Protein Interactions Flashcards Preview

Cellular Biochemistry and Biology > Protein Interactions > Flashcards

Flashcards in Protein Interactions Deck (17)
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1
Q

What can proteins form interactions with?

A
  • Small ligands
  • DNA and RNA
  • Other proteins
  • Lipid membranes
  • Sugars/carbohydrates
2
Q

Where do proteins associate with DNA?

A

In chromatin

3
Q

How can proteins associate with DNA?

A

DNA sequence-specific or DNA sequence non-specific

4
Q

Examples of DNA sequence-specific protein interactions

A
  • Restriction enzymes

- Transcription factors

5
Q

Examples of DNA sequence non-specific protein interactions

A
  • Histones
  • Helicases
  • Polymerases
  • Transcription factors
6
Q

Examples of small ligands

A
  • metabolite
  • metal ion
  • neurotransmitter
  • antigenic
  • peptide
7
Q

Examples of proteins

A
  • hormone
  • receptor
  • subunit in protein assembly
  • cell-surface protein
8
Q

How do proteins interact with lipids?

A

Covalent modification with lipids targets proteins to cell membranes

9
Q

What does Likelihood and strength of binding depend on?

A
  • Availability (concn) & co-localisation
  • Matching non-covalent interactions
  • Competition from alternative partners
10
Q

How do proteins interact with various partners?

A
  • Interaction occurs between compatible structures
  • Proteins can have specialized domains to interact with others
  • Formation of the complex depends on co-localization, concentration of partners, competition, strength of binding
11
Q

What does life time of the complex depend on?

A
  • Extent of contributing stabilising interactions

- Regulators - pH, modification (eg, phosphorylation), other ligands

12
Q

What can protein interactions be influenced by?

A
  • pH, modifications, other ligands, cellular localization

- Proteins can have specialized domains to interact with modified partners

13
Q

How many interaction domains can a protein have?

A
  • 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
14
Q

What is cell signalling based on?

A

Cell signaling is based on protein-ligand and protein-protein interactions and their modification through post-translational modification

15
Q

How do proteins inteact with small ligands?

A
  • Proteins and ligands have a reversible affinity for each other
  • They are in equilibrium – always part of them interacts and part does not
  • Equilibrium is dynamic and regulated by surroundings, other interactors, modification
  • Affinity is indicated by Kd (dissociation constant)–concentration of ligand required to achieve half (50%) saturation of protein population (low is stronger)
16
Q

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

A
  • Using mostly non-covalent interactions: ionic interaction, hydrogen/electrostatic, hydrophobic, van der Waals
  • Rarely two proteins can be joined with covalent disulfide bond (S-S)
  • The more non-covalent interaction the stronger the interaction
17
Q

How can proteins be modified post translation

A
  • phosphorylation, methylation, ubiquitylation, acetylation, SUMOylation, hydroxylation
  • Done by modification-specific protein domains
    • phospho
    • Ubiquitin interacting
    • Acetylated lysine interacting