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1.
Signal peptide amino acid sequences in Escherichia coli contain information related to final protein localization. A multivariate data analysis 总被引:15,自引:1,他引:14
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With few exceptions, the signal peptides from proteins inserted into, or translocated through, the membranes of gram-negative bacteria or the endoplasmic reticulum of eukaryotes have no sequence homologies. Therefore these signal peptides have not been considered to contain information related to the different final localizations of the proteins. In this study, 43 signal peptide amino acid sequences from proteins with different final localizations in Escherichia coli have been subjected to a multivariate data analysis. Each amino acid residue was characterized by 20 physico-chemical properties, yielding a multivariate property profile for each peptide. The similarities/dissimilarities in the property profiles for the signal peptides from different classes were compared with each other by generating few-dimensional partial least squares (PLS) discriminant plots. With this approach, signal peptides from proteins localized to the periplasmic space (PS), the outer membrane (OM), and the extracellular surroundings (excreted proteins), were separated into distinct groups. Signal peptides from pili proteins were not separated from the OM signal peptides and only partly from the PS signal peptides, but were clearly different from the signal peptides of the excreted proteins. Signal peptides from inner membrane proteins were similar to those of the PS peptides. The size and the hydrophobicity of different peptide segments were responsible for the separation of the signal peptide classes. For example, the hydrophobicity of the N-terminal segment of the signal peptides increased with an increased distance from the cytoplasm of the final localization for the corresponding proteins. Thus, many signal peptides from proteins with different final localizations in E. coli have different discernible physico-chemical profiles. 相似文献
2.
Meyer-Arendt K Old WM Houel S Renganathan K Eichelberger B Resing KA Ahn NG 《Journal of proteome research》2011,10(7):3060-3075
When analyzing proteins in complex samples using tandem mass spectrometry of peptides generated by proteolysis, the inference of proteins can be ambiguous, even with well-validated peptides. Unresolved questions include whether to show all possible proteins vs a minimal list, what to do when proteins are inferred ambiguously, and how to quantify peptides that bridge multiple proteins, each with distinguishing evidence. Here we describe IsoformResolver, a peptide-centric protein inference algorithm that clusters proteins in two ways, one based on peptides experimentally identified from MS/MS spectra, and the other based on peptides derived from an in silico digest of the protein database. MS/MS-derived protein groups report minimal list proteins in the context of all possible proteins, without redundantly listing peptides. In silico-derived protein groups pull together functionally related proteins, providing stable identifiers. The peptide-centric grouping strategy used by IsoformResolver allows proteins to be displayed together when they share peptides in common, providing a comprehensive yet concise way to organize protein profiles. It also summarizes information on spectral counts and is especially useful for comparing results from multiple LC-MS/MS experiments. Finally, we examine the relatedness of proteins within IsoformResolver groups and compare its performance to other protein inference software. 相似文献
3.
Food-derived peptides and intestinal functions 总被引:1,自引:0,他引:1
Shimizu M 《BioFactors (Oxford, England)》2004,21(1-4):43-47
Many researchers have reported that food proteins and their peptides expressed a variety of functions in the body, including a reduction of blood pressure, modulation of immune cell functions, and regulation of nerve functions. However, food-derived proteins and peptides also play important roles in the intestinal tract before being absorbed. For example, some of the proteins and peptides can regulate the activity of digestive enzymes in the intestinal tract, thereby modulating the nutrient absorption in the intestines. These proteins and peptides have been used for functional foods with blood glucose- and blood cholesterol-lowering effects. Enhancement of the intestinal calcium absorption by casein-derived peptides is another example, such peptides being used as functional food ingredients. We have recently observed that certain milk peptides might stimulate the calcium transporter in intestinal epithelial cells. Carnosine, a dipeptide contained in skeletal muscles, was observed to suppress the secretion of inflammatory cytokines by intestinal epithelial cells that had been exposed to oxidative stress. Understanding the behavior of dietary proteins and peptides in the intestines is important for designing functional foods with physiological functions. 相似文献
4.
