Refinement of protein cores and protein-peptide interfaces using a potential scaling approach

Refinement of side chain conformations in protein model structures and at the interface of predicted protein-protein or protein-peptide complexes is an important step during protein structural modelling and docking. A common approach for side chain prediction is to assume a rigid protein main chain for both docking partners and search for an optimal set of side chain rotamers to optimize the steric fit. However, depending on the target-template similarity in the case of comparative protein modelling and on the accuracy of an initially docked complex, the main chain template structure is only an approximation of a realistic target main chain. An inaccurate rigid main chain conformation can in turn interfere with the prediction of side chain conformations. In the present study, a potential scaling approach (PS-MD) during a molecular dynamics (MD) simulation that also allows the inclusion of explicit solvent has been used to predict side chain conformations on semi-flexible protein main chains. The PS-MD method converges much faster to realistic protein-peptide interface structures or protein core structures than standard MD simulations. Depending on the accuracy of the protein main chain, it also gives significantly better results compared with the standard rotamer search method.     

Determination of thorium and uranium in ultrapure lead by inductively coupled plasma mass spectrometry

A method for the determination of U and Th at sub-ppt levels in high-purity Pb samples using extraction chromatography with ICPMS detection is described. Following acid digestion, uranium and thorium are separated from the lead matrix using UTEVA resin. Sorption and elution procedures were optimized, the potential reusability of the chromatographic resin was evaluated, and a performance comparison between prepacked and freshly prepared UTEVA column was made. Uranium could be eluted with 0.025 M HCl and Th then recovered using 0.5% oxalic acid. Recovery yields for U exceed 80% whereas those for Th were typically 60%. Procedural detection limits of 0.5 and 1.5 pg g(-)(1) were obtained for U and Th, respectively. For purposes of comparison, GD-MS analysis of samples was also performed, yielding results consistent with those generated by ICPMS but with inferior detection power.     

Method of determining nanoparticle core weight

Polymer-coated metal or metal oxide nanoparticles have a variety of uses in industry, biological research, and medicine. Characterization of nanoparticles often includes determination of the dimensions of the electron-dense core by transmission electron microscopy (TEM), with the weight of the core determined from core volume and core density. However, TEM is labor intensive, has a long turnaround time, and uses equipment that is sometimes not readily available. Here we present an alternative method for determining the weight of nanoparticle cores termed the viscosity/light scattering method, which uses (i) measurements of viscosity over a wide concentration range to obtain the partial specific volume, (ii) measurements of particle diameter by light scattering, to obtain the volume of an individual particle, and (iii) the concentration of nanoparticles (w/v). We have applied this method to determine the weights of nanoparticle cores (iron of amino-CLIO and ferritin), the weights of globular proteins (molecular weight of IgG and albumin), and the weight of polystyrene microspheres. The viscosity/light scattering method is nondestructive of the sample and can be performed with a variety of materials on a routine basis.     

Low molecular weight carboxylic acids in oxidizing porphyry copper tailings

The distribution of low molecular weight carboxylic acids (LMWCA) was investigated in pore water profiles from two porphyry copper tailings impoundments in Chile (Piuquenes at La Andina and Cauquenes at El Teniente mine). The objectives of this study were (1) to determine the distribution of LMWCA, which are interpreted to be the metabolic byproducts of the autotroph microbial community in this low organic carbon system, and (2) to infer the potential role of these acids in cycling of Fe and other elements in the tailings impoundments. The speciation and mobility of iron, and potential for the release of H+ via hydrolysis of the ferric iron, are key factors in the formation of acid mine drainage in sulfidic mine wastes. In the low-pH oxidation zone of the Piuquenes tailings, Fe(III) is the dominant iron species and shows high mobility. LMWCA, which occur mainly between the oxidation front down to 300 cm below the tailings surface at both locations (e.g., max concentrations of 0.12 mmol/L formate, 0.17 mmol/L acetate, and 0.01 mmol/L pyruvate at Piuquenes and 0.14 mmol/L formate, 0.14 mmol/L acetate, and 0.006 mmol/L pyruvate at Cauquenes), are observed at the same location as high Fe concentrations (up to 71.2 mmol/L Fe(II) and 16.1 mmol/L Fe(III), respectively). In this zone, secondary Fe(III) hydroxides are depleted. Our data suggest that LMWCA may influence the mobility of iron in two ways. First, complexation of Fe(III), through formation of bidentate Fe(III)-LMWCA complexes (e.g., pyruvate, oxalate), may enhance the dissolution of Fe(III) (oxy)hydroxides or may prevent precipitation of Fe(III) (oxy)hydroxides. Soluble Fe(III) chelate complexes which may be mobilized downward and convert to Fe(II) by Fe(III) reducing bacteria. Second, monodentate LMWCA (e.g., acetate and formate) can be used by iron-reducing bacteria as electron donors (e.g., Acidophilum spp.), with ferric iron as the electron acceptor. These processes may, in part, explain the low abundances of secondary Fe(III) hydroxide precipitates below the oxidation front and the high concentrations of Fe(II) observed in the pore waters of some low-sulfide systems. The reduction of Fe(III) and the subsequent increase of iron mobility and potential acidity transfer (Fe(II) oxidation can result in the release of H+ in an oxic environment) should be taken in account in mine waste management strategies.     

