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BMS 242 - Advanced Cell and Molecular > Protein interactions > Flashcards

Protein interactions Flashcards

1
Q

What are ‘pockets’ in proteins?

A

Binding sites for ligands - formed by the protein back bone folding to give a specific shape

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2
Q

How do enzymes work?

A

Lower the activation state of a reaction

Making it easier for the substrate to pass over the activation state to product

Reactions happen at a higher rate

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3
Q

What do hydrolyses do?

A

Catalyse a hydrolytic cleavage reaction, using water

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4
Q

What do nucleases do?

A

Break down nucleic acids by hydrolysing bonds between nucleotides

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5
Q

What do proteases do?

A

Break down proteins by hydrolysing bonds between amino acids

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6
Q

What do synthases do?

A

Synthesise molecules in anabolic reactions by condensing 2 smaller molecules to make a larger molecule

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7
Q

What do isomerases do?

What do they change and what do they keep the same?

A

Catalyse the rearrangement of bonds within a single molecule

Change the chemical structure but keep the same chemical formula

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8
Q

What do polymerases do?

A

Catalyse polymerisation reactions, such as the synthesis of DNA and RNA

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9
Q

What do kinases do?

A

Catalyse the addition of phosphate groups to molecules (especially proteins)

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10
Q

What do phosphatases do?

A

Catalyse the hydrolytic removal of a phosphate group from a molecule

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11
Q

What do oxidoreductases do?

A

Catalyse reactions in which one molecules is oxidised, whilst the other is reduced

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12
Q

What can oxidoreductases also be called?

A

Dehydrgenases

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13
Q

What do ATPases do?

A

Hydrolyse ATP

Many proteins with different functions have this as one of their functions

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14
Q

What is dissociation?

A

2 molecules bound together coming apart

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15
Q

What is the dissociation rate defined by?

A

The affinity of the molecules together and the concentration of the bound product at the start [AB]

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16
Q

What is the dissociation rate constant?

How is this used to calculate dissociation rate?

A

Koff

Dissociation rate = Koff x [AB]

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17
Q

What is association?

A

2 molecule coming together

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18
Q

What is association rate proportional to?

A

The concentration of the individual products [A][B]

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19
Q

What is the association rate constant?

How is this used to calculate association rate?

A

Kon

Association rate = Kon x [A][B]

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20
Q

What happens to the association and dissociation rate at equilibrium?

A

They are equal

Association rate = Dissociation rate

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21
Q

What is the equilibrium constant and what is it equal to?

A

K

K = Association rate = Dissociation rate 
K = Kon [A][B] = Koff [AB]
K = Kon/ Koff = [AB] / [A][B]
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22
Q

How can association be measured?

A

1) Hold A constant
2) Gradually increase B in solution

3) Measure the fraction of bound and unbound ([AB] / [A] )
4) Overtime AB increase until SATURATION

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23
Q

What is the shape of an association curve and why?

A
  • Sharp increase in the fraction bound ( [AB] / [A] ), when B is first added
  • Then a slower gradual increase, as the molecules are continuously dissociating
  • Eventually, graph flattens out as the reaction is saturated
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24
Q

What are ‘transient interactions’?

A

Interactions between proteins - they have a dissociation constant and don’t stay bound

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25
Q

Why must the shapes of proteins be compatible?

A

To from many bonds (ionic, hydrophobic, electrostatic)

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26
Q

What are 3 types of protein interaction? (Describe them)

A

1) Surface-string (string is the ligand, fits into a groove)
2) Helix-helix (2 strings wrapped around each other)
3) Surface-surface (complimentary surfaces)

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27
Q

What does binding between proteins often cause? (2 things)

A

A conformational change in shape

A formation of a protein complex

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28
Q

What do signalling pathways rely on?

A

Interactions between a few conserved domains

Eg.

  • Receptors
  • Intracellular proteins which transduce the signal
29
Q

What are protein domains?

A

Modular parts of a protein which have specific purposes and can evolve, function and exist independently of the other proteins in the protein chain

30
Q

What happens to protein domains during evolution?

What does this form?

A

They are swapped with each other - forming many different functional domains which have taken advantage of the specific domains

Forms many different proteins, which can all have the same domain, but are paired with other modular domains

31
Q

What are 6 examples of commonly occurring (conserved) domains?

What do they bind?

A

ALL bind specific substrates

1) SH2
Binds phosphotylated tyrosine

2) SH3
Bind proline-rich motifs (POLY-prolines)

3) PH
Bind phospholipids

4) EF hand
Binds calcium/magnesium in structural of signalling roles

5) Zinc finger
Bind zinc in a structural mode

6) Leucine zipper
Mediated protein-protein or protein-DNA binding

32
Q

Where were the SH2 and SH3 domains originally found?

What is the role of this protein?

A

In Src

Important in cancer - researchers wanted to know what each domain did

33
Q

Where is SH2 domain found?

A

In MANY unrelated different proteins

34
Q

What is the SH2 domain involved in and how?

A

Signalling mechanisms:

- Binds to phospho-tyrosine ligands to form signalling complexes (docking)

35
Q

What can increase binding to SH2?

A

Kinases - by phosphorylating tyrosine

36
Q

What can decrease binding to SH2?

A

Phosphatases - by removing the phosphate from tyrosine

37
Q

How does the SH2 domain bind to phospho-tyrosine?

