that the better milk-clotting activity towards bovine milk of camel chymosin compared with bovine chymosin is related to variations in their surface charges and their substrate-binding clefts.

Integrated database of information from structural genomics experiments

Information from structural genomics experiments has been compiled and published as an integrated database.

Using high-throughput in situ plate screening to evaluate the effect of dehydration on protein crystals

A novel high-throughput in situ plate-screening procedure is used to assess the effect of dehydration on a membrane-associated protein. In this case the dehydration improved the diffraction quality of the crystal.

Visualizing the Invisible: Imaging Techniques for the Structural Biologist