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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.