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Results for “virtual protein profiling”

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PubMed2005

Potential for using isotopically altered metalloproteins in species-specific isotope dilution analysis of proteins by HPLC coupled to inductively coupled plasma mass spectrometry.

The production and evaluation of an isotopically enriched metalloprotein standard for use as a calibrant in species-specific isotope dilution analysis by HPLC coupled to inductively coupled plasma mass spectrometry is described. Using a model system involving the copper-containing protein rusticyanin (Rc) from the bacterium Acido-thiobacillus ferrooxidans, it was possible to demonstrate the analytical conditions that could be used for the measurement of metalloproteins by on-line IDMS analysis. Rc was chosen because it is a well-characterized protein with an established amino acid sequence and can be produced in suitable quantities using a bacterial recombinant system. Three different forms of the protein were studied by organic and inorganic mass spectrometry: the native form of the protein containing a natural isotopic profile for copper, an isotopically enriched species containing virtually all of its copper as the 65Cu isotope, and the nonmetalated apo form. Incorporation of the copper isotopes into the apo form of the protein was determined using a UV-vis spectrophotometric assay and shown to be complete for each of the copper-containing species. The experimental conditions required to maintain the conformational form of the protein with a nonexchangeable copper center were established using +ve electrospray mass spectrometry. A pH 7.0 buffer was found to afford the most appropriate conditions, and this was then used with HPLC-ICP-MS to verify the stability of the copper center by analysis of mixtures of different isotopic solutions. No exchange of the enriched copper isotope from Rc with an added naturally abundant inorganic copper cation was observed under a neutral pH environment, indicating that species-specific ID-MS analysis of metalloproteins is possible.

Acidithiobacillus thiooxidans↗

PubMed1996

Differential protein profiles reflect the different lifestyles of symbiotic and aposymbiotic Anthopleura elegantissima, a sea anemone from temperate waters

Mutualistic associations are prevalent in virtually all environments yet relatively little is known about their complex biochemical and molecular integration and regulation. The endosymbiosis between cnidarians such as the sea anemone Anthopleura elegantissima and the photosynthetic dinoflagellate Symbiodinium californium, in which the algal symbionts are housed in vacuoles within animal endodermal cells, is an ideal model for the study of highly integrated associations at the biochemical and molecular levels. This study describes differential protein synthesis between symbiotic A. elegantissima, collected from environments with high levels of light in the intertidal zone and A. elegantissima that naturally lack symbionts (aposymbiotic), collected from nearby deep-shade habitats. Two-dimensional gel electrophoresis profiles of both steady-state and newly synthesized proteins were compared between the two types of animals using scanning densitometry and image analysis. Symbiotic and aposymbiotic animals share a majority of proteins; however, striking differences in several abundant proteins in steady-state profiles occur. Two proteins are unique to symbiotic animals, one at 32 kDa with an isoelectric point (pI) of 7.9 and another at 31 kDa, pI 6.3. Levels of six proteins with an apparent molecular mass of 25 kDa and pI values ranging from 4.8 to 5.5 are greatly enhanced in aposymbiotic animals. Furthermore, profiles of newly synthesized proteins from symbiotic animals contain a unique cluster of proteins ranging from 25 to 30 kDa and pI 6.6 to 6.9. These marked differences in protein profiles must be a reflection either of underlying differences in the regulation of gene expression or in post-translational modification of common proteins. Identifying the symbiosis-specific products present in A. elegantissima and identifying the inter-partner signaling and cues that result in differential expression will provide an insight into the understanding of these highly integrated associations.

Journal Article↗

PubMed2006

Altered protein profile in chronic myeloid leukemia chronic phase identified by a comparative proteomic study.

Chronic myeloid leukemia is a hematological disorder in which the Ph chromosome is a marker of the disease, detected virtually in all cases. The chimeric transcripts encode a 210-kDa chimeric protein with altered tyrosine kinase activity, responsible for the disease phenotype. In this work, we tried to identify which are the molecular changes common to chronic phase patients, those that represent the chronic phase molecular phenotype. To address this problem we analyzed through a comparative proteomic approach, several CML bone marrow cells protein profile from patients in chronic phase and healthy bone marrow donors. From these results, we identified 31 differentially expressed proteins. Among these proteins, we pointed out c-Myc binding protein 1, 53BP1, Mdm4, OSBP-related protein 3 and Mortalin as putative candidates to BCR-ABL targets in chronic phase. Moreover, we describe for the first time the cytoplasmic protein map from bone marrow cells that helped in the elucidation of the changes we were looking for.

