Sequence and structural proteomics involve the large scale analysis of protein structure. Comparison among the sequence and structure of the protein enable the identification on the function of newly discovered genes (Proteoconsult, n.d.). It consists of two parallel goals which one of the goals is to determine three-dimensional structures of proteins. Determine the structure of the protein help to modeled many other structures by using computational techniques (Christendat et al., 2000). This approach is useful in phylogenetic distribution of folds and structural features of proteins (Christendat et al., 2000). Nuclear magnetic resonance (NMR) spectroscopy is one of the techniques that provide experimental data for those initiatives. It is best applied to proteins which are smaller than 250 amino acids (Yee et al., 2001). Although it is limited by size constraints and also lengthy data collection and analysis time, it is still recommended as it can deliver strong results. There are two types of NMR which are one-dimensional NMR and two-dimensional NMR. One-dimensional NMR provides enough information for assessing the folding properties of proteins (Rehm, Huber & Holak, 2002). It also helps to identify a mixture of folded and unfolded protein by observing both signal dispersion and prominent peak. Observation in one-dimensional spectrum also obtains information on molecular weight and aggregation of molecule under investigation. In spite of this, two-dimensional NMR are used for screening that reveal structural include binding, properties of proteins. It also provides important information for optimizing conditions for protein constructs that are amenable to structural studies (Rehm et al., 2002). NMR is a powerful tool which it w...
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...bioanalytical systems which based on electrochemiluminescence detection and evanescent field fluorescent detection showed the best sensitivities (Dupuy et al., 2009). The power of immunoblotting is extended with this method in order to provide a quantitative analysis of differential expression of active and parental proteins (Tibes et al., 2006). Moreover, by using RPPA, samples can be spotted at same time which is suitable for retrospective analysis of large number of specimens. This technique which can be used to analyze large number of proteins from each sample is suitable to analyze the population of cells that present in low numbers. On the other hand, this technique also has limitation which it only identifies to known proteins or targets only (Tibes et al., 2006). However, it stills a useful technique that use in the study of functional proteomics analysis.
Digestion of the haemolytic and non-haemolytic cells allowed for easier identification of fragments during electrophoresis analysis. Lane 12 in figure 3 show the size markers of SPP1 digested with EcoR1 while lanes 6 and 7 show samples of pK184hlyA and pBluescript digested with EcoR1 and Pst1. Lane 4 was loaded with plasmid DNA from haemolytic cells digested with EcoR1 and Pst1 while lane 5 was loaded with EcoR1 and Pst1 digested DNA from non-haemolytic cells. There was a lack of technical success in both lanes due to no bands appearing in lane 4 and only a single band appearing in lane 5. Theoretically, two bands should appear in both lanes after successful to allow for fragment identification. A possible explanation for the single, large fragment in lane 5 is that successful digestion did not take place and the plasmid was only cut at one restriction site leaving a large linear fragment of plasmid DNA. The absence of bands in lane 4 could be because there was not enough plasmid loaded into the lane. Another possibility could be that low plasmid yield as obtained when eluting the experimental samples in order to purify it. Lanes 8 and 9 belonged to another group and show technical success as two bands were present in both the haemolytic (lane 8) and non-haemolytic (lane 9) lanes. If the
Western blot has been a revolutionary technique for identifying the expression of proteins within relative molecular biological samples that shared the same ancestor. Moreover, the sensitivity and specificity of the western blot (Immunoblotting) enables it a common technique for determining specific protein levels in clinical samples. Since the antibody specific to the antigen immunospecificity), it enables the target protein to be identified. Western blotting can produce quantitative data about that protein, which in this case the difference between bands in each of the protein samples. The western blot is an analytical technique used to detect specific proteins in the given sample of tissue homogenate or extract. The proteins are then transferred to a membrane (in this case, nitrocellulose), where they are stained with antibodies specific to the target protein [1] [2].
The sequence of BRCA1 protein shows that there are quite a few of cysteine residues. These cysteine residues form disulfide bonds which help stabilize the secondary structure of the protein. The secondary structure of BRCA1 protein indicates that there are alpha helices and beta turns which are connected by loops and turns. The 3D structure of BRCA1/BARD1 RING-domain heterodimer is shown in figure 1.
Proteogenomics is a kind of science field that includes proteomics and genomics. Proteomic consists of protein sequence information and genomic consists of genome sequence information. It is used to annotate whole genome and protein coding genes. Proteomic data provides genome analysis by showing genome annotation and using of peptides that is gained from expressed proteins and it can be used to correct coding regions.Identities of protein coding regions in terms of function and sequence is more important than nucleotide sequences because protein coding genes have more function in a cell than other nucleotide sequences. Genome annotation process includes all experimental and computational stages.These stages can be identification of a gene ,function and structure of a gene and coding region locations.To carry out these processes, ab initio gene prediction methods can be used to predict exon and splice sites. Annotation of protein coding genes is very time consuming process ,therefore gene prediction methods are used for genome annotations. Some web site programs provides these genome annotations such as NCBI and Ensembl. These tools shows sequenced genomes and gives more accurate gene annotations. However, these tools may not explain the presence of a protein. Main idea of proteogenomic methods is to identify peptides in samples by using these tools and also with the help of mass spectrometry.Mass spectrometry searches translation of genome sequences rather than protein database searching. This method also annotate protein protein interactions.MS/MS data searching against translation of genome can determine and identify peptide sequences.Thus genome data can be understood by using genomic and transcriptomic information with this proteogenomic methods and tools. Many of proteomic information can be achieved by gene prediction algorithms, cDNA sequences and comparative genomics. Large proteomic datasets can be gained by peptide mass spectrophotometry for proteogenomics because it uses proteomic data to annotate genome. If there is genome sequence data for an organism or closely related genomes are present,proteogenomic tools can be used. Gained proteogenomic data provides comparing of these data between many related species and shows homology relationships among many species proteins to make annotations with high accuracy.From these studies, proteogenomic data demonstrates frame shifts regions, gene start sites and exon and intron boundaries , alternative splicing sites and its detection , proteolytic sites that is found in proteins, prediction of genes and post translational modification sites for protein.