Class I and class II MHC bind self peptide sets that are strikingly different in their evolutionary characteristics 总被引:3,自引:1,他引:2
Comparison of peptides eluted from human class I and class II major histocompatibility complex (MHC) molecules and the proteins
from which they are derived (source proteins) revealed that class I MHC bind peptides derived from proteins that are highly
conserved, hydrophilic, and universally expressed, while the peptides themselves are hydrophobic and even more conserved than
their source proteins. In contrast, source proteins for class II-bound peptides were not significantly more conserved than
a random sample of proteins. Class II-bound peptides were generally more conserved than their source proteins but were significantly
less conserved than class I-bound peptides. The characteristics of class I-bound peptides can probably be explained by the
selectivity of processing and transport of peptides for binding by class I, while the relative lack of selectivity of peptide
binding for class II may explain the high incidence of autoimmune diseases associated with alleles of these molecules.
Received: 17 May 1999 / Revised: 5 August 1999 相似文献
5.
Synthesis of Capsid and Noncapsid Viral Proteins in Response to Encephalomyocarditis Virus Ribonucleic Acid in Animal Cell-Free Systems 总被引:8,自引:6,他引:2
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The polypeptide products formed in two cell-free protein-synthetic systems programmed with encephalomyocarditis (EMC) virus ribonucleic acid (RNA) have been compared with the virus-specific proteins found in EMC-infected cells and with the capsid proteins of the purified virion. Tryptic peptides of (35)S-methioninelabeled proteins from these three sources were compared by co-chromatography and electrophoresis and by isoelectric focussing. Fifty-two methionine-containing peptides were resolved in digests of material from infected cells, of which about one-third were also clearly present in digests of the virion capsid proteins. The product formed in response to EMC RNA in cell-free systems from Krebs mouse ascites tumor cells yielded 26 to 29 such peptides. Most of these peptides were shown to behave identically with virus-specific peptides from infected cells, whereas just under half of them appeared to be identical with peptides from the virion capsid proteins. The product formed in response to EMC RNA in the L-cell cell-free system was similar, whereas six additional EMC-specific peptides were detected in mixed Krebs L-cell systems. The results indicate that the EMC RNA genome is partially translated in the mouse cell-free systems used to yield products containing both virion capsid and virus-specific noncapsid polypeptides. 相似文献
6.
秀丽小杆线虫分泌蛋白组的计算机分析 总被引:2,自引:0,他引:2
结合计算机技术和生物信息学的方法,采用组合的信号肽分析软件SignalP v3.0、TargetP v1.01、Big-PI Predictor和TMHMM v2.0,预测了秀丽小杆线虫(Caenorthaditis elegans ws123)的全基因组19855个ORF编码蛋白的信号肽,同时系统分析了信号肽的特征。结果表明,在19855个秀丽小杆线虫的蛋白中,有1990条为带有信号肽的分泌型蛋白,其中,1936条为典型的分泌型信号肽(即信号肽酶Ⅰ型信号肽),53条为信号肽酶Ⅱ型信号肽,1条为信号肽酶Ⅳ型信号肽;在Ⅰ型信号肽中,有41条为RR-motif亚组型信号肽。在1990条信号肽中,有742条没有典型的N-区,其余1248条包含典型的3个区。比较了秀丽小杆线虫与原核生物分泌蛋白信号肽中20种氨基酸残基在信号肽酶切位点的使用情况,表明:在Ⅰ型信号肽酶切位点,其信号肽中使用的氨基酸总体趋势与原核生物基本相似,但秀丽小杆线虫选用的氨基酸种类更多,变化更大;在Ⅱ型信号肽酶切位点,秀丽小杆线虫脂蛋白信号肽中使用的氨基酸的种类与原核生物有很大的不同。通过与真核单细胞生物比较,作为真核多细胞生物的秀丽小杆线虫,其分泌蛋白信号肽所占比例更高、种类更多,可知线虫信号肽的组成具有很高的多态性,表明该物种的分泌蛋白具有多种功能。此外,分析结果显示,脂蛋白信号肽在结构上比分泌型信号肽更为保守。在秀丽小杆线虫分泌蛋白中出现了少数氨基酸组成完全一致的信号肽,采用BLAST 2 SEQUENECES对具有相同信号肽的分泌蛋白进行了序列比对,结果表明具有相同信号肽的分泌蛋白同源性非常高,它们的存在是生物进化过程中基因倍加(duplication)及环境选择的结果,信号肽特征的详细描述必将对这些蛋白功能的研究提供重要的帮助。
相似文献
7.
