Protein Interactions Flashcards
What can proteins form interactions with?
- Small ligands
- DNA and RNA
- Other proteins
- Lipid membranes
- Sugars/carbohydrates
Where do proteins associate with DNA?
In chromatin
How can proteins associate with DNA?
DNA sequence-specific or DNA sequence non-specific
Examples of DNA sequence-specific protein interactions
- Restriction enzymes
- Transcription factors
Examples of DNA sequence non-specific protein interactions
- Histones
- Helicases
- Polymerases
- Transcription factors
Examples of small ligands
- metabolite
- metal ion
- neurotransmitter
- antigenic
- peptide
Examples of proteins
- hormone
- receptor
- subunit in protein assembly
- cell-surface protein
How do proteins interact with lipids?
Covalent modification with lipids targets proteins to cell membranes
What does Likelihood and strength of binding depend on?
- Availability (concn) & co-localisation
- Matching non-covalent interactions
- Competition from alternative partners
How do proteins interact with various partners?
- 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
What does life time of the complex depend on?
- Extent of contributing stabilising interactions
- Regulators - pH, modification (eg, phosphorylation), other ligands
What can protein interactions be influenced by?
- pH, modifications, other ligands, cellular localization
- Proteins can have specialized domains to interact with modified partners
How many interaction domains can a protein have?
- 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
What is cell signalling based on?
Cell signaling is based on protein-ligand and protein-protein interactions and their modification through post-translational modification
How do proteins inteact with small ligands?
- 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)
How do proteins interact with other proteins or DNA or lipids?
- 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
How can proteins be modified post translation
- phosphorylation, methylation, ubiquitylation, acetylation, SUMOylation, hydroxylation
- Done by modification-specific protein domains
- phospho
- Ubiquitin interacting
- Acetylated lysine interacting
