Nanomechanical In Situ Monitoring of Proteolysis of Peptide by Cathepsin B

Characterization and control of proteolysis of peptides by specific cellular protease is a priori requisite for effective drug discovery. Here, we report the nanomechanical, in situ monitoring of proteolysis of peptide chain attributed to protease (Cathepsin B) by using a resonant nanomechanical microcantilever immersed in a liquid. Specifically, the detection is based on measurement of resonant frequency shift arising from proteolysis of peptides (leading to decrease of cantilever''s overall mass, and consequently, increases in the resonance). It is shown that resonant microcantilever enables the quantification of proteolysis efficacy with respect to protease concentration. Remarkably, the nanomechanical, in situ monitoring of proteolysis allows us to gain insight into the kinetics of proteolysis of peptides, which is well depicted by Langmuir kinetic model. This implies that nanomechanical biosensor enables the characterization of specific cellular protease such as its kinetics.     

Spectral Properties of Chromophore-Containing Fragments Prepared from Pea Phytochrome by Limited Proteolysis

Five chromophore-containing fragments were prepared from peaphytochrome in PR form (monomer mol wt 114,000) by limited proteolysiswith trypsin, thermolysin or chymotrypsin, and their absorptionand circular dichroism (CD) spectra were determined. The fragmentsof mol wt 62,100 and 56,400 showed photoreversible transformationbetween P_R and P_FR like phytochrome. The smaller fragments ofmol wt 40,300, 39,000 and 33,000 showed an absorption maximumat 657–660 nm (P₆₆₀) which was transformed to a bleachedform (P_BL) after a brief red-light exposure. The phototransformationbetween P₆₆₀ and P_BL was repeatedly reversible. Both P₆₆₀ andP_BL showed a negative CD band in red region like P_R, in contrastwith P_FR which has a positive band in far-red region. The natureof a chromophore domain of phytochrome and spectral propertiesof P_BL are discussed. ¹This study is dedicated to the late Professor J. Ashida. ²Permanent address: Department of Botany, Faculty of Science,University of Tokyo, Hongo, Tokyo 113, Japan. (Received August 7, 1982; Accepted March 26, 1983)     

Proteolysis of Microtubule-Associated Protein 2 and Tubulin by Cathepsin D

The in vitro degradation of microtubule-associated protein 2 (MAP-2) and tubulin by the lysosomal aspartyl endopeptidase cathepsin D was studied. MAP-2 was very sensitive to cathepsin D-induced hydrolysis in a relatively broad, acidic pH range (3.0-5.0). However, at a pH value of 5.5, cathepsin D-mediated hydrolysis of MAP-2 was significantly reduced and at pH 6.0 only a small amount of MAP-2 was degraded at 60 min. Interestingly, the two electrophoretic forms of MAP-2 showed different sensitivities to cathepsin D-induced degradation, with MAP-2b being significantly more resistant to hydrolysis than MAP-2a. To our knowledge, this is the first clear demonstration that MAP-2 is a substrate in vitro for cathepsin D. In contrast to MAP-2, tubulin was relatively resistant to cathepsin D-induced hydrolysis. At pH 3.5 and an enzyme-to-substrate ratio of 1: 20, only 35% of the tubulin was degraded by cathepsin D at 60 min. The cathepsin D-mediated hydrolysis of tubulin was optimal only at pH 4.5. These results demonstrate that MAP-2 and tubulin are unequally susceptible to degradation by cathepsin D. These data also imply a potential for rapid degradation of MAP-2 in vivo by cathepsin D either in lysosomes or perhaps autophagic vacuoles of the neuron.     

