Structural influence of metals

Question 1

Increases in intracellular Ca2+ levels are sensed by…

Answer 1

…calcium-binding proteins e.g. calmodulin

Question 2

Calmodulin

Answer 2

Couples changes in intracellular [Ca2+] to the state of activation of a variety of enzymes
Monomeric proteins, 148 AAs
Can bind up to 4 Ca2+ ions at very low [Ca2+]
Each Ca is 7-coordinate! (A Ca-specifc coordination number)
Bound by 3 monodentate Asp/Asn, 1 bidentate Glu, 1 peptide C=O group, 1 H2O

Question 3

What is the nature of the Ca coordination site in calmodulin important for?

Answer 3

Metal-binding specificity
Calmodulin must specifically recognise Ca in the presence of high concentrations of other metals e.g Mg2+
The high coordination number of the metal binding site in calmodulin favours Ca2+ binding over Mg2+ (because Mg2+ smaller)

Question 4

Shape of calmodulin with 4 Ca2+ bound

Answer 4

Dumbbell shaped

A long, exposed alpha-helix connecting the two pairs of EF hand domains that bind Ca2+

Question 5

How is the binding of Ca2+ to calmodulin related to calmodulin function?

Answer 5

Binding of Ca2+ to calmodulin induces a distinct conformational change that allows calmodulin to bind to its protein target
The hydrophobic surfaces on calmodulin that are required for its binding to proteins are probably not well-established prior to Ca binding, precluding their interaction with targets

Question 6

Zinc finger

Answer 6

Structural motif of a small protein characterised by the coordination of one or more Zn2+ ions to stabilise the fold
Vast majority of these proteins function as interacting modules that bind to DNA, RNA, proteins and lipids
(zinc finger proteins fit perfectly into DNA major groove)
Zn2+ generally coordinated with a combination of Cys and His residues
Zn2+ bound 1000-100000x more strongly than other metals

Question 7

Why is Zn a good metal of choice for zinc fingers?

Answer 7

Abundant

No redox activity that could damage DNA

Question 8

Structural influence of magnesium

Answer 8

Electroneutrality demands that cations are coordinated to negatively charged DNA/RNA - counter-cations stablise DNA
This is often fulfilled by Mg2+
Esp in RNA e.g. tRNA - Mg2+ binding determines the secondary structure of RNA