Native polyacrylamide electrophoresis in the presence of Ponceau Red to study oligomeric states of protein complexes

Native polyacrylamide electrophoresis in the presence of two reversible protein anionic stains (Ponceau S and Ponceau 2R) was used to study the oligomeric states of soluble proteins. A mild binding of the used protein stains to nondissociated protein oligomers imposed a charge shift on the proteins resulting into separation of protein species according to their size under physiological conditions. Adsorbed stains could be easily removed after electrophoresis by washing of polyacrylamide gel with buffer and protein complexes could be visualized either by the detection of their enzyme activity or by using a nonspecific protein stain. The specific detection of enzyme activity of glycosidases, lactate dehydrogenase, or phosphatases was shown as an example.     

Energetic preference of 8-oxoG eversion pathways in a DNA glycosylase

Base eversion is a fundamental process in the biochemistry of nucleic acids, allowing proteins engaged in DNA repair and epigenetic modifications to access target bases in DNA. Crystal structures reveal end points of these processes, but not the pathways involved in the dynamic process of base recognition. To elucidate the pathway taken by 8-oxoguanine during base excision repair by Fpg, we calculated free energy surfaces during eversion of the damaged base through the major and minor grooves. The minor groove pathway and free energy barrier (6-7 kcal/mol) are consistent with previously reported results (Qi, Y.; Spong, M. C.; Nam, K.; Banerjee, A.; Jiralerspong, S.; Karplus, M.; Verdine, G. L. Nature 2009, 462, 762.) However, eversion of 8-oxoG through the major groove encounters a significantly lower barrier (3-4 kcal/mol) more consistent with experimentally determined rates of enzymatic sliding during lesion search (Blainey, P. C.; van Oijent, A. M.; Banerjee, A.; Verdine, G. L.; Xie, X. S. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 5752.). Major groove eversion has been suggested for other glycosylases, suggesting that in addition to function, dynamics of base eversion may also be conserved.     

Mechanism of Ketone Allylation with Allylboronates as Catalyzed by Zinc Compounds: A DFT Study

The mechanism of the allylation reaction between 4‐chloroacetophenone and pinacol allylboronates catalyzed by ZnEt₂ with alcohols was investigated using density functional theory (DFT) at the M05‐2X/6‐311++G(d,p) level. The calculations reveal that the reaction prefers to proceed through a double γ‐addition stepwise reaction mechanism rather than a Lewis acid‐catalyzed concerted one. The intermediate with a four‐coordinated boron center, which is formed through proton transfer from EtOH to the ethyl group of ZnEt₂ mediated by the boron center, is the active species and an entrance for the catalytic cycle. The latter is composed of three elementary steps: 1) boron to zinc transmetalation leading to the formation of allylzincate species, 2) electrophilic addition of ketone to allylzincate species, and 3) generation of the final product with recovery of the catalyst. The boron to zinc transmetalation step has the largest energy barrier of 61.0 kJ mol^?1 and is predicted to be the rate‐determining step. The calculations indicate that the additive EtOH plays important roles both in lowering the activation free energy for the formation of the four‐coordinated boron active intermediate and in transforming the low catalytic activity ZnEt₂ into high activity zinc alkoxide species. The alcohols with a less sterically encumbering R group might be the effective additives. The substituted groups on the allylboronates might primarily affect the boron to zinc transmetalation, and the allylboronates with substituents on the C_γ atom is poor in reactivity. The comparison of the catalytic effect between the zinc compounds investigated suggest that Zn(OEt)₂, Zn(OH)₂, and ZnF₂ exhibit higher catalytic efficiency for the boron to zinc transmetalation due to the activation of the B? C_α bond through orbital interactions between the p orbitals of the EtO, OH, F groups and the empty p orbital of the boron center.     

On the Controversial Fitting of Susceptibility Curves of Ferromagnetic CuII Cubanes: Insights from Theoretical Calculations

This paper reports a theoretical analysis of the electronic structure and magnetic properties of a tetranuclear Cu^II complex, [Cu₄(HL)₄], which has a 4+2 cubane‐like structure (H₃L=N,N′‐(2‐hydroxypropane‐1,3‐diyl)bis(acetylacetoneimine)). These theoretical calculations indicate a quintet (S=2) ground state; the energy‐level distribution of the magnetic states confirm Heisenberg behaviour and correspond to an S₄ spin–spin interaction model. The dominant interaction is the ferromagnetic coupling between the pseudo‐dimeric units (J₁=22.2 cm^?1), whilst a weak and ferromagnetic interaction is found within the pseudo‐dimeric units (J₂=1.4 cm^?1). The amplitude and sign of these interactions are consistent with the structure and arrangement of the magnetic Cu 3d orbitals; they accurately simulate the thermal dependence of magnetic susceptibility, but do not agree with the reported J values (J₁=38.4 cm^?1, J₂=?18.0 cm^?1) that result from the experimental fitting. This result is not an isolated case; many other polynuclear systems, in particular 4+2 Cu^II cubanes, have been reported in which the fitted magnetic terms are not consistent with the geometrical features of the system. In this context, theoretical evaluation can be considered as a valuable tool in the interpretation of the macroscopic behaviour, thus providing clues for a rational and directed design of new materials with specific properties.     

