Monitoring cytoplasmic protein complexes with blue native gel electrophoresis and stable isotope labelling with amino acids in cell culture: analysis of changes in the 20S proteasome

Analysis of protein complexes is of increasing interest in the field of proteomics. A challenge is to develop methods for monitoring changes in the quantity and subunit composition of protein complexes on a proteome-wide scale. Here, we describe the combination of 1-D blue native polyacrylamide gel electrophoresis (BN-PAGE) with stable isotope labelling of amino acids in cell culture (SILAC) and tandem mass spectrometry (MS/MS). Cleared lysates from normal and perturbed samples, one incorporating heavy stable isotopes and the other light isotopes, are co-separated by blue native PAGE and then analysed and quantitated with MS/MS and appropriate software. This permits the analysis of cytoplasmic complexes. To demonstrate this technique, we explored how the 20S proteasome changes when the Pre9/α3 subunit, the only non-essential subunit of this complex, was deleted. Our results showed that ΔPre9/α3 cells can form the 20S proteasome complex, although with reduced efficiency. This involves an increase in expression of the α4 subunit. Our findings suggest this technique as an approach for the study of quantitative and qualitative differences in protein complexes, from cleared cell lysates.     

Electrochemical Oxidation of Ibuprofen and Its Voltammetric Determination at a Boron‐Doped Diamond Electrode

The electrochemical oxidation of ibuprofen at a boron‐doped diamond electrode (BDDE) and its voltammetric determination is reported for the first time. A well‐defined oxidation peak was observed at around 1.6 V in 0.1 mol L^?1 H₂SO₄ solution with 10 % (v/v) ethanol at the BDDE surface activated by either cathodic or anodic pretreatments. A differential‐pulse voltammetric method for the determination of ibuprofen in pharmaceutical formulations was optimized with a detection limit of 5 µmol L^?1 and compared with the British Pharmacopeia method.     

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.     

Primary Studies on Variation in Position of Trifluoromethyl Groups in Several Aromatic Group‐14 Derivatives by 19F‐NMR Spectroscopy

Variation in the position of CF₃ groups in several aromatic Group‐14 compounds was studied by ¹⁹F‐NMR spectroscopy. In these compounds R_nECl_4?n (n=1 or 2; E=Si, Ge, or Sn; R=2,4,6‐(CF₃)₃C₆H₂ (=Ar), 2,6‐(CF₃)₂C₆H₃ (=Ar′), or 2,4‐(CF₃)₂C₆H₃ (=Ar″)), Ar, Ar′, and Ar″ are all bulky, strongly electron‐withdrawing ligands. The ¹⁹F‐NMR studies of the variation in position of the CF₃ substituents in these compounds as revealed by chemical shifts could be correlated with the electronegativities of the central elements E, and with intramolecular E–F interactions derived from single‐crystal X‐ray diffraction data. These interactions are considered to play an important role in the stabilization of these compounds.     

An assessment of pure,hybrid, meta,and hybrid‐meta GGA density functional theory methods for open‐shell systems: The case of the nonheme iron enzyme 8R–LOX

The performance of a range density functional theory functionals combined in a quantum mechanical (QM)/molecular mechanical (MM) approach was investigated in their ability to reliably provide geometries, electronic distributions, and relative energies of a multicentered open‐shell mechanistic intermediate in the mechanism 8R–Lipoxygenase. With the use of large QM/MM active site chemical models, the smallest average differences in geometries between the catalytically relevant quartet and sextet complexes were obtained with the B3LYP^* functional. Moreover, in the case of the relative energies between ⁴II and ⁶II , the use of the B3LYP^* functional provided a difference of 0.0 kcal mol^–1. However, B3LYP^± and B3LYP also predicted differences in energies of less than 1 kcal mol^–1. In the case of describing the electronic distribution (i.e., spin density), the B3LYP^*, B3LYP, or M06‐L functionals appeared to be the most suitable. Overall, the results obtained suggest that for systems with multiple centers having unpaired electrons, the B3LYP^* appears most well rounded to provide reliable geometries, electronic structures, and relative energies. © 2012 Wiley Periodicals, Inc.     

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.