A goodness of fit test may be used to assign tandem mass spectra of peptides to amino acid sequences and to directly calculate the expected probability of mis-identification. The product of the peptide expectation values directly yields the probability that the parent protein has been mis-identified. A relational database could capture the mass spectral data, the best fit results, and permit subsequent calculations by a general statistical analysis system. The many files of the Hupo blood protein data correlated by X!TANDEM against the proteins of ENSEMBL were collected into a relational database. A redundant set of 247,077 proteins and peptides were correlated by X!TANDEM, and that was collapsed to a set of 34,956 peptides from 13,379 distinct proteins. About 6875 distinct proteins were only represented by a single distinct peptide, 2866 proteins showed 2 distinct peptides, and 3454 proteins showed at least three distinct peptides by X!TANDEM. More than 99% of the peptides were associated with proteins that had cumulative expectation values, i.e. probability of false positive identification, of one in one hundred or less. The distribution of peptides per protein from X!TANDEM was significantly different than those expected from random assignment of peptides. 相似文献
8.
《Journal of Proteomics》2010,73(1):103-111
A goodness of fit test may be used to assign tandem mass spectra of peptides to amino acid sequences and to directly calculate the expected probability of mis-identification. The product of the peptide expectation values directly yields the probability that the parent protein has been mis-identified. A relational database could capture the mass spectral data, the best fit results, and permit subsequent calculations by a general statistical analysis system. The many files of the Hupo blood protein data correlated by X!TANDEM against the proteins of ENSEMBL were collected into a relational database. A redundant set of 247,077 proteins and peptides were correlated by X!TANDEM, and that was collapsed to a set of 34,956 peptides from 13,379 distinct proteins. About 6875 distinct proteins were only represented by a single distinct peptide, 2866 proteins showed 2 distinct peptides, and 3454 proteins showed at least three distinct peptides by X!TANDEM. More than 99% of the peptides were associated with proteins that had cumulative expectation values, i.e. probability of false positive identification, of one in one hundred or less. The distribution of peptides per protein from X!TANDEM was significantly different than those expected from random assignment of peptides. 相似文献
9.
Böttger A Strasser D Alexandrova O Levin A Fischer S Lasi M Rudd S David CN 《European journal of cell biology》2006,85(9-10):1107-1117
We have screened a Hydra cDNA library for sequences encoding N-terminal signal peptides using the yeast invertase secretion vector pSUC [Jacobs et al., 1997. A genetic selection for isolating cDNAs encoding secreted proteins. Gene 198, 289-296]. We isolated and sequenced 907 positive clones; 88% encoded signal peptides; 12% lacked signal peptides. By searching the Hydra EST database we identified full-length sequences for the selected clones. These encoded 37 known proteins with signal peptides and 40 novel Hydra-specific proteins with signal peptides. Localization of two signal peptide-containing sequences, VEGF and ferritin, to the secretory pathway was confirmed with GFP fusion proteins. In addition, we isolated 105 clones which lacked signal peptides but which supported invertase secretion from yeast. Isolation of plasmids from these clones and retransformation in invertase-negative yeast cells confirmed the phenotype. A GFP fusion protein of one such clone encoding the foot morphogen pedibin was localized to the cytoplasm in transfected Hydra cells and did not enter the ER/Golgi secretory pathway. Secretion of pedibin and other proteins lacking signal peptides appears to occur by a non-classical protein secretion route. 相似文献
10.