双分子荧光互补系统分析S-periaxin蛋白的聚合

S-periaxin蛋白是施旺氏细胞特异性表达的一种蛋白,在维持髓鞘的稳定方面发挥重要作用,该蛋白基因的突变引起腓骨肌萎缩症4F亚型的发生。Periaxin基因由于mRNA剪切方式的不同可以编码两种长短不同的含PDZ结构域的蛋白,即L-periaxin和S-periaxin。两种蛋白在施旺氏细胞的定位存在明显的差异,相对L-periaxin而言,S-periaxin无论是分子结构还是生物学功能均未见相关研究。该文从大鼠的施旺氏细胞系RSC96克隆了S-periaxin基因,构建了原核表达载体pETM-3C-S-periaxin,在大肠杆菌中进行重组表达,经Ni-NTA亲和柱和Sephacryl S-200凝胶层析柱获得电泳纯的目的蛋白。体外戊二醛交联分析蛋白的聚合状态表明,S-periaxin蛋白在体外易于形成不同聚合度的聚合物。免疫共沉淀也表明,S-periaxin蛋白存在同源蛋白间相互作用。另外,构建了原、真核双分子荧光互补系统,并利用该系统分析了细胞内S-periaxin蛋白间的相互作用。     

Critical Evaluation of Product Ion Selection and Spectral Correlation Analysis for Biomarker Screening Using Targeted Peptide Multiple Reaction Monitoring

Introduction  Tandem mass spectrometry (MS/MS) has emerged as a cornerstone of proteomic screens aimed at discovering putative protein biomarkers of disease with potential clinical applications. Systematic validation of lead candidates in large numbers of samples from patient cohorts remains an important challenge. One particularly promising high throughout technique is multiple reaction monitoring (MRM), a targeted form of MS/MS by which precise peptide precursor–product ion combinations, or transitions, are selectively tracked as informative probes. Despite recent progress, however, many important computational and statistical issues remain unresolved. These include the selection of an optimal set of transitions so as to achieve sufficiently high specificity and sensitivity when profiling complex biological specimens, and the corresponding generation of a suitable scoring function to reliably confirm tentative molecular identities based on noisy spectra. Methods  In this study, we investigate various empirical criteria that are helpful to consider when developing and interpreting MRM-style assays based on the similarity between experimental and annotated reference spectra. We also rigorously evaluate and compare the performance of conventional spectral similarity measures, based on only a few pre-selected representative transitions, with a generic scoring metric, termed T _corr, wherein a selected product ion profile is used to score spectral comparisons. Conclusions  Our analyses demonstrate that T _corr is potentially more suitable and effective for detecting biomarkers in complex biological mixtures than more traditional spectral library searches. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. Jian Liu and Johannes A Hewel contributed equally to this study.     

Monitoring Microbial Community Composition by Fluorescence In Situ Hybridization During Cultivation of the Marine Cold-Water Sponge Geodia barretti

To determine the stability and specificity of microbes associated with the marine cold-water sponge Geodia barretti during cultivation, we compared the microbial community of freshly retrieved specimens to that of cultivated explants by fluorescence in situ hybridization (FISH). G. barretti hosts a specific homogeneous microbial community in its mesohyl, which is maintained during a cultivation period of 8 months. In 10-day-old explants, bright colonies of unusually large bacterial cells, located predominantly at canal walls, were observed in addition to the common bacteria. Bacteria of the aberrant type included both lineages present in whole sponges and foreign ones, notably numerous genera of sulfate-reducing bacteria. We assume that these represent infectious bacteria that eluded the innate immune system of the sponge. Explants that resist these microbial attacks during the critical phase of cultivation eliminate infectious bacteria. The intrinsic microbial community of G. barretti is not affected by these infections and remains persistent over a cultivation period of at least several months.     

Intrinsic Protein Fluorescence Interferes with Detection of Tear Glycoproteins in SDS-Polyacrylamide Gels Using Extrinsic Fluorescent Dyes

Intrinsic protein fluorescence may interfere with the visualization of proteins after SDS-polyacrylamide electrophoresis. In an attempt to analyze tear glycoproteins in gels, we ran tear samples and stained the proteins with a glycoprotein-specific fluorescent dye. The fluorescence detected was not limited to glycoproteins. There was strong intrinsic fluorescence of proteins normally found in tears after soaking the gels in 40% methanol plus 1-10% acetic acid and, to a lesser extent, in methanol or acetic acid alone. Nanograms of proteins gave visible native fluorescence and interfere with extrinsic fluorescent dye detection. Poly-L-lysine, which does not contain intrinsically fluorescent amino acids, did not fluoresce.     