Adult↗

PubMed1993

Polypeptides of Treponema pallidum: progress toward understanding their structural, functional, and immunologic roles. Treponema Pallidum Polypeptide Research Group.

Treponema pallidum subsp. pallidum, the spirochete that causes syphilis, is unusual in a number of respects, including its small genome size, inability to grow under standard in vitro culture conditions, microaerophilism, apparent paucity of outer membrane proteins, structurally complex periplasmic flagella, and ability to evade the host immune responses and cause disease over a period of years to decades. Many of these attributes are related ultimately to its protein content. Our knowledge of the activities, structure, and immunogenicity of its proteins has been expanded by the application of recombinant DNA, hybridoma, and structural fractionation techniques. The purpose of this monograph is to summarize and correlate this new information by using two-dimensional gel electrophoresis, monoclonal antibody reactivity, sequence data, and other properties as the bases of polypeptide identification. The protein profiles of the T. pallidum subspecies causing syphilis, yaws, and endemic syphilis are virtually indistinguishable but differ considerably from those of other treponemal species. Among the most abundant polypeptides are a group of lipoproteins of unknown function that appear to be important in the immune response during syphilitic infection. The periplasmic flagella of T. pallidum and other spirochetes are unique with regard to their protein content and ultrastructure, as well as their periplasmic location. They are composed of three core proteins (homologous to the other members of the eubacterial flagellin family) and a single, unrelated sheath protein; the functional significance of this arrangement is not understood at present. Although the bacterium contains the chaperonins GroEL and DnaK, these proteins are not under the control of the heat shock regulon as they are in most organisms. Studies of the immunogenicity of T. pallidum proteins indicate that many may be useful for immunodiagnosis and immunoprotection. Future goals in T. pallidum polypeptide research include continued elucidation of their structural locations and functional activities, identification and characterization of the low-abundance outer membrane proteins, further study of the immunoprotective and immunodiagnostic potential of T. pallidum proteins, and clarification of the roles of treponemal proteins in pathogenesis.

Amino Acid Sequence↗

PubMed1991

Molecular techniques for studying the epidemiology of infection by Helicobacter pylori.

The efficacy of one-dimensional sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) of whole-cell protein patterns for fingerprinting isolates of Helicobacter pylori was assessed by means of computerized numerical analysis. Virtually all strains were found to have unique, stable, and reproducible protein profiles. The application of this technique to a collection of isolates from eight patients showed clearly that each harboured a distinct strain that was present before treatment and persisted after treatment. This suggests that relapse was due to recrudescence of the same strain rather than re-infection with a different strain. Minor differences in protein banding profiles within sets of isolates from the same patient were evident, and this was confirmed by means of both two-dimensional PAGE protein patterns and restriction endonuclease analysis of DNA on the same strains.

DNA Fingerprinting↗

PubMed1984

Drug residue formation from ronidazole, a 5-nitroimidazole. VII. Comparison of protein-bound products formed in vitro and in vivo.

In vivo experiments were conducted with ronidazole radiolabelled in the 2-14CH2-, 4,5-14C-, N-14CH3- and 4-3H-positions. The hepatic protein-bound residues, assessed by the radioactivity of exhaustively washed protein samples, were independent of the radiolabel position and occurred with 4-3H loss (greater than 80%) in excellent agreement to previous results obtained in vitro with anaerobic incubations of liver microsomes (Miwa et al., Chem. Biol. Interact., 41 (1982) 297). HPLC analysis of acid hydrolyzed in vivo protein-bound residues, obtained from [2-14CH2] ronidazole, produced a radiochromatographic profile which was virtually identical to that obtained from a similarly treated in vitro sample. Moreover, almost quantitative (76-96%) liberation of radiolabelled methylamine was obtained from hydrolysates of in vivo and in vitro residue samples formed from [N-14CH3] ronidazole. With 4,5-ring labeled ronidazole the distribution of total radioactivity of the protein hydrolysate on cation exchange resin and the fraction of the residue recovered as oxalic acid were nearly identical for the in vivo and in vitro products. We interpret these data to indicate that ronidazole alkylates proteins with retention of most of the carbon framework of the molecule, in vivo. It is also concluded that the in vitro model, previously used to examine the mechanism of protein alkylation, accurately reflects the salient process initially occurring in the intact animal during the formation of protein-bound residues of this drug.

