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Y1 Cellular Biochemistry and Biology > L5: Protein Interactions > Flashcards

L5: Protein Interactions Flashcards

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1
Q

What can proteins interact with?

A
  • Other proteins - hormones, receptors, subunits in protein assembly, cell-surface proteins
  • Small ligands - metabolites, metal ions, neurotransmitters, antigenic peptide
  • DNA/RNA
  • Membranes - lipids
  • Sugars/carbohydrates
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2
Q

How do proteins interact with other proteins or DNA or lipids?

A
  • Using mostly non-covalent interactions - ionic interaction, hydrogen/electrostatic, hydrophobic and van der Waals
  • Rarely two proteins can be joined with covalent disulphide bonds (S-S)
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3
Q

How does the number of protein interactions affect the strength of the overall interaction?

A

The more interactions, the stronger the bonding
- On their own the interactions are weaker but combined are very strong
- A small number of interactions is still unfavourable to a binding interaction with more interactions as this is stronger

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4
Q

What is an example of a protein interacting with a small ligand?

A

Calmodulin with Ca2+ ions

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5
Q

Describe the interaction of calmodulin with Ca2+

A
  • Calmodulin is the main sensor of Ca2+
  • When calmodulin binds to Ca2+ the calcium changes conformationally, allowing the binding of other targets - can interact and regulate the behaviour with other membrane transport proteins and a range of enzymes, and allow signalling so calcium can interact with other molecules
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6
Q

What are multimeric proteins?

A

When proteins interact and bind with other proteins of the same subunit or very similar subunits; to form a larger protein complex

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7
Q

What are examples of multimeric proteins?

A
  • Structural filaments like microtubules, actin filaments and microfilaments found in cells
  • Form very rigid structures that provide shape and stability to cells
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8
Q

What is an example of a large protein complex formed from protein-protein interactions?

A
  • Helicase in DNA replication
  • Allow the unwinding of the DNA double helix to form the replication fork
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9
Q

How is DNA organised in the nucleus?

A
  • Arranged as chromatin, which is associated with histone proteins - subunit is a nucleosome
  • One nucleosome is made of an octameric core with 146 nucleotides wrapped around one histone
  • These structures are all connected and are further tightly wound into centromeres which make up a chromosome
  • All dependent on DNA protein interactions
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10
Q

What are the 2 types of DNA interaction?

A
  • DNA sequence non-specific - proteins that can interact with any DNA e.g. histones, helicases, polymerases, transcription factors
  • DNA sequence specific - restriction enzymes, transcription factors - recognise very specific sequence of nucleotides and cannot bind to others
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11
Q

Describe protein-lipid associations

A
  • Some integral membrane proteins which anchor and pass through the lipid bilayer. These can have hydrophobic centres that pass through the hydrophobic lipid bilayer
  • Some associate and attach extrinsically through the modification of membrane proteins, to act as receptors in cell signalling - these are glycolipids
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12
Q

Describe protein-sugar associations

A
  • Often seen as glycoproteins on the outside of the phospholipid bilayer
  • These are proteins modified with sugar/carbohydrates
  • Allow interaction and cell signalling with the external matrix
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13
Q

What factors determine proteins interacting with other proteins/molecules?

A
  • Availability (concentration) and co-localisation - proteins and other molecules need to be located in the same place and the higher the conc. the greater the chance of interaction
  • Need to be matching non-covalent interactions
  • Competition of alternative partners - will go with the interaction that will form the strongest bonds
  • Strength of binding/interaction
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14
Q

How is the structure of a protein specialised to interact with other protein/molecules?

A

Often have domains within their structure that specialise in specific interaction

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15
Q

What is a domain?

A

A fragment of a protein that is folded in a particular way and creates a unit that can deliver a specific function

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16
Q

What are some example of a protein-protein interaction domains?

A
  • WD40
  • F-box
  • SH2
17
Q

What are some examples of DNA binding domains?

A
  • HTH (helix ten helix)
  • HMG - leucine zipper
  • Organised to fit into the grooves of the DNA double helix
18
Q

How can pH affect protein interactions?

A
  • pH can change the charge of the amino acids depending on the pKa
  • Can alter the ionic interactions which will destabilise the protein structure and denature it
19
Q

What are post-translational modifications? How can these affect interactions?

A
  • Changes to proteins after they have been synthesised
  • This increases the proteome complexity to provide a diversity in the number of proteins to carry out an increased number of functions
  • e.g. proteins undergo phosphorylation, methylation, acetylation etc
  • Can disrupt interactions and prevent folding, which changes the structure and can destabilise
20
Q

What are some modification-specific protein domains?

A
  • Phospho-
  • Ubiquitin interacting
  • Acetylated lysine interacting
  • All of these can only carry out a function or be recognised by a specific molecule after modification
21
Q

What other group can regulate protein interactions? What is the main example?

A
  • Other ligands
  • e.g. calmodulin with Ca2+ which conformationally changes shape to allow the binding of Ca2+, and provide signalling for calcium to carry out other functions
22
Q

What does DNA polymerase interact with to carry out its function?

A
  • Single-stranded DNA
  • Double-stranded DNA
  • dNTPs
  • Zn and Fe ions - allow catalytic activity
  • Regulatory proteins e.g. exonucleases for proofreading and a beta-clamp to allow binding
23
Q

Summarise protein interactions

A
  • One protein can have many interaction domains
  • One protein can interact at the same time with many substrates and ligands
  • All of the interactions influence each other and form a complex matrix
24
Q

How can protein interactions be measured?

A
  • Proteins and other molecules have a reversible affinity
  • They are in equilibrium - part always interacts and part does not
  • Equilibrium is dynamic and regulated by surroundings
  • Identify the proportion/ percentage of protein bound by other molecules on a graph using a dissociation constant
25
Q

What is the dissociation constant to measure interactions (Kd)?

A

Affinity is indicated by Ka (dissociation constant) -concentration of ligand required to achieve half (50%) saturation of protein population

26
Q

Which ligand has the greatest affinity to the protein?

A
  • The pink has the greatest affinity
  • Achieves the Kd fastest with a low concentration of ligand added - lowest dissociation constant
  • So the pink one has the highest affinity to the ligand and has the strongest interaction

Y1 Cellular Biochemistry and Biology (20 decks)

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