The detectability by India ink staining of proteins and peptides dot-blotted on nitrocellulose paper was assessed before and after fixation. Fixation considerably increased the detectability of proteins and peptides. Denaturation by KOH treatment or baking at 100 degrees C for 15 min gave the best results. Precipitation by isopropanol/acetic acid gave intermediate results, whereas crosslinking with glutaraldehyde improved the detectability of small peptides, but not of proteins. Ferridye and Aurodye were also tested after baking. Both dyes were more sensitive and stained more proteins and peptides than India ink. In all cases the detectability of peptides smaller than Mr 1500 was poor. 相似文献
11.
目的:从大肠埃希氏杆菌UTI89基因组中筛选出全部潜在的分泌蛋白并进行初步研究。方法:使用SignalP3.0、TatP1.0、 SecretomeP2.0等蛋白分析软件对5211个ORF进行预测;对筛选出的信号肽及分泌蛋白的基本特征进行统计学分析;使用Blast 2 Sequences进行同源性分析。结果:共筛选出432个sec途径分泌蛋白,19个Tat途径分泌蛋白,386个非经典分泌蛋白;信号肽、分泌蛋白平均长度分别为25.5aa、282.8aa;信号肽中出现频率最高的3种氨基酸依次为L、A、S;仅有两个信号肽的氨基酸序列完全相同,相应的分泌蛋白高度同源。结论:大肠埃希氏杆菌UTI89基因组中有837个ORF可能编码分泌蛋白;分泌蛋白集中在500aa以下;组成信号肽的氨基酸相对保守,多数为疏水氨基酸;信号肽变异性较大,含相同信号肽的蛋白可能由同源基因编码。 相似文献
12.
Multiple residues with consensus sequence, i.e. motif, on proteins are closely related to protein function. However, there is no effective method for targeted analysis of such proteins. The challenge for analysis of these classes of proteins by MS is how to selectively enrich peptides containing consensus sequence from protein digest. Although enrichment of peptides containing one type of amino acid residue was successfully achieved by chemically labeling followed by chromatographic isolation, however, it is almost impossible to label and isolate signature peptides containing multiple residues with consensus sequence by chemical approach. Herein, we developed an enzymatic approach based on the specific recognition between enzyme and its substrates to enrich such peptides. This approach was realized by modification of a residue in the consensus sequence via enzyme that can recognize the sequence followed by the isolation of the modified peptides. cAMP-dependent protein kinase was used to validate this approach and 168 peptides containing consensus motif were identified with selectivity of 67.2%. Those peptides resulted in the identification of 88 proteins with consensus sequence from serum sample. As this motif-oriented peptide enrichment approach allows targeted analysis of a subset of proteins with consensus sequence, it will have broad application in biological studies. 相似文献
13.
Wang YH Chen CP Chan MH Chang M Hou YW Chen HH Hsu HR Liu K Lee HJ 《Biochemical and biophysical research communications》2006,346(3):758-767
Plasma membranes of plant or animal cells are generally impermeable to peptides or proteins. Many basic peptides have previously been investigated and covalently cross-linked with cargoes for cellular internalization. In the current study, we demonstrate that arginine-rich intracellular delivery (AID) peptides are able to deliver fluorescent proteins or beta-galactosidase enzyme into animal and plant cells, as well as animal tissue. Cellular internalization and transdermal delivery of protein could be mediated by effective and nontoxic AID peptides in a neither fusion protein nor conjugation fashion. Therefore, noncovalent AID peptides may provide a useful strategy to have active proteins function in living cells and tissues in vivo. 相似文献
14.
Information about peptides and proteins in urine can be used to search for biomarkers of early stages of various diseases.
