Structure-based identification and clustering of protein families and superfamilies

Summary We describe an approach to protein structure comparison designed to detect distantly related proteins of similar fold, where the procedure must be sufficiently flexible to take into account the elasticity of protein folds without losing specificity. Protein structures are represented as a series of secondary structure elements, where for each element a local environment describes its relations with the elements that surround it. Secondary structures are then aligned by comparing their features and local environments. The procedure is illustrated with searches of a database of 468 protein structures in order to identify proteins of similar topology to porcine pepsin, porphobilinogen deaminase and serum amyloid P-component. In all cases the searches correctly identify protein structures of similar fold as the search proteins. Multiple cross-comparisons of protein structures allow the clustering of proteins of similar fold. This is exemplified with a clustering of /- and -class protein structures. We discuss applications of the comparison and clustering of three-dimensional protein structures to comparative modelling and structure-based protein design.     

Detector comparison for sulfur and chlorine detection with laser induced breakdown spectroscopy in the near-infrared-region

Laser-induced breakdown spectroscopy has been employed for the investigation of the sulfur and chlorine content of building materials. Both, chloride and sulfate ions are major damaging species affecting the stability and lifetime of a structure. Chlorine and sulfur are mostly detected in the VUV and the NIR. In case of building materials the main elements like calcium or iron have many strong spectral lines over the whole spectral range, so that trace elements can only be detected in spectral windows unaffected from these lines. With regard to a preferably simply, robust against dust and vibrations and portable setup only the NIR spectral features are used for civil engineering applications.

Most detectors, mainly CCD cameras have rapidly decreasing quantum efficiency in the NIR. Also the quantum efficiency of the photocathode of CCD-Detectors with image intensifier is decreasing in the NIR. Different CCD-detectors were tested with respect to high quantum efficiency and high dynamic range, which is necessary for simultaneous detection of weak spectral lines from trace elements and intense spectral lines from main elements.

The measurements are made on reference samples consisting of cement, hydrated cement, cement mortar and concrete with well-defined amounts of the trace elements. Experimental conditions are chosen for an optimum intensity of the trace element spectral lines. The detector systems are compared by limit of detections and the signal to noise ratio.     

Charge calculations in molecular mechanics. Part 8 Partial atomic charges from classical calculations

Summary The CHARGE2 programme, which involves the classical calculation of both the inductive and resonance contributions to the partial atomic charges in molecules is described, and the charges and electrostatic potentials obtained presented for some illustrative examples.In substituted methanes (CH₃X, CF₃X, CCl₃X) the effects of varying the electronegativity of the substituents and the - and -substituent contributions are clearly illustrated for a variety of substituent groups X.The problems involved in the inclusion of silicon into this scheme are detailed, together with the methods of overcoming them. The partial atomic charges ( and contributions) and electrostatic potentials for some silicon oxygen compounds are presented and discussed.The partial atomic charges from CHARGE2 for all the natural amino acids as their N-acetyl, N-methyl-amides are given and compared with those obtained from the AMBER and ECEPP/2 force fields. Considerable differences in these figures are observed, with the AMBER charges consistently much larger than those from the other two methods.The CHARGE2 partial atomic charges and electrostatic potentials for the four common nucleic acids, adenine, cytosine, guanine and thymine, are given and compared with those derived from other calculations. Again there is general similarity but also there are considerable differences, with those from the AMBER force field somewhat larger than the other methods.For previous parts in this series, see Refs. 1-7.     

Bibliometric Analysis of the <Emphasis Type="Italic">Journal of Structural Chemistry</Emphasis>

Bibliometric analysis has been carried out for the Journal of Structural Chemistry (JSC) published since 1960 by the Siberian Branch of the Russian Academy of Sciences. All JSC publications which appeared between 1960 and 2002 have been chosen online from the Chemical Abstracts and Science Citation Index databases of the STN International net and analyzed according to topics, authors, affiliations, and other criteria. JSC authors and publications with the largest numbers of citations have been identified. The impact factor has been determined for JSC 2002.Original Russian Text Copyright © 2004 by V. M. Buznik, I. V. Zibareva, V. N. Piottukh-Peletskii, and N. I. Sorokin__________Translated from Zhurnal Strukturnoi Khimii, Vol. 45, No. 6, pp. 1142–1153, November–December, 2004.     

