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Proteins > Structural determinants of protein function > Flashcards

Structural determinants of protein function Flashcards

1
Q

What does the protein 3D shape determine?

A

How protein works in the cell

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2
Q

What do loop, coil and random coil structures share?

A

They have no regular defining properties in structure

Not Alpha-helices and Beta-sheets

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3
Q

What is the structure of loop and coil?

In line

A

Ordered (not mobile), but not in a systematic or regular way

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4
Q

What is the structure of loop and coil?

American Lines

A

Disordered, mobile, fluctuating set of structures

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5
Q

What % of protein is alpha helix?

A

31%

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6
Q

What % of protein is beta sheet?

A

28%

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7
Q

What is the remaining part of the protein structure?

Doesn’t repeat

A

Rest is non repetitive structure

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8
Q

What are the supersecondary structures (motifs)?

Greeks put in their hair

A

B alpha Beta Motif

Beta Hairpin motif

Alpha Alpha Motif

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9
Q

Helical supersecondary structures have?

looped together

A

4 Helix bundle motif

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10
Q

Describe the structure of Beta Supersecondary Structures

A

The chain is a N to a C with 4 sections.

Beta Hairpin motif

the second and third section folds so it is ordered 3,2,1,4

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11
Q

What are the different folds for Beta supersecondary structures?

A

Immunoglobulin fold
Beta-Barrel fold
Alpha/Beta Barrel (TIM barrel) fold

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12
Q

What is the structure of the immunoglobulin fold?

A 
N to C Beta Hairpin motif
4 folds
1 is bound to 2
2 is bound to 5
4 to 3
3 to 6
6 to 7
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13
Q

What is the structure of the Beta barrel fold?

A

N to C beta hairpin motifs
1,2,3,4,5,6, 7, 8
Wiggly line

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14
Q

What is the structure of the Alpha/Beta Barrel (TIM barrel) fold?

A

N to C
Each is folded with itself in a beta hairpin motif
1,2,3,4,5, 6,7 ,8
So 1 is adjacent to 2

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15
Q

Define and give an example of Protein tertiary structure

A

How the secondary structural elements come together

Each protein structure is different (Unlike DNA)

Whale myoglobin (first structure solved): 
Oxygen carrier, allows whales to store oxygen for long periods while they are diving
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16
Q

Teritary structures that build protein structures may contain?

A

Alpha-helices and or Beta-sheets or neither

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17
Q

What are the features of the side chain location in tertiary structure?

A

Water is largely excluded from interior

Hydrophobic “non-polar” amino acids in the core: Shielded from the aqueous solvent (water)

Hydrophillic “charged” amino acids on the exterior- in contact with the water in the solvant

Uncharged polar amino acids often on surface, but can be found in the inside, but usually buried hydrogen bond donors form bonds with acceptors (sort of neutralizing the polarity)

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18
Q

What amino acids face protein interior?

A

Phe
lle
Leu

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19
Q

What amino acids face protein exterior?

A 
Ala
Asp
Lys
Gly
Glu
Asn
Arg
Gln
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20
Q

What are protein domains?

A

Large polypeptides (200 or more amino acids) Usually fold up into a group of globular domains

E.g. Glyceraldehyde-3-phosphate

21
Q

What helps protein folding?

A

Proteins aren’t a tangled mess because they are hierarchically organised, with domains often divided into subdomains

Thing that need to end up close in 3D start close in 2D

22
Q

What are the common DNA folds?

A

Helix-turn-helix
Zinc finger
Leucine zipper

23
Q

What is the structure of Helix-turn-helix?

A

DNA-binding helix is connected to a Dimer-binding helix (loop de loop) by a turn shaped like a upside down mountain

24
Q

Explain the Amino acid sequence for Helix-turn-helix motif

A

20 AA’s per chain

One Alpha helix for recognition of DNA then beta turn, then another Alpha helix

For DNA-binding helix-turn-helix motifs in the lac repressor (tetramer)

25
Q

Helix-turn-helix: Sequence-specific binding due to?

A

Specific contacts between the recognition helix and major goove

26
Q

What is the structure of the Zinc finger motif?

A

30 AA’s

Finger portion is a peptide loop cross-linked by Zn^2+ ion
Zn^2+ usually coordinated by 4 Cys, or 2Cys , 2 His

27
Q

How does Zinc finger interact with DNA or RNA?

