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Motif

The document defines motifs in bioinformatics as recurring structural arrangements in proteins, often referred to as super-secondary structures or folds. It categorizes various types of motifs, such as β-α-β, β-hairpin, Greek key, and others, detailing their functional descriptions and example proteins. Additionally, it includes an assignment for collecting motifs from real proteins using Pymol software.

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7 views22 pages

Motif

The document defines motifs in bioinformatics as recurring structural arrangements in proteins, often referred to as super-secondary structures or folds. It categorizes various types of motifs, such as β-α-β, β-hairpin, Greek key, and others, detailing their functional descriptions and example proteins. Additionally, it includes an assignment for collecting motifs from real proteins using Pymol software.

Uploaded by

istiake zahan
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Download as PPTX, PDF, TXT or read online on Scribd
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Motif

Bioinformatics
Md. Fazlul Karim Patwary
Definition
• Motif is a recurring subject, theme, idea, etc.,
specially in a literary, artistic, or musical work.

• Motif is the stable arrangements of secondary


structures and the connections between them
commonly found in many proteins.
• It is also termed as “Super-secondary structures” or
as simply “folds”.
Types of Motif
• Name: β-α-β
• Functional Description: Two β-strands forming
parallel β-sheets connected by parallel α-helix.
• Example protein: Triose phosphate isomarase
Types of Motif
• Name: β-α-β
• Parallel beta-strands are connected by longer
regions of chain.
• The chain cross the beta-sheet and frequently
contain alpha-helical segments.
• This motif is found in most proteins that have a
parallel beta-sheet.
• Loop regions linking the strands to the helical
segments can vary greatly in length.
Types of Motif
• Name: β-α-β
• Protein Name: 1IGT
• DNA Sequence: 2nd part of 31-41
Types: searching a Motif
• http://www.genome.jp/tools/motif/
• Protein Name: Protease-induced heterodimer of
human triosephosphate isomerase (4BR1)
Types of Motif
• Name: β-Hairpin
• Functional Description: Two β-strands involved in an
anti-parallel sheet connected by 2~5 residues loop.
• Example protein: Bovine pancreatic trypsin
inhibitors.
Types of Motif
• Name: β-Hairpin
• Protein Name: 1IGT
• DNA Sequence:1-41
Types of Motif
• Name: Greek Key
• Functional Description: Four beta strands in
contagious sequence associated in anti-parallel
beta-sheets. Strand 1 pairs with strand 2, which
pairs with strand 3, strand 4 pairs with strand 1.
• Example protein: Staphylococcal nuclease.
Types of Motif
• Name: Helix-turn-helix

• Functional Description: DNA binding.

• Example protein: DNA binding proteins


Types of Motif
• Name: β-meander motif
• Functional Description: Composed of 2 or more
consecutive anti-parallel β-strands linked together
by hairpin loops

• Example protein:
Types of Motif
• Protein Name: 1IGT
• Name: β-meander motif
• DNA Sequence: 41-126
Types of Motif
• Name: Psi-loop motif
• Functional Description: two antiparallel strands with
one strand in between that is connected to both by
hydrogen bonds.

• Example protein:
Types of Motif
• Protein Name: 1IGT
• DNA Sequence: 126-171
• Name: Psi-loop motif
Types of Motif
• Name: β hairpin
• Functional Description: two anti-parallel strands are
linked by a short loop of two to five residues.

• Example protein:
Types of Motif
• Name: Basic helix-loop-helix

• Functional Description: two α-helices connected by


a loop.
• Example protein: aryl hydrocarbon receptor
nuclear translocator protein
Types of Motif
• Name: E-F hand

• Functional Description: A helix-turn-helix motif


sometimes involved in Ca++ binding.

• Example protein: DNA binding proteins


Types of Motif
• Name: α­helix motif

• Functional Description: Only Alpha helix.

• Example protein: Alpha keratin


Types of Motif
• Name: β- sheet motif

• Functional Description: Only beta sheets.

• Example protein: Ferritin


Types of Motif
• Name: Omega loop
• Functional Description: a loop in which the residues
that make up the beginning and end of the loop are
very close together.
• Example protein: enzyme triosephosphate
isomerase
Types of Motif
• Name: Zinc finger

• Functional Description: Two anti-parallel beta


strands with an alpha helix end folded over to bind
a zinc ion. Important in DNA binding proteins.

• Example protein:
Assignment
• Collect all the motif from a real protein.
• Write the name of protein
• Write motif name
• Give the image of that Motif
• Use Pymol software to do all the above tasks

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