Alkylation↗

PubMed2006

Single amino acid residue changes in subsite -1 of inulosucrase from Lactobacillus reuteri 121 strongly influence the size of products synthesized.

Bacterial fructansucrase enzymes belong to glycoside hydrolase family 68 and catalyze transglycosylation reactions with sucrose, resulting in the synthesis of fructooligosaccharides and/or a fructan polymer. Significant differences in fructansucrase enzyme product specificities can be observed, i.e. in the type of polymer (levan or inulin) synthesized, and in the ratio of polymer versus fructooligosaccharide synthesis. The Lactobacillus reuteri 121 inulosucrase enzyme produces a diverse range of fructooligosaccharide molecules and a minor amount of inulin polymer [with beta(2-1) linkages]. The three-dimensional structure of levansucrase (SacB) of Bacillus subtilis revealed eight amino acid residues interacting with sucrose. Sequence alignments showed that six of these eight amino acid residues, including the catalytic triad (D272, E523 and D424, inulosucrase numbering), are completely conserved in glycoside hydrolase family 68. The other three completely conserved residues are located at the -1 subsite (W271, W340 and R423). Our aim was to investigate the roles of these conserved amino acid residues in inulosucrase mutant proteins with regard to activity and product profile. Inulosucrase mutants W340N and R423H were virtually inactive, confirming the essential role of these residues in the inulosucrase active site. Inulosucrase mutants R423K and W271N were less strongly affected in activity, and displayed an altered fructooligosaccharide product pattern from sucrose, synthesizing a much lower amount of oligosaccharide and significantly more polymer. Our data show that the -1 subsite is not only important for substrate recognition and catalysis, but also plays an important role in determining the size of the products synthesized.

Amino Acid Substitution↗

PubMed2004

Topographic regulation of phosphorylation in giant neurons of the squid, Loligo pealei: role of phosphatases.

In previous studies of phosphorylation in squid stellate ganglion neurons, we demonstrated that a specific multimeric phosphorylation complex characterized each cellular compartment. Although the endogenous protein profile of cell body extracts (giant fiber lobe, GFL), as determined by Coomassie staining, was similar to that of axoplasm from the giant axon, in this study we show that the protein phosphorylation profiles are qualitatively different. Whereas many axoplasm proteins were phosphorylated, including most cytoskeletal proteins, virtually all phosphorylation in perikarya was confined to low molecular weight compounds (<6 kDa). Because phosphorylation of exogenous substrates, histone and casein, was equally active in extracts from both compartments, failure to detect endogenous protein phosphorylation in cell bodies was attributed to the presence of more active phosphatases. To further explore the role of phosphatases in these neurons, we studied phosphorylation in the presence of serine/threonine and protein tyrosine phosphatase (PTP) inhibitors. We found that phosphorylation of axonal cytoskeletal proteins was modulated by okadaic acid-sensitive ser/thr phosphatases, whereas cell body phosphorylation was more sensitive to an inhibitor of protein tyrosine phosphatases, such as vanadate. Inhibition of PTPs by vanadate stimulated endogenous phosphorylation of GFL proteins, including cytoskeletal proteins. Protein tyrosine kinase activity was equally stimulated by vanadate in cell body and axonal whole homogenates and Triton X-100 free soluble extracts, but only the Triton X soluble fraction (membrane bound proteins) of the GFL exhibited significant activation in the presence of vanadate, suggesting higher PTP activities in this fraction than in the axon. The data are consistent with the hypothesis that neuronal protein phosphorylation in axons and cell bodies is modulated by different phosphatases associated with compartment-specific multimeric complexes.

Animals↗

PubMed1978

Isolation and partial characterization of rat CNS axolemma enriched fractions.

