多特征框架下的蛋白质相似性比较与分类

蛋白质的相似性比较是研究蛋白质结构和功能的重要手段。与以往基于构建距离矩阵来研究蛋白质空间结构相似性的方法不同,文章从蛋白质的基本组成单元——氨基酸入手,通过对氨基酸以及蛋白质多肽链中的特殊结构的分析,综合考虑骨架原子Cα数、突变原子数、亲水微粒数、螺旋数四个方面,依托模糊数学等价矩阵理论,运用传递闭包的方法,提出了一种全新的相似性比较与分类方法。     

分形层次及码尺与分辨率的关系

提出了在分形研究中，用计算机进行图像分析时，分形层次和码尺与图像采样分辨率之间的关系。码尺的改变只能通过改变输入的分辨率，同时输入分辨率的选择要综合考虑分形自身的层次要求、输入方法以及测量的要求。给出了实验验证。     

基于多分辨率裁剪纹理的体裁剪技术

为解决单分辨率裁剪纹理的数据规模过大的问题,该文提出了一种具有INDEX-DATA二级结构的多分辨率裁剪纹理。文章主要介绍了多分辨率裁剪纹理的定义和结构,并讨论多分辨率纹理的构建方法和基于多分辨率纹理的体裁剪方法,最后对实验结果进行了分析讨论。该文方法已在自主知识产权可视化软件SVIP中得到应用,取得了令人满意的结果。     

生物信息学资源及其检索述评

生物信息学是在生命科学的研究中,以计算机为工具对生物信息进行储存、检索和分析的科学.其研究重点主要体现在基因组学(Genomics)和蛋白组学(Proteomics)两方面,具体说就是从核酸和蛋白质序列出发,分序列中表达的结构功能的生物信息的科学.美国人类基因组计划实施五年后的总结报告中,对生物信息学作了以下定义:生物信息学是一门交叉科学,它包含了生物信息的获取、处理、存储、分发、分析和解释等在内的所有方面,它综合运用数学、计算机科学和生物学的各种工具,来阐明和理解大量数据所包含的生物学意义.……     

Sn(Sb)O2凝胶结构模型及试验研究

对Sn(Sb)O2干凝胶的结构进行了试验及模拟研究，通过BET－N2吸附及XRD分析，详细研究了SnO2凝胶在200－600℃干燥过程中凝胶骨架纳米结构及其变化规律，并研究了掺杂元素Sb对纳米结构演变的影响。研究发现：SnO2干凝胶为1－10nm的纳米多孔结构，其结构特征符合圆柱体通孔模型；随着固化温度的升高，凝胶骨架粗化，但结构特征相似性不变，孔体积率也基本不变；Sb的增加有细化骨架的作用。     

组织工程用高分子骨架研究的进展

组织工程是一个新兴的交叉学科。结合目前组织工程用高分子骨架研究和发展的最新状况，探讨了高分子骨架材料的本体结构、性能及表面形态与分子结构要求，并对常用的骨架制备方法进行了概述。     

WT-102UV-涂复光纤骨架式光缆填充料的研究和应用

UV-涂复光纤骨架式光缆是目前国内外大力发展的一种不需二次被复工艺的新型光缆。该光缆结构对填充料有特殊要求。本文研究了能满足这种光缆填充要求的新型光缆填充料WT-102的结构和性能,特别从多方面研究了这种光缆填充料对UV-固化光纤涂层、聚乙烯骨架等成缆材料的高度相容性。该材料已开发生产,用于多项光通信工程。     

核磁共振（NMR）法在分子筛的合成,结构及其性能研究上的应用

论述了ＮＭＲ法在分子筛研究领域的应用。通过ＮＭＲ的观测与计算可以确定分子筛骨架的硅铝比，从而分析硅，铝在骨架上的统计分布特征，以及不同结构状态，配位状态和催化机理，进一步对分子筛的合成及其性能的研究提供了重要依据。     

多分辨率社团结构挖掘在故障定位中的应用

由于战场环境下对武器系统自我修复与重构功能的需求,以及分布式系统结构的特殊性,使得分布式武器装备具有众多的功能节点以及复杂的交联关系,对其进行快速故障定位已成为武器系统维修保障的重要研究内容。文中运用复杂网络理论对分布式系统建模,结合复杂网络社团性这一特点,提出了多分辨率模型映射的新观点,并以自律分散自动测试系统作为分析载体,运用多分辨率社团挖掘的方法,进行多分辨率故障回溯推理,为实现新型分布式武器系统的故障定位提供了新思路。     

拱式桥梁的新进展：成渝公路内江提蓝拱桥建成

成渝公路内江新龙坳立交桥，在提蓝拱体系，钢管混凝土劲性骨架，交叉吊杆，骨架侧转施工，管心混凝土泵压灌注等方面，开展了研究和实践；对跨度拱桥的新材料，新结构，新工艺应用进行了成功的探索，本文就此表达了作者的见解。     

Electrochemistry-assisted top-down characterization of disulfide-containing proteins

