This document discusses protein motifs and domains. It defines a motif as a recurring arrangement of secondary structure found in multiple proteins, such as the HTH, HLH, and hairpin motifs. A domain contains one or more well-characterized motifs and has an independent function. Two common motifs are described: the HTH motif, which contains two antiparallel alpha helices connected by a beta turn for DNA binding; and the HLH motif, which contains two helices connected by a loop, with the larger helix binding DNA and the smaller helix aiding folding. Domains are defined as distinct functional units that are evolutionarily conserved and can exist independently; they are classified based on secondary structure composition.

1. MOTIFS AND
DOMAINS
By-Gouthaman PP

2. INTRODUCTION
A particular arrangement of secondary structure that can be found
in other proteins as well can be called a motif
It is a connection of helices and sheets in different combinations
Common motifs are HTH, HLH and Hairpin etc.
A domain can be made up of one or more well characterised
motifs which usually occur together and have independent
function.

3. HTH
2 α-helices connected by a β-turn
The helices are usually antiparallel
Usually found in protein that bind to major and minor groves of
DNA
Best characterized motif for DNA binding domain
One helix helps in recognition of DNA while the other stabilizes
the DNA-Protein interaction
Mainly involved in cell proliferation, establishment of DNA
structure etc.

4. β-turnα-helices
β-turn
α-helices

5. HLH
2 α-helices connected by a loop
The two helices tend to be of different size
The larger helix aids in binding to DNA while the smaller one
helps in folding and packing
Associated with transcription
240 types have been identified
Involved in cellular differentiation
Regulation of transcription of immunoglobulins

6. Loop
Long Helix
Small Helix

7. DOMAINS
Distinct functional units
Spatially separated unit of protein
Have structural and sequence resemblance to other proteins
From 50-250 residues long
Building blocks of molecular evolution
Can be isolated by genetic engineering as they are independently
stable entities
Classified as α-domains, β-domains, α+β-domains and α/β-
domains

8. α-domains are made of α-helices coming up and down with folds
β-domains are composed of antiparallel β-sheets and generate
various patterns
α+β-domains are a mixture of all α and all β motifs
α/β-domains are a combination of β-α-β motifs that form parallel
β-sheets surrounded by antiparallel α-helices
Used by nature to generate new sequences
The C and N terminals of domains are close together and allows
easy slotting into parent proteins

12. THANK YOU