L5 - Protein Interactions Flashcards
What forms the binding site in a protein?
The folding of the protein
Hydrogen bonds form between side chains
How do enzymes work?
Lower the activation energy of the reaction - catalyst
- Bring substrate into close proximity
- Bending substrate
- Providing electron donor/acceptors
Hydrolases
Catalyse a hydrolytic cleavage reaction
Nucleases
Break down nucleic acids by hydrolysing bonds
Proteases
Break down proteins by hydrolysing bonds
Synthases
Synthesis molecules in anabolic reactions
Isomerases
Catalyse the rearrangement of bonds within a single molecule
Polymerases
Catalyse polymerisation reactions
Kinases
Catalyse the addition of a phosphate group to a molecule
Phosphatases
Catalyse the hydrolytic removal of a phosphate group
Oxido-reductases
Catalyse reactions in which one molecule is oxidised and one is reduced
ATPases
Hydrolyse ATP
Kinetics of protein interactions for not covalent interactions
Dissociation rate = dissociation rate constant x concentration of AB
Association rate = association rate constant x concentration A x concentration B
At equilibrium association rate = dissociation rate
Equilibrium constant
[AB]/[A]x[B]
Protein-protein interactions require complementary surfaces
Surface-string
Helix-helix
Surface-surface
Protein-protein binding enables
The formation of enough weak bonds to withstand thermal jolting.
Enables formation of protein complexes
Often causes a conformational change
Activation of GTP
EF-Tu binds to GTP to become activated
GTP hydrolyses to GDP resulting in inactivation of EF-Tu
SH2 domain
Binds phosphorylated tyrosine
SH3 domain
Binds proline rich motifs
PH domain
Binds phospholipids
EF hand domain
Binds calcium/magnesium in structural or signalling mode
Zinc finger domain
Bind zinc in structural mode
Leucine zipper domain
Protein-protein or protein-DNA binding
SH2 domain role
Formation of signalling complexes
Kinases and phosphatases modulate the level of tyrosine phosphorylation
- Helps regulate binding
Specificity between the phosphate of the protein tyrosine - SH2 domain
Ionic interactions between - phosphate and + amino acids
Some hydrogen bonds
SH3 domain role
Linking signalling components
Structural role in maintaining multiprotein complexes
Minimum consensus sequence for SH3 binding is
P-x-x-P
2 amino acids
SH3 domain contains
Several aromatic residues - interdigitate between prolines of PxxP
- Stabilised by aromatic stacking
- Electrostatic interactions due to aromatic stacking of proline and tyrosine
PH domain role
Lipid binding
Signalling
Anchoring proteins to membrane
Kinases modify phospholipids to create binding sites for proteins containing PH domains
Spectrin
Structural protein
Combination of hydrophobic and charged interactions bind phospholipid an drive association with membrane surface
Metal ion binding domain role
Structural - Zn
Regulatory - Ca
Catalytic - iron and copper
Size and valencies of metal ion
These are liganded by different numbers of amino acid
Have different structural requisites
EF hand binding domain role
Regulatory - binding Ca
Structural - binding Ca/Mg
How do they accommodate tight turn in EF hands?
Octadentate - 7 oxygen containing side chains
Invariant glycine chains
Calmodium structure and regulation
Ca binding exposes hydrophobic patch which enables binding to amphipathic alpha helix
Protein DNA binding domain classes
Zinc fingers
Leucine zipper motifs - dimers of short coiled sequence and a specific DNA recognition helix
Basic helix-loop-helix - charged residues in the helix interact with charged groups on DNA
Beta sheet
Protein DNA binding domain role
Basic charge to mediate interaction with acidic DNA strand through interactions with major groove
Zinc fingers role
Structural function in protein-DNA or protein-protein interactions
Zn is coordinated tetrahedrally by cysteine or histidine residues
Protein DNA binding domain often form
Homo or hetero dimers increasing the repertoire of available DNA binding proteins
