Proteins - EF-Hand/Calmodulin

Question 1

EF-Hand

Answer 1

This is a motif of 30 amino acids folding in a helix-loop-helix structure, ressembling a right hand with index and thumb extended.

Question 2

How are the two EF-hand helicies ocnnected?

Answer 2

Calcium binding loop which binds Ca ions through acidic residues(aspartate or glutamate_

Question 3

What happens when Ca binds?

Answer 3

Exposes binding sites for protein/membrane interactions

Question 4

How does Ca interact with acidic residues?

Answer 4

Form a sequence with carboxylate groups forming co-ordination complex

Question 5

Motifs

Answer 5

Conserved amino acid sequence alignments, corresponding to a region whose function or structure is known, or its signifcance may be unknonw.

Question 6

Kd(Dissociation constant)

Answer 6

This quantifies equilibrium between ligand(L) being free in solution and bound to a site in the protein(EL) corresponding to ligand-binding site affinity.

Question 7

How can Kd be mathematically described?

Answer 7

Ratio of rate constants for disassociation and association of the ligand-receptor complexes.

Question 8

What is the equation for kD

Answer 8

K2/K1 Where K2 is rate of dissociation and K1 rate of association

Question 9

What does a low kD mean?

Answer 9

A very high receptor-ligand affinity.

Question 10

What is kD used to describe?

Answer 10

Concentraiton at which 50% of the ligand is free and 50% bound to a receptor.

Question 11

Law of Mass Action

Answer 11

This states that rate of a chemical reaciton is proportional to the concentration of the reacting substance.

Question 12

What is the binding affinity of EF-hand for Ca?

Answer 12

Kd = 10^6 M

Question 13

How does kD for EF-hand and ca binding affinity change?

Answer 13

Whether found intracelluarly(10^-3) or extracellularly (10^-7-10^-6)

Question 14

Why are EF-hand rarely found extracellularly?

Answer 14

Calcium binding loops contain several anionic AA and cytosol has higher Ca concentration

Question 15

Why are Asp and Glu anioninc?

Answer 15

Carboxylate groups.

Question 16

Why does Ca bind anions?

Answer 16

Two valence electrons forming co-ordination complexes.

Question 17

What is the amino acid structure of EF-hand?

Answer 17

29 residues with a Glu at position 1 at first alpha helix, with hydrophobic molecules facting core at 2,5,6, and 9.

Question 18

What are the important amino acids in the second helix?

Answer 18

Glu at position 21 and hydrophobic molecules at 22,25,26 and 19

Question 19

Why is Gly15 important?

Answer 19

Permits a sharp bend in the loop.

Question 20

Why is glycine useful?

Answer 20

Smallest AA with a single hydrogen side hcane, allowing flexibility of protein for many conformations.

Question 21

Why is position 17 Ile important?

Answer 21

Attahcing loop the hydrophobic core of the molecule.

Question 22

Calmodulin

Answer 22

This is important in mediation of actions of calcium in many cellular processes.

Question 23

What is the general structure of calmodulin?

Answer 23

Two identical globular domains, each containing two EF-hand motifs mediating interactions with Ca ions.

Question 24

What is the primary sequence structure of Calmodulin?

Answer 24

17kDa with 75 AA

Question 25

What secondary structures does each Calmodulin domain contain?

Answer 25

Four alpha helicies bound by flexibilie loops

Question 26

What is the structure of Calmodulin without Ca?

Answer 26

A long, central alpha helix mediates connections of the two domains between them forming a dumbbell shaped structure.

Question 27

What does Ca binding to calmodulin do?

Answer 27

Exposes hydrophobic residues, reorientating the domains, allowing interactions with target protein

Question 28

What does calmodulin CC expose?

Answer 28

Hydrophobic patch in each globular domain, for interaction with other proteins.

Question 29

What does unfolding of calmodulin lobes do?

Answer 29

Enfold an alpha helical target peptide when four CA ions have bound with hydrophobic patches on each lobe contacting the hydrophobic side of the target peptide.

Question 30

Where are the EF hand domains found in calmodulin?

Answer 30

NTD and CTD have two each