Modular Structure of Proteins

Question 1

What is a motif?

Answer 1

A motif is an Element of structure or pattern that recurs in many contexts. Specifically, a motif is a minimum arrangement of secondary structures combining folds & is a small structural unit that can be recognized in a variety of proteins.

Question 2

What are domains?

Answer 2

Domains are distinct functional and/or structural units in a protein. Usually they are responsible for a particular function or interaction, contributing to the overall role of a protein.
Motifs can be combined to make a larger structural and functional domain.

Question 3

What is the difference between motifs and domains?

Answer 3

Domains more clearly define a functional unit than a motif. Domain can be defined as a more complex structure at the tertiary or quaternary level, often involving interaction between distant parts of a protein or motifs. Both are evolutionarily conserved and are modular in nature.

Question 4

List four examples of protein motifs.

Answer 4

• EF HAND: It resembles a helix-turn-helix, but combines with a metal ion such as calcium (eg. Calmodulin, Troponin, etc. Calmodulin contains four EF hands, each binding to a single calcium ion)
• GREEK KEY MOTIF: these consist of antiparallel β strands, but it is a motif that is so common that it isn’t generally associated with a specific function
• BETA BARREL: β strands wrapped around to form a circular tunnel
• β-α-β MOTIF: parallel strands of a β sheet interlinked with an α helix

Question 5

How do DNA binding motifs work?

Answer 5

The helices can be inserted into the major groove of DNA in a sequence specific manner.

Question 6

What are the four DNA binding motifs?

Answer 6

• helix-loop-helix
• helix-turn-helix
• leucine zipper
• zinc finger

Question 7

Expand on transcription factors and motifs/domains.

Answer 7

There are many different transcription factors but they each contain a small number of conserved motifs which combine to form domains that interact with the DNA.
These motifs are conserved across all phyla (ie huge variety of eukaryotes, ranging from fungi to plants and animals).
These motifs form DNA binding domains that allow the regulatory function of their respective proteins.

Question 8

Why are α helices important in DNA binding?

Answer 8

Alpha helices can fit within the major groove of DNA.
The amino acid sequence of a DNA binding motif provides specificity.
Different DNA binding domains & motifs present the binding helix using different arrangements of the structural motif.

Question 9

Describe the helix-loop-helix motif.

Answer 9

• It only binds to DNA in the dimeric form. It can exist as hetero- (different monomers) or homodimers (same monomer).
• The central portion formed from overlapping helices form a structure that enables dimerisation.
• The terminal part of the lower opposing helices contain basic (positively charged) amino acids that interact with the major groove of the DNA (negatively charged) – giving rise to the b/HLH functional domain.
  Examples include mad, max, myc, myoD, etc.

Question 10

Describe the leucine zipper motif.

Answer 10

• This motif is formed from 2 contiguous alpha helices and like the HLH, is a dimeric protein formed from two polypeptide chains.
• The dimers “zip” together in the top “stalk” to form a short “coiled-coil”
• The coil is held together by hydrophobic interactions down opposing sides of the helix.
• As in the b/HLH, basic amino acids dominate the lower part of the helix (forming a motif) and interact with the DNA major groove.
• Heterodimerisation expands the regulatory potential of leucine zippers.

Question 11

Describe the helix-turn-helix motif.

Answer 11

• The structural appearance of this motif is quite different. - It consists of two short helices (one of which is the recognition helix) orientated at right angles to each other & connected by a “turn”.
• The motif is found in both prokaryotic and eukaryotic DNA binding proteins, for example, the CRO repressor.
• The CRO protein is a homodimer.
• CRO recognises palindromic sequence and, by binding to DNA, represses transcription.
• Only the recognition helix interacts with the nucleotide sequence itself and, like other DNA binding motifs, it locates within the major groove.
• (also in lac repressors)

Question 12

Describe the zinc finger motif.

Answer 12

This motif is an α helix and a βsheet held together by non-covalent interactions with zinc.
The zinc atoms stabilise the recognition helix and the loop structure.
The alpha helix of each motif interacts with the major groove of DNA and recognises a specific DNA sequence.
Many proteins that possess the motif are hormone receptors, including Glucocorticoid, Mineralocorticoid, Oestrogen, Progesterone, Vit D receptors, etc.

Question 13

Explain the domains involved in membrane bound receptors.

Answer 13

The 7-transmembrane arrangement of alpha helices contains:

• EXTRACELLULAR REGION (ligane binding protein)
• TRANSMEMBRANE REGION (domain) embedded in the lipid bilayer.
• INTRACELLULAR REGION (domain) interacts with GPCR

Question 14

Whats domain shuffling?

Answer 14

• Individual domains can be found in different proteins
• Domain shuffling in the genome results in modular units of function being conserved
  (e. g mammalian phospholipase C contains 4 recognisible domains that are found individualy in other proteins)