Identifying potential binding modes and explaining partitioning behavior using flexible alignments and multidimensional scaling

A method is described for the rapid and automatic analysis of flexible molecular alignments using multidimensional scaling and a normalized scoring scheme. A projection scheme was devised to separate orientational and conformational effects. It is shown that the approach can be utilized for the identification of common binding orientations or to the study of differences in partioning behavior. It is suggested that the method can be employed as a novel approach exploring molecular similarity as a dynamic property, so that it includes aspects of motion (by way of mutual orientations), conformations and molecular properties.     

脑神经退行性疾病中的有机化学-朊病毒(疯牛病)中的蛋白物理有机化学和自由基化学

通过关于“普里昂”蛋白病毒疾病的已有临床、医学生理、免疫和化学等方面的现象，讨论了朊病毒当中的部分蛋白氧化损伤和蛋白自由基化学本质。     

Synthesis and X-ray crystal structures of six [TeL4][MF6] salts, where L is ethylene- or trimethylene-thiourea, and M is Si, Ge or Sn. Five Te(II) complexes with a novel type of structure linked together by unusual N–HF hydrogen bonds

The complexes [Te(etu)₄][SiF₆] (1), [Te(etu)₄][SiF₆] · H₂O (2), [Te(trtu)₄][SiF₆] (3), [Te(etu)₄][GeF₆] · H₂O (4), [Te(trtu)₄][GeF₆] (5) and [Te(etu)₄][SnF₆] (6) (etu = ethylenethiourea, trtu = trimethylenethiourea) have been prepared and their crystal structures determined by X-ray crystallographic methods. The crystals of 1, 3 and 5 are tetragonal; space groups P4cc (No. 103) with Z = 4 for 1, P4nc (No. 104) with Z = 2 for 3, and I4 (No. 79) with Z = 2 for 5. The crystals of 2, 4 and 6 are orthorhombic, space group Pccn (No. 56) with Z = 8 for 2 and 4 and Z = 4 for 6; those of 2 and 4 being isomorphous. The cations contain square planar or slightly distorted square planar TeS₄ coordination groups. In 1, 3 and 5 the Te atoms are located on fourfold rotation axes; the cations have fourfold rotational symmetry and the four thiourea ligands extend to the same side of the TeS₄ plane. These are the first examples of [TeL₄]²⁺ conformers of this type. In 2 and 4 the Te atoms lie on general positions; the cations are distorted versions of those in 1, and also in these the four ligands extend to the same side of the TeS₄ plane. In 6 the Te atoms are located on twofold rotation axes, the conformation of the cations corresponds to the point group C₂ with two neighbouring ligands extending to one side of the coordination plane and the remaining two to the opposite side. In 1–5 each of the four ligands forms a N–HF bond to the same F atom in the counter ion. The crystals of 1–5 are red, and those of 6 are yellow. The red colour is attributed to interactions of Te and S lone electron pairs caused by ligand TeS₄/TeSC tilt angles markedly different from 90°.     

Genetic engineering to enhance the selectivity of protein separations

The ability to recover and purify natural and recombinant proteins, and the costs of doing so remain a major task in introducing the potential products of biotechnology. The bases for separation range from specific binding onto tailored reagents to solubility and partitioning behavior governed by a mixed bag of size, charge, and hydrophobicity. In most cases, a combination of methods is used in sequence, and improvements in the selectivity at an early stage can enhance the effectiveness of subsequent (and usually more costly) steps. Genetic engineering provides a means of improving the selectivity within the context of existing separation methods. By this strategy, improvements in selectivity are sought by bestowing a distinctive property on the protein of interest. The primary sequence of amino acids is altered, such that the protein can be selectively removed from other components of the multicomponent mixture in which such products are commonly found. In this article, the range of these “distinctive properties” and their pairing with various separation methods will be reviewed. Specific examples from our work, in which a distinctive charge is provided via a polypeptide “purification” fusion tail, will be discussed. Separation methods we have used with these fusion proteins are precipitation, two-phase aqueous extraction, reversed micellar extraction, and ion exchange using both resins and membranes.     

N-Amino Derivatives of Condensed Imidazole Systems

The previously unknown 1-amino- and 3-aminonaphtho[1,2-d]imidazoles, 1-aminonaphtho[2,3-d]imidazole, 1-aminophenanthro[9,10-d]imidazole and the N-amino-N'-methylimidazolium picrates corresponding to them have been obtained by direct amination of a series of condensed imidazoles with O-picrylhydroxylamine. An X-ray structural investigation of 1-amino-3-methylnaphtho[1,2-d]imidazolium picrate showed that, in difference to 1-aminobenzimidazolium salts, a conformation exists in it in which the hydrogen atoms of the N-NH₂ group are directed to the side of the meso carbon atom.     

Molecular and crystal structure of 2-(N-benzyl-N-phenylhydrazinoethylidene)-3-(2H)-benzo[b]-thiophenone

X-ray structural analysis was used to determine the molecular and crystal structure of 2-(N-benzyl-N-phenylhydrazinoethylidene)-3-(2H)-benzo[b]thiophenone. The crystals are monoclinic, the space group isC2/c,a=16.022(6),b=11.202(3),c=22.111(4) Å, =81.08(3)°, and andZ=8. It was shown that the ability of hydrazones of a similar class to exhibit photochromic properties is a function of the steric stresses in the molecules and their confirmation.Institute of Chemical Physics in Chernogolovka, Russian Academy of Sciences, 142432 Chernogolovka. Translated fromIzvestiya Akademii Nauk, Seriya Khimicheskaya, No. 12, pp. 2805–2809, December, 1992.     

