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.     

Effects of solute-matrix interaction on monitoring the conformational changes of immobilized proteins by surface plasmon resonance sensor

A real-time and labeling-free surface plasmon resonance (SPR) sensor was used to monitor the conformational changes of immobilized globule proteins (RNase A and lysozyme) in chemical unfolding and refolding. The effects of chemical denaturants on the protein structures were investigated. The methodology in protein conformational study on the solid surface is refined through the theoretic calculations and the conformational information of native/denatured proteins in solution. Additionally, our observation illustrates that the ambient buffer solution is merit to influence the refractive index of immobilized protein films and directly be observed from the SPR resonance angle shifts.     

Use of D–T-produced fast neutrons for in vivo body composition analysis: a reference method for nutritional assessment in the elderly

Body composition has become the main outcome of many nutritional intervention studies including osteoporosis, malnutrition, obesity, AIDS, and aging. Traditional indirect body composition methods developed with healthy young adults do not apply to the elderly or diseased. Fast neutron activation (for N and P) and neutron inelastic scattering (for C and O) are used to assess in vivo elements characteristic of specific body compartments. Non-bone phosphorus for muscle is measured by the ³¹P(n,)²⁸Al reaction, and nitrogen for protein via the ¹⁴N(n,2n)¹³N fast neutron reaction. Inelastic neutron scattering is used to measure total body carbon and oxygen. Body fat is derived from carbon after correcting for contributions from protein, bone, and glycogen. Carbon-to-oxygen ratio (C/O) is used to measure the distribution of fat and lean tissue in the body and to monitor small changes of lean mass. A sealed, D–T neutron generator is used for the production of fast neutrons. Carbon and oxygen mass and their ratio are measured in vivo at a radiation exposure of less than 0.06 mSv. Gamma-ray spectra are collected using large BGO detectors and analyzed for the 4.43 MeV state of carbon and 6.13 MeV state of oxygen, simultaneously with the irradiation. P and N analysis by delayed fast neutron activation is performed by transferring the patient to a shielded room equipped with an array of NaI(Tl) detectors. A combination of measurements makes possible the assessment of the quality of fat-free mass. The neutron generator system is used to evaluate the efficacy of new treatments, to study mechanisms of lean tissue depletion with aging, and to investigate methods for preserving function and quality of life in the elderly. It is also used as a reference method for the validation of portable instruments of nutritional assessment.     

Silicone-modified starch/protein microparticles: protecting biopolymers with a hydrophobic coating

Silicone-coated starch/protein (human serum albumin, HSA) microparticles were prepared by precipitation of a starch/HSA/DMSO/water (water-in-oil) emulsion into acetone containing a silicone: the silicone polymer was either unfunctionalized (SiMe₃ terminated, PDMS) or functionalized at its termini with Si(OEt)₃ groups (TES-PDMS). The microparticles of approximate diameter 2–7 μm were highly hydrophobic with advancing contact angles 115°. Over several minutes, however, the contact angle decreased to ca. 40–70°. Soxhlet extraction with water led to degradation of the microparticles, irrespective of the nature of their silicone coating, as evidenced by release of the protein from them. Intraperitoneal (IP) or gastric administration of the two different particles to mice, however, showed a clear difference between the two silicones. The microparticles coated with either PDMS or TES-PDMS led to very different immune responses. Oral administration of the microparticles prepared with functionalized silicone elicited a significant production of antibodies, whereas the particles prepared with the unfunctionalized silicone (PDMS) were only weakly active. By contrast, the IP results demonstrated that particles coated with PDMS elicited an immune response that was established much more rapidly than with the particles modified with TES-PDMS. It is proposed that the TES-PDMS forms a physically adhering film or covalent bond to the protein molecules, which serves to protect the microparticle from biological degradation in the gut and/or facilitates the microparticle/protein interaction with the immune system.     

