Section 1 – Predicting the hydrophilicity of the protein 1. How a computer algorithm can be used to predict the characteristic. In order to predict the characteristics of a protein, computer algorithms use the following method. The databases contain scales such as hydrophobicity scales which have been derived using data obtained from experimental studies carried out on proteins. The experiments are carried out with the purpose of predicting sections that are highly hydrophobic. Apart from hydrophobicity, algorithms also use many other scales based on physical and chemical properties of amino acids. The algorithm used in this assignment was ProtScale. This algorithm contains 50 scales that have been obtained from literature. Each of these scales has a value for each amino acid. In order to obtain the data, the algorithm scans the entered protein sequence with a window of specified size. Next, at every position, the mean scale value of the amino acids within that window is calculated. These values are then used to generate the plot as seen in figure 1 (Gasteiger E. 2005). 2. Reasons for choosing the algorithm and brief explanation of the algorithm. The algorithm that was used to find out the hydrophilicity of the protein was the Hopp-Woods algorithm. This algorithm was chosen because it gives the regions of maximum and minimum hydrophilicity. The algorithm has scale values for all 20 amino acids. They are as follows. Amino acid Scale value Ala -0.500 Arg 3.000 Asn 0.200 Asp 3.000 Cys -1.000 Gln 0.200 Glu 3.000 Gly 0.000 His -0.500 Ile -1.800 Leu -1.800 Lys 3.000 Met -1.300 Phe -2.500 Pro 0.000 Ser 0.300 Thr -0.400 Trp -3.400 Tyr -2.300 Val -1.500 Table 1 – Table showing the scale values for each amino acid on the Hopp-Wodds scale (Hopp T.P.). Based on these values and using the method described previously in part 1, the algorithm generates results that give the regions of maximum and minimum hydrophilicity. The scale gives the non-polar amino acids negative values. Therefore, the region which has the highest value can be considered as the most hydrophilic region. Also, according to (Bowen 1998) when a window of 6 is used, the region of maximal hydrophilicity is likely to be an antigenic site. The protein sequence that was used in this assignment is as follows. MPRAPRCRAVRSLLRSHYREVLPLATFVRRLGPQGWRLVQRGDPAAFRA LVAQCLVCVPWDARPPPAAPSFRQVSCLKELVARVLQRLCERGAKNVLA FGFALLDGARGGPPEAFTTSVRSYLPNTVTDALRGSGAWGLLLRRVGDD VLVHLLARCALFVLVAPSCAYQVCGPPLYQLGAATQARPPPHASGPRRR LGCERAWNHSVREAGVPLGLPAPGARRRGGSASRSLPLPKRPRRGAAPE PERTPVGQGSWAHPGRTRGPSDRGFCVVSPARPAEEATSLEGALSGTRH SHPSVGRQHHAGPPSTSRPPRPWDTPCPPVYAETKHFLYSSGDKEQLRP SFLLSSLRPSLTGARRLVETIFLGSRPWMPGTPRRLPRLPQRYWQMRPL FLELLGNHAQCPYGVLLKTHCPLRAAVTPAAGVCAREKPQGSVAAPEEE DTDPRRLVQLLRQHSSPWQVYGFVRACLRRLVPPGLWGSRHNERRFLRN TKKFISLGKHAKLSLQELTWKMSVRGCAWLRRSPGVGCVPAAEHRLREE ILAKFLHWLMSVYVVELLRSFFYVTETTFQKNRLFFYRKSVWSKLQSIG IRQHLKRVQLRELSEAEVRQHREARPALLTSRLRFIPKPDGLRPIVNMD YVVGARTFRREKRAERLTSRVKALFSVLNYERARRPGLLGASVLGLDDI HRAWRTFVLRVRAQDPPPELYFVKVDVTGAYDTIPQDRLTEVIASIIKP QNTYCVRRYAVVQKAAHGHVRKAFKSHVSTLTDLQPYMRQFVAHLQETS PLRDAVVIEQSSSLNEASSGLFDVFLRFMCHHAVRIRGKSYVQCQGIPQ GSILSTLLCSLCYGDMENKLFAGIRRDGLLLRLVDDFLLVTPHLTHAKT FLRTLVRGVPEYGCVVNLRKTVVNFPVEDEALGGTAFVQMPAHGLFPWC GLLLDTRTLEVQSDYSSYARTSIRASLTFNRGFKAGRNMRRKLFGVLRL KCHSLFLDLQVNSLQTVCTNIYKILLLQAYRFHACVLQLPFHQQVWKNP TFFLRVISDTASLCYSILKAKNAGMSLGAKGAAGPLPSEAVQWLCHQAF LLKLTRHRVTYVPLLGSLRTAQTQLSRKLPGTTLTALEAAANPALPSDF KTILD 3. Results interpretation The sequence was 1132 amino acids in length and the result that was generated is as follows.
Moreover, the class average curve shows a similar trend, as the curve flattens, at 70% but with an enzyme activity of 5.3 x10-3 seconds. This indicates that even though the saturation point is the same it was considerably lower than our results, which could indicate sources of systematic error in the design of the practical.
It is composed of polymers of amino acids. An enzyme has an optimum pH and temperature. When an enzyme is at its optimum conditions, the rate of reaction is the fastest. In their globular structure, one or more polypeptide chains twist and fold, bringing together a small number of amino acids to form the active site, or the location on the enzyme where the substrate binds and the reaction takes place. An enzyme has an active site, which has a unique shape into which only a substrate of the exact same unique shape can fit.
Still, I thought, surveying my comatose family, there must be something to this turkey thing. And I'd eaten the ham, so I was still awake enough to dig up the truth. As my family slept and my dog stared down at the leftovers, I learned the truth about tryptophan. Tryptophan is an essential amino acid, one of the building blocks of protein. It is termed essential because the body cannot manufacture it on its own.
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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.
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...
the resulting amino acid would be sodium glycinate (see fig. 3), an example of a
In this case only when sufficient quantities have been ingested, are we able to synthesise the remaining non-essential amino acids.
"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.
Then the sequence was loaded into Velvet where it was trimmed to the desired k-mer length for alignment and contig formation. Mitos and MEGA alignment Explorer were also used in order to get the DNA sequence to a
Its many contains disulphide bonds, which make it an extremely stable protein. References Website’s used :. www.Intelihealth.com - www. Inteli www.dentistry.leeds.ac.uk/biochem/lectures/nutrition. www.healthy.net/library/books/haas/funct.htm.
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
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
There are four main levels of a protein, which make up its native conformation. The first level, primary structure, is just the basic order of all the amino acids. The amino acids are held together by strong peptide bonds. The next level of protein organization is the secondary structure. This is where the primary structure is repeated folded so that it takes up less space. There are two types of folding, the first of which is beta-pleated sheets, where the primary structure would resemble continuous spikes forming a horizontal strip. The seco...
In the hierarchial organisation of proteins, domains are found at the highest level of tertiary structure. Since the term was first used by Wetlaufer (1973) a number of definitions exist reflecting author bias, however all of the definitions agree that domains are independently folding compact units. Domains are frequently coded by exons and therefore have specific functionality. Among the many descriptions of protein domains the two most striking and simple are " Protein evolutionary units" and "Basic currency of Proteins".