Axolemma-enriched fractions were prepared from rat brain by osmotic shock of a purified preparation of myelinated axons and subsequent separation of myelin, two axolemma-enriched fractions and myelin-free axons by density gradient centrifugation. Compared with the starting whole homogenate, the fractions were enriched in specific activity of Na+K+ ATPase, acetylcholinesterase, 5'nucleotidase as well as 2',3'-cyclic nucleotide 3'phosphohydrolase. Compared with myelin, the axolemmal fractions are greatly enriched in high molecular weight proteins. The 1.0/1.2 fraction has a predominant peak of fucose-labeled glycoprotein with a molecular weight between that of the myelin associated glycoprotein and the Wolfgram protein which is absent from the myelin glycoprotein profile. Polyacrylamide gel electrophoresis showed that the protein profile of myelin isolated by this procedure was similar to that of myelin isolated by other procedures and that the myelin specific basic and proteolipid proteins were virtually absent in the axolemma-enriched fractions. Both axolemma fractions were enriched in higher MW proteins, some of which resembled proteins in the myelin protein profile. Both axolemma-enriched fractions specifically bind between 2 and 3 pmoles of [3H]tetrodotoxin per mg protein. The axolemma-enriched fractions incorporated [3H]leucine and [14C]fucose exclusively into high molecular weight proteins and glycoproteins. In contrast myelin concomitantly isolated with the axolemma-enriched fractions had a significant amount of [3H]leucine labeled protein in myelin proteolipid and basic proteins. In addition to the myelin associated g-ycoprotein the [14C]fucose labeled a glycoprotein of slightly larger apparent molecular weight than proteolipid protein was found in the myelin fraction while the comparable labeled glycoprotein was absent in the axolemma-enriched fractions. The possible extent of contamination of these fractions by myelin or myelin subfractions and relationship of these axolemma-enriched fractions to other axolemma preparations are discussed.

2',3'-Cyclic-Nucleotide Phosphodiesterases↗

PubMed1980

Intracytoplasmic neuronal inclusions in the human thalamus. Light-microscopic, histochemical, and ultrastructural observations.

Intracytoplasmic eosinophilic inclusions were found by light microscopy in the thalamic neurons of 35 consecutive normal adult brains and in a case of myotonic dystrophy, but not in six newborn children, including one with myotonic dystrophy. Histochemical tests suggested a protein composition. Ultrastructurally, the inclusions were composed of stacks of parallel alternating dark and light rectilinear profiles not surrounded by a limiting membrane. Such inclusions are a virtually constant finding in the adult human thalamus and probably represent sites of neuronal protein storage.

Adult↗

PubMed1984

Purification, characterization, and pituitary regulation of the sex-specific cytochrome P-450 15 beta-hydroxylase from liver microsomes of untreated female rats.

A sex-differentiated form of cytochrome P-450 has been purified to electrophoretic homogeneity from liver microsomes of untreated female rats. The purified preparation contained 17 nmol of P-450/mg of protein and had a minimum molecular weight of 50,000. The final preparation was active in the hydroxylation of 5 alpha-[3H]androstane-3 alpha, 17 beta-diol 3,17-disulfate in the 15 beta position, with a turnover number of 2.6 nmol/min/nmol P-450 and is designated "P-450 15 beta" on the basis of this activity. Cytochrome P-450 15 beta is isolated essentially in the low-spin state and has a CO-reduced difference spectral maximum at 449 nm. Comparison of the female protein with the corresponding P-450 fraction from male rats revealed an absence of the 15 beta band in the male electrophoretic profile. Specific antibodies to isozyme 15 beta were used with a Western blot technique to demonstrate the virtual absence of the protein in male microsomes. This method was also used to demonstrate that hypophysectomy of female rats resulted in undetectable levels of the 15 beta-hydroxylase, while continuous infusion of growth hormone to normal male animals increased the 15 beta-hydroxylase level to that of female. P-450 15 beta is proposed to be the enzyme responsible for the predominance of 15 beta-hydroxylated steroid sulfate metabolites in excreta of female rats, and their absence in males. The same purification procedure for female rat liver microsomes also yielded another purified cytochrome P-450 characterized by a minimum molecular weight of 52,500, termed P-450 DEa, which was inefficient in the 15 beta-hydroxylation of 5 alpha-[3H]androstane-3 alpha, 17 beta-diol 3, 17-disulfate. No evidence was obtained that this form is sexually differentiated.

Animals↗

PubMed2006

Cardiac genomic response following preconditioning stimulus.