The structural frame considers that right roles and relationship for people working in an organization to be one of the main keys to success. According to Bolman and Deal (2008), organizations are characterized by goals and objectives, well defined structure and division of labor, various forms of coordination and control, rational conduct and policies. These features help to make an organization more efficient and improve its performance. When an organization faces problems, they are resolved through analysis and restructuring.
The Double Helix by James Watson is his personal reflection on discovering the structure of the DNA molecule. With contributions of other scientists, James Watson and Francis Crick were able to solve the structure of DNA. Through contributions and integral relationships of Watson and Crick to Maurice Wilkins, Rosalind Franklin, Linus Pauling, and other smaller contributors the DNA structure was finally solved.
The Database of Genotypes and Phenotypes (dbGaP) was developed by National Center for Biotechnology Information (NCBI) to archive and distribute the results of various studies that have examined the interaction of genotype and phenotype. It is public repository for individual level phenotype, exposure, genotype, sequence data and the associations between them. Searching relevant studies of particular interest accurately and completely is challenging task due to keyword based search method of dbGaP Entrez system. Text mining is emerging research field which enable users to extract useful information from text documents and deals with retrieval, classification, clustering and machine learning techniques to classify different text document.
Myoglobin consist of single polypeptide chain that made up of 153 amino acid and ahs a size of 18 kDa. Its three-dimensional structure was first determined by X-ray crystallography by John Kendrew in 1957. Myoglobin is a typical globular protein in that it is a highly folded compact structure with most of the hydrophobic amino acid residues buried in the interior and many of the polar residues on the surface. X-ray crystallography revealed that the single polypeptide chain of myoglobin consist of entirely of eight (labelled A-H) alpha-helical. Within a hydrophobic crevice formed by the folding polypeptide chain is the heme prosthetic group. This nonopolypepetide unit is noncovalently bound to myoglobin and is essential for the biological activity of the protein.
"The Species of the Secondary Protein Structure. Virtual Chembook - Elmhurst College. Retrieved July 25, 2008, from http://www.cd http://www.elmhurst.edu/chm/vchembook/566secprotein.html Silk Road Foundation. n.d. - n.d. - n.d.
A polypeptide chain is a series of amino acids that are joined by the peptide bonds. Each amino acid in a polypeptide chain is called a residue. It also has polarity because its ends are different. The backbone or main chain is the part of the polypeptide chain that is made up of a regularly repeating part and is rich with the potential for hydrogen-bonding. There is also a variable part, which comprises the distinct side chain. Each residue of the chain has a carbonyl group, which is good hydrogen-bond acceptor, and an NH group, which is a good hydrogen-bond donor. The groups interact with the functional groups of the side chains and each other to stabilize structures. Proteins are polypeptide chains that have 500 to 2,000 amino acid residues. Oligopeptides, or peptides, are made up of small numbers of amino acids. Each protein has a precisely defined, unique amino acid sequence, referred to as its primary structure. The amino acid sequences of proteins are determined by the nucleotide sequences of genes because nucleotides in DNA specify a complimentary sequence in RNA, which specifies the amino acid sequence. Amino acid sequences determine the 3D structures of proteins. An alteration in the amino acid sequence can produce disease and abnormal function. All of the different ways
Gel electrophoresis is used in a variety of settings, particularly in molecular biology. Besides being used to separate nucleic acids, such as DNA and RNA, gel electrophoresis is also employed to divide proteins (Gel Electrophoresis). According to research, electrophoresis is applied for the following reasons, "To get a DNA fingerprint for forensic pur...
Cheminformatics term was coined for the first time by F.K. Brown and it's defined as "the field of chemistry that integrates chemical data with analytic and molecular design tools finding the 'best- fitting' compounds to address particular targets". It can be called also "chemoinformatics", "chemioinformatics" or "chemical informatics". In silico techniques are used in cheminformatics for a wide range of applications, such as in rotational drug design or in drug diversity, using the structure for predication of the activity and in virtual screening. This was first applied in the making of the period table
Protein is configured to detect a specific analyte and ensuing signal is read by detection instrument for example fluorometer or luminometer.
Shapiro AL, V. E. (1967). Molecular weight estimation of polypeptide chains by electrophoresis in SDS-polyacrylamide gels. Biochem Biophys Res Commun , 815-820.
"Within a single subunit [polypeptide chain], contiguous portions of the polypeptide chain frequently fold into compact, local semi-independent units called domains." - Richardson, 1981