Lecture 2.1: Intro to Soluble Transport Proteins Flashcards
Many of protein functions involve binding
Binding occurs between?
- Enzymes & their substrates
- receptors & signal molecules
- transporters & small molecules (for transport)
A ligand is a
small molecule that forms a complex with a protein to serve a biological function
The binding of ligands to proteins occurs by [—] interactions
weak non-covalent interactions
ligand binding is a [—] association
Reversible
Ka
association constant/ equilibrium constant for the association (or binding of the protein and ligand)
Keq = Ka
[products]/[reactants] = [protein-ligand complex]/[protein][ligand]
Large Ka = [—]
high binding affinity
Small Ka = [—]
low binding affinity
Kd
dissociation constant/ equilibrium constant for the dissociation of ligand from protein-ligand complex
Keq = Kd
[reactants]/[products] = [protein][ligand]/[protein-ligand complex]
Large Kd = [–]
low binding affinity
small Kd = [–]
high binding affinity
fractional saturation
the fraction of protein binding sites that are occupied
fractional saturation equation
theta =(occupied binding site)/(total binding sites)=[PL]/([PL]+[P])=[L]/([L]+Kd )
Order of Protein Dissociation Constants from Low to High
Biotin-advin
Enzyme-substrate
Typical receptor-ligand interactions
Sequence-specific protein-DNA
Antibody-antigen
[High Affinity]
1. Biotin-avidin
2. Antibody-antigen
3. Sequence-specific protein-DNA
4. Typical receptor-ligand interactions
5. Enzyme-substrate
[Low Affinity]
Myoglobin has very [–] Kd for O2 binding
low Kd
high binding affinity
Myoglobin facilitates oxygen diffusion in [–]
muscles
Myoglobin structure
tertiary
single polypeptide globin
1 heme
MW ~17 kDa
8 alpha helices (75% alpha helices)
hemoglobin facilitates oxygen diffusion in [–]
red blood cells
hemoglobin structure
quaternary
4 globin chains (tetramer)
2 alpha and 2 beta subunits
alpha and beta subunits associate to form alpha-beta dimers
What type of group is heme?
prosthetic group
what is a prosthetic group?
A non-protein molecule which is permanently attached to a protein and is required for protein function
tightly bound, specific non-polypeptide unit
What state must iron be in to bind to O2
Fe2+
Each heme group can bind [–] ligand
one (O2, CO2, CO)
Two critical histidine residues and their functions
Distal His = stabilizes the O2
Proximal His = forms the other coordinate bond
Steps of O2 binding
- Distal His stabilizes the O2 with H-bonds
- oxygen bonds to the heme Fe2+ with one coordinate bond
- proximal his forms the other coordinate bond
