The role of entropy in initializing the aggregation of peptides: a first principle study on oligopeptide oligomerization

The initiation and progression of Alzheimer's disease is coupled to the oligo- and polymerization of amyloid peptides in the brain. Amyloid like aggregates of protein domains were found practically independent of their primary sequences. Thus, the driving force of the transformation from the original to a disordered amyloid fold is expected to lie in the protein backbone common to all proteins. In order to investigate the thermodynamics of oligomerization, full geometry optimizations and frequency calculations were performed both on parallel and antiparallel β-pleated sheet model structures of [HCO-(Ala)(1-6)-NH(2)](2) and (For-Ala(1-2)-NH(2))(1-6) peptides, both at the B3LYP and M05-2X/6-311++G(d,p)//M05-2X/6-31G(d) levels of theory, both in vacuum and in water. Our results show that relative entropy and enthalpy both show a hyperbolic decrease with increasing residue number and with increasing number of strands as well. Thus, di- and oligomerization are always thermodynamically favored. Antiparallel arrangements were found to have greater stability than parallel arrangements of the polypeptide backbones. During our study the relative changes in thermodynamic functions are found to be constant for long enough peptides, indicating that stability and entropy terms are predictable. All thermodynamic functions of antiparallel di- and oligomers show a staggered nature along the increasing residue number. By identifying and analyzing the 6 newly emerging dimer vibrational modes of the 10- and 14-membered building units, the staggered nature of the entropy function can be rationalized. Thus, the vanishing rotational and translational modes with respect to single strands are converted into entropy terms "holding tight" the dimers and oligomers formed, rationalizing the intrinsic adherence of natural polypeptide backbones to aggregate.     

Bioprocessing of sweet sorghum within situ-produced enzymes

Applied Biochemistry and Biotechnology - Enzyme-assisted ensiling (ENLAC), usingin situ-produced enzymes fromGliocladium sp. TUB-F-498, preserved 80% of the sugar content of sweet sorghum, and...     

Comparative study of the thermal behavior of Sr–Cu–O gels obtained by sol–gel and microwave-assisted sol–gel method

Journal of Thermal Analysis and Calorimetry - In the literature data, several papers reported the synthesis by various chemical or physical methods of the SrCu2O2 (SCO) having possible applications...     

Comparative bioanalytical study of3H-deramciclane in dog plasma, using a gas chromatography-nitrogen-selective detection (GC-NPD), a new GC-radiochemical detection (GC-RD) and a liquid scintillation method

Summary A new, highly sensitive and selective gas chromatography method, using radiochemical detection (GC-DR) was developed for the selective determination of³H-labelled deramciclane and its N-desmethyl metabolite in dog plasma. Inter-day accuracy and precision, as well as system suitability of the GC-RD method was investigated during the method validation. The calibration curve was proved to be linear (r=0.9986) in a wide concentration range (13–1000 ngeqv mL⁻¹) The lower limit of quantitation (LLOQ) was 13.7 ngeqv mL⁻¹, and the limit of the detection (LOD) was 1 ngeqv mL⁻¹. Using this new GC-RD method, plasma levels of³H-labelled deramciclane and its metabolite were determined in dogs, after the administration of a single 10 mg kg⁻¹ oral dose. Pharmacokinetic curves and the calculated pharmacokinetic parameters were compared to those obtained using a previously elaborated gas chromatography-nitrogen selective detection method (GC-NPD) and to those obtained by measuring the plasma level of total radioactivity (liquid scintillation counting, LSC). Pharmacokinetic curves and the calculated pharmacokinetic parameters obtained with the two different gas chromatography detection methods (NPD and RD) showed good correlation. Comparison of these results to those acquired by total radioactivity measurement demonstrated that deramciclane was intensively metabolised. Moreover, the biological half-life (t ₁ ^2/β ) of the unknown metabolites proved to be more than a magnitude longer than the half-life of the parent compound or that of N-desmethyl metabolite. Presented at: Balaton Symposium on High-Performance Separation Methods, Siófok, Hungary, September 3–5, 1997.     

