Protein Interactions Flashcards
What can proteins form interactions with?
- small ligands
- DNA and RNA
- proteins
- membranes=lipids
- sugars/carbohydrates
What are protein interactions that occur which are sequence specific?
- restriction enzymes
- transcription factors
What are protein interactions which are not sequence specific?
- histone
- helicase
- polymerase
How do proteins interact with other proteins or DNA or lipids?
- usually using non-covalent interactions such as ionic, Hydrogen, van der waals bonding/forces
- sometimes two proteins can be joined by disulphide bonds
What affects the likelihood and strength of binding of protein interactions?
- availability (conc) and co-localisation
- matching non-covalent interactions
- competition from other partners
What affects the lifetime of the complex and therefore its affect?
- extent of contributing stabilising interactions
- regulators= PH, modification, other ligands
What are some examples of post-translational modification of proteins?
- phosphorylation
- methylation
- ubiquitylation
- acetylation
- SUMOylation
- hydroxylation
How does calmodulin work?
-once it binds to calcium it changes structure in a way that enables it to bind to other partners
What factors make protein interactions more complicated to understand?
- 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
What can we measure ligand-protein interaction?
- proteins and ligands have reversible affinity for each other
- they are in equilibrium because always part of them interacts and part does not
- the equilibrium is dynamic and regulated by surroundings, other interactors and modification
What is Protein interaction affinity indicated by?
Kd (disassociation constant)
What is the Kd?
the concentration of substrate/ligand required to achieve half (50%) saturation of protein population
What does a low value of Kd mean?
that the interaction is strong
What are protein-protein complexes?
Proteins interacting with other proteins forming multimers/multimeric proteins.
There proteins have a quaternary structure
What are protein-lipid associations?
Proteins associate themselves with phospholipids in the membrane producing integral/peripheral transmembrane proteins.
What are protein sugar interactions?
Some membrane proteins may get modified to form glycoproteins.
What does more non-covalent interactions between a protein and its ligand mean?
There is a stronger interaction between them
What interaction stabilies 2’ structure of proteins?
Hydrogen bonds either intra in alpha helicies or inter in beta sheets
What interaction stabilise 3’ structure of proteins?
Ionic bonds between 2 ionisable R groups of amino acids.
What are protein domains?
Specific fragments /domains that have evolved to interact with specific proteins.
They have specialised and specfic domains
One protein may have multiple different domains each with a different job.
What are some properties of protein interactions?
Highly Regulated
Highly fluid
Both associate and dissociate with its substrates.
What is the saturation point of a protein?
The point where the addition of a ligand will not affect the percentage bound to a protein.
How do you measure protein affinity?
Have an amount of protein
React with varying substrate concentrations
Measure the proportion of ligand bound to the protein
Draw a graph.
