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- Proteomics/Introduction to Proteomics
- What is Proteomics?
- Proteomics | SCIEX
Wheat proteins causes allergic reactions in susceptible individuals that have been traced in foods to protect wheat-sensitive individuals using commercially available ELISA kits Western blotting is an important and powerful technique for detection of low abundance proteins that involve the separation of proteins using electrophoresis, transfer onto nitrocellulose membrane and the precise detection of a target protein by enzyme-conjugated antibodies Western blotting is a dominant tool for antigen detection from various microorganisms and is quite helpful in diagnosis of infectious diseases.
The seroprevalence of Herpes Simplex Virus type 2 HSV-2 in African countries was investigated by measuring the specific immunoglobulin G in the sera of patients Leishmania donovani is responsible for visceral leishmaniasis, which is classically diagnosed by the presence of Hsp83 and Hsp70 antigens in the bone marrow, spleen and liver Western blotting was carried out by Li et al.
Kollerova et al. The expression of PfCP Specific IgE against Ara h1, Ara h2 and Ara h3 was determined in peanut allergic patients through western blotting Edman sequencing was developed by Pehr Edman in to determine the amino-acid sequence in peptides or proteins. The method comprises chemical reactions that eliminate and identify amino acids residue that is present at the N-terminus of polypeptide chain. Edman sequencing played a major role in development of therapeutic proteins and quality assurance of biopharmaceuticals Brucella suis survive and replicate in macrophage due to the acidification.
The proteins that are involved in this acidification were identified.
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Edman degradation and comparison of 13 N-terminal amino-acid sequences revealed that these were signal peptides for its periplasmic location. The protein in B. The causative agent of hemorrhagic fever, Lassa virus belongs to family of Arenaviridae. The Lassa virus synthesis glycoproteins which are cleaved into GP-1 amino-terminal subunit and GP-2 Carboxy-terminal subunit after translation and are primarily involved in pathogenesis.
The prevalence of sesame seed allergy has been increasing due to the use of bakery products and fast-food. IgE binding epitopes of these proteins were identified that might be helpful in immunotherapeutic approaches The proteins from leaf sheaths of rice were extracted and analyzed through MS and Edman sequencing to determine its function. The amino-acid sequence of majority of proteins analyzed by both techniques have similar results, therefore suggesting the use of these techniques in combination for the identification of plant protein Protein microarrays also known as protein chips are the emerging class of proteomics techniques capable of high-throughput detection from small amount of sample.
Protein microarrays can be classified into three categories; analytical protein microarray, functional protein microarray and reverse-phase protein microarray Antibody microarray is the most representative class of analytical protein microarray. After antibody capture, proteins are detected by direct protein labeling. These are typically used to measure the expression level and binding affinities of proteins 17 , 61 , High-throughput proteome analysis of cancer cells was carried out through antibody microarray for differential protein expression in tissues derived from squamous carcinoma cells of oral cavity Antibody array was also used for protein profiling of bladder cancer Microarray immunoassay was used for detection of Staphylococcal enterotoxin B, cholera toxin, Bacillus globigii and B.
Analytical and experimental approaches have been developed for identification of cellular signaling pathways and to characterize the plant kinases through protein microarray MAPKs are highly conserved single transduction and universal molecules in plants that respond to wide range of extracellular stimuli Functional protein microarray is constructed by means of purified protein, thus permits the study of various interactions including protein—DNA, protein—RNA and protein—protein, protein—drug, protein—lipid, enzyme—substrate relationship The first use of functional protein microarray was to analyze the substrate specificity of protein kinases in yeast Functional protein microarray characterized the functions of thousands of proteins.
The protein—protein interaction of A. Cell lysates obtained from different cell states are arrayed on nitrocellulose slide that are probed with antibodies against target proteins.
Afterwards, antibodies are detected with fluorescent, chemiluminescent and colorimetric assays. For protein quantification, reference peptides are printed on slides. These microarrays are used to determine the altered or dysfunction protein indicative of a certain disease The analysis of hematopoietic stem cell and primary leukemia samples through reverse-phase protein microarray was found to be highly reproducible and reliable for large-scale analysis of phosphorylation state and protein expression in human stem cells and acute myelogenous leukemia cells Reverse-phase protein microarray approach was evaluated for quantitative analysis of phosphoproteins and other cancer-related proteins in non-small cell lung cancer NSCLC cell lines by monitoring the apoptosis, DNA damage, cell-cycle control and signaling pathways SDS-PAGE is a high resolving technique for the separation of proteins according to their size, thus facilitates the approximation of molecular weight.
Proteins are capable of moving with electric field in a medium having a pH dissimilar from their isoelectric point. Different proteins in mixture migrate with different velocities according to the ratio between its charge and mass. However, addition of sodium dodecyl sulfate denatures the proteins, therefore separate them absolutely according to molecular weight The protein profiling of Mycoplasma bovis and Mycoplasma agalactiae through SDS-PAGE has high diagnostic value as these species are difficult to differentiate with routine diagnostic procedures The outer membrane proteins from E.
