Systematic localisation of proteins fused to the green fluorescent protein in Bacillus subtilis: identification of new proteins at the DNA replication factory

Construction and microscopic imaging of protein fusions to green fluorescent protein (GFP) have revolutionised our understanding of bacterial structure and function. We have undertaken a systematic study of the localisation of over 100 Bacillus subtilis proteins, following the development of high-throughput construction and analysis procedures. We focused on proteins linked in various ways to the DNA replication machinery, as well as on proteins exemplifying a range of other cellular functions and structures. The results validate the approach as a way of obtaining systematic protein localisation information. They also provide a range of novel biological insights, particularly through the identification of a number of proteins not previously known to be associated with the DNA replication factory.     

Construction of bioactive chimeric MHC class I tetramer by expression and purification of human-murine chimeric MHC heavy chain and beta(2)m as a fusion protein in Escherichia coli

Major histocompatibility (MHC) class I tetramers are used in the quantitative analysis of epitope peptide-specific CD8+ T-cells. An MHC class I tetramer was composed of 4 MHC class I complexes and a fluorescently labeled streptavidin (SA) molecule. Each MHC class I complex consists of an MHC heavy chain, a beta(2)-microglobulin (beta(2)m) molecule and a synthetic epitope peptide. In most previous studies, an MHC class I complex was formed in the refolding buffer with an expressed MHC heavy chain molecule and beta(2)m, respectively. This procedure inevitably resulted in the disadvantages of forming unwanted multimers and self-refolding products, and the purification of each kind of monomer was time-consuming. In the present study, the genes of a human/murine chimeric MHC heavy chain (HLA-A2 alpha1, HLA-A2 alpha2 and MHC-H2D alpha3) and beta(2)m were tandem-cloned into plasmid pET17b and expressed as a fusion protein. The recombinant fusion protein was refolded with each of the three HLA-A2 restricted peptides (HBc18-27 FLPSDFFPSI, HBx52-60 HLSLRGLPV, and HBx92-100 VLHKRTLGL) and thus three chimeric MHC class I complexes were obtained. Biotinylation was performed, and its level of efficiency was observed via a band-shift assay in non-reducing polyacrylamide gel electrophoresis (PAGE). Such chimeric MHC class I tetramers showed a sensitive binding activity in monitoring HLA/A2 restrictive cytotoxic T lymphocytes (CTLs) in immunized HLA/A*0201 transgenic mice.     

Automated segmentation of molecular subunits in electron cryomicroscopy density maps

Electron cryomicroscopy (cryoEM) is capable of imaging large macromolecular machines composed of multiple components. However, it is currently only possible to achieve moderate resolution at which it may be possible to computationally extract the individual components in the machine. In this work, we present application details of an automated method for detecting and segmenting the components of a large machine in an experimentally determined density map. This method is applicable to object with and without symmetry and takes advantage of global and local symmetry axes if present. We have applied this segmentation algorithm to several cryoEM data sets already deposited in EMDB with various complexities, symmetries and resolutions and validated the results using manually segmented density and available structures of the components in the PDB. As such, automated segmentation could become a useful tool for the analysis of the ever-increasing number of structures of macromolecular machines derived from cryoEM.     

Why iron–dithiocarbamates ensure detection of nitric oxide in cells and tissues

The in vivo mechanism of NO trapping by iron-dithiocarbamate complexes is considered. Contrary to common belief, we find that in biological systems the NO radicals are predominantly trapped by ferric iron-dithiocarbamates. Therefore, the trapping leads to ferric mononitrosyl complexes which are diamagnetic and cannot be directly detected with Electron Paramagnetic Resonance spectroscopy. The ferric mononitrosyl complexes are far easily reduced to ferrous state with L-cysteine, glutathione, ascorbate or dithiocarbamate ligands than their non-nitrosyl counterpart. When trapping NO in oxygenated biological systems, the majority of trapped nitric oxide is found in diamagnetic ferric mononitrosyl iron complexes. Only a minority fraction of NO is trapped in the form of paramagnetic ferrous mononitrosyl iron complexes with dithiocarbamate ligands. Subsequent ex vivo reduction of biological samples sharply increases the total yield of the paramagnetic mononitrosyl iron complexes. Reduction also eliminates the overlapping EPR spectrum from Cu(2+)-dithiocarbamate complexes. This facilitates the quantification of yields from NO trapping.     

Syntheses, structures, and mesomorphism of a series of Ni(II) salen complexes with 4-substituted long alkoxy chains

A series of nickel(II) salen complexes containing 4-substituted alkoxy chains of aromatic rings, [Ni((4-C_nH_2n + 1O)₂salen)] (n = 3 (1), 4 (2), 6 (3), 8 (4), 10 (5), 12 (6), 14 (7), 16 (8), 18 (9), and 20 (10)), and their parent complex, [Ni((4-HO)₂salen)] (11) (salen = N,N′-ethylenebis(salicylideneiminato)), have been prepared and mesomorphic properties have been investigated. An X-ray crystallographic analysis revealed that complex 11 · 2DMF has one-dimensional stacking structure supported by the π-π interaction between the six-membered chelate and aromatic rings with the NiNi distances of alternatively 3.3957 and 3.7224 Å and that complex 3 is formed by one-dimensional stacking by weak CH?O type hydrogen bonded interaction between the five-membered chelate ring and phenoxo atoms of the dramatically distorted salen moieties with the NiNi distance of 5.994 Å. Complexes 1-6 did not exhibit any mesophases. On the other hand, complexes 7-10 with longer alkoxy chains of n = 14-20 showed an unusual metallomesogen of a lamello-columnar mesophase within the smectic layers with an interlamellar distance of 31.1 Å (7), 33.6 Å (8), 37.1 Å (9), and 39.5 Å (10) and nearly constant stacking distance of 6.19-6.24 Å between the inter-dimers, irrespective of the variation of the alkoxy chain lengths by the X-ray diffraction measurements of the liquid crystal. The relationship between molecular assemblies and mesomorphic properties is discussed.     