Covalent disulfide bond linkage in a protein represents an important challenge for mass spectrometry (MS)-based top-down protein structure analysis as it reduces the backbone cleavage efficiency for MS/MS dissociation. This study presents a strategy for solving this critical issue via integrating electrochemistry (EC) online with a top-down MS approach. In this approach, proteins undergo electrolytic reduction in an electrochemical cell to break disulfide bonds and then undergo online ionization into gaseous ions for analysis by electron-capture dissociation (ECD) and collision-induced dissociation (CID). The electrochemical reduction of proteins allows one to remove disulfide bond constraints and also leads to increased charge numbers of the resulting protein ions. As a result, sequence coverage was significantly enhanced, as exemplified by β-lactoglobulin A (24 vs 75 backbone cleavages before and after electrolytic reduction, respectively) and lysozyme (5 vs 66 backbone cleavages before and after electrolytic reduction, respectively). This methodology is fast and does not need chemical reductants, which would have an important impact in high-throughput proteomics research.     

Spatially resolved protein hydrogen exchange measured by matrix-assisted laser desorption ionization in-source decay

Mass spectrometry has become a powerful tool for measuring protein hydrogen exchange and thereby reveal the structural dynamics of proteins in solution. Here we describe the successful application of a matrix-assisted laser desorption ionization (MALDI) mass spectrometry approach based on in-source decay (ISD) to measure spatially resolved amide backbone hydrogen exchange. By irradiating deuterated protein molecules in a crystalline matrix with a high laser fluence, they undergo prompt fragmentation. Spatially resolved deuteration levels are readily obtained by mass analysis of consecutive fragment ions. MALDI ISD analysis of deuterated cytochrome c yielded an extensive series of c-fragment ions which originate from cleavage of nearly all N-C(α) bonds (Cys17 to Glu104) allowing for a detailed analysis of the deuterium content of the backbone amides. While hydrogen scrambling can be major concern when using mass spectrometric fragmentation to obtain detailed information on protein hydrogen exchange, we show that the level of hydrogen scrambling in our MALDI ISD measurements is negligible and that the known dynamic behavior of cytochrome c in solution is accurately reflected in the deuterium contents of the fragment ions. The developed method combines several attractive features from a practical point of view as it is simple to perform and it readily provides a detailed mapping of the dynamic structure of a protein in solution.     

From local structure to a global framework: recognition of protein folds

Protein folding has been a major area of research for many years. Nonetheless, the mechanisms leading to the formation of an active biological fold are still not fully apprehended. The huge amount of available sequence and structural information provides hints to identify the putative fold for a given sequence. Indeed, protein structures prefer a limited number of local backbone conformations, some being characterized by preferences for certain amino acids. These preferences largely depend on the local structural environment. The prediction of local backbone conformations has become an important factor to correctly identifying the global protein fold. Here, we review the developments in the field of local structure prediction and especially their implication in protein fold recognition.     

Ultrasensitive characterization of site-specific glycosylation of affinity-purified haptoglobin from lung cancer patient plasma using 10 μm i.d. porous layer open tubular liquid chromatography-linear ion trap collision-induced dissociation/electron transfer dissociation mass spectrometry

Site-specific analysis of protein glycosylation is important for biochemical and clinical research efforts. Glycopeptide analysis using liquid chromatography-collision-induced dissociation/electron transfer dissociation mass spectrometry (LC-CID/ETD-MS) allows simultaneous characterization of the glycan structure and attached peptide site. However, due to the low ionization efficiency of glycopeptides during electrospray ionization, 200-500 fmol of sample per injection is needed for a single LC-MS run, which makes it challenging for the analysis of limited amounts of glycoprotein purified from biological matrixes. To improve the sensitivity of LC-MS analysis for glycopeptides, an ultranarrow porous layer open tubular (PLOT) LC column (2.5 m × 10 μm i.d.) was coupled to a linear ion trap (LTQ) collision-induced dissociation/electron transfer dissociation mass spectrometer to provide sensitive analysis of N-linked protein glycosylation heterogeneity. The potential of the developed method is demonstrated by the characterization of site-specific glycosylation using haptoglobin (Hpt) as a model protein. To limit the amount of haptoglobin to low picomole amounts of protein, we affinity purified it from 1 μL of pooled lung cancer patient plasma. A total of 26 glycoforms/glycan compositions on three Hpt tryptic glycopeptides were identified and quantified from 10 LC-MS runs with a consumption of 100 fmol of Hpt digest (13 ng of protein, 10 fmol per injection). Included in this analysis was the determination of the glycan occupancy level. At this sample consumption level, the high sensitivity of the PLOT LC-LTQ-CID/ETD-MS system allowed glycopeptide identification and structure determination, along with relative quantitation of glycans presented on the same peptide backbone, even for low abundant glycopeptides at the ～100 amol level. The PLOT LC-MS system is shown to have sufficient sensitivity to allow characterization of site-specific protein glycosylation from trace levels of glycosylated proteins.     

