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.

O LEVEL MATHEMATICS NEW SYLLABUS

New syllabus will be published soon.