KSH HW1 Protein analysis

Motif, Pattern, Profiling, Signature

Sequence motif - amino acid sequence pattern that is widespread and has a biological significance

Cf) Structural motif - connectivity between secondary structure elements¹⁾ - The simplest structural motif is a helical bundle

(http://www.proteinstructures.com/Structure/Structure/protein-motifs.html)

Pattern - Characters that appear in common in one protein family

two or more patterns are associated with a single motif ²⁾

Protein Profiling - the detection of the character or quantity of specific sets of proteins

Signature - a part of whole pattern. Short diagnostic pattern that we can find the character of specific protein

1. PROSITE (prosite.expasy.org)

³⁾A protein database which consists of the protein families, domains, functional sites, amino acid patterns and profiles.

They are manually curated by a team of Swiss Institute of Bioinformatics

 

 

 

5. PRINTS (bioinf.man.ac.uk/dbbrowser/PRINTS)

 

PSI-BLAST(blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE=Proteins&PROGRAM=blastp&RUN_PSIBLAST=on)

To search similarity among amino acid sequences . PIR - Protein Informatics Resourse , PSI - Position Specific Iterated

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Example

Human Serotonin Receptor

1. Search the amino acid sequence from NCBI

2. Get the FASTA format information from the sample

3. Do analysis using the analysis tools

 

Result

1. Using CPHmodels

 

2. Using SWISS-MODELS

Although the identity is not high (~ 40 %), they assumes the sample as a 5' hydroxytryptamine receptor. It is exactly  correct because human serotonine receptor is known as 5' hydroxytryptamin receptor⁴⁾

 

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Reference

*** All these websites are listed in the book called 'Bioinformatics with bioperl' authored by Young-chang Kim

1) http://www.proteinstructures.com/Structure/Structure/protein-motifs.html

2) https://en.wikipedia.org/wiki/Sequence_motif

3) https://en.wikipedia.org/wiki/PROSITE

4) https://en.wikipedia.org/wiki/5-HT_receptor

 

Seung-hoon Kim