It exhibited varied degree of susceptibility to the human serum. Extracellular protein profile of Staphylococcus spp. The antigenic proteins of Streptococcus agalactiae have been characterized to test the immunogenicity of mastitis vaccine The cleome spp. The comparative analysis of leaf and seed proteins of cleome spp. The profiling of seed and leaf storage proteins of chickpea Cicer arientinum was conducted under drought stress and non-stress conditions The seed storage proteins of Brassica species are also identified to evaluate the genetic divergence in different genotypes The influence of heat treatment and addition of demineralized whey on the soluble protein composition of the skim milk was investigated [ 88 ].
High molecular weight complexes were formed during the addition of demineralized whey as well as heat treatment which was determined by SDS-PAGE Large-scale production of insulin is helpful for the management of diabetes, therefore different approaches and species have been used for the production of insulin. Elamin et al. The two-dimensional polyacrylamide gel electrophoreses 2D-PAGE is an efficient and reliable method for separation of proteins on the basis of their mass and charge. The proteins are separated by charge in the first dimension while in second dimension separated on the basis of differences between their mass.
Proteomics/Introduction to Proteomics
The 2-DE is successfully applied for the characterization of post-translational modifications, mutant proteins and evaluation of metabolic pathways. Neidhardt and van Bogelen introduced the highly sensitive technique of 2-DE into the bacterial physiology The membrane proteins from the cell wall of Listeria innocua and Listeria monocytogenes involved in the host—pathogen interactions were analyzed with 2-DE and 30 different proteins of two strains were identified This approach was useful for the comparative study of exotoxins and virulence factors released by enterotoxigenic strains of two food-derived Staphylococcus aureus strains Pseudomonas aeruginosa secrete numerous proteins during different stages of infection as seen in isolates obtained from cystic fibrosis patients Large number of proteins were detected during the seed development in Ocotea catharinensis , and profile was constructed by characterizing these proteins during each developmental stage Protein extraction from grapes is challenging due to the low concentration of proteins, high activity of proteases and high level of interfering compounds such as polyphenols, flavonoids, terpenes, lignans and tannins; however, Marsoni et al.
Islam et al. The proteins are also involved in regulation, adaptation to harsh condition and transportation The characterization of proteins expressed in rat neurons have been carried to understand the pathogenesis of West Nile virus The plasma membrane responds to the biotic and abiotic stress in plants, therefore the characterization of plasma proteins provides new perception about the plant-specific biological functions. The role of apoplastic proteins of day-old rice plants in salt stress response was investigated. For differential analysis, soluble apoplastic proteins from rice shoot stem were extracted and compared with untreated and were found to be involved in oxidation-reduction reaction, carbohydrate metabolism and protein degradation and processing During ovule development of Pinus tabuliformis , female gametophyte cellularization is a vital process regulated by multiple proteins, which were first extracted in anaphase and prophase then separated through 2D-DIGE The biological drugs produced during cell culture technology constitute host cell proteins HCP as most important group of impurities.
The HCP has diverse molecular and immunological properties and should be effectively monitored and removed during downstream processing. The quantitative changes in red blood cell membrane proteins in sickle cell disease were analyzed and the contents of 49 gel spots were found altered by 2. The 2-DE remains a method of choice in proteomic research, though certain limitations enervate its potential as a principal separation technique in modern proteomics.
Therefore, the state of the art instrumentation and techniques are rapid expanding as a new means of gel-free analytical techniques. The advancement of MS coupled with shotgun proteomics can find newer directions for sensitive and high quantity protein profiling with more accurate quantification. The chemical label-based approaches remained popular in quantitative proteomics, these methods also have certain drawbacks.
The quantitative plant proteomics is more challenging due to problems associated with protein extraction, abundance of proteins in some plants tissues and the lack of well-marked genome sequences. The higher resolution power of MS, exact mass measurements, higher scanning rates and precise chromatogram alignment are essential feature for the successful use of MS in proteomics The ICAT is an isotopic labeling method in which chemical labeling reagents are used for quantification of proteins. The ICAT has also expanded the range of proteins that can be analyzed and permits the accurate quantification and sequence identification of proteins from complex mixtures.
The ICAT reagents comprise affinity tag for isolation of labeled peptides, isotopically coded linker and reactive group The combination of techniques offers comprehensive understanding of biological system and provides additional information.
The systemic proteome quantification was carried out possible through ICAT during cell cycle of Saccharomyces cerevisiae that supported the cognition of gene functions The levels of reactive nitrogen species and reactive oxygen species increase in living cells during abiotic and biotic stress. The reversible oxidation of protein residues may assist as redox sensors and signal transducers for transmission of anti-stress responses.
The thiol group on cysteine residue is sensitive to oxidative species and upon oxidation can modulate protein function.
What is Proteomics?
ICAT reagents precisely react with thiol group of cysteine residues, therefore the technique coupled with MS is useful to quantify the thiol-containing redox proteins The tumor-specific proteins were analyzed through ICAT and MS from the aspirated fluid of breast tumor patients at earlier stages. Beta-globin, hemopexin, lipophilin B and vitamin D-binding proteins were overexpressed while Alpha2HS-glycoprotein was under expressed.
