'Carbon-Monoxide-Releasing Molecule-2 (CORM-2)' Is a Misnomer: Ruthenium Toxicity, Not CO Release, Accounts for Its Antimicrobial Effects.

Carbon monoxide (CO)-releasing molecules (CORMs) are used to deliver CO, a biological 'gasotransmitter', in biological chemistry and biomedicine. CORMs kill bacteria in culture and in animal models, but are reportedly benign towards mammalian cells. CORM-2 (tricarbonyldichlororuthenium(II) dimer, RuCl(CO)), the first widely used and commercially available CORM, displays numerous pharmacological, biochemical and microbiological activities, generally attributed to CO release.

Chain-folded lamellar structure and dynamics of the crystalline fraction of Bombyx mori silk fibroin and of (Ala-Gly-Ser-Gly-Ala-Gly) model peptides.

Solid-state NMR is a powerful analytical technique to determine the composite structure of Bombyx mori silk fibroin (SF). In our previous paper, we proposed a lamellar structure for Ala-Gly copolypeptides as a model of the crystalline fraction in Silk II. In this paper, the structure and dynamics of the crystalline fraction and of a better mimic of the crystalline fraction, (Ala-Gly-Ser-Gly-Ala-Gly) (n = 2-5, 8), and C selectively labeled [3-C]Ala-(AGSGAG) in Silk II forms, were studied using structural and dynamical analyses of the Ala Cβ peaks in C cross polarization/ magic angle spinning NMR and C solid-state spin-lattice relaxation time (T) measurements, respectively.

Structure of a Wbl protein and implications for NO sensing by M. tuberculosis.

Mycobacterium tuberculosis causes pulmonary tuberculosis (TB) and claims ~1.8 million human lives per annum. Host nitric oxide (NO) is important in controlling TB infection.

Conserved asymmetry underpins homodimerization of Dicer-associated double-stranded RNA-binding proteins.

Double-stranded RNA-binding domains (dsRBDs) are commonly found in modular proteins that interact with RNA. Two varieties of dsRBD exist: canonical Type A dsRBDs interact with dsRNA, while non-canonical Type B dsRBDs lack RNA-binding residues and instead interact with other proteins. In higher eukaryotes, the microRNA biogenesis enzyme Dicer forms a 1:1 association with a dsRNA-binding protein (dsRBP).

MYT1L mutations cause intellectual disability and variable obesity by dysregulating gene expression and development of the neuroendocrine hypothalamus.

Deletions at chromosome 2p25.3 are associated with a syndrome consisting of intellectual disability and obesity. The smallest region of overlap for deletions at 2p25.

Ferrous Iron Binding Key to Mms6 Magnetite Biomineralisation: A Mechanistic Study to Understand Magnetite Formation Using pH Titration and NMR Spectroscopy.

Formation of magnetite nanocrystals by magnetotactic bacteria is controlled by specific proteins which regulate the particles' nucleation and growth. One such protein is Mms6. This small, amphiphilic protein can self-assemble and bind ferric ions to aid in magnetite formation.

Synthesis of Chlorophyll-Binding Proteins in a Fully Segregated Δycf54 Strain of the Cyanobacterium Synechocystis PCC 6803.

In the chlorophyll (Chl) biosynthesis pathway the formation of protochlorophyllide is catalyzed by Mg-protoporphyrin IX methyl ester (MgPME) cyclase. The Ycf54 protein was recently shown to form a complex with another component of the oxidative cyclase, Sll1214 (CycI), and partial inactivation of the ycf54 gene leads to Chl deficiency in cyanobacteria and plants. The exact function of the Ycf54 is not known, however, and further progress depends on construction and characterization of a mutant cyanobacterial strain with a fully inactivated ycf54 gene.

The Polycystin-1, Lipoxygenase, and α-Toxin Domain Regulates Polycystin-1 Trafficking.

Mutations in polycystin-1 (PC1) give rise to autosomal dominant polycystic kidney disease, an important and common cause of kidney failure. Despite its medical importance, the function of PC1 remains poorly understood. Here, we investigated the role of the intracellular polycystin-1, lipoxygenase, and α-toxin (PLAT) signature domain of PC1 using nuclear magnetic resonance, biochemical, cellular, and in vivo functional approaches.

