Chemical basis of peptidoglycan discrimination by PrkC, a key kinase involved in bacterial resuscitation from dormancy

Bacterial Ser/Thr kinases modulate a wide number of cellular processes. In Bacillus subtilis , the Ser/Thr kinase PrkC has been shown to induce germination of bacterial spores in response to DAP-type but not Lys-type cell wall muropeptides. Muropeptides are a clear molecular signal that growing conditions are promising, since they are produced during cell wall peptidoglycan remodeling associated with cell growth and division of neighboring bacteria. However, whether muropeptides are able to bind the protein physically and how the extracellular region is able to distinguish the two types of muropeptides remains unclear. Here we tackled the important question of how the extracellular region of PrkC (EC-PrkC) senses muropeptides. By coupling NMR techniques and protein mutagenesis, we exploited the structural requirements necessary for recognition and binding and proved that muropeptides physically bind to EC-PrkC through DAP-moiety-mediated interactions with an arginine residue, Arg500, belonging to the protein C-terminal PASTA domain. Notably, mutation of this arginine completely suppresses muropeptide binding. Our data provide the first molecular clues into the mechanism of sensing of muropeptides by PrkC.     

Ultrasonic frequency analysis of antibody-linked hydrogel biosensors for rapid point of care testing

Analyte quantification in highly scattering media such as tissue, blood, and other biological fluids is challenging using conventional spectroscopic methods. Ultrasound easily penetrates these opaque samples, yet currently provides little chemical information. We have developed a general approach for creating hydrogel biosensors based on antibody-linked cellulose polymers. Target recognition induces changes to the sensor stiffness and size, which is accompanied by characteristic changes to a measured ultrasonic frequency profile. Using this technique, nM sensitivity for acetaminophen is demonstrated in a series of biofluids including whole blood, blood plasma, saliva, and urine. Likewise, this methodology is attractive for point of care diagnostics due to the short measurement time, simple methodology which excludes pretreatment of samples, and has minimal chemical or buffer requirements.     

A flexible synthesis of C-6 and N-1 analogues of a 4-amino-1,3-dihydroimidazo[4,5-c]pyridin-2-one core

A flexible route which enables access to derivatives of 4-amino-1,3-dihydroimidazo[4,5-c]pyridin-2-ones is described. Issues of selectivity, reaction safety, and low yields in original routes are overcome with the key improvements to the route, including a Negishi cross-coupling and use of a carbamate as a protecting group and intrinsic carbonyl source. The new route enables variation of C-6 and N-1 substituents.     

Top-down proteomics reveals novel protein forms expressed in methanosarcina acetivorans

Combining our previous work with current platforms presented here that identified 99 new proteins (Supplemental Table 1), a total of 200 protein identities in M. acetivorans have been confirmed. Of these, five proteins were unannotated, 15 were mispredicted, two exhibited variable removal of the start methionine, and one was a proteolysis fragment from the identical C-terminus of two possible proteins. The incorporation of LC-MS/MS and offline automation speeds up the processing of samples through automation of the top-down process. For five data files that were automatically processed and iteratively searched, 2 h were required to complete analysis. In these, a total of 835 identifications were detected by the search algorithm in this time period. The expanded use of top-down will use both online and offline strategies, with increasingly sophisticated data acquisition strategies tailored for the challenges of top-down fragmentation [[16], [18], [19], [32] and [33]].     

Towards stable analogues of inositol phosphates: stereoselective syntheses of (alpha,alpha-difluoromethyl)phosphonic acid (DFMPA)-containing cyclohexanes

Diels-Alder and conjugate addition reactions were used to prepare precursors to a range of fully functionalized and deoxy inositol phosphate analogues.     

Selective anion binding by a cofacial binuclear zinc complex of a Schiff-base pyrrole macrocycle

The synthesis of the new cofacial binuclear zinc complex [Zn(2)(L)] of a Schiff-base pyrrole macrocycle is reported. It was discovered that the binuclear microenvironment between the two metals of [Zn(2)(L)] is suited for the encapsulation of anions, leading to the formation of [K(THF)(6)][Zn(2)(μ-Cl)(L)]·2THF and [Bu(n)(4)N][Zn(2)(μ-OH)(L)] which were characterized by X-ray crystallography. Unusually obtuse Zn-X-Zn angles (X = Cl: 150.54(9)° and OH: 157.4(3)°) illustrate the weak character of these interactions and the importance of the cleft preorganization to stabilize the host. In the absence of added anion, aggregation of [Zn(2)(L)] was inferred and investigated by successive dilutions and by the addition of coordinating solvents to [Zn(2)(L)] solutions using NMR spectroscopy as well as isothermal microcalorimetry (ITC). On anion addition, evidence for deaggregation of [Zn(2)(L)], combined with the formation of the 1:1 host-guest complex, was observed by NMR spectroscopy and ITC titrations. Furthermore, [Zn(2)(L)] binds to Cl(-) selectively in THF as deduced from the ITC analyses, while other halides induce only deaggregation. These conclusions were reinforced by density functional theory (DFT) calculations, which indicated that the binding energies of OH(-) and Cl(-) were significantly greater than for the other halides.     

Statistical Examination of the <Emphasis Type="Italic">a</Emphasis> and <Emphasis Type="Italic">a</Emphasis> + 1 Fragment Ions from 193 nm Ultraviolet Photodissociation Reveals Local Hydrogen Bonding Interactions

Dissociation of proteins and peptides by 193 nm ultraviolet photodissociation (UVPD) has gained momentum in proteomic studies because of the diversity of backbone fragments that are produced and subsequent unrivaled sequence coverage obtained by the approach. The pathways that form the basis for the production of particular ion types are not completely understood. In this study, a statistical approach is used to probe hydrogen atom elimination from a + 1 radical ions, and different extents of elimination are found to vary as a function of the identity of the C-terminal residue of the a product ions and the presence or absence of hydrogen bonds to the cleaved residue.

Open image in new window

Graphical Abstract ?