Mannose‐Binding Geometry of Pradimicin A

Pradimicins (PRMs) and benanomicins are the only family of non‐peptidic natural products with lectin‐like properties, that is, they recognize D ‐mannopyranoside (Man) in the presence of Ca²⁺ ions. Coupled with their unique Man binding ability, they exhibit antifungal and anti‐HIV activities through binding to Man‐containing glycans of pathogens. Notwithstanding the great potential of PRMs as the lectin mimics and therapeutic leads, their molecular basis of Man recognition has yet to be established. Their aggregate‐forming propensity has impeded conventional interaction analysis in solution, and the analytical difficulty is exacerbated by the existence of two Man binding sites in PRMs. In this work, we investigated the geometry of the primary Man binding of PRM‐A, an original member of PRMs, by the recently developed analytical strategy using the solid aggregate composed of the 1:1 complex of PRM‐A and Man. Evaluation of intermolecular distances by solid‐state NMR spectroscopy revealed that the C2–C4 region of Man is in close contact with the primary binding site of PRM‐A, while the C1 and C6 positions of Man are relatively distant. The binding geometry was further validated by co‐precipitation experiments using deoxy‐Man derivatives, leading to the proposal that PRM‐A binds not only to terminal Man residues at the non‐reducing end of glycans, but also to internal 6‐substituted Man residues. The present study provides new insights into the molecular basis of Man recognition and glycan specificity of PRM‐A.     

Stabilization of Large Adsorbates by Rotational Entropy: A Time‐Resolved Variable‐Temperature STM Study

Investigating the dynamics in an adlayer of the oligopyridine derivative 2‐phenyl‐4,6‐bis(6‐(pyridine‐2‐yl)‐4‐(pyridine‐4‐yl)pyridine‐2‐yl)pyrimidine (2,4′‐BTP) on Ag(111) by fast scanning tunneling microscopy (video‐STM), we found that rotating 2,4′‐BTP adsorbates coexist in a two‐dimensional (2D) liquid phase (β‐phase) in a dynamic equilibrium with static adsorbate molecules. Furthermore, exchange between an ordered phase (α‐phase) and β‐phase leads to fluctuations of the domain boundary on a time scale of seconds. Quantitative evaluation of the temperature‐dependent equilibrium between rotating and static adsorbates, evaluated from a large number of STM images, gains insight into energetic and entropic stabilization and underlines that the rotating adsorbate molecules are stabilized by an entropy contribution, which is compatible with that derived by using statistical mechanics. The general validity of the concept of entropic stabilization of rotating admolecules, favoring rotation already at room temperature, is tested for other typical small, mid‐size and large adsorbates.     

Self‐Assembly of Anionic Porphyrins and Alkaline or Alkaline Earth Metal Ions Mediated by Cucurbit[7,8]uril

Nanoscaled coordination polymers based on biologically prevalent ions have potential applications in drug delivery and biomedical imaging. Herein, coordination polymer nanoparticles of anionic porphyrins, including meso‐tetra(4‐carboxyphenyl)‐porphyrin (H₂TCPP^4?) and meso‐tetra(4‐sulfonatophenyl)‐porphyrin (H₂TPPS^4?), and alkaline or alkaline earth metal cations, such as K⁺ and Ca²⁺, were constructed in aqueous solution in the presence of cucurbit[7]uril (CB7) or cucurbit[8]uril (CB8). UV/Vis absorption and fluorescence spectroscopy, dynamic light scattering (DLS), scanning electron spectroscopy (SEM), and atomic force microscopy (AFM) were applied to explore the assembly and particle formation of porphyrin anions and metal cations mediated by CBn. The particle size depends on the kinds of CBn and metal cations and their concentrations. The uptake of H₂TPPS^4? particles by tumor cells (A549 cells) was found to be more efficient than H₂TPPS^4? at 37 °C, showing the application potential of such assembled particles in biology and medicine.     

Nitrogen‐Doped Carbon Dots: A Facile and General Preparation Method,Photoluminescence Investigation,and Imaging Applications

Carbon dots (Cdots) are an important probe for imaging and sensing applications because of their fluorescence property, good biocompatibility, and low toxicity. However, complex procedures and strong acid treatment are often required and Cdots suffer from low photoluminescence (PL) emission. Herein, a facile and general strategy using carbonization of precursors and then extraction with solvents is proposed for the preparation of nitrogen‐doped Cdots (N‐Cdots) with 3‐(3,4‐dihydroxyphenyl)‐L ‐alanine (L ‐DOPA), L ‐histidine, and L ‐arginine as precursor models. After they are heated, the precursors become carbonized. Nitrogen‐doped Cdots are subsequently extracted into N,N′‐dimethylformamide (DMF) from the carbogenic solid. A core–shell structure of Cdots with a carbon core and the oxygen‐containing shell was observed. Nitrogen has different forms in N‐Cdots and oxidized N‐Cdots. The doped nitrogen and low oxidation level in N‐Cdots improve their emission significantly. The N‐Cdots show an emission with a nitrogen‐content‐dependent intensity and Cdot‐size‐dependent emission‐peak wavelength. Imaging of HeLa cells, a human cervical cancer cell line, and HepG2 cells, a human hepatocellular liver carcinoma line, was observed with high resolution using N‐Cdots as a probe and validates their use in imaging applications and their multicolor property in the living cell system.     

Formation and Properties of Self‐Assembly‐Driven Fluorescent Nanoparticle Sensors

Fluorescent nanoparticles (FNPs) are obtained in water by self‐assembly from a polymeric ionic liquid, fluorescent carboxylate moiety, and a surfactant through two main supramolecular interactions, that is, ionic bonds and hydrophobic/hydrophilic interactions. The hydrophobicity of the surfactant is tunable and a highly hydrophobic surfactant increases the fluorescence intensity and stability of the FNPs. The fluorescence of the FNPs is sensitive to a quenching effect by various ions with high selectivity, and consequently, they may be used as sensors. The self‐assembly approach used to generate the FNPs is considerably simpler than other methods based on more challenging synthetic methods and the flexibility of the approach should allow a wide and diverse range of FNPs to be prepared with specific sensor applications.