Conformational analysis of [Met5]-enkephalin: Solvation and ionization considerations

[Met5]-Enkephalin has the sequence Tyr-Gly-Gly-Phe-Met. Only the extended conformation of the peptide has been observed by X-ray crystallography. Nuclear magnetic resonance spectroscopy supports the presence of a turn at Gly 3 and Phe 4 in dimethyl sulfoxide. In this study, the peptide conformational states and thermodynamic properties are understood in terms of ionization state and solvent environment. In the calculation, final conformations obtained from multiple independent Monte Carlo simulated annealing conformational searches are starting points for molecular dynamics simulations. In an aqueous environment given by the use of solvation free energy and the zwitterionic state, dominant structural motifs computed are G-P Type II bend, G-G Type II bend, and G-G Type I bend motifs, in order of increasing free energy. In the calculation of the peptide with neutral N- and C-termini and solvation free energy, the extended conformer dominates (by at least a factor of 2.5), and the conformation of another low free energy conformer superimposes well on the pharmacophoric groups of morphine. Neutralization of charge and solvation induce and stabilize the extended conformation, respectively. A mechanism of inter-conversion between the extended conformer and three bent conformers is supported by /-scatter plots, and by the conformer relative free energies. An estimate of the entropy change of receptor unbinding is 8.3 cal K-1 mol-1, which gives rise to a -2.5 kcal/mol entropy contribution to the free energy of unbinding at 25 °C. The conformational analysis methodology described here should be useful in studies on short peptides and flexible protein surface loops that have important biological implications.     

Computer based screening of compound databases: 1. Preselection of benzamidine-based thrombin inhibitors

We present a computational protocol which uses the known three-dimensional structure of a target enzyme to identify possible ligands from databases of compounds with low molecular weight. This is accomplished by first mapping the essential interactions in the binding site with the program GRID. The resulting regions of favorable interaction between target and ligand are translated into a database query, and with UNITY a flexible 3D database search is performed. The feasibility of this approach is calibrated with thrombin as the target. Our results show that the resulting hit lists are enriched with thrombin inhibitors compared to the total database.     

Characterisation of botulinum toxins type C, D, E, and F by matrix-assisted laser desorption ionisation and electrospray mass spectrometry

In a follow-up of the earlier characterisation of botulinum toxins type A and B (BTxA and BTxB) by mass spectrometry (MS), types C, D, E, and F (BTxC, BTxD, BTxE, BTxF) were now investigated. Botulinum toxins are extremely neurotoxic bacterial toxins, likely to be used as biological warfare agent. Biologically active BTxC, BTxD, BTxE, and BTxF are comprised of a protein complex of the respective neurotoxins with non-toxic non-haemagglutinin (NTNH) and, sometimes, specific haemagglutinins (HA). These protein complexes were observed in mass spectrometric identification. The BTxC complex, from Clostridium botulinum strain 003-9, consisted of a 'type C1 and D mosaic' toxin similar to that of type C strain 6813, a non-toxic non-hemagglutinating and a 33 kDa hemagglutinating (HA-33) component similar to those of strain C-Stockholm, and an exoenzyme C3 of which the sequence was in full agreement with the known genetic sequence of strain 003-9. The BTxD complex, from C. botulinum strain CB-16, consisted of a neurotoxin with the observed sequence identical with that of type D strain BVD/-3 and of an NTNH with the observed sequence identical with that of type C strain C-Yoichi. Remarkably, the observed protein sequence of CB-16 NTNH differed by one amino acid from the known gene sequence: L859 instead of F859. The BTxE complex, from a C. botulinum isolated from herring sprats, consisted of the neurotoxin with an observed sequence identical with that from strain NCTC 11219 and an NTNH similar to that from type E strain Mashike (1 amino acid difference with observed sequence). BTxF, from C. botulinum strain Langeland (NCTC 10281), consisted of the neurotoxin and an NTNH; observed sequences from both proteins were in agreement with the gene sequence known from strain Langeland. As with BTxA and BTxB, matrix-assisted laser desorption/ionisation (MALDI) MS provided provisional identification from trypsin digest peptide maps and liquid chromatography-electrospray (tandem) mass spectrometry (LC-ES MS) afforded unequivocal identification from amino acid sequence information of digest peptides obtained in trypsin digestion.     

