Visualization of Protein‐Specific Glycosylation inside Living Cells

Protein glycosylation is a ubiquitous post‐translational modification that is involved in the regulation of many aspects of protein function. In order to uncover the biological roles of this modification, imaging the glycosylation state of specific proteins within living cells would be of fundamental importance. To date, however, this has not been achieved. Herein, we demonstrate protein‐specific detection of the glycosylation of the intracellular proteins OGT, Foxo1, p53, and Akt1 in living cells. Our generally applicable approach relies on Diels–Alder chemistry to fluorescently label intracellular carbohydrates through metabolic engineering. The target proteins are tagged with enhanced green fluorescent protein (EGFP). Förster resonance energy transfer (FRET) between the EGFP and the glycan‐anchored fluorophore is detected with high contrast even in presence of a large excess of acceptor fluorophores by fluorescence lifetime imaging microscopy (FLIM).     

A Puckered Singlet Cyclopentane‐1,3‐diyl: Detection of the Third Isomer in Homolysis

In the photochemical denitrogenation of 1,4‐diaryl‐2,3‐diazabicyclo[2.2.1]heptane ( AZ6 ) bearing sterically hindered substituents, a curious new absorption band at about 450 nm was observed under low‐temperature matrix conditions, together with the previously well‐characterized planar singlet diradical pl‐¹ DR6 with λ_max=≈580 nm. The 450 nm species was electron paramagnetic resonance (EPR)‐silent. Instead of generating the planar diradical pl‐¹ DR6 and the precursor azoalkane AZ6 upon warming, the ring‐closed bicyclo[2.1.0]pentane derivative SB6 , that is, the AZ6 denitrogenation product was identified. Based on product analysis, low‐temperature spectroscopic observations, high‐level quantum‐mechanical computations, viscosity effect, and laser‐flash photolysis, the puckered singlet diradicaloid puc‐¹ DR6 was assigned to the new 450 nm absorption. The latter was detected experimentally at the same time as the planar singlet diradical pl‐¹ DR6 . Sterically demanding substituents as well as viscosity impediments were essential for the detection of the experimentally hitherto unknown puckered singlet cyclopentane‐1,3‐diyl diradicaloid puc‐¹ DR6 , that is, the third isomer in homolysis. The present findings should stimulate future work on the mechanistically fascinating stereoselectivity documented in the formation of bicyclo[2.1.0]pentanes during the 2,3‐diazabicyclo[2.2.1]heptane denitrogenation.     

Chlorophyll‐Derived Yellow Phyllobilins of Higher Plants as Medium‐Responsive Chiral Photoswitches

The fall colors are signs of chlorophyll breakdown, the biological process in plants that generates phyllobilins. Most of the abundant natural phyllobilins are colorless, but yellow phyllobilins (phylloxanthobilins) also occur in fall leaves. As shown here, phylloxanthobilins are unique four‐stage photoswitches. Which switching mode is turned on is controlled by the molecular environment. In polar media, phylloxanthobilins are monomeric and undergo photoreversible Z/E isomerization, similar to that observed for bilirubin. Unlike bilirubin, however, the phylloxanthobilin Z isomers photodimerize in apolar solvents by regio‐ and stereospecific thermoreversible [2+2] cycloadditions from self‐assembled hydrogen‐bonded dimers. X‐ray analysis revealed the first stereostructure of a phylloxanthobilin and its hydrogen‐bonded self‐templating architecture, helping to rationalize its exceptional photoswitch features. The chemical behavior of phylloxanthobilins will play a seminal role in identifying biological roles of phyllobilins.     

Metadynamics in essential coordinates: free energy simulation of conformational changes

We propose an approach that combines an extraction of collective motions of a molecular system with a sampling of its free energy surface. A recently introduced method of metadynamics allows exploration of the free energy surface of a molecular system by means of coarse-grained dynamics with flooding of free energy minima. This free energy surface is defined as a function of a set of collective variables (e.g., interatomic distances, angles, torsions, and others). In this study, essential coordinates determined by essential dynamics (principle component analysis) were used as collective variables in metadynamics. First, dynamics of the model system (explicitly solvated alanine dipeptide, Ace-Ala-Nme) was simulated by a classical molecular dynamics simulation. The trajectory (1 ns) was then analyzed by essential dynamics to obtain essential coordinates. The free energy surface as a function of the first and second essential coordinates was then explored by metadynamics. The resulting free energy surface is in agreement with other studies of this system. We propose that a combination of these two methods (metadynamics and essential dynamics) has great potential in studies of conformational changes in peptides and proteins.     

Effect of selenium oxidation state on cadmium translocation in chamomile plants

Syntheses and spectral characteristics of cadmium(II) compounds (CdSeO₄, CdSeO₃, and Cd(NCSe)₂(nia)₂) containing selenium in oxidation states (VI), (IV), and (-II) are described. In Cd(NCSe)₂(nia)₂, nicotinamide (nia) and selenocyanate anions are bonded to Cd atom as N-donor monodentate ligands. Nicotinamide is coordinated through the ring nitrogen atom. The effects of these selenium compounds as well as Cd(NCS)₂(nia)₂ on the growth and Cd accumulation in roots and shoots of hydroponically cultivated chamomile plants (cultivar Lutea) were studied. In the applied concentration range (12–60 μmol dm⁻³) Cd(NCS)₂(nia)₂ affected neither the length nor the dry mass of roots and shoots. Other compounds applied at 24 μmol dm⁻³ and 60 μmol dm⁻³ significantly reduced dry mass of roots and shoots. Selenium oxidation state in the cadmium compounds affected Cd accumulation in plant organs as well as Cd translocation within the plants, which was reflected in the values of bioaccumulation (BAF) and translocation factors (S/R). Cd amount accumulated by shoots was lower than that in the roots. The highest BAF values determined for Cd accumulation in shoots were obtained with CdSeO₄. Substitution of S with Se in the Cd(NCX)₂(nia)₂ (X = Se or S) caused an increase of Cd translocation into the shoots. Presented at the XVIIIth Slovak Spectroscopic Conference, Spišská Nová Ves, 15–18 October 2006.     

Validation of the density-functional based tight-binding approximation method for the calculation of reaction energies and other data

We investigated the performance of the approximative density functional method DFTB versus BLYP and G2 with respect to zero-point corrected reaction energies, vibrational frequencies, and geometry parameters for a set of 28 reactions and 22 representative molecules containing C, H, N, and O (DFTB--density-functional based tight-binding approximation). The DFTB reaction energies show a mean absolute deviation versus the G2 reference of 4.3 kcalmol only. The corresponding value for the vibrational frequencies amounts to 75 cm(-1) versus BLYP/cc-pVTZ. With very few exceptions bond lengths and angles are in excellent agreement with the results of higher-level methods.