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Predict potential cleavage sites cleaved by proteases or chemicals in a given protein sequence.

EXPERIMENT #13        

OBJECT:-

Predict potential cleavage sites cleaved by proteases or chemicals in a given protein sequence.

THEORY:-

Peptide cutter predicts potential cleavage sites , cleaved by proteases or chemicals in a given protein sequence.

Proteins are biological polymers , composed of aminoacids. Aminoacids, linked together by peptide bonds, form a poly peptide chains.One or more polypeptide chain twisted into a 3 dimensional shape to form a protein.

NEB cutter is also a search tool, it will take a DNA sequence and find the lare non overlapping open reading farme using E.coli  genetic code and the sites for all type 2 and commercially available type 3 restriction enzyme that cuts the sequence just once.Restriction enzymes are those enzymes , which are restricted to specific sequences,in a protein or DNA molecule.

Procedure:-

1.From expasy peptide cutter was selected.

2.Sequence of protein from fasta format was taken and pasted in input box.

3.Where the selection or the whole list of proteases and chemicals can be used.

4.By which cleavage specification of selected enzymes and chemicals can be known.

DISCUSSION:-

In this practical peptide cutter was used to observe different cleavage sites, cleaved by different available enzymes or chemicals,in a given protein sequence.The table showed list of enzymes (that cuts our protein sequence),number of cuts and position of cuts and specific sequences recognized by enzymes to make a cut.Peptide cutter returns the query sequence with the possible cleavage sites mapped on it and a table of cleavage site positions by different enzymes e.g  Protinase k,Pn-2 etc.List of enzymes were also found which do not   cleaved our protein sequence because of lack of availability of specific sequences , required for their cleavage-potential.There are some overlapping regions through which we can concluded about the complete sequence.           

Retrieve a sequence using UniprotKB.

EXPERIMENT #09

OBJECT:-

Retrieve a sequence using UniprotKB.

THEORY:

What is UniProt?

UniProt provides the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information. UniProt is a comprehensive, high-quality and freely accessible database of protein sequence and functional information, many entries being derived from genome sequencing projects. It contains a large amount of information about the biological function of proteins derived from the research literature.

Why do we need UniProt?

As the number of completely sequenced genomes continues to increase, huge efforts are being made in the research community to understand as much as possible about the proteins encoded by these genomes. This work is critical to many areas of science including biology, medicine and biotechnology - and is generating a wealth of data. UniProt provides an up-to-date, comprehensive body of protein information. The resource facilitates scientific discovery by collecting, interpreting and organising this information, which saves researchers countless hours of work.

What can I do with UniProt?

You can use UniProt for a wide range of tasks, from finding out about your protein of interest and comparing its protein sequence with other proteins, to mapping a list of identifiers from an external database to UniProtKB or vice versa.

UniProt is a comprehensive, high-quality and freely accessible database of protein sequence and functional information, many entries being derived from genome sequencing projects. It contains a large amount of information about the biological function of proteins derived from the research literature.

PROCEDURE:-

1.Www.uniprot.org/uniprot/P21543 was opened.

2.Name of protein was written.

3.All the information about protein was noted.

RESULTS:-

DISCUSSION:-

UniProt is a comprehensive, high-quality and freely accessible database of protein sequence and functional information, many entries being derived from genome sequencing projects. It contains a large amount of information about the biological function of proteins derived from the research literature. It provides all the information related to that protein(amylase),the name of organism (Bacillus licheniformis), function of that protein. It showed the position of active site of protein and also its graphical view. It gives information about the position of signal peptide that was from 1-29 and functional chain that was at 30-512 position. Blue color showed alpha helix and red color showed Beta strand. There were some repeated strands which meant that in evolution perhaps there is duplication.

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To observe O-glycosylation in eukaryotic sequence.

Experiment #12   

Object:-

To observe O-glycosylation in eukaryotic sequence.

Theory:-

O- glycosylation occurs at Ser or Thr-residues, usually in sequence-stretches rich in hydroxy amino acids, but there has been no consensus sequence determined for this modification. In addition, O-glycosylation lacks a common core structure: mammalian proteins have been reported bearing O-linked N-acetylgalactosamine, fucose, glucose, and corresponding elongated structures, as well as N-acetylglucosamine. Chemical methods are used to liberate these oligosaccharides because no enzyme has been discovered that would cleave all the different O-linked carbohydrates. Glycosylation , a common PTM, plays a role in protein folding, transport and half-life, as well as being involved in cell-cell interactions and antigenicity. Glycosylation is an enzymatic process, with the exception of glycation, and involves the addition of sugars to the protein to build up glycan chains.

Procedure:-

1.NetOGly1.0 server was opened.

2. Fasta format was pasted in input box.

3.Result was noted.

DISCUSSION:-

In this experiment O-Glycosylation was observed.There is no any seqon.It has limited application.This tool is only for eukaryotic protein.O- glycosylation occurs at Ser or Thr-residues, usually in sequence-stretches rich in hydroxy amino acids, but there has been no consensus sequence determined for this modification. In addition, O-glycosylation lacks a common core structure.

TO CHECK THE ANTI MICROBIAL ACTIVITY OF TEN ANTI MICROBIAL AGENT AGAINST MICRO ORGANISMS ISOLATED FROM HEN'S LIVER AND MEAT OF GOAT AND SHEEP

To observe N-glycosylation in eukaryotic sequence.

Experiment#11

Object:-

To observe N-glycosylation in eukaryotic sequence.

