Lecture 23 - Protein function and regulation Flashcards
Common activity of all proteins
Binding
Name of what proteins bind to and consequence of binding
Bind to ligand -> Conformational change that may result = the protein does its function
2 important properties in ligand-binding
Specificity and Affinity
What do we mean by the specificity of a protein
Its abiliy to bind a particular ligand even when in presence of many irrelevant molecules
What do we mean by the affinity of a protein and how is measured
Strength of binding. Dissociation constand (Kd). Lower Kd = stronger binding
What makes binding possible (how is it possible if bonds between molecules are very weak)
Summation of all interactions between 2 protein surfaces makes binding
4 things that are good for binding of 2 surfaces
1) Surfaces have complementary shapes
2) H bonds
3) Complementary charges (plus one side, minus other)
4) Hydrophobic interactions
Best molecules for specificity and affinity + how they bind
Antibodies. Bind with CDR (complementarity determining region)
Where CDR found on antibody/what it’s made of
On both ends of the Y, made of loops of heavy chain and light chain that are highly variable
Enzymes : Special thing about their ligands
Are the substrates of the reactions they catalyze
General scheme of reaction from energy POV
Reactants energy, Transition state (activation energy). Products energy
What enzymes change in a reaction (2)
1) Reduce activation energy
2) Therefore, increase reaction rate
where on enzyme do substrate (ligand) binding and reaction catalysis occur 2 components of this region
In enzyme’s active site. Has a substrate binding site and a catalytic site
How rigid is the binding of an enzyme to its substrates + name of phenomenon by which they fit together
Fluid. There is some molecular flexibility which allows an induced fit of substrate in its binding site
What makes up an enzyme’s catalytic site and substrate binding site
Amino acids that are close by on its surface (3D shape) but that could be far in the linear polypeptide
What are proteases
Proteases cleave proteins (hydrolyze peptide bonds).
what kind of protease trypsin is + why
Trypsin = serine protease cause catal. mechanism involves key serine (serine 195) w/ OH group
Specific activity of trypsin (where it cuts)
Cuts between lysine and arginine residues
Special name of substrate binding site in trypsin
Side-chain-specificity binding pocket
What goes in the side-chain-specificity binding pocket and how it’s held there
Arg or Lys positively charged side chain. Held by negatively charged aspartate
Beside interaction on the substrate binding site, how can interactions also occur between substrate and enzyme
Possible interactions between enzyme and substrate backbones (H bonds) elsewhere
What determines specificity of the enzyme
ONLY the interaction between peptide and substrate binding site (aspartate and side chain of residue at Arg position)
2 other serine proteases like trypsin but with different specificities
Chymotrypsin and elastase
Chymotrypsin substrate binding site (side-chain-specificity binding pocket)
Contains a serine so less specificity than trypsin for basic residues