A

Has a binding pocket, which is lined with positively charged amino acids
(phosphate on the tyrosine is NEGATIVELY charged)

38
Q

What does the SH3 domain do?

What is it involved in?

A

Act as an adaptor to LINK proteins, bringing them together in a non-regulated fashion

Involved in signalling and has a structural role (holds proteins together - maintaining a mul-tiprotein complex)

39
Q

What is the minimum consensus of a target of SH3?

A

P-x-x-P

with x being another amino acid

40
Q

How does the SH3 domain interact with the target?

A

NOT through phosphorylated tyrosine!!

SH3 domain contains many AROMATIC residues, which interdigitate between the prolines of the PxxP motif

Stabilised through AROMATIC STACKING (as proline is also aromatic)

41
Q

What is ‘aromatic sticking’?

A

Non-covalent interactions between aromatic rings

Causing stabilisation of the aromatic side chains into a LOW ENERGY state

42
Q

What is the difference between the interactions of SH2 to its target and SH3 to its target?

A

SH2 - mostly IONIC bonding (H bonding or charged attraction)

SH3 - ELECTROSTATIC interactions (Van Der Waals)

43
Q

What is the PH domain involved in and how?

A

Signalling and anchoring proteins to the membrane

As binds to phosphorylated lipids

44
Q

How does the PH domain bind to different lipids?

A

Lipids show different states/levels of phosphorylation, which is recognised by the PH domain

45
Q

Where does the PH domain sit in the cell and why?

A

Close to the membrane - binds to phosphorylated lipids (in the membrane)

46
Q

What creates binding sites for proteins containing PH domains?

A

Kinases - phosphorylates lipids

47
Q

What pathways are PH domains involved in? (5 things)

A

1) Actin rearrangement
2) Vesicular trafficking

3) Gene expression
4) Cell growth

5) Survival

48
Q

What is Spectrin?

A

A structural protein with a PH domain

49
Q

How does the PH domain in Spectrin bind to the target?

A

Has amino acids to make the binding site ‘hydrophillic’

Pocket is +ve charged to interact with the -ve phospholipids

To make the protein ‘comfortable’ against the hydrophilic heads of the lipids in the membrane

50
Q

What function do Zn ions have in the cell?

A

Structural - holds proteins in a certain confirmation

51
Q

What function do Ca ions have in the cell?

A

Regulatory - Tightly controlled concentrations within the cell

52
Q

What function do iron and copper ions have in the cell?

A

Enzymatic - found within enzymes

53
Q

What do EF hands do?

A

Bind Ca ions to have a regulatory function

Bind Ca or Mg ions to have a strutural function

54
Q

What does calcium binding to EF hands cause?

A

Induces a structural change

55
Q

How does the size or valency (charge) of a metal ion change its binding?

A

Different sizes and valencies of metal ions need to be liganded by different numbers of amino acids and have DIFFERENT structures

56
Q

What is the structure of an EF hand?

A

Octadentate (has 8 atoms in the binding site which can interact with the calcium ion)

7 oxygen containing side chains

Invarient glycine residue to accommodate for the oxygen which encircles the calcium - tight turns

2 alpha helices

57
Q

What purpose does the oxygen in the side chains in the EF hand serve?

A

They are negatively charged - to shield the positively charged calcium ion, which is embedded tightly in a pocket with a bed of oxygen

58
Q

What is calmodulin?

A

A regulatory protein which is involved in many signalling pathways

Commonly binds to calcium

59
Q

What is the structure of calmodulin?

A

2 binding domains with 2 EF hands - can bind to 4 calcium in total (2 on either side)

Glycine - to allow the sharp bend

60
Q

What happens when calcium binds to calmodulin?

What does this allow?

A

Conformational change to expose a hydrophobic patch of amino acids on each EF hand

Allows the interaction with amphipathic alpha helices (have BOTH hydrophobic and hydrophilic parts)

61
Q

Why do proteins need to interact with DNA?

A

To regulate:

  • DNA activity
  • Gene expression
  • DNA replication
  • RNA synthesis
62
Q

How are DNA binding domains similar?

A
  • Overall basic charge (have basic amino acids) as DNA is acidic
  • Recognises DNA strand mostly through interactions with the major groove (wider - easier for amino acids to interact)
63
Q

What are 4 examples of DNA binding motifis, which are present in DNA binding proteins?

A

1) Zinc fingers
2) Leucine zippers
3) Basic helix-loop-helix (bHLH)
4) Beta-sheet

64
Q

Why do many DNA binding proteins have several DNA binding motifs in a row?

A

For increased affinity and a more stable and specific interaction

Interact with multiple places on the DNA

65
Q

What do zinc finger bind to?

A

DNA

Zn

66
Q

How and why do zinc fingers bind to Zn?

A

To stabilise the DNA binding structure - holds the alpha helices and beta sheet together in the tertiary structure

4 amino acids (histidine and/or cystine) separated by at least 2 residues bind to the Zn ion

Zn ions are also positively charged - DNA is negatively charged

67
Q

Which part of the Zinc finger interacts with the DNA and how?

A

The alpha helice, interacts with the major groove

68
Q

What is proline?

A

An amino acid

BMS 242 - Advanced Cell and Molecular (24 decks)

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