The de novo design of median molecules within a property range of interest

Summary In this paper an application is presented of the median molecule workflow to the de novo design of novel molecular entities with a property profile of interest. Median molecules are structures that are optimised to be similar to a set of existing molecules of interest as an approach for lead exploration and hopping. An overview of this workflow is provided together with an example of an instance using the similarity to camphor and menthol as objectives. The methodology of the experiments is defined and the workflow is applied to designing novel molecules for two physical property datasets: mean molecular polarisability and aqueous solubility. This paper concludes with a discussion of the characteristics of this method.     

Relative stability of major types of beta-turns as a function of amino acid composition: a study based on Ab initio energetic and natural abundance data

Folding properties of small globular proteins are determined by their amino acid sequence (primary structure). This holds both for local (secondary structure) and for global conformational features of linear polypeptides and proteins composed from natural amino acid derivatives. It thus provides the rational basis of structure prediction algorithms. The shortest secondary structure element, the beta-turn, most typically adopts either a type I or a type II form, depending on the amino acid composition. Herein we investigate the sequence-dependent folding stability of both major types of beta-turns using simple dipeptide models (-Xxx-Yyy-). Gas-phase ab initio properties of 16 carefully selected and suitably protected dipeptide models (for example Val-Ser, Ala-Gly, Ser-Ser) were studied. For each backbone fold most probable side-chain conformers were considered. Fully optimized 321G RHF molecular structures were employed in medium level [B3LYP/6-311++G(d,p)//RHF/3-21G] energy calculations to estimate relative populations of the different backbone conformers. Our results show that the preference for beta-turn forms as calculated by quantum mechanics and observed in Xray determined proteins correlates significantly.     

Expression and Characterization of Catalytic Domain of T Cell Protein Tyrosine Phosphatase（△TC-PTP） —— Immunohistochemical Study of △TC-PTP Expression in Non-small Cell Lung Carcinomas

This study objective was to express and characterize the catalytic domain of the human T cell protein tyrosine phosphatase（△TC-PTP） and to study immunohistochemically the expression of △TC-PTP in human non-small cell lung cancers. △TC-PTP gene was PCR amplified with the cDNA of human TC-PTP as template, and cloned into the pT7 expression vector. The recombinant pT7-△TC-PTP was expressed in E. coli Rosetta （ DE3 ） host cells and puri- fied. The enzymatic characteristics of △TC-PTP including enzyme activity and kinetics assay were measured. The antiserum was prepared by immunizing rabbit with the purified recombinant △TC-PTP. Rabbit polyclonal antibody against △TC-PTP was purified by PVDF immobilized antigen affinity chromatography. Immunohistochemical staining of lung cancer tissues was performed with antibody against △TC-PTP protein. △TC-PTP gene was correctly cloned, expressed, and purified. The recombinant △TC-PTP had a highly catalytic activity of PTPase. Squamous cell lung carcinoma showed a significantly higher expression rate of △TC-PTP （76. 92%, 10/13 ） than adenocarcinoma （57.14%, 4/7） and normal lung tissue（20%, 1/5 ）. This study represents the first demonstration that △TC-PTP is highly expressed in human squamous cell lung carcinomas. In addition, this study provides an important basis for further studying the biological function of TC-PTP and its relationship with lung carcinomas and other diseases.     

Structural Changes of Cellulose Crystallites Induced by Mercerisation in Different Solvent Systems; Determined by Powder X-ray Diffraction Method

The completeness of mercerisation can be evaluated by investigating the changes in the crystalline regions of cellulose from cellulose I (C-I) to cellulose II (C-II) by the X-ray powder diffraction method. Mercerisation experiments in four different solution systems: ethanol/water, acetone, DMSO and xylene, are reported. Also the effect of some additives, external pressure, treatment time and alkalisation temperature were studied. In two-phase solvent systems, structural changes of cellulose crystallites depended primarily on the distribution and solubility of sodium hydroxide in the solvent phases. The sodium hydroxide concentration in the hydrophilic phase must exceed 7–8 w/w-% before complete crystal change from C-I to C-II can occur. The precipitation of sodium hydroxide due to high concentration prevents the successful use of one-phase ethanol/water system in slurry process. On the contrary, the 2-propanol/water/sodium hydroxide system separates into two layers; to the water-rich lower layer and the 2-propanol-rich upper layer, where the sodium hydroxide remains mainly in the water-rich lower layer. This prevents the precipitation of sodium hydroxide and promotes the alkalisation of cellulose. Ammonium chloride and ammonium hydroxide clearly had a positive effect by promoting the crystal changes, however, the urea concentration used in this study was obviously too small. In the advantageous two-phase 2-propanol/water systems, the alkalisation time was only 15 min when the treatment temperature was kept between 0 and 10 °C. Reduced external pressure was found to have a small but still detectable positive effect on cellulose alkalisation while over-pressure prevented crystal changes.     

