Crystal structure of a transition state mimic for Tdp1 assembled from vanadate,DNA, and a topoisomerase I-derived peptide

Tyrosyl-DNA phosphodiesterase (Tdp1) is a member of the phospholipase D superfamily and acts as a DNA repair enzyme that removes stalled topoisomerase I- DNA complexes by hydrolyzing the bond between a tyrosine side chain and a DNA 3' phosphate. Despite the complexity of the substrate of this phosphodiesterase, vanadate succeeded in linking human Tdp1, a tyrosine-containing peptide, and a single-stranded DNA oligonucleotide into a quaternary complex that mimics the transition state for the first step of the catalytic reaction. The conformation of the bound substrate mimic gives compelling evidence that the topoisomerase I-DNA complex must undergo extensive modification prior to cleavage by Tdp1. The structure also illustrates that the use of vanadate as the central moiety in high-order complexes has the potential to be a general method for capturing protein-substrate interactions for phosphoryl transfer enzymes, even when the substrates are large, complicated, and unusual.     

Effect of quality characteristics of single sample preparation steps in the precision and coverage of proteomic studies—A review

Proteomic profiling and biomarker search are analytical tools as many other. Nevertheless, in the proteomic discovery phase considerable sample fractionation is inevitable before readout. Since these procedures are of notable complexity, proteomic tools need in particular analytical quality validation standards as prevail for other analytical methods. With acceptance of the rule of error propagation the values of imprecision and yield of each preparation step determine overall reproducibility and therewith information harvest of a propagated method series. Thereto, we examined recent proteomic reports with reproducibility data and with parallelization, and automation approaches. Based on the data available from literature it is highly probable, that at least a part of current proteomic platforms actually suffer from high technical variance.     

Convenient Synthesis of tert‐Butyl Esters of Indole‐5‐carboxylic Acid and Related Heterocyclic Carboxylic Acids

The tert‐butyl esters of indole‐5‐carboxylic acid and related compounds such as benzofuran‐ and benzothiophene‐5‐carboxylic acid were readily accessed by reacting the appropriate carboxylic acids with tert‐butyl trichloroacetimidate. To obtain the tert‐butyl esters of the 5‐carboxylic acids of 1H‐benzotriazole and 1H‐benzimidazole, position 1 of these heterocycles had to be protected by acetylation prior to reaction with tert‐butyl trichloroacetimidate. Cleavage of the acetyl residue of the obtained intermediates by dilute aqueous NaOH in ethanol led to the desired tert‐butyl 1H‐benzotriazole‐and 1H‐benzimidazole‐5‐carboxylates.     

catena‐Poly[[chloro­dipyridine­manganese(II)]‐μ3‐6‐oxo‐1,6‐dihydro­pyridine‐2‐carboxyl­ato]

The title one‐dimensional chain polymer complex, [Mn(C₆H₄NO₃)Cl(C₆H₅N)₂]_n, was isolated from the reaction of MnCl₂ with 6‐oxo‐1,6‐dihydro­pyridine‐2‐carboxylic acid (HpicOH) in pyridine. The asymmetric unit contains one [Mn(HPicO)Cl(py)₂] moiety (py is pyridine), with the (HpicO)⁻ ligand acting in a tridentate manner via the two carboxyl­ate O atoms and the pyridone O atom. The operation of inversion centres generates eight‐ and 14‐membered rings and, in conjunction with an a‐axis translation, leads to an infinite chain extending along [100]. The Mn⋯Mn separations in this chain are 5.1069 (6) and 7.1869 (6) Å. The Mn^II atom has a distorted octahedral coordination, with trans‐axial pyridine ligands and with three O atoms and the Cl atom in the equatorial plane. The conformation of the 14‐membered ring is stabilized by pairs of inversion‐related N—H⋯O hydrogen bonds.     

Targeting Cancer with PCPA‐Drug Conjugates: LSD1 Inhibition‐Triggered Release of 4‐Hydroxytamoxifen

Targeting cancer with small molecule prodrugs should help overcome problems associated with conventional cancer‐targeting methods. Herein, we focused on lysine‐specific demethylase 1 (LSD1) to trigger the controlled release of anticancer drugs in cancer cells, where LSD1 is highly expressed. Conjugates of the LSD1 inhibitor trans‐2‐phenylcyclopropylamine (PCPA) were used as novel prodrugs to selectively release anticancer drugs by LSD1 inhibition. As PCPA‐drug conjugate (PDC) prototypes, we designed PCPA‐tamoxifen conjugates 1 a and 1 b , which released 4‐hydroxytamoxifen in the presence of LSD1 in vitro. Furthermore, 1 a and 1 b inhibited the growth of breast cancer cells by the simultaneous inhibition of LSD1 and the estrogen receptor without exhibiting cytotoxicity toward normal cells. These results demonstrate that PDCs provide a useful prodrug method that may facilitate the selective release of drugs in cancer cells.     

Structure elucidation of β-carotene isomers by HPLC-NMR coupling using a C30 bonded phase

The separation of cis/trans isomers of β-carotene has been performed with a C₃₀ stationary phase employing ¹H NMR spectroscopy as an on-line detection technique. 1D as well as 2D NMR spectra have been recorded in the stopped-flow mode for the predominant chromatographic peaks. Structural assignment of the five identified isomers was performed via comparison of simulated 1D ¹H NMR spectra on the basis of the structures of β-carotene cis/trans isomers with the experimental data, and also by the analysis of the proton-proton connectivities in the 2D NMR spectra of three isomers with the highest concentration. The chromatographic retention behaviour of the isomers agreed well with previously reported data. The advantage of the applied hyphenated coupling technique compared to conventional off-line techniques lies in the fact that chromatographic separation and NMR detection are performed in a closed system, so that reisomerization of the separated compounds is inhibited. Received: 29 May 1996 / Revised: 1 July 1996 / Accepted: 4 July 1996     

Charge transport through extended molecular wires with strongly correlated electrons

Electron–electron interactions are at the heart of chemistry and understanding how to control them is crucial for the development of molecular-scale electronic devices. Here, we investigate single-electron tunneling through a redox-active edge-fused porphyrin trimer and demonstrate that its transport behavior is well described by the Hubbard dimer model, providing insights into the role of electron–electron interactions in charge transport. In particular, we empirically determine the molecule''s on-site and inter-site electron–electron repulsion energies, which are in good agreement with density functional calculations, and establish the molecular electronic structure within various oxidation states. The gate-dependent rectification behavior confirms the selection rules and state degeneracies deduced from the Hubbard model. We demonstrate that current flow through the molecule is governed by a non-trivial set of vibrationally coupled electronic transitions between various many-body ground and excited states, and experimentally confirm the importance of electron–electron interactions in single-molecule devices.

Experimental studies of electron transport through an edge-fused porphyrin oligomer in a graphene junction are interpreted within a Hubbard dimer framework.     

Background removal from polarized Raman spectra of tooth enamel using the wavelet transform

A wavelet transformation method is introduced to remove the large fluorescence background from polarized Raman spectra of stained tooth enamel. This method exploits the wavelet multiresolution decomposition where the experimental Raman spectrum is decomposed into signals with different frequency components, and where the lowest frequency background and highest frequency noise are removed. This method is optimized using a simulated collection of parallel‐polarized and cross‐polarized Raman spectra of the enamel and then applied to a set of experimental data. The results show that the wavelet transform technique can extract the pure spectra from background and noise, with the depolarization ratio used to discriminate between early dental caries and sound enamel preserved. Copyright © 2010 Crown in the right of Canada. Published by John Wiley & Sons, Ltd.