Molecular basis for bacterial peptidoglycan recognition by LysM domains.

Carbohydrate recognition is essential for growth, cell adhesion and signalling in all living organisms. A highly conserved carbohydrate binding module, LysM, is found in proteins from viruses, bacteria, fungi, plants and mammals. LysM modules recognize polysaccharides containing N-acetylglucosamine (GlcNAc) residues including peptidoglycan, an essential component of the bacterial cell wall.

Solution structure of the Q41N variant of ubiquitin as a model for the alternatively folded N2 state of ubiquitin.

It is becoming increasingly clear that proteins transiently populate high-energy excited states as a necessary requirement for function. Here, we demonstrate that rational mutation based on the characteristics of the structure and dynamics of proteins obtained from pressure experiments is a new strategy for amplifying particular fluctuations in proteins. We have previously shown that ubiquitin populates a high-energy conformer, N2, at high pressures.

Reprogramming of Escherichia coli K-12 metabolism during the initial phase of transition from an anaerobic to a micro-aerobic environment.

Background: Many bacteria undergo transitions between environments with differing O₂ availabilities as part of their natural lifestyles and during biotechnological processes. However, the dynamics of adaptation when bacteria experience changes in O₂ availability are understudied. The model bacterium and facultative anaerobe Escherichia coli K-12 provides an ideal system for exploring this process.

Experimental evidence that the membrane-spanning helix of PufX adopts a bent conformation that facilitates dimerisation of the Rhodobacter sphaeroides RC-LH1 complex through N-terminal interactions.

The PufX polypeptide is an integral component of some photosynthetic bacterial reaction center-light harvesting 1 (RC-LH1) core complexes. Many aspects of the structure of PufX are unresolved, including the conformation of its long membrane-spanning helix and whether C-terminal processing occurs. In the present report, NMR data recorded on the Rhodobacter sphaeroides PufX in a detergent micelle confirmed previous conclusions derived from equivalent data obtained in organic solvent, that the α-helix of PufX adopts a bent conformation that would allow the entire helix to reside in the membrane interior or at its surface.

Signature active site architectures illuminate the molecular basis for ligand specificity in family 35 carbohydrate binding module.

The deconstruction of the plant cell wall is an important biological process that is attracting considerable industrial interest, particularly in the bioenergy sector. Enzymes that attack the plant cell wall generally contain one or more noncatalytic carbohydrate binding modules (CBMs) that play an important targeting function. While CBMs that bind to the backbones of plant structural polysaccharides have been widely described, modules that recognize components of the vast array of decorations displayed on these polymers have been relatively unexplored.

A polycystin-2 (TRPP2) dimerization domain essential for the function of heteromeric polycystin complexes.

Autosomal dominant polycystic kidney disease (ADPKD) is caused by mutations in two genes, PKD1 and PKD2, which encode polycystin-1 (PC1) and polycystin-2 (PC2), respectively. Earlier work has shown that PC1 and PC2 assemble into a polycystin complex implicated in kidney morphogenesis. PC2 also assembles into homomers of uncertain functional significance.

Dimerisation of the UBA domain of p62 inhibits ubiquitin binding and regulates NF-kappaB signalling.

The ubiquitin (Ub)-binding p62 scaffold protein (encoded by the SQSTM1 gene) regulates a diverse range of signalling pathways leading to activation of the nuclear factor kappa B (NF-kappaB) family of transcription factors and is an important regulator of macroautophagy. Mutations within the gene encoding p62 are commonly found in patients with Paget's disease of bone and largely cluster within the C-terminal ubiquitin-associated (UBA) domain, impairing its ability to bind Ub, resulting in dysregulated NF-kappaB signalling. However, precisely how Ub-binding is regulated at the molecular level is unclear.

Activation of the global gene regulator PrrA (RegA) from Rhodobacter sphaeroides.

PrrA is a global transcription regulator activated upon phosphorylation by its cognate kinase PrrB in response to low oxygen levels in Rhodobacter sphaeroides. Here we show by gel filtration, analytical ultracentrifugation, and NMR diffusion measurements that treatment of PrrA with a phosphate analogue, BeF(3)(-), results in dimerization of the protein, producing a protein that binds DNA. No dimeric species was observed in the absence of BeF(3)(-).

