lecture 35/36 - ice binding proteins Flashcards
what are the two groups of ice binding proteins?
antifreeze proteins (AFPs) and antifreeze glycoproteins (AFGPs)
what do all AFPs/AFGPs bind?
ice - the same ligand
are AFPs diverse? describe their evolution.
- very diverse grp of structures
- convergent evolution (didn’t evolve from the same source but have the same function)
generally describe the structure of AFPs
mostly repetitive sequences and structures
what is the function of most AFPs?
to slow or stop ice crystal growth by directly interacting with ice
where are these proteins found?
found in fish, plants, insects, fungi, bacteria
what are ice nucleation proteins? what is there function?
- bacteria that infect plants
- nucleate (accelerate) ice growth
explain how AFPs work to slow ice growth
- AFP binds to the ice surface, hindering growth at the site where it is bound
- this results in growth as a cruved surface (instead of straight uniform growth - have indents where AFPs are)
- this is energetically less favourable for ice to continue growing
- results in depression of the freezing point
describe (generally) the first discovered AFP structure
- 37 aa residues
- alpha helix
- no tertiary structure associated with them
- have the sequential repeat: (TAA XAX AAA XX) 3.5 times where X = variable (usually hydrophilic) res
describe the helical wheel of type 1 AFP proteins
- top face was more variable, generally consisting of hydrophilic residues - not as important
- bottom face was more conserved, generally hydrophobic - important for struct/function
how did we test functional importance of type 1 AFPs?
what did we discover? (2)
mutagenesis experiments:
-mutated A17 -> L = inactive protein
-mutated A19 -> L = active protein
suggested that theres an “active face” of the alpha helix
-mutated T -> S = not active
-mutated T -> V = active
suggested the methyl groups of the A and T residues on the active face are the groups that are essential for binding
discuss the methyl residues on the active face of the type 1 AFP alpha helix
- these are conserved residues
- form a ~flat, hydrophobic surface
describe the “intrahelical h-bonding” of type 1 AFPs
what does this do?
- intrahelical h-bonds (i+4) occur btwn amine and carbonyl grps of the backbone stabilizing the protein
- as you get into the inner loop - can have aa with 2 h-bonds within each res (can donate from amine and accept w carbonyl grp)
- BUT first 4 can only h-bond via their c-term
- BUT last 4 can only h-bond via their n-term
what is the first aa residue of type 1 AFPs?
asp
what is the last aa residue of type 1 AFPs?
arg
describe “helix capping” of type 1 AFPs
what does this do?
- asp side chain folds in (forward) to form h-bonds with the first couple n-term aa of the alpha helix
- arg side chain folds in (back) to from h-bonds with the last couple c-term aa of the alpha helix
- stabilizes alpha helix
describe “dipole compensation” of type 1 AFPs
what does this do?
- recall: peptide bonds can rearrange electrons (resonance) to create structures with a dipole
- this creates overall dipole in the alpha helix
- neg charged asp (at pos end of helical dipole) and pos charged arg (at neg end of helical dipole) offset the dipole - stabilizing the alpha helix
describe the “i+4 salt bridge” of type 1 AFPs
what does this do?
- gluatmic acid (E) and lysine (K) on the hydrophilic face of the amino acid can form a salt bridge
- stabilizes the alpha helix
explain the general structure of Spruce Budworm AFPs
- sequential repeats of 15-17 aa residues
- within the repeats - get the formation of 3 beta strand structures
- within the first beta strand - see a TxT repeat, where x is variable and usually hydrophobic
- three beta strands are then folded into a triangle (3 parallel beta sheets (makes 1 strand) - have 7 strands) - forming a triangular prism - called a beta-solenoid
describe the arrangement of amino acids in the beta solenoid structure
- hydrophobic side chains face inwards forming a hydrophobic core
- hydrophilic side chains face out (includes TxT repeat- where Ts are outside and X is inside)
where does water align to the spruce budworm AFP
aligns to Ts from the TxT repeat
do other “beta-solenoid” structures exist? describe.
- yes
- can be varying lenghts or have varied # of repeats
- my be two beta strands (cylinder)
- may be triangular with certain indents
what is the key property of all AFPs?
- all have flat hydrophobic surface
- allows water molecules to organize as a clathrate around hydrophobic groups (trapped)
- seems that AFPs bind and pre-organize water to look more like ice structures (similar geometry of ice crystal)
- allows h2o molecules to readily h-bond onto ice surface, allowing AFPs to bind ice surface
describe snow flea AFPs
-rich in gly, ala and some pro
-GXY repeat, where X is vairable but some = Gly and Y= ala
-thus, have collagen like left-handed helical structure
(6 helices folded with pro at the turns)
-have flat hydrophobic face, rich in ala side chains, that organizes water into an ice like geometry, allowing them to bind ice surfaces