Correlation of the 680 to 672 nm Spectral Shift and the Halving of the Apparent Molecular Weight for Chlorophyll(ide) Holochrome from Barley

Protochlorophyll(ide) holochrome was isolated from dark-grown barley (Hordeum vulgare L.) leaves and photoconverted. When the chlorophyll(ide) absorption maximum had decreased from 680 to 676 nm the preparation was chromatographed on a Sephadex-gel column under conditions which strongly inhibited a further decrease in the absorption maximum. The absorption properties of the column fractions and the shape of the chlorophyll(ide) elution-profile indicated the presence of two distinct chlorophyll(ide)-bearing molecular species with apparent molecular weights of c. 74,000 and 29,000 and absorption maxima at 680 and 672 nm, respectively. It is concluded that: (1) no long-lived species with intermediate absorption maximum is formed during the 680 to 672 nm shift of the absorption maximum of newly photoconverted holochrome; (2) no long-lived pigment-protein complexes with intermediate molecular weights are formed during the approximate halving of the molecular weight; (3) the shift in the absorption maximum and the decrease in molecular weight are closely correlated.     

Benzodiazepine-Mediated Structural Changes in the Multidrug Transporter P-Glycoprotein: An Intrinsic Fluorescence Quenching Analysis

P-glycoprotein expressed in Pichia pastoris was used to study the drug binding sites of different benzodiazepines. The effect of bromazepam, chlordiazepoxide, diazepam and flurazepam on P-glycoprotein structure was investigated by measuring the intrinsic fluorescence of the transporter tryptophan residues. Purified mouse mdr1a transporter in mixed micelles of 3-[(3-cholamidopropyl)-dimethylammonio]-1-propanesulfonic acid and 1,2-dimiristoyl-sn-glycerol-3-phosphocholine emitted fluorescence at 340 nm indicative of the fluorophores in a relatively apolar environment. Acrylamide and iodide ion were used as collisional quenchers toward distinct regions of the transporter, the protein and the interface protein-surface, respectively. Binding of ATP induced conformational changes at the protein surface level in accordance with the location of the nucleotide binding sites. Bromazepam interaction with the transporter was located at the protein-surface interface, diazepam at the membrane region and chlordiazepoxide at the protein surface. Only the flurazepam interaction site was not detected by the quenchers used. All benzodiazepines were able to elicit reorientation of the protein fluorophores on the P-glycoprotein—ATP complex.     

Spectral Tuning of the Photoactive Yellow Protein Chromophore by H-Bonding

Spectral tuning in the photoactive yellow protein (PYP) is investigated by performing gas-phase absorption measurements on a PYP-model chromophore with two water molecules hydrogen-bonded to it. The photoabsorption maximum shows an unusually large blue shift of 0.71 eV in going from the bare to the hydrogen-bonded chromophore. It is concluded that several interactions within the PYP protein are mutually canceling each other, yielding an absorption maximum that is close to the absorption maximum of the bare chromophore. The system breaks apart upon photoexcitation in the gas phase by releasing the two water molecules, leaving the chromophore itself intact. The hydrogen-bonding interactions thus play an important role in stabilizing the gas phase chromophore against photofragmentation. The relaxation dynamics for the breakup process was also studied, and the timescale of relaxation via fragmentation was found to be <25 ns.     

