modular structure of proteins

Question 1

how many amino acids are there?

Answer 1

20

Question 2

what is a motif?

Answer 2

→a combination of two or more secondary structures to form a recognizable folded arrangement that appears across different proteins

Question 3

what is a domain?

Answer 3

→A conserved part of the sequence that can function independently to the rest of the protein chain.

→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.

Question 4

what is the difference between motifs and domains?

Answer 4

→domains more clearly define a functional unit than a motif.

→Both are evolutionarily conserved and are modular in nature.

→A 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.

Question 5

give examples of motifs

Answer 5

→EF hand motif
→greek key motif
→beta barrel
→DNA binding motifs

Question 6

what are properties of the EF hand motif? and give an example

Answer 6

→ resembles alpha 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)

Question 7

what are properties of a greek key motif?

Answer 7

→ consist of antiparallel β strands

→motif that is so common that it isn’t generally associated with a specific function

Question 8

what are properties of a β barrel and β-α-β MOTIF?

Answer 8

→ 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 9

how do DNA binding motifs work?

Answer 9

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

Question 10

what are the four DNA binding motifs?

Answer 10

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

Question 11

what is domain shuffling?

Answer 11

→Domain shuffling is where gene segments coding for functional domains are shuffled between different genes during evolution

Question 12

what do transcription factors have in common across eukaryotes?

Answer 12

→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 13

why are α helices important in DNA binding?

Answer 13

→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 14

give some properties of the helix loop helix motif including what the central and terminal parts are made of and give examples

Answer 14

→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 15

describe the leucine zipper motif

Answer 15

→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 16

describe the helix-turn-helix motif and where is this motif found (example)

Answer 16

→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

→e.g the CRO repressor.

Question 17

what does the CRO repressor do?

Answer 17

→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.

Question 18

describe the zinc finger motif and give examples

Answer 18

→This motif is an α-helix and a β-sheet held together by non-covalent interactions with zinc.

→ 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.