Using a process-centered approach to minimize the effort of compliance

 The complexity of different quality standards can, in principle, be covered by different approaches and strategies. In-depth process mapping of quality control (QC) work streams was used by the analytical laboratories of Lonza AG to show up the principle differences in being compliant to different quality systems. The results identified two main drivers for all necessary actions: process-related activities and infrastructure-related activities. In addition, a clear indication of the economic impact of these driving forces was gained, which led the laboratories to decide on a process-oriented approach. This approach has the advantage of being able to reflect the different demands of different quality assurance (QA) regulations within the same QC organizational structure. Following the process helps avoid unnecessary efforts in analytical work and represents a very economical approach, at the same time, providing high flexibility to react to different QA or customer demands. Received: 5 July 2002 Accepted: 12 November 2002 Acknowledgements The process-oriented approach resulted from many, very challenging discussions for which I would like to thank the staff of my organization (Analytics & QC), especially, the QA staff and the LIMS team. Presented at Analytica Conference, 23–26 April 2002, Munich, Germany Correspondence to B. Ciommer     

Controlled enzyme-immobilisation on capillaries for microreactors for peptide mapping

In the present paper, the covalent immobilisation of the digesting enzyme trypsin has been achieved through photo-immobilisation on a portion of a silica capillary, thus leading to the construction of a capillary electrophoretic (CE)-microreactor for peptide mapping. The CE-microreactor is characterised by being a single piece, thus ensuring no fluidic or electrical leakage. The enzyme was immobilised with a surface density of 15.8 g/cm², the stability was high (80% after 38 days) and the rate of conversion was 0.2 ng/s. On-line protein mapping was tested with proteins of different dimensions, showing competitiveness in terms of time (completed map within 15 min) and exhaustive maps of small proteins. The results of the CE-microreactor and the potential to immobilise biocomponents easily on a desired portion of the capillary indicate further developments towards the construction of a variety of miniaturised enzymatic screening devices for high-throughput screening analysis.     

声音转换技术的研究与进展

声音转换是一项改变说话人声音特征的技术,可以将一人的语音模式转换为与其特性不同的另一人语音模式.声音转换算法的目标是确定一个什么样的模式转换规则,使转换语音保持第一个说话人原有语音信息内容不变,而具有第二个说话人的声音特点.本文介绍了当前声音转换技术领域的研究状态,主要分析现有声音转换技术中各种转换算法的实现原理,描述声音转换系统性能的各种评估方法,最后给出了对声音转换技术的简要评述和展望.     

Mixing tone mapping operators on the GPU by differential zone mapping based on psychophysical experiments

In this paper, we present a new technique for displaying High Dynamic Range (HDR) images on Low Dynamic Range (LDR) displays in an efficient way on the GPU. The described process has three stages. First, the input image is segmented into luminance zones. Second, the tone mapping operator (TMO) that performs better in each zone is automatically selected. Finally, the resulting tone mapping (TM) outputs for each zone are merged, generating the final LDR output image. To establish the TMO that performs better in each luminance zone we conducted a preliminary psychophysical experiment using a set of HDR images and six different TMOs. We validated our composite technique on several (new) HDR images and conducted a further psychophysical experiment, using an HDR display as the reference that establishes the advantages of our hybrid three-stage approach over a traditional individual TMO. Finally, we present a GPU version, which is perceptually equal to the standard version but with much improved computational performance.     

Progressive filling partitioning and mapping algorithm for Spark based on allocation fitness degree

The job execution mechanism of Spark was analyzed,task efficiency model and Shuffle model were established,then allocation fitness degree (AFD) was defined and the optimization goal was put forward.On the basis of the model definition,the progressive filling partitioning and mapping algorithm (PFPM) was proposed.PFPM established the data distribution scheme adapting Reducers’ computing ability to decrease synchronous latency during Shuffle process and increase cluster the computing efficiency.The experiments demonstrate that PFPM could improve the rationality of workload distribution in Shuffle and optimize the execution efficiency of Spark.     

Real-time sensing and three-dimensional display of far outdoor scenes based on asymmetric integral imaging

A new asymmetric integral imaging (AII) system for real-time pickup and three-dimensional (3-D) display of far outdoor scenes based on dynamic-pixel-mapping (DPM) is proposed. DPM is a digital process to transform the elemental images captured with a lens array into the perspective-variant object images (POIs) whose structures are matched with those of display lenses, where the orders of pixels in each POI are reversely mapped, and then capture a set of virtual elemental images (EIs) at the specific depth planes from the back-propagated POIs. This DPM enables an asymmetrical use of pickup and display lens arrays, allowing the long-ranged pickup of far outdoor scenes and their resolution-enhanced 3-D reconstruction. Experiments with a pair of pickup and display lens arrays whose pitches and focal lengths are given by 7.5 mm, 30 mm and 1.2 mm, 8 mm, respectively, show that the effective pickup-range and resolution of the proposed system have been increased up to 6 m and 1600×1600 pixels, respectively, from 0.064 m and 480×480 pixels of the conventional systems employing the same pickup and display lens arrays. In addition, experiments with an implemented test bed confirms that the proposed system can provide real-time 3-D images in 25 frames per second.     

Bounds for the fundamental solutions of elliptic and parabolic equations

It is shown that any elloptic or parabolic operator in nondivergence form with measurable coefficients has a global fundamental solution verifying certain pointwise bounds.