Resistance to Surfactant and Protein Fouling Effects at Conducting Diamond Electrodes

Boron‐doped diamond thin‐film electrodes display negligible fouling effects in the presence of high levels of surface‐active materials, including proteins. Dramatic improvements in the stability of the analyte response (compared to common glassy carbon and carbon paste electrodes) are illustrated using bovine serum albumin (BSA), gelatin, and Triton X‐100 in connection with repetitive square‐wave voltammetric (SWV) measurements. The voltammetric response of ascorbic acid at the diamond electrode exhibits negligible shifts in peak potentials and minimal depressions of current signals over a wide range of surfactant concentrations (0–750 ppm). For example, the diamond electrode exhibited 70, 50 and 60 mV potential shifts for 10 repetitive voltammetric scans in the presence of 100 ppm BSA, gelatin and Triton X‐100, respectively, compared to 120, 190, and 280 mV shifts observed at the glassy carbon electrode. Furthermore, only 4.3 and 6.2% of the initial current decays were observed in the presence of 100 ppm Triton X‐100 and gelatin, respectively (compared to 45.2 and 34.4% diminutions at the glassy carbon electrode). Such improved performance was also confirmed from the SWV measurements of uric acid, dihydroxyphenylacetic acid, and catechol. The greatly improved resistance to surfactant interference reflects the fact that the as‐grown diamond thin film, composed of oxide‐free and hydrogen‐terminated surface, has a relatively lower surface energy and minimal electrostatic attributes, either specific or general, so that little adsorption of surface‐active agents occurs. The topographic AFM images of the diamond electrode surface confirm a negligible BSA fouling effect after repetitive SWV measurements. Such enhanced antifouling features make diamond electrodes very attractive for numerous real‐life electroanalytical applications.     

氨-碘酸盐介质中白喉类毒素的平行催化氢波

在 0 .4mol/LNH3 NH4Cl (pH 8.3 1 )介质中 ,白喉类毒素 (DT)于 - 1 .89V(vs.SCE)处产生的极谱催化氢波可被碘酸钾进一步催化 ,峰电流明显增大 ,但峰电位不变 ,产生一种氢的新动力波 ,建议称其为平行催化氢波。在 0 .4mol/LNH3 NH4Cl(pH 8.3 1 ) - 5 .0× 1 0 - 3 mol/LKIO3介质中 ,DT平行催化氢波的二阶导数峰电流与其浓度在 0 .2 μg/mL～ 1 .0 μg/mL内呈线性关系 ,可用于生物制品中DT含量的测定。     

傅里叶变换近红外光谱法测定大麦中蛋白质、淀粉和赖氨酸含量

采用傅里叶变换近红外光谱法测定大麦中蛋白质、淀粉、赖氨酸的含量，并用光谱影响值法(leverage)对异常值进行判断和处理。蛋白质、淀粉和赖氨酸含量近红外光谱分析模型的测定系数R。分别为0．985、0．973和0．978；检验集的化学值与模型预测值的相关系数r分别为0．9853、0．9644和0．9172，分析模型的预测相对标准偏差RSD分别为4．0％、2．4％和5．4％，该结果可替代经典分析方法，满足农产品快速分析的需要。     

蛋白质在固体表面吸附的研究进展

蛋白质在固体表面的吸附有多种理论模型和实验分析.蛋白质吸附主要包括分子传递、吸附、重排、交换、解吸等步骤.蛋白质在表面的状态由表面性能、静电作用及蛋白质自身性质等因素决定.蛋白质分子在界面吸附后发生构象改变,引起熵增.     

UV-VIS and CD-spectroscopic investigations of intermolecular interactions of bile pigments with small proteins

Summary The intermolecular complex formation of bilirubin and biliverdin with two proteins (basic pancreatic trypsin inhibitor and lysozyme) were studied by optical and chiroptical methods. Evidence for specific intermolecular interactions of biliverdin with both proteins was found. Bilirubin forms a soluble complex only with lysozyme.

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UV-VIS und CD-spektroskopische Untersuchungen intermolekularer Wechselwirkungen von Gallenpigmenten mit kleinen Proteinen

Zusammenfassung Die intermolekulare Komplexbildung von Bilirubin und Biliverdin mit zwei Proteinen (basischer pankreatischer Trypsininhibitor und Lysozym) wurden mittels optischer und chiroptischer Spektroskopie untersucht. Für Biliverdin konnten intermolekulare Wechselwirkungen mit beiden Proteinen nachgewiesen werden. Bilirubin bildet nur mit Lysozym einen löslichen Komplex.

     

Analyzing functional similarity of protein sequences with discrete wavelet transform

This paper applies discrete wavelet transform (DWT) with various protein substitution models to find functional similarity of proteins with low identity. A new metric, 'S' function, based on the DWT is proposed to measure the pair-wise similarity. We also develop a segmentation technique, combined with DWT, to handle long protein sequences. The results are compared with those using the pair-wise alignment and PSI-BLAST.