This review focuses on the genomic response following a preconditioning stimulus. Initial studies demonstrated that classical ischemic preconditioning mediated by cyclic episodes of short durations of reversible ischemia and reperfusion could result in the reprogramming of gene expression. Some of these genes are translated into proteins during the late preconditioning or so-called "second window of protection". Subsequent studies determined a unique similarity of the expressed gene profiles between diverse varieties of preconditioning including ischemic/hypoxic, heat shock, and oxidative stress. The most common genes that are expressed by virtually any kind of stress conditioning include antioxidants like superoxide dismutase, glutathione peroxidase and heme oxygenase and heat shock proteins such as HSP70. At a later date, differential display and subtractive hybridization techniques revealed the identities of many other genes including those belonging to mitochondrial respiratory chain such as ATPases. More recently, gene array profiles using gene chips determined several other genes triggered by preconditioning including the mitochondrial genes. The results of the studies present in the literature clearly indicate the existence of a strong resemblance between the patterns of gene expression profiles induced by diverse preconditioning stimuli, oxidative stress being situated at the cross-roads of all forms of the stresses. Redox signaling appears to be responsible for the conversion of the ischemia/reperfusion-induced "death signal" into preconditioning-mediated "survival signal".

Animals↗

PubMed1985

Synthesis of aerobactin and a 76,000-dalton iron-regulated outer membrane protein by Escherichia coli K-12-Shigella flexneri hybrids and by enteroinvasive strains of Escherichia coli.

One of the chromosomal segments associated with the virulence of Shigella flexneri and transferred to Escherichia coli K-12 by conjugation has been shown to code for the production of aerobactin and for the synthesis of an iron-regulated 76,000-dalton (76K) outer membrane protein. Analysis of various E. coli K-12-S. flexneri transconjugants showed that the genes involved with the synthesis of aerobactin and with the production of the 76K protein were linked to the mtl region of the S. flexneri chromosome. S. flexneri itself synthesized a 76K protein in its outer membrane under iron restriction as well as traces of 81K and 74K proteins. An examination of four enteroinvasive strains of E. coli showed that each produced aerobactin and a 76K outer membrane protein during iron-restricted growth. The profile of the iron-regulated proteins expressed by the enteroinvasive strains of E. coli was virtually identical to that expressed by the laboratory-constructed E. coli K-12-S. flexneri hybrids under the same growth conditions.

Animals↗

PubMed1999

BOCILLIN FL, a sensitive and commercially available reagent for detection of penicillin-binding proteins.

We describe a new, sensitive, rapid, and nonradioactive method involving the use of the commercially available BOCILLIN FL, a fluorescent penicillin, as a labeling reagent for the detection and study of penicillin-binding proteins (PBPs). This method allowed rapid detection of 30 ng of a purified PBP protein under UV light and of 2 to 4 ng of the protein with the aid of a FluorImager. This method also allowed rapid determination of the PBP profiles of Escherichia coli, Pseudomonas aeruginosa, and Streptococcus pneumoniae. The PBP profiles obtained are virtually identical to those reported previously with 3H-, 14C-, or 125I-labeled penicillin. Using this method enabled us to determine the 50% inhibitory concentrations of the penicillin-sensitive and -resistant PBP2x proteins of S. pneumoniae for penicillin G, thereby allowing a direct evaluation of their relative affinities for penicillin G. Finally, this method also allowed us to compare relative affinities of a PBP2x protein for different beta-lactam antibiotics with the aid of fluorescence polarization technology and to monitor a PBP2x protein during purification.

Bacteria↗

PubMed1999

Application of mass spectrometry for target identification and characterization.

Mass spectrometry-based methodologies span the vast expanse of drug discovery. Both electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) support proteomics-based research projects by identifying proteins separated and isolated by polyacrylamide gel electrophoresis. MALDI-MS-based surface scanning of one-dimensional isoelectric focusing gels, "virtual 2-D gel electrophoresis," represents a potentially high throughput means to map proteins and to determine protein profiles. Mass spectrometry can also be used to directly study the covalent and noncovalent interactions of drug molecules and biomolecule targets. Drug binding examples discussed include the binding of covalent and noncovalent inhibitors to src SH2 domain protein, and the interaction of aminoglycoside antibiotic neomycin and HIV Tat peptide-TAR RNA.

Drug Design↗

PubMed2026

Identifying JAK2 and ANXA5 as Key Genes Linking Obstructive Sleep Apnea and Oxidative Stress via Machine Learning and Multilayer Transcriptomic Integration With Functional Validation.

