Globular Proteins Flashcards
ligand
molecule that reversibly binds to a protein
binding site
- site where ligand docks
- specific size, shape, charge, hydrophilic/hydrophobic
- noncovalent forces
induced fit
binding results in conformational change
myoglobin: function
- store O2 for metabolism
- protein side chains lack affinity for O2
myoglobin: structure
- peptide bond in trans-config.
- all a-domain: 8 a-helices (A-H)
- 3 or 4 proteins at bends
- hydrophobic residues interior
- Fe(II) at center of heme coordinated by 4 porphyrin bond to Fe, O2-Fe
Ka equation
[PL]/[P][L]
Kd equation
[P][L]/[PL]
fractional saturation equation
θ=protein occupied by ligand/total protection
= [PL]/[P]+[PL]
hyperbolic curve equation
θ=[L]/Kd+[L]
carbon monoxide
- binds 20,000x better than O2 because of lone electron pair that donates to Fe 3+
- similar size and shape to O2 because of lone electron pair
- blocks myoglobin and hemoglobin
myoglobin as O2 transporter
- pO2 in lungs is ~13 kPa (100 mmHg)
- myoglobin binds oxygen well
- pO2 in tissues is ~ 4 kPa (20 mmHg)
- myoglobin won’t release oxygen
hemoglobin as O2 transporter
- affinity has to vary with pO2 for effective transport
- hemoglobin binds in lungs well, releases about 1/2 of O2 in tissues
hemoglobin: physiochemical info
- tetrameric protein (a2B2)
- Mr 64,000 (subunit 16,000)
- 4 total
hemoglobin: function
- sensitive response to changes in [O2], [CO2], [H+], [BPG]
cooperativity
positive
- first binding event increases affinity at remaining sites (hemoglobin is positive)
hemoglobin: quaternary structure
- a2B2 dissociates to two aB dimers in presence of urea
- strong interactions between unlike subunits
- conformations
- oxyhemoglobin
- deoxyhemoglobin
oxyhemoglobin
HbO2
- R (relaxed) state
- greater affinity for O2
Deoxyhemoglobin
Hb
- T (tense) state
- lower affinity for O2
- stabilized by greater number of ion pairs than R-state
T to R transition
- movement of heme iron by 0.039 nm (0.39 Å)
- O2 binds, Fe2+ pulled into heme plane, dragging HisF8 and F helix in
- spin state high to low
- upon O2 binding, F helix tilts and translates by ~ 1Å to avoid crashing into heme
- subunits tightly coupled, large tertiary changes in subunit cannot occur with full molecule quaternary changes
- one O2 in each aB: strain sufficient to tear away C-terminal
allosteric proteins: concerted
- 2 conformations in equilibrium
- ligand can bond to either
- molecular symmetry conserved
allosteric proteins: sequential
- ligand binding to subunit causes conformational change
- may cause changes in adjacent subunits
- the more ligand bound, the more likely subsequent conformational changes will occur
bohr effect
- affinity for O2 decreases with decreasing pH
- Hb releases 10% more O2 at pH 7.2 than 7.4
- increased [H+] favors in pair conformation, driving R–>T transition and releasing O2
bohr effect in tissues
H+ is generated as a consequence of HCO3- formation
bohr effect in lungs
O2 binds, driving T–>R, releasing H+ and driving CO2 evolution
hemoglobin variants: HbS
- Glu6 is Val6 in beta-subunit
- interactions between hydrophobic val side chains at position B6 and hydrophobic pockets of neighboring side chains
hemoglobin variants: HbA
adult hemoglobin
- a2B2
hemoglobin variants: HbF
fetal hemoglobin
- a2Y2
- His143 is Ser143
- BPG binds to T-state, interacts with His143 well, not Ser143 (lower affinity in HbF)
