L5 - Protein Interactions Flashcards
What presents after folding which allows protein interactions to occur
Pockets
What are found within the pockets
Side chains that are exposed
Describe how an enzyme may affect a reaction
Lower the activation energy so it is easier for the substrate to pass through slightly higher energy state
What can be said of the energy state of the products of an enz controlled reaction
Products will have a lower energy state than the initial substrates
What do hydrolases do
Catalyses hydrolytic cleavage reactions
What do nucleases do
Break down of nucleic acids by breaking bonds between the nucleotides
What do proteases do
Breakdown proteins by hydrolysing peptide bonds between amino acids
What do synthases do
Involved in synthetic reactions (anabolic) by condensing two smaller molecules
What do isomerases do
Involved in the rearrangement of bonds within a single molecule
What do polymerases do
Involved in polymerisation reactions such as with DNA and RNA
What do kinases do
Phosphorylate other molecules
What do phopsphatases do
Hydrolytic removal of a phosphate molecule
What do oxido-reductases do
Involved in a reaction where one molecule is oxidised and one molecule is reduced
ATPase carry out what type of reactions, give an example
Hydrolysis reactions of ATP
Myosin head
What is the equation for dissociation
AB –> A + B
What does Koff represent
The dissociation constant
What equation gives the rate of dissociation
Koff [AB] = rate of dissociation
What is the equation for association
A + B –> AB
What does Kon represent
Constant of association
What equation gives the rate of association
Kon [A] [B]
At equilibrium what can be said about the two rates
What is the algebraic representation of this
Ass. rate = dis rate
Kon [A] [B] = Koff [AB]
Give the equation for the equilibrium constant when the system is at equillibrium
[AB] / [A] [B] = Kon/Koff = K
What can be said at Kd
Fraction of protein associated is 0.5
What affects the binding rate
Protein concentration
At low conc of B what will be the ammount of AB complexes formed
Very low
Will fraction bound exceed 1
No saturable
What will occur in terms of interactions if surfaces are a poor match
Very few interactions
What will occur in terms of interactions if surfaces are a good match
Many interactions
What type of forces are involved in protein interactions
Ionic, hydrophobic
What are three types of protein-protein interactions which involve complementary surfaces
Surface - string
Helix - helix
Surface - surfac
What is an example of a protein which interactions lead to the formation of complexes (it also carries oxygen)
Hemocyanin
Describe how Ef-Tu is an example of a protein which undergoes confrontational changes
When GTP is bound it is active - the switch helix is at one end associated closely with the 3rd phosphate allows close association with the second domain
When GDP bound no longer as close interaction with the switch helix –> second domain no longer as close
Describe the role of different domains in signalling pathways
Many domains at the PM
Many domains in the downstream pathwway
Explain what a SH2 domain binds to
Phosphorylated tyrosines
Explain what an SH3 domain binds to
Proline rich motifs P-XX-P
What does a PH domain bind to
Phospholipids
What does an EF domain bind to
Binds Ca/Mg in a structurual or signalling mode
What does a zinc finger bind
Zn in a strcutral mode
What does a leucine zipper bind to
Protein-pr otein or protein DNA `
Where does SH2 get its name
Src homology 2 domain
What is SH2 important in
Phospho-tyrosine binding
What is the SH2 domain often involved in
Signalling mechanisms
Where the the prototypical SH2 domain found
Where else is it found
Src tyrosine kinase
Found in many other signalling and adaptor proteins
What does the binding od the SH2 domain cause
Formation of signalling complexes
What enzymes regulate SH2 binding - how is this achieved
Kinases and phosphatases act to either phosphorylate or dephosphorylate tyrosines - this determines the activity as SH2 domains are only able to bind to tyrosines
Where does Sh3 get its name
Src homology 3 domain
What does SH3 bind
Poly-proline binding motifs
What is the minimum binding consensus
P -XX- P
Proline separated by two amino acids
Where is the prototypical SH3 domain found
From the Src tyrosine kinase
What is the SH3 involved in
Linking signalling complexes also has a strucutural role in maintianing multi protein complexes
What do the aromatic residues add for the SH3 domain, how?
Interdigitate between the prolines of the P-XX-P motif.
this aromatic stacking gives them a much lower energy state
Where does a PH domain get its name from
Pleckstrin homology domain
What is the PH doamin involved in
Lipid binding, roles in signalling and anchoring proteins to the membrane
How to kinases have a regulatory effect on PH domain
Kinases modify phospholipids to create binding sites for proteins which have a PH domain
Describe the PH domain in PLC-gamma
PH domain is anchored to membrane PI(3,4,5)P2
3 metal bound in proteins in different contexts
Structural - Zn
Regulatory - Ca
Catalytic - Fe and Cu
What different combinations of ions may be found in EF hands
Ca –> regulatory function
Ca/Mg –> Structural role
Describe the EF motif
Octadentate - (8 atoms in the binding site)
Invariant glycine residues to accomodate the turn
Describe calmodulin
How does it activate when Ca is bound
Strucutral and regualtion requiring Ca
Ca binding exposes a hydrophobic patch - this then allows interaction with an amphipathic a-helix to flexible linker helix
What must be the charge of protein-DNA binding domains
Must maintain a basic charge in order to act with the acidic DNA strand through interactions with the major groove
What do the different classes of DNA binding proteins containing
Zinc fingers
Leucine zipper
Basic-helix-loop-helix
B-sheet
What are leucine zippers dimers of
Dimers of short coiled-coil sequences (the leucine zipper) and a specific recognition helix
Describe Zn finger domains
Central Zn ion
Includes two beta sheets (antiparrallel) and an alpha helix
