Protein Motifs

Question 1

What is a protein motif

Answer 1

Arrangements of limited numbers of secondary structure elements
Form part of larger regions of proteins-domains
In multi-domain proteins each domain has a role

Question 2

What are ß-α-ß motifs

Answer 2

Found in almost every structure that contains parallel b-sheet
a-helix connects the C-terminus of one b-strand with the N-terminus of a second
b-a-b contains two b-strands, two loop regions and one a-helix.
Can be found in larger, repeating domains
Found in repeating units in proteins

Question 3

What are some different types of protein motifs

Answer 3

Helix-loop-helix
Zinc finger
EF hand motif
Greek key motif
b-a-b motif
Leucine rich motif
Rossman fold

Question 4

What is y- crystallin

Answer 4

Y-crystallin protein is in lens of the eye
Responsible in part for transparency and refractive power
Contains 2 domains
Each domain contains two Greek key motifs

Question 5

what is the structure of a pyruvate uinase

Answer 5

530 amino acids
Tetramer, only a monomer is shown
4 different domains

N-terminal domain key in oligomer formation
a/b barrel is core functional domain

Question 6

Why are proteins multi domain

Answer 6

One suggestion is that it makes evolving new proteins easier- Easier than single point mutations
A domain in one protein can be transposed to another protein-should do the same job
Multidomain organisation makes it easy to introduce control and regulation

Multidomain construction simplifies folding and assembly
Stabilizes the protein
Large single domain protein would take a long time to fold
Domains fold independently

Question 7

What can domains be

Answer 7

Domains can be a-helical, b-strand or a mixture of both.

Question 8

Why are oligomers important

Answer 8

Important for function
Stabilises proteins
Cooperativity

Question 9

What are the characteristics of protein motifs

Answer 9

Question 10

What is a helix-loop-helix motif

Answer 10

Question 11

What do transcription factors do

Answer 11

Question 12

What is the zinc finger domain

Answer 12

Question 13

What is a 4 helix bundle

Answer 13

Question 14

What are the 4 different ways for a 4 helix bundle to be arranged

Answer 14

Question 15

What is the EF hand motif

Answer 15

Question 16

What is a Greek key motif

Answer 16

Question 17

How can motifs be identified

Answer 17

Can be identified by sequencing primary structure
Sequencing a motif can allow identification of other EF hand hoop motifs in the absence of structure

Question 18

Why are motifs important

Answer 18

They’re important for fold and function
Proteins with similar functions will contain the same motif

Question 19

What is the problem with a protein having a large loop

Answer 19

Less stability

Question 20

Why are there many glycine residues in active site regions of proteins

Answer 20

It makes the active site more flexible

Question 21

how do you compare the structure of two domains

Answer 21

Superposition allows comparisons of different domains ( overlaying the structures in 3D/ putting them ontop of each other)
Root mean square deviation- gives a quantitative measure of how similar the two protein structures are

Question 22

What are domains in proteins

Answer 22

Domains are combined to make proteins