Studies on the Spectral Behavior between Protein with Poniacyl Carmine 2B and its Analytical Application

In this paper, the spectral behavior of protein and Poniacyl Carmine 2B (PC 2B) has been studied by spectrophotometric method. The conditional constants, apparent combination constant K and maximum binding number n, were used to express the combination ability of the reactions between PC 2B and protein under a set of given conditions. The Sandell index s was used to express the sensitivity of the determination of protein. The factors, acidity, PC 2B concentration and the ionic strength, were discussed by the change of apparent combination constant and maximum binding number. It was found that acidity of the solution, PC 2B concentration and ionic strength had a significant effect on the sensitivity of the assay of protein. Under the optimal conditions, the apparent combination constant K and the maximum binding number n were 2.36 × 10⁶ L mol^?1 and 95, respectively. With further investigation, it was found that the Scatchard model was suitable in treating the data obtained in the experiments. In the buffer medium of HCl‐KCl at 1.87, the addition of protein made the maximum absorption of the system move from 527 nm to 513 nm. Its apparent molar absorptivity is 4.46 × 10⁵ Lmol^?1 cm^?1 at 513 nm. Beer's law is obeyed in the range of 0 ? 55 μg mL^?1. The system developed in this paper has been used for the determination of protein in milk powder successfully.     

Composting and biodegradation of thermally processed feather keratin polymer

Proteins obtained from agricultural sources represent a unique feedstock from which to prepare thermally processable polymers. In this study, thermally processed feather keratin films were composted with three-month-old compost inoculum in self-heating laboratory composters for 30 days and temperature and carbon dioxide development monitored. About 24% of the available carbon in the feather keratin polymer (FKP) was metabolized in this time and this may not be high enough for some applications. Degradation of the feather keratin polymers was observed within 10 days with concurrent molecular weight reduction measured using FT-IR. Visual inspection of the polymers also showed destruction of the films. A change in crystallinity was observed in DSC analysis and some degradation processes could be inferred from this as well.     

Optimization of a portable microanalytical system to reduce electrode fouling from proteins associated with biomonitoring of lead (Pb) in saliva

There is a need to develop reliable portable analytical systems for on-site and real-time biomonitoring of lead (Pb) from both occupational and environmental exposures. Saliva is an appealing matrix since it is easily obtainable, and therefore a potential substitute for blood due to existing reasonably good correlation between Pb levels in blood and saliva. The microanalytical system is based on flow-injection/stripping voltammetry with a wall-jet (flow-onto) microelectrochemical cell. Samples that contain as little as 1% saliva can cause electrode fouling, resulting in significantly reduced responsiveness and irreproducible quantitations. In addition, incomplete Pb release from salivary protein can also yield a lower Pb response than expected. This paper evaluates the extent of in vitro Pb-protein binding and the optimal pretreatment for releasing Pb from the saliva samples. Even in 50% by volume of rat saliva, the electrode fouling was not observed, due to the appropriate sample pretreatment and the constant flow of the sample and acidic carrier that prevented passivation by the protein. The system offered a linear response over a low Pb range of 1-10 ppb, low detection limit of 1 ppb, excellent reproducibility, and reliability. It also yielded the same Pb concentrations in unknown samples as did the ICP-MS. These encouraging results suggest that the microanalytical system represents an important analytical advancement for real-time non-invasive biomonitoring of Pb.     

Determination of the thiol redox state of organisms: new oxidative stress indicators

This study describes a new methodology by which the concentrations of non-protein (NP) thiols glutathione (GSH), cysteine (CSH), N-acetylcysteine (AcCSH), and protein (P) thiols (PSH), as well as the contribution of these components to symmetric and mixed disulfides (NPSSR, NPSSC, NPSSCAc, PSSR, PSSC, PSSCAc, PSSP) can reliably be measured. The methodology consists of a strict sequence of methods which are applied to every sample. Free thiols at any given state of the procedure are measured by Ellmans assay, the CSH fraction is measured by its unique response in the ninhydrin assay, AcCSH is selectively measured with ninhydrin after enzymatic deacylation, proteins are separated from non-protein thiols/disulfides by precipitation with trichloroacetic or perchloric acid, disulfides are reduced into free thiols with borohydride, mixed disulfides between a protein and a non-protein component are measured by extracting the non-protein thiol from the protein pellet after borohydride treatment, and protein thiols/disulfides are measured after resolubilization of the protein pellet.When this method was applied to animal and fungal tissue, new molecular indicators of the thiol redox state of living cells were identified. The findings of the present study clearly show that the new parameters are very sensitive indicators of redox state, while at the same time the traditional parameters GSH and GSSG often remain constant even upon dramatic changes in the overall redox state of biological tissue. Therefore, unbiased assessment of the redox state also requires explicit measurement of its most sensitive thiol indicators.Electronic Supplementary Material Supplementary material is available in the online version of this article at . A link in the frame on the left on that page takes you directly to the supplementary material.