A

Binding is weak, so several zinc fingers often act in tandem

Binding can range from sequence specific to random

28
Q

Explain the structure of Leucine Zipper Motif

A

Dimer of two amphipathic Alpha helices plus a DNA-binding domain

Each helix is hydrophobic on one side and hydrophillic on the other

Hydrophobic side is the contact between the two monomers

Apparently every seventh residue in helices is leu

29
Q

What is the job of the Leucine Zipper motif?

A

The two helices wrap around each other in a gently coiled coil. The interacting Leu side chains and the conserved residues in the DNA-binding region are coloured to correspond to the sequence

30
Q

What are EF hands and how do they bind calcium?

A

They are 40 AA’s forming a helix-loop-helix motif

present in > 100 proteins

Often found in multiple pairs, for example four in calmodulin (CAM)

Each EF hand binds to a single Ca^2+ ion

31
Q

What is the first step in the activation of Calmodulin?

A

Calmodulin binds to four Calcium ions

32
Q

What is the second step in the activation of Calmodulin?

A

Calmodulin changes conformation, resulting in an active complex

33
Q

What is the third step in the activation of Calmodulin?

A

The two globular hands of the complex wrap around a binding site on a target protein

34
Q

Src family kinases are a family of?

A

Non-receptor tyrosine kinases

35
Q

SH2 and SH3 both play a part in?

A

Protein-protein interactions

36
Q

Kinase catalytic domain contains?

A

The kinase active site

37
Q

How is the kinase active site switched from inactive to active?

A

Through phosphorylation state, or protein interactions

38
Q

How is Src inactivated?

A

Critical site phosphorylation site: Tyr527, CSK kinases (phosphorylates), or SHP-1 phosphorylase (dephosphorylates)

This inactivates Src through the interaction of P-tyr527 with the SH2 domain, which effectively folds Src up into a closed, accessible bundle.

39
Q

How is Src activated?

A

Desphosphorylation of Tyr527 releases this bond, opening up the molecule to an active state

40
Q

How does the Src family kinases interact with cellular cytosolic, nuclear and membrane proteins?

A

Modifying the proteins by phosphorylation of tyrosine residues

41
Q

What does a Src-homolgy 2 domain compose of?

A

Comprises a central antiparallel Beta-strand surrounded by two Alpha-helices

Conserved AA contribute to pY recognition, variable AA recognise residues C-terminal to pY-provides specificity

42
Q

What are the functions of SH2 domain?

A

modules of 100 AA

Widely distributed in metazoan proteins including PLCy (Phosphinositide phospholipase C, signaling) and Grb2 (Growth factor receptor-bound protein 2, signalling)

Recognise and bind pY-containing motifs of 4-7 amino acids (phosphopeptides)

Enable proteins with diverse functions such as Grb2 (adapter), PLCy (phospholipase) and Src (protein kinase) to interact with autophosphorylated domains of receptor tyrosine kinases. (RTKs).

43
Q

What is the structure of the Sh3 domains?

A

60 AAs

Five Antiparallel Beta-strands form two perpendicular Beta sheets

Recognise pro-rich peptides with minimum sequence Pro-X-X-Pro

Found in various proteins that include Src (kinase), PLCy (phospholipase) and adapter proteins (Grb2)

44
Q

Explain Protein folding

A

Molecular chaperones may be required to fold proteins, either newly synthesized or misfolded for a reason

Some chaperones bind to the amino terminus of the growing polypeptide chain during translation, stabilzing it in an unfolded configuration until synthesis is completed

45
Q

What is the function of the E.coli chaperone: GroEl

A

it is bacterial protein which is a little folding machine

Takes unfolded or miss-folded proteins and refolds them

Its shape is like a rubbish bind with a lid

46
Q

Two conformations of chaperones: Explain A

A

The hydrophobic patch attracts/binds incorrectly folded protein

it has a hydrphobic surfact that binds unfolded proteins

Lid closes with the client inside

47
Q

Two conformations of chaperones: Explain B

A

Structural re-arrangment (uses ATP) exposing hydrphillic surface

Lid then opens and protein is released

48
Q

What are the Macromolecular 4’ Structures?

A

Calcium Channel, GPCR and G protein

Proteins (10 decks)

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