Rapid calculation of protein chemical shifts using bond polarization theory and its application to protein structure refinement

Although difficult to analyze, NMR chemical shifts provide detailed information on protein structure. We have adapted the semi-empirical bond polarization theory (BPT) to protein chemical shift calculation and chemical shift driven protein structure refinement. A new parameterization for BPT amide nitrogen chemical shift calculation has been derived from MP2 ab initio calculations and successfully evaluated using crystalline tripeptides. We computed the chemical shifts of the small globular protein ubiquitin, demonstrating that BPT calculations can match the results obtained at the DFT level of theory at very low computational cost. In addition to the calculation of chemical shift tensors, BPT allows the calculation of chemical shift gradients and consequently chemical shift driven geometry optimizations. We applied chemical shift driven protein structure refinement to the conformational analysis of a set of Trypanosoma brucei (the causative agent of African sleeping sickness) tryparedoxin peroxidase Px III structures. We found that the interaction of Px III with its reaction partner Tpx seems to be governed by conformational selection rather than by induced fit.     

Mechanistic Studies on the Gas‐Phase Dehydrogenation of Alkanes at Cyclometalated Platinum Complexes

In the ion/molecule reactions of the cyclometalated platinum complexes [Pt(L? H)]⁺ (L=2,2′‐bipyridine (bipy), 2‐phenylpyridine (phpy), and 7,8‐benzoquinoline (bq)) with linear and branched alkanes C_nH_2n+2 (n=2–4), the main reaction channels correspond to the eliminations of dihydrogen and the respective alkenes in varying ratios. For all three couples [Pt(L? H)]⁺/C₂H₆, loss of C₂H₄ dominates clearly over H₂ elimination; however, the mechanisms significantly differs for the reactions of the “rollover”‐cyclometalated bipy complex and the classically cyclometalated phpy and bq complexes. While double hydrogen‐atom transfer from C₂H₆ to [Pt(bipy? H)]⁺, followed by ring rotation, gives rise to the formation of [Pt(H)(bipy)]⁺, for the phpy and bq complexes [Pt(L? H)]⁺, the cyclometalated motif is conserved; rather, according to DFT calculations, formation of [Pt(L? H)(H₂)]⁺ as the ionic product accounts for C₂H₄ liberation. In the latter process, [Pt(L? H)(H₂)(C₂H₄)]⁺ (that carries H₂ trans to the nitrogen atom of the heterocyclic ligand) serves, according to DFT calculation, as a precursor from which, due to the electronic peculiarities of the cyclometalated ligand, C₂H₄ rather than H₂ is ejected. For both product‐ion types, [Pt(H)(bipy)]⁺ and [Pt(L? H)(H₂)]⁺ (L=phpy, bq), H₂ loss to close a catalytic dehydrogenation cycle is feasible. In the reactions of [Pt(bipy? H)]⁺ with the higher alkanes C_nH_2n+2 (n=3, 4), H₂ elimination dominates over alkene formation; most probably, this observation is a consequence of the generation of allyl complexes, such as [Pt(C₃H₅)(bipy)]⁺. In the reactions of [Pt(L? H)]⁺ (L=phpy, bq) with propane and n‐butane, the losses of the alkenes and dihydrogen are of comparable intensities. While in the reactions of “rollover”‐cyclometalated [Pt(bipy? H)]⁺ with C_nH_2n+2 (n=2–4) less than 15 % of the generated product ions are formed by C? C bond‐cleavage processes, this value is about 60 % for the reaction with neo‐pentane. The result that C? C bond cleavage gains in importance for this substrate is a consequence of the fact that 1,2‐elimination of two hydrogen atoms is no option; this observation may suggest that in the reactions with the smaller alkanes, 1,1‐ and 1,3‐elimination pathways are only of minor importance.     

Multivalent Design of Apoptosis‐Inducing Bid‐BH3 Peptide–Oligosaccharides Boosts the Intracellular Activity at Identical Overall Peptide Concentrations

Multivalent peptide–oligosaccharide conjugates were prepared and used to investigate the multivalency effect concerning the activity of Bid‐BH3 peptides in live cells. Dextran oligosaccharides were carboxyethylated selectively in the 2‐position of the carbohydrate units and activated for the ligation of N‐terminally cysteinylated peptides. Ligation through maleimide coupling was found to be superior to the native chemical ligation protocol. Monomeric Bid‐BH3 peptides were virtually inactive, whereas pentameric peptide conjugates induced apoptosis up to 20‐fold stronger at identical peptide concentrations. Comparison of lowly multivalent and highly multivalent peptide dextrans proved a multivalency effect in life cells which was specific for the BH3 peptide sequence.     

Rocky core solubility in Jupiter and giant exoplanets

Gas giants are believed to form by the accretion of hydrogen-helium gas around an initial protocore of rock and ice. The question of whether the rocky parts of the core dissolve into the fluid H-He layers following formation has significant implications for planetary structure and evolution. Here we use ab initio calculations to study rock solubility in fluid hydrogen, choosing MgO as a representative example of planetary rocky materials, and find MgO to be highly soluble in H for temperatures in excess of approximately 10,000 K, implying the potential for significant redistribution of rocky core material in Jupiter and larger exoplanets.     

On-line determination of mercury in river water at the German monitoring station Schnackenburg/Elbe

A monitor is described which provides the on-line determination of mercury in river water at concentrations from 20 to 1000 ng/L. The measurement includes an on-line digestion with Br^–/BrO₃ ^– and UV-radiation. Each determination is controlled by an on-line addition of 50 and 100 ng/L mercury carried out by pre-dilution of a 500 and 1000 ng/L stock solution using sequential injection analysis (SIA). One cycle of analysis takes 20 min and results in nine signals. A five days stand-alone operation has been performed successfully. Details are also published at web page: “http/www.rzbd.fh-hamburg.de/¶～prmercol”     

Spin-Labeled Riboswitch Synthesized from a Protected TPA Phosphoramidite Building Block

The nitroxide TPA (2,2,5,5-tetramethyl-pyrrolin-1-oxyl-3-acetylene) is an excellent spin label for EPR studies of RNA. Previous synthetic methods, however, are complicated and require special equipment. Herein, we describe a uridine derived phosphoramidite with a photocaged TPA unit attached. The light sensitive 2-nitrobenzyloxymethyl group can be removed in high yield by short irradiation at 365 nm. Based on this approach, a doubly spin-labeled 27mer neomycin sensing riboswitch was synthesized and studied by PELDOR. The overall thermal stability of the fold is not much reduced by TPA. In-line probing nevertheless detected changes in local mobility.     

The principal block idempotent

Dedicated to Walter Feit