The main technology currently used for identification of peptides and proteins is tandem mass spectrometry, in which peptides
are identified by mass spectra of their fragmentation products. However, the presence of the fragmentation stage decreases
sensitivity of analysis and increases its duration. We have developed a method for identification of human urinary proteins
and peptides. This method based on the accurate mass and time tag (AMT) method does not use tandem mass spectrometry. The
database of AMT tags containing more than 1381 AMT tags of peptides has been constructed. The software for database filling
with AMT tags, normalizing the chromatograms, database application for identification of proteins and peptides, and their
quantitative estimation has been developed. The new procedures for peptide identification by tandem mass spectra and the AMT
tag database are proposed. The paper also lists novel proteins that have been identified in human urine for the first time. 相似文献
15.
Mathiesen G Sveen A Piard JC Axelsson L Eijsink VG 《Journal of applied microbiology》2008,105(1):215-226
Aims: To test seven selected putative signal peptides from Lactobacillus plantarum WCFS1 in terms of their ability to drive secretion of two model proteins in Lact. plantarum, and to compare the functionality of these signal peptides with that of well‐known heterologous signal peptides (Usp45, M6). Methods and Results: Signal peptide functionality was assessed using a series of modular derivatives of the pSIP vectors for peptide pheromone‐controlled high‐level gene expression in lactobacilli. Several of the constructs with homologous signal peptides yielded similar or higher reporter protein activities than constructs with heterologous signal peptides. Two of the homologous signal peptides (Lp_0373 and Lp_0600) appeared as especially promising candidates for directing secretion, as they were among the best performing with both reporter proteins. Conclusions: We have identified homologous signal peptides for high‐level secretion of heterologous proteins in Lact. plantarum. With the model proteins, some of these performed better than commonly used heterologous signal peptides. Significance and Impact of the Study: The homologous signal peptides tested out, in this study, could be useful in food‐grade systems for secretion of interesting proteins in Lact. plantarum. The constructed modular secretion vectors are easily accessible for rapid signal peptide screening. 相似文献
16.
Cell-penetrating peptides (CPPs) constitute a family of peptides with the characteristic ability to cross biological membranes and deliver cargo into the intracellular milieu. Several CPPs have been proposed for delivery of polypeptides and proteins into cells through either of two strategies: covalent or complexed in a non-covalent fashion. Members of the PEP family are primary amphipathic peptides which have been shown to deliver peptides and proteins into a wide variety of cells through formation of non-covalent complexes. CADY is a secondary amphipathic peptide which has been demonstrated to deliver short nucleic acids, in particular siRNA with high efficiency. Here we review the characteristics of the PEP and CADY carriers and describe a novel derivative of CADY termed CADY2, which also presents sequence similarities to Pep1. We have compared Pep1, CADY and CADY2 in their efficiency to interact with and internalize short fluorogenic peptides and proteins into cultured cells, and provide evidence that CADY2 can interact with proteins and peptides and deliver them efficiently into living cells, similar to Pep1, but in contrast to CADY which is unable to deliver any peptide, even short negatively charged peptides. This is the first study to investigate the influence of the cargo on the interactions between PEP and CADY carriers, thereby providing novel insights into the physicochemical parameters underlying interactions and cellular uptake of peptides and proteins by these non-covalent CPPs. 相似文献
17.
SDS-polyacrylamide gel electrophoresis of anti-glucose-6-phosphate dehydrogenase immunoprecipitates from radiolabeled uterine tissue extracts previously revealed three proteins: A, B and C, which were tentatively identified as a 60-64 kDa precursor form, a 57 kDa predominant form, and a 40-42 kDa nascent peptide form of the enzyme, respectively. A peptide-mapping technique was used to examine structural homologies among A, B and C. Following the labeling of uterine proteins with [35S]methionine, labeled proteins A, B and C were isolated by immunoprecipitation and electrophoresis. Each protein was individually co-digested with authentic, [3H]methionine-labeled glucose-6-phosphate dehydrogenase using papain, the resulting peptides were resolved by isoelectric focusing and the peptides from the two sources on each gel were compared using double-label counting methods. Proteins A, B and C had at least eight peptides in common, both proteins A and C had two additional peptides in common that were not present in protein B, and B protein had two peptides that were either absent or present in reduced amounts in digests of proteins A and C. The extensive structural homology and immunoreactivity of these proteins indicated that proteins A, B and C were all related to glucose-6-phosphate dehydrogenase. The presence of two extra peptides in proteins A and C suggested that these peptides may be derived from a common NH2-terminal leader sequence which was present in both the precursor and nascent peptide chains. The presence of two peptides that were present in protein B and absent from proteins A and C is easiest to explain if they are derived from the two ends of the molecule, with the corresponding peptides in proteins A and C containing additional peptide sequences that are 'normally' removed by endogenous proteolytic processing enzymes. Based on the relative time-course of synthesis of the three glucose-6-phosphate dehydrogenase-related proteins in control and estrogen-treated uteri, it appears that estradiol promotes an increase in the relative rate of transfer of label from protein A into B by stimulating the rate of processing of the precursor to the predominant form of the enzyme and enhances the rate of translational conversion of protein C into higher molecular weight forms. 相似文献
18.