Enthalpies of solution in sodium octanoate + water + alcohol mixtures

Enthalpies of solution of sodium octanoate in water, 1-propanol and aqueous mixtures of 1-propanol, 1-butanol, 1-pentanol and 1-hexanol, and of the alcohols in aqueous solutions of sodium octanoate at various concentrations were determined calorimetrically at 35 °C. MostH(soln) values are exothermic and strongly dependent on the solute concentration. The main energetic factor governing the process of dissolution of the surfactant is associated with changes in the water structure caused by the presence of alcohol. That governing the process of the alcohol dissolution in surfactant solutions is due to the effect alcohols have on the CMC of the octanoate. There is no indication of the alcohol being either solubilized in the interior of the aqueous micelle, or becoming part of the micellar film.The solubility at 35 °C of sodium octanoate in water, 1-propanol and their mixtures has also been determined.     

Study on the Phase Diagram of CsCl-CeCl3-HCl(11%)-H2O System and the Properties of the Compounds

The equilibrium solubility of CsCl-CeCl3-HCl(11%)-H2O qua-ternary system at 25℃ has been determined by the physicchemical analysis method ,and the phase diagram was plotted, Two new double salts 3CsCl.CeCl3.3H2O and CsCl.CeCl3.4H2O obtained from the complicated system were identified and characterized by XRD,TG-DTA ,DSC,UV and fluorescence spectroscopy, Studies on the fluorescence excitation and emission show that 3CsCl.CeCl3.3H2O and CsCl.CeCl3.4H2O have upconversion luminescence of infrared-visible range,and the upconversion emission intensity increases with the increase of ratio of CeCl3 in CsCl.     

Rapid Protein Hydrolysis by Microwave Irradiation Using Heat-Resistant Teflon-Pyrex Tubes

A rapid peptide-bond hydrolysis by means of microwave irradiation is introduced for the facile preparation of protein hydrolysates used for amino acid analysis. The optimal hydrolysis condition has been determined using several enzymes with known amino acid compositions. The effects of hydrolysis time on the recovery of various labile and hydrophobic amino acids are also exemplified in the microwave heating of standard amino acids. The method has been applied to the complete amino acid analysis with a single nonvolatile solvent of methanesulfonic acid with good recovery of tryptophan and half-cystine. It provides a radical expedition of protein and peptide hydrolysis via commercial microwave ovens and specially-designed Teflon-Pyrex tubes, circumventing the tedious procedures using vacuum-sealed pyrex lubes heating at 110°C for more than 24 h. This novel type of microwave chemistry associated with rapid peptide-bond cleavage is of great potential in the automation of the complete process of amino acid analysis starting from the preparation of protein hydrolysates.     

New methods for data analysis of isothermal titration calorimetry

Heat divided by ligand concentration vs. heat, similar to the Scatchard plot, was introduced to obtain the equilibrium constant (K) and the enthalpy of binding (DH) using isothermal titration calorimetry data. Values of K and DH obtained by this linear pseudo-Scatchard plot for a system with a set of independent binding sites (such as binding fluoride ions on urease and monosaccharide methyl a-D-mannopyranoside on concavalin A) were remarkably like that obtained from a normal fitting Wiseman method and other our technical methods. On applying this graphical method to study the binding of copper ion on myelin basic protein (MBP), a concave downward curve obtained was consistent with the positive cooperativity in the binding. A graphical fitting by simple method for determination of thermodynamic parameters was also introduced. This method is general, without any assumption and restriction made in previous method. This general method was applied to the product inhibition study of adenosine deaminase. This revised version was published online in July 2006 with corrections to the Cover Date.     

Concerning the Thermal Diastereomerization of the Green Fluorescent Protein Chromophore

Summary. Two model compounds for the green fluorescent protein chromophore were prepared. One of them incorporates the natural 4-hydroxybenzylidene group of the natural tyrosin derived chromophore, the other one bears a methyl group instead of the hydroxy group. Whereas the photochemically prepared (E)-diastereomer of the first compound very effectively reverted thermally (room temperature) to the thermodynamically stable (Z)-diastereomer, the (E)-diastereomer of the second derivative proved to be stable even at elevated temperatures for more than a day. This finding can be rationalized by constructing the appropriate resonance structures showing that only in the first case an effective delocalization enables partial single bond character of the benzylidene double bond. From the standpoint of chemical etiology, only Nature’s choice of the tyrosin derived chromophore of the green fluorescent protein provides an efficient radiationless thermal relaxation channel for the unwanted photo-diastereomerization product formed after excitation besides the dominating fluorescence channel of its chromophore.