Theory:-

Most proteins do not perform their function without undergoing some form of post translational modification (PTM) . PTMs occur after the mRNA has been translated into peptide sequence and the polypeptide has begun to fold . The importance of PTMs in protein function makes their characterization of particular interest . Accurate prediction, using computational methods, of sites in a protein sequence where PTM occurs would facilitate protein annotation and would contribute to efforts in functional genomics Glycosylation , a common PTM, plays a role in protein folding, transport and half-life, as well as being involved in cell-cell interactions and antigenicity. Glycosylation is an enzymatic process, with the exception of glycation, and involves the addition of sugars to the protein to build up glycan chains. N-linked glycosylation consists of the addition of a pre-assembled glycan chain to Asn. This occurs co-translationally and influences protein folding. After its addition, the glycan chain undergoes a maturation process, which can produce a glycan of the high mannose, hybrid or complex types. The sequence motif Asn-Xxx-Ser/Thr , or in some rare cases Asn-Xxx-Cys, where Xxx is any amino acid except Pro, is required for N-glycosylation, although not sufficient on its own. This Web Service implements NetNGlyc 1.0b. It predicts N-Glycosylation sites in human proteins using artificial neural networks that examine the sequence context of Asn-Xaa-Ser/Thr sequons.The traditional server offers more detailed output (graphics), extended functionality and comprehensive documentation. It is suitable for close investigation of few proteins while this service is recommended for high throughput projects.

Procedure:-

1.NetNGly1.0 server was opened.

2. Fasta format was pasted in input box.

3.Result was noted.

DISCUSSION:-

In this experiment N-Glycosylation was observed. This Web Service implements NetNGlyc 1.0b. It predicts N-Glycosylation
sites in human proteins using artificial neural networks that examine
the sequence context of Asn-Xaa-Ser/Thr sequons.

The traditional server offers more detailed output (graphics), extended
functionality and comprehensive documentation. Glycosylation mainly depends on nature of amino acids and environment around specific aminoacids .N glycosylation occur where basic aminoacids like Asparigin is present.We observed that N glycosylation occurred at many positions of given sequence.

Discussion:-

In this experiment N-Glycosylation was observed. N-linked glycosylation consists of the addition of a pre-assembled glycan chain to Asn. This occurs co-translationally and influences protein folding. After its addition, the glycan chain undergoes a maturation process, which can produce a glycan of the high mannose, hybrid or complex types. The sequence motif Asn-Xxx-Ser/Thr , or in some rare cases Asn-Xxx-Cys, where Xxx is any amino acid except Pro, is required for N-glycosylation, although not sufficient on its own. The traditional server offers more detailed output (graphics), extendedfunctionality and comprehensive documentation.We observed that N glycosylation occurred at many positions of given sequence.

To predict signal peptide in eukaryotic sequence

EXPERIMENT#10

OBJECT:-

To predict signal peptide in eukaryotic sequence.

Theory:-

A signal peptide (some time referred to as signal sequence, targeting signal, localization signal ,transit peptide , leader sequence or leader peptide)is a short (5-30 amino acid)peptide present at the N terminal of the majority of newly synthesized proteins that are destined towards the secretary pathway. These proteins include those that reside either inside certain organelles (endoplasmic reticulum golgi bodies or   endosomes),secreted from the cells or inserted into most cellular membranes. In eukaryotes , signal sequences direct the insertion of proteins into the membrane of the endoplasmic reticulum and are usually cleaved off by signal peptidase. The resulting signal peptide are presumably rapidly degraded but some still have function on their own. SignalP 4.1 server predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive prokaryotes, Gram-negative prokaryotes, and eukaryotes. The method incorporates a prediction of cleavage sites and a signal peptide/non-signal peptide prediction based on a combination of several artificial neural networks. Organism group:
It is important for performance that you choose the correct organism group — Eukaryotes, Gram-negative bacteria or Gram-positive bacteria — since the signal peptides of these three groups are known to differ from each other.
Gram-positive bacteria correspond to Actinobacteria and Firmicutes in the NCBI Taxonomy.
Gram-negative bacteria are all other eubacteria, except Tenericutes (including Mycoplasma), which seem to lack a type I signal peptidase and therefore do not have standard signal peptides You can see which cutoff values are being used in the boxes marked "D-cutoff". They will change if you change the setting for "D-cutoff values" or "Organism group".
If you want to experiment with your own cutoff values, select "User defined" and the boxes will go blank, ready for you to fill in values between 0 and 1.

PROCEDURE:-

1.In Expasy signal peptide was selected.

2. Fasta sequence of protein was pasted in input box.

3.After tat group of organism was selected (gram negative, gram positive, eukaryotes)

4.Result was noted.

Dicussion:-

In this experiment we predicted signal peptide in eukaryotic sequence, by using expasy  search tool, for that purpose , we pasted protein sequence of a eukaryotic organism in a bar of search and found a graph, we observed a peak (blue colored), it indicated site of proteolytic cleavage. In graph green line showed hydrphobicity residues.

We have to consider those lines which are above the base-line. Green and blue line played basic role in signal peptide.

We observed cleavage site between 23 and 24^th amino acids ,it indicates that signal peptide is present in given sequence. Signal peptide helps the protein to reach its destination, than through cleavage it cleaved out from protein.

Discussion:-

In this experiment we predicted signal peptide in eukaryotic sequence, by using expasy  search tool, for that purpose , we pasted protein sequence of a eukaryotic organism in a bar of search and found a graph, we observed a peak (blue colored), it indicated site of proteolytic cleavage. In graph green line showed hydrphobicity residues.

Any thing above cut off line is significant. The software looked for 3 parameters(1.short stretch of hydrophobic amino acids,2.short peptide,3.cleavage site).It only look 70 begining aminoacids because if sinal peptide present it would be in begining.In translated protein Met is first amino acid but in functional it is not the first aminoacid. By looking the graph we can predict the presence and absence of signal peptide.If signal peptide not present reason might be that protein may be cytoplasmic or there is only functional sequence uploaded or may be there is partial sequence not complete sequence.

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