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Proteins Structure and Function > Lecture 12 - 16 > Flashcards

Lecture 12 - 16 Flashcards

1
Q

Advantages of NMR over X-ray Crystallography

A

Protein can be in solution - natural state
Can study protein dynamics
Can see interactions that protein makes

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2
Q

Atoms used

A

1H, 13C, 15N - spin of 1/2

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3
Q

Halpha chemical shift in secondary structure

A

Lower for alpha helix than beta sheet

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4
Q

How to determine alpha helix/beta sheet from chemical shift index

A

4 or more consecutive -1/+1

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5
Q

J

A

spin-spin coupling constant - when nearby nuclei split a signal

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6
Q

Relaxation

A

Time (T) taken for NMR signal to disappear - shorter T means there are other nuclei nearby

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7
Q

Nuclear Overhauser Effect (NOE)

A

Depends on relaxation between spins - if you saturate one nuclei, the nuclei nearby will have a stronger signal

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8
Q

R

A

Distance between 2 relaxing nuclei

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9
Q

NOE signal + distance between nuclei

A

Strong - 1.8 - 2.7A
Medium - 2.7 - 3.5A
Weak - 3.5 - 5A

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10
Q

Amide protection

A

When amide protons are involved in hydrogen bonds in a folded protein, they are protected from exchange with solvent and exchange more slowly

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11
Q

Protonation factor

A

Rate of expected change (unfolded)/ Rate of actual exchange

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12
Q

Problems with large molecule NMR

A 
Issues with unresolved signals
Overlapping signals
Complex multiplets
Low sensitivity - use high B0
Large quantity of info - use computational methods
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13
Q

Ligand

A

Non-macromolecules that interact with proteins - water not normally counted as ligand e.g. peptides nucleotides, ions

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14
Q

Surface characteristics of protein

A

Size, shape, charge, hydrophobicity, dynamics e.g. flexibility

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15
Q

Most favourable protein shape

A

Globular/spherical

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16
Q

Protein crystallisation steps

A 
Purify protein
Crystallise protein
Collect data
Evaluate data
Model building
3D structure
17
Q

Why is it hard to crystallise proteins?

A

Proteins not evolved to crystallise, may be dynamic, every protein requires different parameters, can be unstable

18
Q

Structural proteins

A

Keratin, collagen, fibroin

19
Q

Motor proteins

A

Actin/myosin, kinesin, ATP synthase

20
Q

Fibroin

A

Antiparallel beta sheets with ala and gly side chains

21
Q

To get pure spider silk

A

Ligate consensus sequence into expression vector, transform into e.coli and express and purify

22
Q

MotA/MotB

A

convert proton gradient into energy for movement

23
Q

FliG, FliM and FliN

A

Interact with MotA/B to cause a direction change

24
Q

FliF

A

self-assembled, forms template for rest of structure to assemble from

25
Q

Amino acid in outlier range in ramachandran plot

A

Glycine - so small that doesn’t really have many steric clashes

26
Q

Protein homeostasis maintained by…

A

protein folding/unfolding

27
Q

Folding is exothermic/endothermic

A

exothermic

28
Q

Half unfolding point

A

melting point - Tm. sharp change between folded and unfolded state due to cooperative binding

29
Q

Excreted misfolded proteins

A

Aggregate, which can form amyloids - result in disease

30
Q

Promiscuous activity

A

duplicated gene has a small degree of secondary activity , this can become the main activity if beneficial through mutation.

31
Q

Glycosyl hydrolases involved in..

A

Degredation of poly/oligosaccherides

32
Q

Saccherification

A

hydrolysis into soluble sugar

33
Q

Hydrophobic cluster analysis

A

shows folding similarities through hydrophobic/hydrophillic residues - can determine structural families

34
Q

Digestive protease

A

Low specificity, works well in acidic environment

35
Q

General proteases

A

high specificity, only cleave at one specific peptide bond in one specific molecule. adapted to specific environment

36
Q

How do mutations make drug ineffective?

A

Change in sequence, change in structure, change in binding site = ligand/drug can no longer bind

Proteins Structure and Function (5 decks)

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