Normal carbon acid referencing for protein amide hydrogen exchange

Measurement of the exchange kinetics for amide hydrogens along the protein backbone continues to offer valuable insights into structural stability and conformational dynamics. Since such studies routinely compare samples that differ in solution conditions or mechanical handling, normalization of the relative exchange rates can present a potentially significant source of experimental uncertainty. The carbon acids 1,3-dimethylimidazolium cation and thiomethylacetonitrile exhibit base catalyzed exchange rates similar to those of the slowly exchanging amides, under conditions typical for protein studies. With 13C enrichment at the acidic carbon position to facilitate selective observation, such carbon acids offer practical internal calibration of exchange.     

The ubiquitin proteasome system in Huntington's disease and the spinocerebellar ataxias

Huntington's disease and several of the spinocerebellar ataxias are caused by the abnormal expansion of a CAG repeat within the coding region of the disease gene. This results in the production of a mutant protein with an abnormally expanded polyglutamine tract. Although these disorders have a clear monogenic cause, each polyglutamine expansion mutation is likely to cause the dysfunction of many pathways and processes within the cell. It has been proposed that the ubiquitin proteasome system is impaired in polyglutamine expansion disorders and that this contributes to pathology. However, this is controversial with some groups demonstrating decreased proteasome activity in polyglutamine expansion disorders, some showing no change in activity and others demonstrating an increase in proteasome activity. It remains unknown whether the ubiquitin proteasome system is a feasible therapeutic target in these disorders. Here we review the conflicting results obtained from different assays performed in a variety of different systems. Publication history: Republished from Current BioData's Targeted Proteins database (TPdb; http://www.targetedproteinsdb.com).     

Electroluminescent networks via photo "click" chemistry

The use of thiol-ene click chemistry is demonstrated for the first time as a suitable method for cross-linking thin films of 4-phenylethenyl end-capped poly(fluorene). Cross-linking was accomplished by a simple, brief UV curing step at modest temperatures. This chemistry provides an advantage over similar schemes employed for cross-linking conjugated polymers since it does not require elevated temperature or produce potentially detrimental side products. Thiol-ene cross-linking was found to preserve the emissive color integrity of the poly(fluorene) films and allowed for facile photopatterning of the active polymer layer. Furthermore, the investigated cross-linking chemistry was shown to be fully compatible with fabrication of polymer light-emitting diodes (PLEDs) whose performance was comparable to noncross-linked devices. Multicolor PLEDs were also demonstrated by taking advantage of the photopatternability of the thiol-ene based system.     

Iron(II) PARACEST MRI contrast agents

The first examples of Fe(II) PARACEST magnetic resonance contrast agents are reported (PARACEST = paramagnetic chemical exchange saturation transfer). The iron(II) complexes contain a macrocyclic ligand, either 1,4,7-tris(carbamoylmethyl)-1,4,7-triazacyclononane (L1) or 1,4,7-tris[(5-amino-6-methyl-2-pyridyl)methyl]-1,4,7-triazacyclononane (L2). The macrocycles bind Fe(II) in aqueous solution with formation constants of log K = 13.5 and 19.2, respectively, and maintain the Fe(II) state in the presence of air. These complexes each contain six exchangeable protons for CEST which are amide protons in [Fe(L1)](2+) or amino protons in [Fe(L2)](2+). The CEST peak for the [Fe(L1)](2+) amide protons is at 69 ppm downfield of the bulk water resonance whereas the CEST peak for the [Fe(L2)](2+) amine protons is at 6 ppm downfield of bulk water. CEST imaging using a MRI scanner shows that the CEST effect can be observed in solutions containing low millimolar concentrations of complex at neutral pH, 100 mM NaCl, 20 mM buffer at 25 °C or 37 °C.     

On the chlorenium source in the asymmetric chlorolactonization reaction

N-Acylated N-chlorohydantoins are shown to be competent chlorenium sources in the (DHQD)(2)PHAL-mediated asymmetric chlorolactonization. The derivatives demonstrate the exact role of the N1 and N3 chlorine atoms in the parent dichlorohydantoins with the N1 chlorine serving as an inductive activator and the N3 chlorine being delivered to the substrate. The putative associated catalyst/chlorine source complex was experimentally demonstrated through a series of matched/mismatched experiments employing chiral N-chlorinated hydantoins.     

Discovery of kibdelomycin, a potent new class of bacterial type II topoisomerase inhibitor by chemical-genetic profiling in Staphylococcus aureus

Bacterial resistance to known therapeutics has led to an urgent need for new chemical classes of antibacterial agents. To address this we have applied?a Staphylococcus aureus fitness test strategy to natural products screening. Here we report the discovery of kibdelomycin, a novel class of antibiotics produced by a new member of the genus Kibdelosporangium. Kibdelomycin exhibits broad-spectrum, gram-positive antibacterial activity and is a potent inhibitor of DNA synthesis. We demonstrate through chemical genetic fitness test profiling and biochemical enzyme assays that kibdelomycin is a structurally new class of bacterial type II topoisomerase inhibitor preferentially inhibiting the ATPase activity of DNA gyrase and topoisomerase IV. Kibdelomycin is thus the first truly novel bacterial type II topoisomerase inhibitor with potent antibacterial activity discovered from natural product sources in more than six decades.     

