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MSF1 > Protein Folding 1 > Flashcards

Protein Folding 1 Flashcards

1
Q

How are proteins converted from polypeptide chains to an active form?

A

Protein folding.

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2
Q

What is the process of protein folding mediated by?

A

A complex energy landscape that directs the unfolded state conformations into the encoded native structure.

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3
Q

Why is it not possible to code a set of amino acids to produce a specific 3D structure?

A

Because the mechanism of how this works is not fully understood - unsure of how the 3D structure is encoded in amino acids.

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4
Q

What are intrinsically disordered proteins?

A

Proteins that manage to have biological function without having 3D structure.

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5
Q

How many eukaryotic proteins possess a significant level of structural disorder?

A

~30%

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6
Q

What can IDPs be associated with?

A

Neurodegenerative diseases.

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7
Q

Which neurodegenerative disease is alpha sinuclein associated with?

A

Parkinson’s

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8
Q

Which neurodegenerative disease is AlphaBeta protein associated with?

A

Alzheimer’s

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9
Q

Which neurodegenerative disease is Tau protein associated with?

A

Taupathies

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10
Q

Which neurodegenerative disease is Prion protein associated with?

A

Prion disease.

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11
Q

What other disease are IDPs associated with?

A

Cancer - P53.

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12
Q

Why is it interesting to study IDPs?

A

Can help target the diseases more specifically.

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13
Q

What allows the amino acid code rather than the DNA code to encode protein fold ?

A

It is much more complex than DNA (which only has 4 bases)

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14
Q

Who defined the general principle of protein folding?

A

Anfinsen.

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15
Q

What protein did Anfinsen use to define protein folding?

A

Ribonuclease A.

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16
Q

How many amino acids are there in ribonuclease A and how is it folded?

A

~120 amino acids

Folded via disulphide bridges - 8 cysteines that combine with a very specific pattern of 4 disulphide bonds.

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17
Q

What drives the protein to fold into its native structure?

A

because this state is the most stable

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18
Q

What defines the conformational of the native state?

A

The difference in free energy between the native and unfolded states - (Delta)G(NU).

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19
Q

What is chemical stability?

A

The stability by which a pattern of bonds between atoms is conserved.

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20
Q

What is the main stability that protein folding is focused on?

A

Conformational stability.

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21
Q

What is conformational stability?

A

Refers primarily to the ability of adopting a well defined conformation rather than random coil (unfolded) state.

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22
Q

What are the angles in the backbone of the amino acids?

A

Phi – the angle between alpha carbon and nitrogen.
Psi – the angel between the alpha carbon and carboxyl group.
(omega - peptide bond)

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23
Q

Which amino acids has the greatest available conformations?

A

Glycine

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24
Q

Give examples of things that result in chemical instability.

A

Deamination
Hydrolysis of peptide bonds
Oxidation (of Met at high temperatures)
Elimination/randomisation of disulphide bonds/

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25
Q

What is the energy change in protein folding?

A

Goes from high energy to low energy state.

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26
Q

What does protein need to have to be spontaneous?

A

A negative delta G

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27
Q

Which part of protein folding is not favourable?

A

Entropy - negative entropy when going from disordered to ordered state.

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28
Q

Which conditions influence protein folding strongly?

A

Temperature and pH

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29
Q

Why is protein affected by temperature and pH?

A

Proteins have been selected by evolution to be folded under very specific conditions.

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30
Q

What does optimum conditions for folding depend on?

A

The environment that the organisms live in - mesophile/thermophile/extremophile

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31
Q

What is the average stability of a protein?

A

5-10kcal/mol

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32
Q

Why is the average stability of a protein so low despite all the favourable covalent interactions?

A

It is a balance of the unfavourable interactions and destabilising ones.

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33
Q

Why is it advantageous for proteins to be minimally stable?

A

This means they can be degraded easily - would be too costly otherwise.
Also allows for dynamic conformational changes which may involve partial unfolding.

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34
Q

What is an example of covalent interaction in proteins?

A

Disulphide bonds - can occur inter/intra molecularly.

35
Q

What is an example of inter molecular disulphide bond formation?

A

Antibody light and heavy chains.

36
Q

Are disulphide bonds reversible?

A

Yes.

37
Q

Which enzyme sometimes assists disulphide bond formation?

A

Protein disulphide isomerases.

38
Q

What is the main driving force of protein folding (contributing towards compaction)?

A

The hydrophobic effect - proteins very compact because of this.

39
Q

Which residues can be mutated in a protein without much effect on folding?

A

Surface residues.

40
Q

Which is the most variable part of the protein?

A

The loops.

41
Q

What type of mutations effect folding normally?

A

Internal residue mutations.

