Mapping of possible prion protein self-interaction domains using peptide arrays

Background  

The common event in transmissible spongiform encephalopathies (TSEs) or prion diseases is the conversion of host-encoded protease sensitive cellular prion protein (PrP^C) into strain dependent isoforms of scrapie associated protease resistant isoform (PrP^Sc) of prion protein (PrP). These processes are determined by similarities as well as strain dependent variations in the PrP structure. Selective self-interaction between PrP molecules is the most probable basis for initiation of these processes, potentially influenced by chaperone molecules, however the mechanisms behind these processes are far from understood. We previously determined that polymorphisms do not affect initial PrP^C to PrP^Sc binding but rather modulate a subsequent step in the conversion process. Determining possible sites of self-interaction could elucidate which amino acid(s) or amino acid sequences contribute to binding and further conversion into other isoforms. To this end, ovine – and bovine PrP peptide-arrays consisting of 15-mer overlapping peptides were probed with recombinant sheep PrP^C fused to maltose binding protein (MBP-PrP).     

Ab initio and DFT modeling of stereoselective deamination of aziridines by nitrosyl chloride

The stereochemical course of the deamination of cis‐2,3‐dimethylaziridine by nitrosyl chloride was investigated at the QCISD/6‐31G(d) level. Calculations reveal that the reaction takes place in two steps. In the first step, the reactants form a pre‐reactive complex, followed by a spiro‐type bicyclic transition state, which on dissociative cycloelimination gives the N‐nitrosoaziridine intermediate. In the second step, this intermediate undergoes cycloreversion through a slightly asynchronous concerted transition state to form an alkene with the same stereochemistry, which is in total agreement with experiment. In the whole reaction, the denitrosation step is found to be rate‐determining. For comparison, geometry optimizations and energies were also obtained at the B3LYP/6‐31G(d) level. It was found that the B3LYP energy results differed significantly from the QCISD ones. To analyze the reason for this difference, B3LYP calculations were repeated by varying the contribution of exact exchange in the Becke functional. With respect to the QCISD results, it has been shown that the functional with 0% exact exchange yields the best activation barriers, whereas the functional with 30% exact exchange is the most suitable one to carry out the complexation and reaction energy calculations. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Ring cleavage of aziridines by difluoroamine: mechanistic insights from ab initio and DFT study

cis-2,3-Dimethylaziridine reacts with difluoroamine to give the corresponding alkene and nitrogen with retention of configuration. We have carried out a DFT study of this reaction to clarify the reaction mechanism by considering a multistep reaction pathway with possible intermediacy of several three- and four-membered cyclic intermediates and transition states (TSs). The energetics of this reaction shows that the reaction takes place in four steps including a three-membered azamine intermediate. Both the energetics and the stereochemical outcome of this reaction rule out the formation of a four-membered diazetine intermediate during the reaction. Although the first N-N bond formation step is rate determining, the final step, asynchronous concerted cleavage of the azamine intermediate, explains the stereochemistry of this reaction. The asynchronous nature of the final step makes the reaction Woodward-Hoffmann allowed, as reported by Yamabe and Minato (J. Phys. Chem. A 2001, 105, 7281). Computations at HF and MP2 levels confirm the same trends in energetics. Single point energy computations at B3LYP, MP2, and QCISD levels with the 6-311++G(d,p) and cc-pVTZ basis sets show that the larger basis sets predict higher free energies of activation and less negative free energies of reaction. Intrinsic reaction coordinate (IRC) analyses reveal the asynchronous nature of the first and the last steps of the reaction. The deamination of trans-2,3-dimethylaziridine was shown to follow a course of reaction similar to that of the cis isomer.     

Acceptor tuning effect on TPA-based organic efficient sensitizers for optoelectronic applications—quantum chemical investigation

Structural Chemistry - A new series of triphenylamine (TPA)-based organic dyes (A1-A4) are characterized and implemented as photosensitizers for dye-sensitized solar cells (DSSCs). In the...     

Effect of Substituents and Dopants on the Structure–Property Relationship of Poly(Aniline)—A Comparative Study

Effects of substituents and dopants on the structure–property relationships of poly(aniline) (PANI)-type homopolymers are analyzed. The gravimetric method was used for the estimation of rate of polymerization (R_p). FTIR spectroscopy was used for the calculation of relative intensities (RI) of benzenoid (RI_[B/CH]), quinonoid (RI_[Q/CH]), and their internal conversion (RI_[B/Q]). Thermogravimetric analysis (TGA) characterized the thermal stability of PANIs. A standard four probe method was employed for the conductivity measurements. The results are analyzed and critically compared.