The Campylobacter jejuni PEB1a adhesin is an aspartate/glutamate-binding protein of an ABC transporter essential for microaerobic growth on dicarboxylic amino acids.

The PEB1a protein of the gastrointestinal pathogen Campylobacter jejuni mediates interactions with epithelial cells and is an important factor in host colonization. Cell fractionation and immunoblotting showed that PEB1a is most abundant in the periplasm of C. jejuni, and is detectable in the culture supernatant but not in the inner or outer membrane.

Redox-responsive in vitro modulation of the signalling state of the isolated PrrB sensor kinase of Rhodobacter sphaeroides NCIB 8253.

Prr is a global regulatory system that controls a large and diverse range of genes in Rhodobacter sphaeroides in response to changing conditions of environmental redox potential. PrrB is the membrane-bound sensor kinase and previously we showed that the purified, detergent-solubilised intact membrane protein is functional in autophosphorylation, phosphotransfer and phosphatase activities. Here we confirm that it also senses and responds directly to its environmental signal, redox potential; strong autophosphorylation of PrrB occurred in response to dithiothreitol (DTT)-induced reducing conditions (and levels increased in response to a wide 0.

Creaming in black tea.

Tea cream is the precipitate formed as tea cools. Its formation has been studied by X-ray scattering, and it is shown that a higher tea concentration leads to earlier onset of creaming and larger particles and that addition of theaflavin and calcium promotes creaming. Association constants between the major components of black tea have been obtained using NMR and show that calcium and glucose enhance the self-association of caffeine, polyphenols, and theaflavin but have little effect on hetero-association.

Probing the mechanism of ligand recognition in family 29 carbohydrate-binding modules.

The recycling of photosynthetically fixed carbon, by the action of microbial plant cell wall hydrolases, is integral to one of the major geochemical cycles and is of considerable industrial importance. Non-catalytic carbohydrate-binding modules (CBMs) play a key role in this degradative process by targeting hydrolytic enzymes to their cognate substrate within the complex milieu of polysaccharides that comprise the plant cell wall. Family 29 CBMs have, thus far, only been found in an extracellular multienzyme plant cell wall-degrading complex from the anaerobic fungus Piromyces equi, where they exist as a CBM29-1:CBM29-2 tandem.

Multiple binding modes of the camptothecin family to DNA oligomers.

The binding constants of camptothecin, topotecan and its lactone ring-opened carboxylate derivative to DNA octamers were measured by UV and NMR spectroscopy. The self-association of topotecan (TPT) was also measured. The carboxylate form of TPT binds in the same way as the lactone, but more weakly.

Solution structure and DNA binding of the effector domain from the global regulator PrrA (RegA) from Rhodobacter sphaeroides: insights into DNA binding specificity.

Prr/RegA response regulator is a global transcription regulator in purple bacteria Rhodobacter sphaeroides and Rhodobacter capsulatus, and is essential in controlling the metabolic changes between aerobic and anaerobic environments. We report here the structure determination by NMR of the C-terminal effector domain of PrrA, PrrAC. It forms a three-helix bundle containing a helix-turn-helix DNA binding motif.

Many residues in cytochrome c populate alternative states under equilibrium conditions.

A curved temperature dependence of an amide proton NMR chemical shift indicates that it explores discrete alternative conformations at least 1% of the time; that is, it accesses conformations that lie within 5 kcal/mol(-1) of the ground state. The simulations presented show how curvature varies with the nature of the alternative state, and are compared to experimental results. From studies in different denaturant concentrations, it is concluded that at least 25% of residues in reduced horse cytochrome c, covering most of the protein, with the exception of the center of the N- and C-terminal helices, visit alternative states under equilibrium conditions.

The solution structure of bovine pancreatic trypsin inhibitor at high pressure.

The solution structure of bovine pancreatic trypsin inhibitor (BPTI) at a pressure of 2 kbar is presented. The structure was calculated as a change from an energy-minimized low-pressure structure, using (1)H chemical shifts as restraints. The structure has changed by 0.