42
Q

What does ‘protein structure and folding is hierarchical’ mean?

A

Sub domains fold independently of domains - then assemble to form domains.

43
Q

Give an example of a protein that folds hierarchically?

A

GroEL.

44
Q

Which protein is able to withstand many internal residue mutations?

A

T4 lysozyme

45
Q

How does lysozyme withstand internal residue mutations?

A

Local shifts in packing.

46
Q

What percentage of identity tends to mean identical protein fold?

A

> 40%

47
Q

What lower percentage of identity can also confer identical fold?

A

20%

48
Q

Does identical fold mean identical functionality?

A

No - the number of folds is not infinite so identical folds need to give different functions.

49
Q

What is an example of two proteins that have 50% identity but different folds?

A

GB1 and Rop - can be mutated to 80% identity and still fold differently.

50
Q

What is required for a technique to measure protein folding?

A

Must give two different signals for folded and unfolded state.

51
Q

How can folding being induced in the lab?

A

Temperature increase
pH extremes
Organic solvent
denaturing agent

52
Q

What must be considered when denaturing protein using temperature?

A

Its origin - what is its optimum conditions.

53
Q

Give an example of a denaturing agent.

A

Guanidinium hydrochloride (GuHCl).

54
Q

Define melting point.

A

Point at which 50% of protein is folded and 50% is unfolded.

55
Q

What has distinct signals in CD when absorbing circularly polarised light?

A

The three different states - alpha helices, beta sheets and random coil.

56
Q

Define light.

A

A oscillating wave of electric and magnetic fields.

57
Q

In CD which field of light are you concerned with

A

Electric field.

58
Q

What are the different types of oscillations light can have?

A

Planar, circular or elliptic.

59
Q

What are the different types of oscillations light can have in its electric field?

A

Planar, circular or elliptic.

60
Q

How do you polarise light?

A

Oscillating the light in one specific plane.

61
Q

Is circularly polarised light chiral?

A

Yes

62
Q

What are the two kinds of circularly polarised light?

A

Left handed and right handed - chiral.

63
Q

Which kinds of molecule absorb the two kinds of polarised light differently?

A

Chiral molecules

64
Q

What is a good wavelength to measure a CD spectrum and why?

A

220nm - largest gap between alpha helices (-15) and random coil (1) - easy to follow transition.

65
Q

What is a bad wavelength to measure CD at and why?

A

~204nm - this an isodichroic point

alpha signal = random coil, no transition to follow.

66
Q

What is the sum of the two polarised lights before they hit the sample?

A

Linearly polarised light.

67
Q

What happens is one form of light is completely absorbed by sample?

A

Circularly polarised light is produced

68
Q

What happens if there is equal absorption of both types of light?

A

linearly polarised light is produced.

69
Q

What happens if the two types are absorbed differently?

A

Elliptically polarised light is produced.

70
Q

What does a modern CD spectrometer allow you to do?

A

Set angles of light you want.

71
Q

Advantages of CD.

A

Fast and cheap and there are programs for deciphering results.

72
Q

What makes protein folding so fast?

A

Protein fold is encoded in the amino acids.

73
Q

Other than time, why would a protein not want to sample all conformations?

A

Some conformations are harmful to proteins - prevent protein reaching native fold or conformations can aggregate.

74
Q

Define FRET efficiency.

A

How much the acceptor is being excited.

75
Q

Describe protein ensemble.

A

Protein place in denaturing agent - water added in, diluting the denaturing agent and causes protein to refold due to conditions being below Tm. Can measure exponential phase of refolding to gain kinetic constant.

76
Q

What do FRET and Protein ensemble not give you information about?

A

The transition state.

77
Q

Is the transition state the highest energy state?

A

Yes.

78
Q

What defines the kinetics from going between states?

D->TS->N

A

The energy gap between states corresponds to the kinetics required to interchange between them.

79
Q

Describe the general principle of phi value analysis.

A

The mutation of residues using alanine scanning to determine which ones are already folded in the TS.

80
Q

If you mutate a residue and get a phi value of 1 mean?

A

Transition state and native state have been disrupted - residue is already folded in TS.

81
Q

If you mutate a residue and get a phi value of 0 mean?

A

TS is unaffected - amino acid not yet folded in transition state.

82
Q

What did phi value analysis of the PDZ domain show?

A

Denatured (unfolded) state could go through two different TSs. One of these resulted in intermediate which caused aggregation.

83
Q

What in the intermediate TS of PDZ domain folding caused aggregation?

A

Difference in N terminal beta hairpin - it was warped and so could not dock onto rest of protein.

84
Q

What was it about the intermediate state of PDZ domain that allowed it to form?

A

It was very stable

MSF1 (12 decks)

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