Subsurface examination of a foliar biofilm using scanning electron- and focused-ion-beam microscopy

The dual beam scanning electron microscope, equipped with both a focused ion- and scanning electron-beam (FIB SEM) is a novel tool for the exploration of the subsurface structure of biological tissues. The FIB can remove a predetermined amount of material from a selected site to allow for subsurface exploration and when coupled with SEM or scanning ion-beam microscopy (SIM) could be suitable to examine the subsurface structure of bacterial biofilms on the leaf surface. The suitability of chemical and cryofixation was examined for use with the FIB SEM to examine bacterial biofilms on leaf surfaces. The biological control agent, Burkholderia pyroccinia FP62, that rapidly colonizes the leaf surface and forms biofilms, was inoculated onto geranium leaves and incubated in a greenhouse for 7 or 14 days. Cryofixation was not suitable for examination of leaf biofilms because it created a frozen layer over the leaf surface that cracked when exposed to the electron beam and the protective cap required for FIB milling could not be accurately deposited. With chemically fixed samples, it was possible to precisely FIB mill a single cross section (5μm) or sequential cross sections from a single site without any damage to the surrounding surface. Biofilms, 7 days post-inoculation (DPI), were composed of 2-5 bacterial cell layers while biofilms 14 DPI ranged from 5 to greater than 30 cell layers. Empty spaces between bacteria cells in the subsurface structure were observed in biofilms 7- and 14-DPI. Sequential cross sections inferred that the empty spaces were often continuous between FP62 cells and could possibly make up a network of channels throughout the biofilm. FIB SEM was a useful tool to observe the subsurface composition of a foliar biofilm.     

The effect of bromine scanning around the phenyl group of 4‐phenylquinolone derivatives

Three quinolone compounds were synthesized and crystallized in an effort to study the structure–activity relationship of these calcium‐channel antagonists. In all three quinolones, viz. ethyl 4‐(4‐bromophenyl)‐2,7,7‐trimethyl‐5‐oxo‐1,4,5,6,7,8‐hexahydroquinoline‐3‐carboxylate, (I), ethyl 4‐(3‐bromophenyl)‐2,7,7‐trimethyl‐5‐oxo‐1,4,5,6,7,8‐hexahydroquinoline‐3‐carboxylate, (II), and ethyl 4‐(2‐bromophenyl)‐2,7,7‐trimethyl‐5‐oxo‐1,4,5,6,7,8‐hexahydroquinoline‐3‐carboxylate, (III), all C₂₁H₂₄BrNO₃, common structural features such as a flat boat conformation of the 1,4‐dihydropyridine (1,4‐DHP) ring, an envelope conformation of the fused cyclohexanone ring and a bromophenyl ring at the pseudo‐axial position and orthogonal to the 1,4‐DHP ring are retained. However, due to the different packing interactions in each compound, halogen bonds are observed in (I) and (III). Compound (III) crystallizes with two molecules in the asymmetric unit. All of the prepared derivatives satisfy the basic structural requirements to possess moderate activity as calcium‐channel antagonists.     

Tethered dinuclear europium(III) macrocyclic catalysts for the cleavage of RNA

Dinuclear europium(III) complexes of the macrocycles 1,3-bis[1-(4,7,10-tris(carbamoylmethyl)-1,4,7,10-tetraazacyclododecane]-m-xylene (1), 1,4-bis[1-(4,7,10-tris(carbamoylmethyl)-1,4,7,10-tetraazacyclododecane]-p-xylene (2), and mononuclear europium(III) complexes of macrocycles 1-methyl-,4,7,10-tris(carbamoylmethyl)-1,4,7,10-tetraazacyclododecane (3), 1-[3'-(N,N-diethylaminomethyl)benzyl]-4,7,10-tris(carbamoylmethyl)-1,4,7,10-tetraazacyclododecane (4), and 1,4,7-tris(carbamoylmethyl)-1,4,7,10-tetraazacyclododecane (5) were prepared. Studies using direct excitation ((7)F0 --> (5)D0) europium(III) luminescence spectroscopy show that each Eu(III) center in the mononuclear and dinuclear complexes has two water ligands at pH 7.0, I = 0.10 M (NaNO3) and that there are no water ligand ionizations over the pH range of 7-9. All complexes promote cleavage of the RNA analogue 2-hydroxypropyl-4-nitrophenyl phosphate (HpPNP) at 25 degrees C (I = 0.10 M (NaNO3), 20 mM buffer). Second-order rate constants for the cleavage of HpPNP by the catalysts increase linearly with pH in the pH range of 7-9. The second-order rate constant for HpPNP cleavage by the dinuclear Eu(III) complex (Eu2(1)) at pH 7 is 200 and 23-fold higher than that of Eu(5) and Eu(3), respectively, but only 7-fold higher than the mononuclear complex with an aryl pendent group, Eu(4). This shows that the macrocycle substituent modulates the efficiency of the Eu(III) catalysts. Eu2(1) promotes cleavage of a dinucleoside, uridylyl-3',5'-uridine (UpU) with a second-order rate constant at pH 7.6 (0.021 M(-1) s(-1)) that is 46-fold higher than that of the mononuclear Eu(5) complex. Methyl phosphate binding to the Eu(III) complexes is energetically most favorable for the best catalysts, and this supports an important role for the catalyst in stabilization of the developing negative charge on the phosphorane transition state. Despite the formation of a bridging phosphate ester between the two Eu(III) centers in Eu2(1) as shown by luminescence spectroscopy, the two metal ion centers are only weakly cooperative in cleavage of RNA and RNA analogues.