The Effect of Silver Perchlorate of the Reaction of Trialkyl Phosphite with α-Halogenoketones

Abstract

Trialkyl phosphites are known to react with α-halogenoketones to yield β-ketophosphonates (Arbuzov product) or vinyl phosphates (Perkow product) according to coniiitions.¹ α-Hydroxyphosphonate may be formed in addition, in prcltic media.² We have now shown that none of these products is formed in the presence of silver perchlorate (in benzene sclutim); nor could we detect the ketophosphonium perchlorate reported previously. Phosphorus-31 nmr showed the formation of trimethyl phosphate and tetramethyl pyrophosphate as the exclusive phosphorus-containing products. The sequence of possible reaction is complex and the overall stoichiometry may vary somewhat according to the rate and order of rixing. Trialkyl phosphate could be formed by elimination of alkyne from vinyloxyphosphonium intermediate produced together with silver iodine in first stage of the interaction. Pyrophosphate formation would then result from nucleophilic attack of trimethyl phosphate on the trimethoxy(1-nethylvinyloxy)phosphoniun ion, which may be formed as a reactive intermediate. Evidence for formation of methyl perchlorate in the final dealkylation of the quasiphosphonium intermediate is provided by proton nmr spectroscopy and by the formation of the N-methylquino-linium salt on addition of quinoline. No change in the ³¹P nmr spectrum occurs at this stage. Other by-products of the main reactions include the dehalogenated ketone (acetone from iodoacetone or acetnphenone from α-iodoacetophenone).     

Cinchona based squaramide catalysed enantioselective Michael addition of α-nitrophosphonates to aryl acrylates: enantioselective synthesis of quaternary α-aminophosphonates

Several cinchona based squaramide catalysts were applied to the asymmetric Michael addition of α-nitroethylphosphonates to acrylic acid aryl esters, resulting in high yields and enantioselectivities. The absolute configuration of one of the quaternary α-nitrophosphonate adducts was deduced from its experimental and calculated CD spectra. The adducts were reduced to their cyclic aminophosphonates by catalytic hydrogenation.     

A Multicolumn Ion Chromatographic Determination of Nitrate and Sulfate in Waters Containing Humic Substances

Abstract

A three-column ion chromatographic system for the removal of humic substances from natural waters, and subsequent on-line concentration and determination of nitrate and sulfate using non-suppressed ion chromatography is presented. Humic substances are removed using disposable adsorption columns packed with chemically bonded amine silica material. The sample is directly transfered to an ion exchange column where the anions are concentrated ca 10 times. After reversing the flow, the ions are transferred to a third column where they are separated and quantified. The detection limit is less than 1 mg L^?1 of nitrate or sulfate in water containing 45mgL^?1 of humic acid.     

Reaction of Trialkyl Phosphites with α,β-Unsaturated Carbonyl Compounds

Abstract

Reaction of trialkyl phosphites 1 with α,β-unsaturated oxo-compounds 2 gives oxaphospholenes 3 or/and two types of Arbuzov products, γ-keto-phosphonates 4 and alkyl-enol-ethers 5.     

Effects of different alkali metal ions on the cationization of poly(ethylene glycol)s in matrix-assisted laser desorption/ionization mass spectrometry: a new selectivity parameter

The cationization of poly(ethylene glycol)s, PEG 4000 and PEG 6000, under matrix-assisted laser desorption/ionization conditions was studied by using different concentration ratios of the sodium ion, as the reference ion, and another alkali metal ion (Li(+), K(+), Rb(+), Cs(+)). A linear correlation was found between the intensity ratio of the sodiated PEGs and PEGs cationized with alkali metal ions versus the initial concentration ratio of sodium and alkali metal ions. The slopes of these straight lines are proposed as a novel selectivity ratio for the ionization process. The intensity distribution of the cationized PEGs was also investigated. It was found that the cationized oligomers follow Poisson statistics. The M(n) and M(w) values were also evaluated. An explanation for the observed effects is given.