Uncertainties associated with global effects of atmospheric CO2

Although the evidence is quite clear that the increase in atmospheric CO₂ is at least to a large degree a result of fossil fuel burning, and it is equally clear that this increase will result in some change in the global climate, there are quantitative uncertainties that require additional understanding before full assessments can be made. There are quantitative uncertainties in the natural carbon cycle as well as uncertainties in the behaviour of the various reservoirs when perturbed by man. There are questions about the terrestrial biosphere and about the rate at which the oceans can assimilate and store carbon.There are uncertainties in regard to the climate change that can result from increased atmospheric CO₂. Progress in modelling the atmosphere must continue to narrow these uncertainties before the impacts of climate change on man can be adequately determined.The future demands for fossil fuels are uncertain. The growth of the developing world will be closely linked to fossil energy for the next five to eight decades, and rates of growth in these world segments are dependent on many ill-defined quantities.Only the observed increase in the atmospheric concentration and the present (and recent past) rate of production of CO₂ from fossil fuels provide data without uncertainties.     

Effect of information feedback on matrices learning for differing socioeconomic levels.

Examined the differential effect of 2 kinds of information feedback on performance when used to train matrix completion strategies. A matrices training task was administered to 120 white male Ss representing Grades 1 and 3 and low- and middle-socioeconomic status (SES) levels. After 4 enclosure-type items had been learned under 1 of 2 feedback conditions, Ss responded to a transfer set of 10 similar items. Results indicate that the 3rd-grade Ss learned more quickly than the 1st-grade Ss (p 1969-02983-001) concerning differential conceptual performance abilities characteristic of different SES levels. (28 ref) (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Coulometric determination of organic acids

A system has been devised for the coulometric titration of organic acids in a non-aqueous medium. The solvent system is benzene-methanol, 1∶1, containing LiCl as the electrolyte. The acid is titrated by reducing hydrogen ion at a platinum cathode. The anode reaction involves the formation of AgCl on silver. The endpoint is detected by an antimony-glass electrode pair and the derivative of the electrode output is used to effect automatic current shut-off. Alternative reference electrodes are discussed. Usual sample size titrated is 0.01 meq but the method can be applied to both larger and smaller amounts. The method has been applied to the determination of acid value and free fatty acid in fatty materials. The advantages of the coulometric determination are: 1) No standard solutions are required. 2) The titration is conducted without analyst attention. 3) The technique is simple and rapid. Presented at the fall meeting. American Oil Chemists’ Society, Chicago, Illinois, October 30 to November 1, 1961.     

Fatty acid distribution in the bovine pre- and postpartum testis

Testes from fetuses, calves, bulls and recently castrated animals were analyzed for total lipids, lecithin, cephalin, triglycerides, diglycerides, cholesteryl esters and cholesterol. Total lipids increase somewhat with age, but in the castrated animal the increase is more marked. Phospholipid content increases with age, but decreases in the castrated animal. Cholesterol decreases and triglyceride increases after birth and in the castrated animal. Polyunsaturated acids increase with age in all lipid classes. Eicosatrienoic acid is more abundant in fetal testicular lipids than in testes removed after birth. In the castrated testis there is a general decrease in the unsaturated fatty acids. Acids of the ω6 family are the predominant polyunsaturated acids and increase somewhat with age in all lipids. The ω3 family of polyunsaturated acids appears mostly toward the end of fetal life and increases after birth. Acids of the linoleate family reach approximately 25% of total acids in most lipid classes at maturity whereas the ω3 acids range from 1 to 9%. Presented at the American Dairy Science Association Meeting, Lexington, Ky., June 1965.