Structural biology of SMC complexes across the tree of life

Structural maintenance of chromosomes (SMC) complexes guard and organize the three-dimensional structure of chromosomal DNA across the tree of life. Many SMC functions can be explained by an inherent motor activity that extrudes large DNA loops while the complexes move along their substrate. Here, we review recent structural insights into the architecture and conservation of these molecular machines, their interaction with DNA, and the conformational changes that are linked to their ATP hydrolysis cycle.     

Peptide Presentation to T Cells: Solving the Immunogenic Puzzle

The vertebrate immune system uses an impressive arsenal of mechanisms to combat harmful cellular states such as infection. One way is via cells delivering real-time snapshots of their protein content to the cell surface in the form of short peptides. Specialized immune cells (T cells) sample these peptides and assess whether they are foreign, warranting an action such as destruction of the infected cell. The delivery of peptides to the cell surface is termed antigen processing and presentation, and decades of research have provided unprecedented understanding of this process. However, predicting the capacity for a given peptide to be immunogenic—to elicit a T cell response—has remained both enigmatic and a long sought-after goal. In the era of big data, a point is being approached where the steps of antigen processing and presentation can be quantified and assessed against peptide immunogenicity in order to build predictive models. This review presents new findings in this area and contemplates challenges ahead.     

Refinement of protein-protein complexes in contact map space with metadynamics simulations

Accurate protein-protein complex prediction, to atomic detail, is a challenging problem. For flexible docking cases, current state-of-the-art docking methods are limited in their ability to exhaustively search the high dimensionality of the problem space. In this study, to obtain more accurate models, an investigation into the local optimization of initial docked solutions is presented with respect to a reference crystal structure. We show how physics-based refinement of protein-protein complexes in contact map space (CMS), within a metadynamics protocol, can be performed. The method uses 5 times replicated 10 ns simulations for sampling and ranks the generated conformational snapshots with ZRANK to identify an ensemble of n snapshots for final model building. Furthermore, we investigated whether the reconstructed free energy surface (FES), or a combination of both FES and ZRANK, referred to as CS_α, can help to reduce snapshot ranking error.     

Infinite zig-zag and cyclic-tetranuclear isomeric imidazolate-bridged polynuclear copper(II) complexes: Magnetic properties, catalytic activity and electrospray mass and tandem mass spectrometry characterization

Two mononuclear copper(II) complexes 1 and 2 with the unsymmetrical tridentate ligands 2- and 4-[((imidazol-2-ylmethylidene)amino)ethyl]pyridine have been prepared. In alkaline solution, deprotonation of the imidazole moiety in 1 and 2 promotes self-assembly, which yielded two structurally different species. Depending on the binding site in the imidazole ring, a polymeric complex with an infinite zig-zag-chain 3, or a cyclic-tetranuclear complex 4 is formed, as shown by spectroscopic and spectrometric analysis. Herein, structural characterization of these isomeric polynuclear complexes was performed by electrospray mass (ESI-MS) and tandem mass spectrometric experiments (ESI-MS/MS). Each isomer was shown to be stable in methanolic solutions and to display unique mass spectra with characteristic multiply charged molecular and fragment ions, corroborating previous data by EPR measurements. Magnetic data in the solid state fit a typical curve for an one-dimensional infinite regular chain system, with J = −(32.4 ± 1.2) cm⁻¹ and g = 2.03 for 3, and that of a cyclic-tetranuclear structure with J = −(55.5 ± 0.4) cm⁻¹ and g = 2.29 for 4. In the oxidation of 3,5-di-tert-butylcatechol (3,5-DTBC) by molecular oxygen, both complexes were shown to act as efficient catalysts, exhibiting very similar ratios: k_cat/K_M = 9.12 × 10⁶ mol⁻¹ dm³ min⁻¹ for 3 and 8.73 × 10⁶ mol⁻¹ dm³ min⁻¹ for 4. These similar ratios indicate that interactions between the metal centres in 3 or 4 and the substrate in solution occur predominantly at the outside of the catalyst framework.     

Synthesis and characterization of heteroscorpionate dioxo-tungsten(VI) complexes

Twelve new dioxo W(VI) complexes of a family of heteroscorpionate ligands of the type [(L)WO₂Y], where L = N₂X ligand and Y = Cl or OR, have been synthesized and characterized. With the more sterically bulky ligands we show that these complexes exist as isolable cis and trans isomers and compare the rate of such isomerization with their corresponding dioxo Mo(VI) analogs.