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It seems that ICAT has potent applications to designate appropriate biomarkers for cancer diagnosis SILAC is an MS-based approach for quantitative proteomics that depends on metabolic labeling of whole cellular proteome. The SILAC has been developed as an expedient technique to study the regulation of gene expression, cell signaling, post-translational modifications. Additionally, SILAC is a vital technique for secreted pathways and secreted proteins in cell culture More than 1, proteins were identified and quantified in the two tested states.
Moreover, 10 phosphorylation sties were quantified under phosphate starvation while 35 phosphorylation sites under growth on succinate Highly purified mutant adenovirus deficient in protein V internal protein component , wild-type adenovirus and recombinant virus were quantified through SILAC. Viral protein composition and abundance were constant in all types of viruses except virus deficient in protein V which also resulted in reduced amount of another viral core protein Expression of glutathione S-transferase was analyzed in response to abiotic stress due to salicylic acid and consequent proteins were quantified Salt stress response and protein dynamics in photosynthetic organism Chlamydomonas reinhardtii have been studied to establish the proteome turnover rate and changes in metabolism under salt stress conditions.
RuBisCO was found as the most prominent protein in C. Tissue regeneration is imperative in many diseases such as lung disease, heart failure and neurodegenerative disorders. The tissue regeneration and protein turnover rate were quantitatively analyzed in zebra fish. Proteome analysis showed that fin, intestine and liver have high regenerative capacity while heart and brain have the lowest.
The proteins in tissue regeneration were mainly involved in transport activity and catalytic pathways , This technique relies on labeling the protein with isobaric tags 8-plex and 4-plex for relative and absolute quantitation. The technique comprises labeling of the N-terminus and side chain amine groups of proteins, fractionated through liquid chromatography and finally analyzed through MS.
It is essential to find the gene regulation to understand the disease mechanism, therefore protein quantitation using iTRAQ is an appropriate method that helps to identify and quantify the protein simultaneously About membrane and cytosolic proteins were quantified during cellulosic hydrolysis. The quantified protein in cellulosic medium was involved in pentose phosphate pathway, glycolysis, citric acid cycle, starch, amino acid, fatty acid, purine, pyrimidine and energy metabolism.
Consequently, these proteins have a functional role in cell wall synthesis, transcription, translation and replication The huge amount of oxidative and hydrolytic enzymes is secreted by Phanerochaete chrysosporium that degrade lignin, cellulose and mixture of lignin and cellulose. The secretory proteins were quantified from P. The role of hydrogen peroxide H 2 O 2 in growth of wheat was identified through iTRAQ-based quantitative approach that showed that the increased concentration of H 2 O 2 restrained the growth of roots and seedlings of wheat.
Several proteins such as superoxide dismutase, intrinsic protein 1 and fasciclin-like arabinogalactan protein could possibly be involved in H 2 O 2 tolerance Membrane bound proteins of NK cells from CD3-depleted adult peripheral blood cells and umbilical cord blood stem cells were quantified. Ontology analysis exhibited that many of these proteins were involved in nucleic acid binding, cell signaling and mitochondrial functions Protein profiling was carried out in mouse liver regeneration following a partial hepatectomy.
A total of identified proteins, were quantified as well.
Proteomics | SCIEX
X-ray crystallography is the most preferred technique for three-dimensional structure determination of proteins. The highly purified crystallized samples are exposed to X-rays and the subsequent diffraction patterns are processed to produce information about the size of the repeating unit that forms the crystal and crystal packing symmetry.
X-ray crystallography has an extensive range of applications to study the virus system, protein—nucleic acid complexes and immune complexes. Further, the three-dimensional protein structure provides detailed information about the elucidation of enzyme mechanism, drug designing, site-directed mutagenesis and protein—ligand interaction ZipA and FtsZ are the vital components of spatial ring structure that facilitates cell division in E. ZipA is a membrane anchored protein while FtsZ is homologous of eukaryotic tubulin and their interaction is facilitated by C-terminal domains.
The structure of Norwalk virus that causes gastroenteritis in humans was determined through X-ray crystallography, which revealed that viral capsid consists of repeating units of single protein. The two domains; shell S domain and protruding P domain of capsid protein are connected by flexible hinge. These domains are the key determinants responsible of cell binding and strain specificity The movement of phospholipids, glycolipids, steroids and fatty acids between membranes occurs due to non-specific lipid transfer proteins nsLTPs. The comparative structure of maize nsLTP in complex with numerous ligands revealed variations in the volume of the hydrophobic cavity depending on the size of bound ligands The microsomal cytochrome P 3A4 catalyzes the drug—drug interaction in humans that induce or inhibit the enzymes and metabolically clear the clinically used drugs.
The protein structure was analyzed through X-ray crystallography that exhibited a large substrate binding cavity capable to oxidize huge substrates such as statins, cyclosporin, macrolide antibiotics and taxanes The X-ray crystallography revealed the 3D structure of recombinant horseradish peroxidase in complex with benzohydroxamic acid BHA. The electron density for BHA was detected in active site of peroxidase along with hydrophobic pocket adjacent to aromatic ring of the BHA The overall process comprises three steps.
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