Modular structure of proteins

Question 1

Describe Motifs and Domains

Answer 1

• Simple secondary structures (folds) combine to form structural motifs or larger functional domains
• These are different from sequence motifs (pattern of amino acids that are found in related genes or proteins).
• Motifs and Domains are an independent order of structure.
• They are an independent order of structure different from primary, secondary, tertiary and quaternary.
• Such units of protein structure are commonly found and are conserved across functionally related proteins.

Question 2

Define Motif

Answer 2

o A motif is an element of structure or pattern that recurs in many contexts. Specifically, a motif is a minimum arrangement of secondary structure combining folds & is a small structural unit that can be recognised in a variety of proteins.
o Motifs are organised or combined into larger structural and functional domains.

Question 3

Define domain

Answer 3

o A functional unit than a motif but both are evolutionarily conserved and are modular in nature.
o A domain is generally a more complex structure that has a tertiary or quaternary structure of its own.
o A functional domain is typically larger and may or may not be contiguous (being in actual contact: touching along a boundary) segments of the polypeptide chain.
o A domain is a combination of folds at a higher level, often involving many folds that defines a functional unit.
o Larger proteins are generally composed of several domains, domains can be thought of as functional units that are found across different genes and phyla

Question 4

Give and describe examples of motifs

Answer 4

• Many different structural motifs exist.
• EF hand - Ca2+ binding e.g. Calmodulin & Troponin-C resembles a helix turn helix but combines with a metal ion such as calcium. At either end EF hand present (two motifs).
• Greek Key motif consists of antiparallel beta strands but is one motif. It is very common, and it doesn’t have a specific function.
• Beta barrel – beta strands wrapped around to form circular tunnel.
• Parallel strands of a beta sheet interlinked with an alpha helix to form a beta-alpha-beta motif (named after structure).

Question 5

Describe motifs as one element in domain

Answer 5

• Proteins involved in transcription contain 4 main different motifs.
• They are not exclusive to DNA binding/ transcription factors.
• DNA binding motifs – helices can be inserted into the major groove of DNA in a sequence specific manner.
• Helix loop helix – e.g. Max & Mad also Ca2+ binding
• Helix turn helix –e.g. Cro, tryptophan, & lac repressors
• Leucine Zipper – e.g. GCN4 (translation in yeast), cFos & cJun
• Zinc Finger – e.g. hormone receptors (transcriptional regulation as a result of hormone regulation)

Question 6

Describe structural and functional domains

Answer 6

On image

Question 7

Describe Transcription factors

Answer 7

• Proteins that bind to DNA and regulate transcription.
• 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 (i.e. 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

Describe a helix loop helix

Answer 8

o Binds DNA only in the dimeric form.
o Exists as hetero (different monomers) and homodimers (identical monomers).
o The central portion is made from overlapping helices that form a structure enabling dimerization.
o The terminal part of the lower opposing helices contains basic amino acids that interact with the major groove of the DNA – giving rise to the b/HLH functional domain.
o Examples include mad, max, myc, myoD.

Question 9

Describe helix turn helix

Answer 9

o Although the name suggests some similarity to the leucine zipper and Helix-loop-helix motifs the structural appearance of this motif quite different.
o Consists of two short helices orientated at right angles to each other & connected by a “turn”
o The motif is found in both prokaryotic and eukaryotic DNA binding proteins e.g. CRO repressor, & homeobox proteins.
o The CRO protein is a homodimer.
o CRO recognises palindromic sequence and by binding DNA represses transcription.
o Only the recognition helix interacts with the nucleotide sequence itself and like other DNA binding motifs it locates within the major groove.

Question 10

Describe leucine zipper

Answer 10

o This motif is formed from 2 contiguous alpha helices and like the HLH, is a dimeric protein formed from two polypeptide chains.
o The dimers “zip” together in the top “stalk” to form a short “coiled-coil”.
o The coil is held together by hydrophobic interactions down opposing sides of the helix.
o 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.
o Heterodimerisation expands the regulatory potential of leucine zippers the example right is cFos partnered with cJun

Question 11

Describe zinc finger

Answer 11

o This motif is an alpha helix and a beta sheet held together by non-covalent interactions with zinc.
o The diagram shows a dimer with 2 motifs on separate polypeptide chains each containing two zinc atoms stabilising the recognition helix and loop structure.
o The alpha helix of each motif interacts with the major groove of DNA and recognises a specific DNA sequence.
o Of note among the proteins that have zinc fingers include many of the hormone receptors such as:
o Glucocorticoid, Mineralocorticoid oestrogen, progesterone, Vit D receptors.