lecture 35/36 - ice binding proteins Flashcards

1
Q

what are the two groups of ice binding proteins?

A

antifreeze proteins (AFPs) and antifreeze glycoproteins (AFGPs)

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2
Q

what do all AFPs/AFGPs bind?

A

ice - the same ligand

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3
Q

are AFPs diverse? describe their evolution.

A
  • very diverse grp of structures

- convergent evolution (didn’t evolve from the same source but have the same function)

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4
Q

generally describe the structure of AFPs

A

mostly repetitive sequences and structures

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5
Q

what is the function of most AFPs?

A

to slow or stop ice crystal growth by directly interacting with ice

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6
Q

where are these proteins found?

A

found in fish, plants, insects, fungi, bacteria

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7
Q

what are ice nucleation proteins? what is there function?

A
  • bacteria that infect plants

- nucleate (accelerate) ice growth

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8
Q

explain how AFPs work to slow ice growth

A
  • 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
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9
Q

describe (generally) the first discovered AFP structure

A
  • 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
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10
Q

describe the helical wheel of type 1 AFP proteins

A
  • top face was more variable, generally consisting of hydrophilic residues - not as important
  • bottom face was more conserved, generally hydrophobic - important for struct/function
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11
Q

how did we test functional importance of type 1 AFPs?

what did we discover? (2)

A

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

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12
Q

discuss the methyl residues on the active face of the type 1 AFP alpha helix

A
  • these are conserved residues

- form a ~flat, hydrophobic surface

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13
Q

describe the “intrahelical h-bonding” of type 1 AFPs

what does this do?

A
  • 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
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14
Q

what is the first aa residue of type 1 AFPs?

A

asp

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15
Q

what is the last aa residue of type 1 AFPs?

A

arg

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16
Q

describe “helix capping” of type 1 AFPs

what does this do?

A
  • 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
17
Q

describe “dipole compensation” of type 1 AFPs

what does this do?

A
  • 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
18
Q

describe the “i+4 salt bridge” of type 1 AFPs

what does this do?

A
  • gluatmic acid (E) and lysine (K) on the hydrophilic face of the amino acid can form a salt bridge
  • stabilizes the alpha helix
19
Q

explain the general structure of Spruce Budworm AFPs

A
  • 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
20
Q

describe the arrangement of amino acids in the beta solenoid structure

A
  • 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)
21
Q

where does water align to the spruce budworm AFP

A

aligns to Ts from the TxT repeat

22
Q

do other “beta-solenoid” structures exist? describe.

A
  • yes
  • can be varying lenghts or have varied # of repeats
  • my be two beta strands (cylinder)
  • may be triangular with certain indents
23
Q

what is the key property of all AFPs?

A
  • 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
24
Q

describe snow flea AFPs

A

-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