Obstructive sleep apnea (OSA) is a common and severe sleep disorder closely associated with oxidative stress (OS). This study aims to identify and validate potential OS-related genes associated with OSA through bioinformatics methods. We successfully identified OS-related differentially expressed genes (OS-DEGs) by combining the limma test, weighted correlation network analysis (WGCNA), and OS-related genes from the GeneCards database. Key genes and potential biological roles were further identified using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), enrichment analysis, protein-protein interaction (PPI) network analysis, Lasso regression analysis, random forest algorithm, and support vector machine recursive feature elimination (SVM-RFE) method. Evaluate and validate the accuracy of key genes through receiver operating characteristic (ROC) curve analysis. The human single-cell RNA sequencing (scRNA-seq) dataset is used for cell classification annotation, analysis of key gene single-cell expression profiles, and virtual gene knockout experiments based on the scTenifoldKnk algorithm. Integrating scRNA-seq sequencing, pseudotime trajectory inference, cell-cell communication analysis, and bulk immune infiltration deconvolution reveals monocyte subtype remodeling in OSA. Finally, the expression levels of key genes in clinical samples were validated using real-time quantitative PCR (RT-qPCR) and Western blotting. A total of 57 common DEGs, indicating significant enrichment in OS, inflammation, and tumor pathways, particularly prominent in the immunometabolism pathway. By integrating DEGs, WGCNA, PPI results, and machine learning methods, key genes Janus kinase 2 (JAK2) and ANXA5 were screened out. JAK2 was significantly upregulated under disease conditions, while ANXA5 was significantly downregulated. ROC curve exhibited high accuracy (area under the curve [AUC] > 0.85). Human scRNA-seq analysis revealed that key genes were predominantly highly expressed in monocytes. Virtual knockout experiments demonstrated that these key genes play a crucial role in regulating immune responses and inflammatory reactions. PPI networks and enrichment analysis verified that downstream genes S100P, ALOX5AP, PROK2, and PADI4 may collaboratively participate in immune response and inflammation regulation. Finally, clinical sample experiment further validated the results of bioinformatics analysis. This study provides new research insights for the diagnosis, mechanism research, and treatment development of OSA in the future by integrating multilayer transcriptomic and machine learning techniques.

Humans↗

PubMed2005

A microarray data-based semi-kinetic method for predicting quantitative dynamics of genetic networks.

BACKGROUND: Elucidating the dynamic behaviour of genetic regulatory networks is one of the most significant challenges in systems biology. However, conventional quantitative predictions have been limited to small networks because publicly available transcriptome data has not been extensively applied to dynamic simulation. RESULTS: We present a microarray data-based semi-kinetic (MASK) method which facilitates the prediction of regulatory dynamics of genetic networks composed of recurrently appearing network motifs with reasonable accuracy. The MASK method allows the determination of model parameters representing the contribution of regulators to transcription rate from time-series microarray data. Using a virtual regulatory network and a Saccharomyces cerevisiae ribosomal protein gene module, we confirmed that a MASK model can predict expression profiles for various conditions as accurately as a conventional kinetic model. CONCLUSION: We have demonstrated the MASK method for the construction of dynamic simulation models of genetic networks from time-series microarray data, initial mRNA copy number and first-order degradation constants of mRNA. The quantitative accuracy of the MASK models has been confirmed, and the results indicated that this method enables the prediction of quantitative dynamics in genetic networks composed of commonly used network motifs, which cover considerable fraction of the whole network.

Amino Acid Motifs↗

PubMed2002

Prediction, assessment and validation of protein interaction maps in bacteria.

High-throughput proteomics technologies, especially the yeast two-hybrid system, produce large volumes of protein-protein interaction data organized in networks. The complete sequencing of many genomes raises questions about the extent to which such networks can be transferred between organisms. We attempted to answer this question using the experimentally derived Helicobacter pylori interaction map and the recently described interacting domain profile pair (IDPP) method to predict a virtual map for Escherichia coli. The extensive literature concerning E.coli was used to assess all predicted interactions and to validate the IDPP method, which clusters protein domains by sequence and connectivity similarities. The IDPP method has a much better heuristic value than methods solely based on protein homology. The IDPP method was further applied to Campylobacter jejuni to generate a virtual interaction map. An in-depth comparison of the chemotaxis pathways predicted in E.coli and C.jejuni led to the proposition of new functional assignments. Finally, the prediction of protein-protein interaction maps across organisms enabled us to validate some of the interactions on the original experimental map.

Bacterial Proteins↗