Implementation of traceability – needs and perspective of the in-vitro-diagnosticum industry

Manufacturers support the concept of traceability. However, only a small number of the medically relevant measurands can be traced to the highest metrological order. In many cases, the measured substances are heterogeneous mixtures where traceability can be established only to either an international conventional reference measurement procedure or to a manufacturers own in-house reference system. The traceability concept needs to be seen in the context that the results of medical laboratories are not an aim per se, but are meant to provide useful medical information to clinicians, and that pre- and post-analytical steps may also contribute significantly to errors. There is a need for the further development of suitable reference measurement systems, but in view of the multitude of tasks and limited resources, priorities need to be set.Presented at BERM-9 – 9^th International Symposium on Biological and Environmental Reference Materials, 15–19 June 2003, Berlin, Germany     

Visualisation of interlaboratory comparison results in PomPlots

In this work a novel graphical method is applied to the presentation of intercomparison results. This is demonstrated with the results of a recent intercomparison in measuring the ¹³⁷Cs, ⁴⁰K, and ⁹⁰Sr activity concentration in milk powder. The “PomPlot”, an intuitive graphical method, is used for producing a summary overview of the participants’ results of a common measurand. The “PomPlot” displays (relative) deviations of individual results from the reference value on the horizontal axis and (relative) uncertainties on the vertical axis.     

高中有机化学教材“烃类化合物”的国际比较研究

基于闫春更等建立的二维度四指标教材难度微观评价模型，重点对中国、美国、新加坡、澳大利亚、日本、英国的高中化学教材中"烃类化合物"内容的整合广度、表征深度进行测评和比较。研究发现6国教材内容的整合广度整体上差异不大，但其表征深度差异明显；美国教材注重学生认识物质的思路和方法的渗透，日本教材注重基本知识与技能的掌握，中国教材将概念诠释与样例分析相融合；英国、新加坡、美国教材注重情境推理或比较等信息处理策略的运用，对学习者学习的引导性较强。     

QbD approached comparison of reaction mechanism in microwave synthesized gold nanoparticles and their superior catalytic role against hazardous nirto‐dye

Microwave irradiation (MI) process characteristically enables extremely rapid “in‐core” heating of dipoles and ions, in comparison to conventional thermal (conductance) process of heat transfer. During the process of nanoparticles synthesis, MI both modulates functionality behaviors as well as dynamic of reaction in favorable direction. So, MI providing a facile, favorable and alternative approach during nanoparticles synthesis nanoparticles with enhanced catalytic performances. Although, conventionally used reducing and capping reagents of synthetic origin, are usually environmentally hazardous and toxic for living organism. But, in absence of suitable capping agent; stability, shelf life and catalytic activity of metallic nanoparticles adversely affected. However, polymeric templates which emerged as suitable choice of agent for both reducing and capping purposes; bearing additional advantages in terms of catalyst free one step green synthesis process with high degree of biosafety and efficiency. Another aspect of current works was to understand role of process variables in growth mechanism and catalytic performances of microwave processed metallic nanoparticles, as well as comparison of these parameters with conventional heating method. However, due to poor prediction ability with previously published architect OFAT (One factor at a time) design with these nanoparticles as well as random selection of process variables with their different levels, such comparison couldn't be possible. Hence, using gum Ghatti (Anogeissus latifolia) as a model bio‐template and under simulated reaction conditions; architect of QbD design systems were integrated in microwave processed nanoparticles to establish mechanistic role these variables. Furthermore, in comparison to conventional heating; we reported well validated mathematical modeling of process variables on characteristic of nanoparticles as well as synthesized gold nanoparticles of desired and identical dimensions, in both thermal and microwave‐based processes. Interestingly, despite of identical dimension, MI processed gold nanoparticles bearing higher efficiency (kinetic rate) against remediation of hazardous nitro dye (4‐nitrophenol), into safer amino (4‐aminophenol) analogues.