LEC3: Protein Structure and Ligand Binding Flashcards
why is the binding of a ligand to its binding partner not a permanent interaction?
because binding sets off a signaling pathway - do not want this always turned on
need binding to re-occur to signal again
For a drug that binds to a receptor to be efficacious, should it have a lower or higher KD than the natural ligand? Why?
drug should have a lower KD
because KD is dissociation constant - so a lower KD means greater affinity
How would removing the tetramerization domain from a protein that forms a four-subunit complex affect its function?
it woudl become nonfunctional or less effective?
Explain why cooperative binding of oxygen to hemoglobin is important for the normal transport of oxygen from lungs to tissues.
because it allows for most efficient delivery of oxygen to tissues
What is an allosteric effector?
molecule that binds to a protein on 1 site, causing a conformational change in the protein that affects its fxn at a distant site
what is tertiary structure of a protein? what does it enable?
the overall 3D conformation of a protein
enables protein to become function
i.e. amino acid side chains in a particular region of the protein can form a binding pocket for a ligand
what is a ligand, and what does it do? examples of types of ligands?
ligand: molecule that binds reversibly to specific site in proteins, with extremely high specificity
protein, lipid, small molecules, ions, gases
what is the beta-adrenergic receptor?
what binds to what?
what is the effect?
example of a ligand-receptor interaction
hormone, epinephrine (aka adrenaline) binds to its cell surface receptor, the beta-adrenergic receptor
b-adrenergic receptor is a **transmembrane protein **w/ 7 membrane-spanning regions of **alpha-helices **
epinephrine-receptor binding activates signaling pathway that controls: blood prssure, cardiac output, breakdown of energy stores
what is the equilibrium reaction re: ligand-binding partner?
protein (P) + ligand (L) (PL)
Association: P + L PL
Dissociation: PL P + L
KD = [P] [L] / [PL]
what is KD? definition, meaning
what does a low KD mean?
KD: is the dissociation constant for the dissociation reaction between a ligand & its binding partner
the concentration of the ligand at which 1/2 of the protein is bound to the ligand
lower KD = higher affinity of ligand for protein, because it takes smaller amt of ligand to 1/2 saturate the binding partner
what is oxygen-hemoglobin binding an example of?
ligand binding
it’s reversible
what is the structure of adult hemoglobin?
4 globin chains: 2 alpha-globin chains + 2 beta-globin chains
each chain has heme as a tightly bound prosthetic group
how does oxygen bind to hemoglobin?
ferrous iron (Fe2+) in heme group can form 6 potential bonds
oxygen binds to Fe2+ in heme group and it H-bonds w/ histidine in globin
what is the structure of myoglobin?
only 1 subunit, rather than a quarternary structure, like hemoglobin
has oxygen-binding site
how do oxygen-hemoglobin bind? what does this mean? what does it enables?
example of cooperative binding/allosteric effect/allosteric binding
binding of an oxygen molecule to 1 heme group increases oxygen affinity of remaining heme groups in the same hemoglobin molecule (4th oxygen has 100x affinity as 1st)
enables hemoglobin to very efficiently combine oxygen in the lungs & release it into the tissues
how much of oxygen from lungs by myoglobin, hemoglobin, or hypothetically no cooperative binding oxygen is released into tissue?
what does this demonstrate?
what is the shape of this relationship’s curve?
myoglobin: 7%
hemoglobin: 66%
hypothetical: 38%
demonstrates that cooperative binding allows hemoglobin to most efficiently uptake oxygen from lungs, release it in the tissues
SIGMOIDAL relationship
in which state does hemoglobin bind to oxygen? when doesn’t it bind to oxygen?
binds in the relaxed (R) state
does not bind in the taut (T) state
explain this:
binding of oxygen to hemoglobin
partial pressure of oxygen pO2 (torr) (x) vs. fractional saturation of hemoglobin (y)
when binding occurs in a cooperative manner, plot produces a sigmoidal curve
cooperative binding allows hemoglobin to become completely saturated w/ oxygen in the lungs, release it in the tissues
what are allosteric effectors?
molecules that bind to a protien on a site, & cause a conformational change in the protein that affects its function at a distant site
what molecules are allosteric effectors of oxygen-hemoglobin interaction?
1) oxygen itself affects binding of oxygen thru cooperative binding
2) Bohr effect: Low pH
3) High CO2
4) 2,3-biphosphoglycerate (2,3-BPG)
What is the Bohr effect? How does it work?
High concentration of dissolved CO2shifts equilibrium toward bicarbonate plus protons, aka lowered pH
**Lowered pH causes decrease in affinity of hemoglobin for oxygen **(therefore increased KD)
This effect allows more oxygen to be released from hemoglobin in active tissues where pH is low
what is this?
Bohr effect
higher CO2 > lowered pH > increased KD / less hemoglobin-oxygen affinity > more oxygen released to O2-deficient tissues
how does CO2 have an allosteric effect on hemoglobin?
when does this occur?
CO2 can bind directly to hemoglobin, stabilize a conformation w/ a lower affinity for oxygen
occurs in conditions of lower pH, were KD is higher
allows for more release of oxygen into tissues (88%)!
what is 2,3-BPG? its allosteric effect on hemoglobin? the result?
2,3-BPH is a highly negative molecule, a metabolic product of glucose breakdown
it binds to positive part of B-chain of hemoglobin
binding of 2,3-BPG decreases the affinity of hemoglobin for oxygen
what pathological conditions does 2,3-BPG matter for? why?
high levels of 2,3-BPH in individuals w/ anemia or chronic hypoxia due to lung disease
2,3-BPH causes decreased hemoglobin-oxygen affinity, aka
presence of 2,3-BPH results in relase of oxygenf rom hemoglobin at higher partial pressures of oxygen
how does 2,3-BPG impact individuals at high altitude?
2,3-BPH increases in reponse to decrease in partial pressure of oxygen in the air
so it allows adaptation at high altitudes
presence of 2,3-BPH results in relase of oxygenf rom hemoglobin at higher partial pressures of oxygen
is hemoglobin structure the same throughout development?
no
diff types of hemoglobin are expressed at diff times during development
what is the structure of fetal hemoglobin (HbF)?
what is its affinity for oxygen like re: adult hemoglobin (HbA)
HbF= 2 alpha-globin chains, 2 gamma-globin chains
does not bind strongly to 2,3-BPH, therefore has a **higher affinity for oxygen **than HbA
means oxygen is efficiently transferred from maternal RBC > fetal RBC
explain this:
fetal hemoglobin does not bind 2,3-BPG
it therefore has a higher affinity for oxygen than adult hemoglobin
it therefore transfers O2 more efficiently to RBC
O2 flows from maternal oxyhemoglobin > fetal deoxyhemoglobin
genetic basis for sickle cell anemia?
single ntd change from** **in beta-globin gene
results in single amino acid change from glutamate to valine in beta-globin protein
glutamate = positively charged, usually on outside, vs valine = hydrophobic, usually in center of globulin
valine on outside of
why do sickled cells manifest?
amino acid change in B-globin protein from glutamate to valine promotes **polymerization **of variant hemoglobin (HbS) b/c of hydrophobic interactions btwn B-globin subunits per valine
HbS polymerization produces long fibers, which distory shape of RBC into curved, sickled appearance
how does RBC change shape in sickle cell anemia? what is the result?
usually flexible, compact, round RBC can go through capillaries easily
sickled RBC cannot, clogs small capillaries