双向凝胶电泳银染蛋白质点的肽质谱指纹图分析

对双向凝胶电泳后银染显色的蛋白质点经脱色与原位还原和烷基化处理后,用ＴＰＣＫ胰蛋白酶进行酶解,采用带有Ｃ１８反相载体的ＺｉｐＴｉｐ＾ＴＭ吸头进行脱盐处理,再进行ＭＡＬＤＩ－ＴＯＦ肽质谱指纹纹图分析,然后将肽质数据在ＥＭＢＬ数据库中进行搜寻从而对蛋白南点进行鉴定。结果表明用该实验程序可对银染的单一蛋白南点进行快速肽质谱指纹图ｉｐＴｉｐ＾ＴＭ的应用可以明显增加质谱分析的信噪比,提高分析灵敏度。用以上方     

Regulation of Bone Morphogenetic Protein 9 (BMP9) by Redox-dependent Proteolysis

BMP9, a member of the TGFβ superfamily, is a homodimer that forms a signaling complex with two type I and two type II receptors. Signaling through high-affinity activin receptor-like kinase 1 (ALK1) in endothelial cells, circulating BMP9 acts as a vascular quiescence factor, maintaining endothelial homeostasis. BMP9 is also the most potent BMP for inducing osteogenic signaling in mesenchymal stem cells in vitro and promoting bone formation in vivo. This activity requires ALK1, the lower affinity type I receptor ALK2, and higher concentrations of BMP9. In adults, BMP9 is constitutively expressed in hepatocytes and secreted into the circulation. Optimum concentrations of BMP9 are essential to maintain the highly specific endothelial-protective function. Factors regulating BMP9 stability and activity remain unknown. Here, we showed by chromatography and a 1.9 Å crystal structure that stable BMP9 dimers could form either with (D-form) or without (M-form) an intermolecular disulfide bond. Although both forms of BMP9 were capable of binding to the prodomain and ALK1, the M-form demonstrated less sustained induction of Smad1/5/8 phosphorylation. The two forms could be converted into each other by changing the redox potential, and this redox switch caused a major alteration in BMP9 stability. The M-form displayed greater susceptibility to redox-dependent cleavage by proteases present in serum. This study provides a mechanism for the regulation of circulating BMP9 concentrations and may provide new rationales for approaches to modify BMP9 levels for therapeutic purposes.     

Specificity Analysis of Protein Lysine Methyltransferases Using SPOT Peptide Arrays

Lysine methylation is an emerging post-translation modification and it has been identified on several histone and non-histone proteins, where it plays crucial roles in cell development and many diseases. Approximately 5,000 lysine methylation sites were identified on different proteins, which are set by few dozens of protein lysine methyltransferases. This suggests that each PKMT methylates multiple proteins, however till now only one or two substrates have been identified for several of these enzymes. To approach this problem, we have introduced peptide array based substrate specificity analyses of PKMTs. Peptide arrays are powerful tools to characterize the specificity of PKMTs because methylation of several substrates with different sequences can be tested on one array. We synthesized peptide arrays on cellulose membrane using an Intavis SPOT synthesizer and analyzed the specificity of various PKMTs. Based on the results, for several of these enzymes, novel substrates could be identified. For example, for NSD1 by employing peptide arrays, we showed that it methylates K44 of H4 instead of the reported H4K20 and in addition H1.5K168 is the highly preferred substrate over the previously known H3K36. Hence, peptide arrays are powerful tools to biochemically characterize the PKMTs.     

Brightness Analysis by Z-Scan Fluorescence Fluctuation Spectroscopy for the Study of Protein Interactions within Living Cells

Fluorescence fluctuation spectroscopy (FFS) quantifies interactions of fluorescently labeled proteins inside living cells by brightness analysis. Conventional FFS implicitly requires that the sample thickness exceeds the size of the observation volume. This condition is not always fulfilled when measuring cells. Cytoplasmic sections, especially, can be thinner than the axial size of the observation volume. The finite sample thickness introduces a brightness bias which, if not recognized, leads to an erroneous interpretation of the data. To avoid this artifact, we introduce z-scan FFS which consists of a fluorescence intensity z scan through the sample followed by an FFS measurement. To model the experimental z-scan data, a new PSF model had to be introduced. We use the intensity z scan together with the PSF model to determine the geometry of the sample and then extract the brightness from the FFS data. Cells expressing EGFP serve as a model system for testing the experimental approach. We demonstrate that z-scan FFS abolishes the brightness artifact and use the method to determine the oligomerization of cytoplasmic nuclear transport factor 2.