共查询到20条相似文献,搜索用时 31 毫秒
1.
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
2.
The direction of discharge of the nascent peptides of NADPH-cytochrome c reductase and cytochrome b5 from bound polyribosomes of rough microsomes was investigated in order to elucidate the mechanism of separation of these membrane proteins from secretory proteins, which are also synthesized by the same class of ribosomes of rough endoplasmic reticulum. The nascent peptides of NADPH-cytochrome c reductase and cytochrome b5 in intact rough microsomes were accessible to externally added 125I-Fab's against these proteins, and were susceptible to trypsin digestion, whereas the nascent peptides of serum albumin were not. The nascent peptides of these two microsomal proteins were released into the cytoplasm by puromycin treatment of intact rough microsomes, while the nascent peptides of serum albumin were retained in the microsomal lumen. These observations suggest that the nascent peptides of microsomal proteins, which are present on the cytoplasmic surface of the endoplasmic reticulum membrane, are exposed on the surface of microsomal vesicles, while those of secretory proteins are enclosed inside the vesicles. Therefore, the topographical separation of microsomal membrane proteins from secretory proteins is accomplished at the step of their synthesis by the bound polyribosomes of rough endoplasmic reticulum. 相似文献
3.
Peptides and proteins from fungi 总被引:2,自引:0,他引:2
Ng TB 《Peptides》2004,25(6):1055-1073
The peptides and proteins secreted by fungi are reviewed in this article. They include ribosome inactivating peptides and proteins, antifungal peptides and proteins, lectins, ubiquitin-like peptides and proteins, peptides and proteins with nucleolytic activity, proteases, xylanases, cellulases, sugar oxidoreductases, laccases, invertases, trehalose phosphorylases, and various enzymes with applications in food industry, chemical production and the medical sector. 相似文献
4.
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
5.
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.
Shuji Ye Khoi Tan Nguyen Stphanie V. Le Clair Zhan Chen 《Journal of structural biology》2009,168(1):61
Sum frequency generation (SFG) vibrational spectroscopy has been demonstrated to be a powerful technique to study the molecular structures of surfaces and interfaces in different chemical environments. This review summarizes recent SFG studies on hybrid bilayer membranes and substrate-supported lipid monolayers and bilayers, the interaction between peptides/proteins and lipid monolayers/bilayers, and bilayer perturbation induced by peptides/proteins. To demonstrate the ability of SFG to determine the orientations of various secondary structures, studies on the interactions between different peptides/proteins (melittin, G proteins, alamethicin, and tachyplesin I) and lipid bilayers are discussed. Molecular level details revealed by SFG in these studies show that SFG can provide a unique understanding on the interactions between a lipid monolayer/bilayer and peptides/proteins in real time, in situ and without any exogenous labeling. 相似文献
8.
Shpakov AO 《Tsitologiia》2011,53(8):633-644
The peptide strategy, a new direction of molecular endocrinology, includes the synthesis of peptides corresponding to functional regions of signal proteins, the use of the peptides for study of the molecular mechanisms of transduction of hormonal signal into cell ant the development of selective regulators of hormonal signaling systems on the basis of these peptides. The peptide strategy is used for study a wide spectrum of the proteins, components of signal systems, the proteins possessing the catalytic activity in particular, such as tyrosine kinases receptors, the enzymes generating the second messengers, serine/threonine protein kinase, phosphatases. In the first time in the review the data concerning the synthetic peptides, derivatives of the primary structure of proteins with the enzymatic activity, their application for study of the structural-functional organization and the molecular mechanisms of action of signal proteins, and the construction of regulators of fundamental cell processes on the basis of these peptides are analyzed and summarized. 相似文献
9.
Noninvasive intracellular delivery of functional peptides and proteins 总被引:10,自引:0,他引:10
Hawiger J 《Current opinion in chemical biology》1999,3(1):89-94
10.
Hickman HD Luis AD Bardet W Buchli R Battson CL Shearer MH Jackson KW Kennedy RC Hildebrand WH 《Journal of immunology (Baltimore, Md. : 1950)》2003,171(1):22-26
Class I MHC molecules bind intracellular peptides for presentation to cytotoxic T lymphocytes. Identification of peptides presented by class I molecules during infection is therefore a priority for detecting and targeting intracellular pathogens. To understand which host-encoded peptides distinguish HIV-infected cells, we have developed a mass spectrometric approach to characterize HLA-B*0702 peptides unique to or up-regulated on infected T cells. In this study, we identify 15 host proteins that are differentially presented on infected human T cells. Peptides with increased expression on HIV-infected cells were derived from multiple categories of cellular proteins including RNA binding proteins and cell cycle regulatory proteins. Therefore, comprehensive analysis of the B*0702 peptide repertoire demonstrates that marked differences in host protein presentation occur after HIV infection. 相似文献
11.