Use of vapor-phase acid hydrolysis for mass spectrometric peptide mapping and protein identification

A method for mass spectrometric peptide mapping was developed, based on hydrolysis of a solid protein by acid vapor followed by mass spectrometric analysis of the cleavage products. The method is applicable to lyophilized samples as well as proteins present in gels after separation by SDS-PAGE. The cleavage specificity was established using a number of standard proteins. Three different types of cleavages were observed: specific internal backbone cleavages at Asp, Ser, Thr, and Gly and N- and C-terminal sequence ladders. On the basis of the observed cleavage characteristics, a strategy for protein identification based on the peptide mass maps was developed. The identification strategy utilizes the specific internal backbone cleavages as well as the partial sequence information, obtained from the sequence ladders.     

Thin films of a self-assembling peptide on TiO2 and Au studied by NEXAFS,XPS and IR spectroscopies

EAK16 is a 16 amino acid peptide consisting of an alternation of polar and non-polar pending groups and of positively and negatively charged residues, that makes this material capable of self-assembling, producing an extended ordered structure.Thin films of EAK16 were prepared on TiO₂ and Au surfaces and investigated by surface-sensitive techniques such as XPS (X-ray photoelectron spectroscopy), NEXAFS (near edge X-ray absorption fine structure) and IR spectroscopies.XPS analysis allowed to check the chemical structure of the samples and to determine the film thickness. IR experiments yielded evidence of the β-sheet conformation of the peptide backbone. Polarization dependent NEXAFS measurements allowed estimating the angle between the axis of the peptide backbone and the sample surface.     

Distinguishing channel-type crystal structure from dispersed structure in β-cyclodextrin based polyrotaxanes via FTIR spectroscopy

Combining with XRD analysis, Fourier transform infrared (FTIR) spectroscopy is employed to discern the self-assembled structures of β-cyclodextrins (β-CDs) threaded onto the polymer backbone in the polyrotaxanes (PRs) by means of the relative changes of absorption intensity of the characteristic peaks of β-CDs at 1153 and 1025 cm^-1. For quantitative analysis, six parameters are proposed to describe the relative absorption intensity variations of these peaks associated with a channel-type crystal structure or a dispersed structure of β-CDs entrapped. Among them, absorbance ratio (AR), relative absorbance difference (RAD) and transmittance difference (TD) values are suitable. When the AR, RAD and TD data get below 1.04, 4.8 and 1.27, respectively, the PRs obtained would possess a dispersed structure. If these values go beyond 1.32, 34.5 and 9.47, respectively, they would hold a channel-type crystal structure. This finding provides a useful judgment to distinguish the self-assembled structures of β-CDs residing along the polymer backbone in the PRs.     

Pyrolytic conversion of methyl- and vinylsilane polymers to Si-C ceramics

Poly(methylsilane) and poly(vinylsilane) were synthesized using a titanocene catalyst, and their pyrolytic conversion to ceramics was followed using a combination of thermal analysis and infrared spectroscopy. The two polymers have distinctly different backbone structures, as determined by²⁹Si NMR; methylsilane polymerizes to a polysilane, while vinylsilane polymers have a predominately polycarbosilane backbone, with some polysilane structure as well. The pyrolysis path and char yield were dependent primarily on backbone structure, with little influence of polymer molecular weight. The majority of the weight loss on conversion occurs below 650 °C, although bond rearrangement continues to 1400 °C. Poly(vinylsilane) produced a carbon-rich Si-C ceramic in which the carbon was dispersed on a sufficiently fine level to show resistance to oxidation on heating in air to 1400 °C. Copolymerization of methyl- and vinylsilane produced stoichiometric SiC; however, polymers of methylsilane were sensitive to oxygen incorporation and sometimes pyrophoric. Polymerization of vinylsilane with disilylethane permitted control of rheology and imparted thermoset behaviour.     

Kinematic analysis of tendon-driven robotic mechanisms using oriented graphs

Summary In this paper, the kinematic structure of tendon-driven robotic mechanisms is investigated with the aid of oriented graphs. The relation between the graph representation of the kinematic structure and the mechanism is established. It is shown that the kinematic structure of tendon-driven kinematic chains is similar to that of robotic bevel-gear trains, and angular velocity equations of tendon-driven robotic mechanisms can be systematically obtained from the graph representation of the kinematic structure by using the concept of fundamental circuit equations. The theory is demonstrated by the kinematic analysis of two articulated robotic mechanisms.     

Automated proteomics of E. coli via top-down electron-transfer dissociation mass spectrometry

Electron-transfer dissociation (ETD) has recently been introduced as a fragmentation method for peptide and protein analysis. Unlike collisionally induced dissociation (CID), fragmentation by ETD occurs randomly along the peptide backbone. With the use of the sequences determined from the protein termini and the parent protein mass, intact proteins can be unambiguously identified. Because of the fast kinetics of these reactions, top-down proteomics can be performed using ETD in a linear ion trap mass spectrometer on a chromatographic time scale. Here we demonstrate the utility of ETD in high-throughput top-down proteomics using soluble extracts of E. coli. Development of a multidimensional fractionation platform, as well as a custom algorithm and scoring scheme specifically designed for this type of data, is described. The analysis resulted in the robust identification of 322 different protein forms representing 174 proteins, comprising one of the most comprehensive data sets assembled on intact proteins to date.