The human pathogen Staphylococcus aureus requires cell wall anchored surface proteins to cause disease. During cell division, surface proteins with YSIRK signal peptides are secreted into the cross-wall, a layer of newly synthesized peptidoglycan between separating daughter cells. The molecular determinants for the trafficking of surface proteins are, however, still unknown. We screened mutants with non-redundant transposon insertions by fluorescence-activated cell sorting for reduced deposition of protein A (SpA) into the staphylococcal envelope. Three mutants, each of which harboured transposon insertions in genes for transmembrane proteins, displayed greatly reduced envelope abundance of SpA and surface proteins with YSIRK signal peptides. Characterization of the corresponding mutations identified three transmembrane proteins with abortive infectivity (ABI) domains, elements first described in lactococci for their role in phage exclusion. Mutations in genes for ABI domain proteins, designated spdA, spdB and spdC (surface protein display), diminish the expression of surface proteins with YSIRK signal peptides, but not of precursor proteins with conventional signal peptides. spdA, spdB and spdC mutants display an increase in the thickness of cross-walls and in the relative abundance of staphylococci with cross-walls, suggesting that spd mutations may represent a possible link between staphylococcal cell division and protein secretion. 相似文献
19.
Food proteins have been identified as a source of bioactive peptides. These peptides are inactive within the sequence of the parent protein and must be released during gastrointestinal digestion, fermentation, or food processing. Of bioactive peptides, multifunctional cationic peptides are more useful than other peptides that have specific activity in promotion of health and/or the treatment of diseases. We have identified and characterized cationic peptides from rice enzymes and proteins that possess multiple functions, including antimicrobial, endotoxin-neutralizing, arginine gingipain-inhibitory, and/or angiogenic activities. In particular, we have elucidated the contribution of cationic amino acids (arginine and lysine) in the peptides to their bioactivities. Further, we have discussed the critical parameters, particularly proteinase preparations and fractionation or purification, in the enzymatic hydrolysis process for producing bioactive peptides from food proteins. Using an ampholyte-free isoelectric focusing (autofocusing) technique as a tool for fractionation, we successfully prepared fractions containing cationic peptides with multiple functions. 相似文献
20.
Mass spectrometric profiling using ProteinChip and magnetic beads has rapidly grown over the past years, particularly to generate serum profiles for cancer diagnosis. The molecular weights of these distinguishing peaks are usually under 30 kDa. To identify those low molecular weight proteins and peptides is important for specific assays to be developed and increases biological insight. In this study, low molecular weight proteins and peptides from serum were purified by a combination of weak cation exchange magnetic beads and high performance liquid chromatography. The purified proteins and peptides were analyzed by 1D SDS PAGE, SELDI and LC-MS/MS. 246 proteins were identified from the HPLC fractions by LC-MS/MS. 95(38.62%) proteins were first identified in serum compare with Sys-BodyFluid database. 11(11/96) proteins were documented cancer associated proteins. We also observed about 109 proteins/peptides in SELDI mass spectrum, and 13 of the SELDI features were identified. 相似文献