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
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.
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
14.
Cole AM 《Protein and peptide letters》2005,12(1):41-47
Cationic antimicrobial peptides and proteins are among the earliest molecular effectors of the innate arm of immunity in humans and other vertebrates. This review, inspired by recent emphasis on the development of topical preventatives for sexually transmitted infections, describes antimicrobial peptides and proteins in the context of microbicide design and development. Particular emphasis is placed on the defensin family of peptides. 相似文献
15.
Priscille Giron Loïc Dayon Fabrice David Jean-Charles Sanchez Keith Rose 《Journal of Proteomics》2009,71(6):647-661
The detection of low abundance proteins in complex biological samples is still a challenge in proteomics. To circumvent this obstacle a number of strategies involving the targeting of subsets of proteins or peptides were developed.The following work describes a new approach to simplify peptide mixtures by enrichment of N-terminal cysteinyl peptides (and to some extent N-terminal threonine peptides). The strategy is based on the use of an isolation method, so-called covalent capture (CC), which relies on the formation of a covalent bond between an N-terminal free cysteine or N-terminal free threonine and an aldehyde fixed on a solid support. The CC is highly selective. It permits extensive washes of the resin for the elimination of non-specific moieties before the release of the captured peptides. The application of the CC to proteomics was evaluated on tryptic peptides of standard proteins and test protein mixtures. The procedure demonstrated a significant reduction in sample complexity, while allowing the identification of N-terminal cysteinyl peptides hidden in the non-fractionated samples.This new strategy provides an efficient tool to existing proteomics approaches to reduce sample complexity and potentially identify less abundance proteins. 相似文献
16.
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
17.
《Journal of Proteomics》2008,71(6):647-661
The detection of low abundance proteins in complex biological samples is still a challenge in proteomics. To circumvent this obstacle a number of strategies involving the targeting of subsets of proteins or peptides were developed.The following work describes a new approach to simplify peptide mixtures by enrichment of N-terminal cysteinyl peptides (and to some extent N-terminal threonine peptides). The strategy is based on the use of an isolation method, so-called covalent capture (CC), which relies on the formation of a covalent bond between an N-terminal free cysteine or N-terminal free threonine and an aldehyde fixed on a solid support. The CC is highly selective. It permits extensive washes of the resin for the elimination of non-specific moieties before the release of the captured peptides. The application of the CC to proteomics was evaluated on tryptic peptides of standard proteins and test protein mixtures. The procedure demonstrated a significant reduction in sample complexity, while allowing the identification of N-terminal cysteinyl peptides hidden in the non-fractionated samples.This new strategy provides an efficient tool to existing proteomics approaches to reduce sample complexity and potentially identify less abundance proteins. 相似文献
18.
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
19.
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
20.
Intrinsically disordered proteins have a wide variety of important functional roles. However, the relationship between sequence and function in these proteins is significantly different than that for well-folded proteins. In a previous work, we showed that the propensity to be disordered can be recognized based on sequence composition alone. Here that analysis is furthered by examining the relationship of disorder propensity to sequence complexity, where the metrics for these two properties depend only on composition. The distributions of 40 amino acid peptides from both ordered and disordered proteins are graphed in this disorder-complexity space. An analysis of Swiss-Prot shows that most peptides have high complexity and relatively low disorder. However, there are also an appreciable number of low complexity-high disorder peptides in the database. In contrast, there are no low complexity-low disorder peptides. A similar analysis for peptides in the PDB reveals a much narrower distribution, with few peptides of low complexity and high disorder. In this case, the bounds of the disorder-complexity distribution are well defined and might be used to evaluate the likelihood that a peptide can be crystallized with current methods. The disorder-complexity distributions of individual proteins and sets of proteins grouped by function are also examined. Among individual proteins, there is an enormous variety of distributions that in some cases can be rationalized with regard to function. Groups of functionally related proteins are found to have distributions that are similar within each group but show notable differences between groups. Finally, a pattern matching algorithm is used to search for proteins with particular disorder-complexity distributions. The results suggest that this approach might be used to identify relationships between otherwise dissimilar proteins. 相似文献