BIOC 503 - Protein Functions I

reversible

___ binding of ligands is critical for protein/enzyme function

induced fit model

• ligand is coupled to conformational changes, sometimes dramatically

• conformational changes may occur upon ligand binding model

• discovered by Daniel Koshland in 1958

• allows for tighter binding and high affinity

• both ligand and protein can change their conformation

cooperativity

in multisubunit proteins, conformational changes in one subunit can affect the others

functions of globular proteins

• storage of ions and molecules (myoglobin, ferritin)

• transport of ions and molecules (hemoglobin, serotonin transporter)

• defense against pathogens (antibodies, cytokines)

• muscle contractions (actin, myosin)

• biological catalysis (chymotrypsin, lysozyme)

ligand

molecule binding to a protein

• typically small

binding site

region in the protein where the ligand can associate with it

noncovalent

ligands bind via the same ___ interactions that dictate protein structure, as they allow the interactions to be transient

• hydrophobic effect

• Van Der Waals

association rate constant

ka

rate at which the protein and the ligand bind to form the protein-ligand complex

dissociation rate

kd

rate at which the protein-ligand complex breaks off into the protein and the ligand as separate elements

equilibrium

when the association and dissociation rates are equal

rate

small k used to designate ___ constant

equilibrium constant

big K used to designate ____

Ka

__ = [PL]/([P]*[L]) = 1/Kd

theta

the fraction of occupied binding site

__ = [PL]/([PL]+[P]) = bound/total = [L]/([L]+Kd)

free ligand, Kd

the fraction of bound site (theta) depends on the ___ concentration and ___

Y

fractional occupancy symbol

saturation binding curve

fractional occupancy plotted against (usually experimentally known) substrate concentration

50

On a saturation binding curve, Kd corresponds to the intersection between the ___% line and the curve

equal

At equilibrium, when 50% of protein is bound, the concentration of unbound protein and the concentration of protein complexes are ___

• [P] = [PL] AT EQUILIBRIUM

kon

formation of complexes

M^-1 s^-1

quick bonding/recognition

koff

dissociation of complexes

s^-1

stability

koff,kon

Kd = __/__=stability/recognition

affinity

__ and kinetics are related

• complexes can have the same __ aka same Kd despite being made of different combinations of kon & koff rates, and thus either more stability or quick recognition.

decrease

to increase affinity, you need to ___ Kd

partial pressures

when the ligand is a gas, binding is expressed in terms of ___

low

myoglobin has a very ___ Kd, aka a very high affinity for O2, which makes sense because its function is to store it

molarity

dissociation constant Kd is expressed in units of ___ (M)

kJ/mol

free binding energy delta G^o is expressed in units of ___

• DG^o = DH^o −TDS^o

• DG^o = −RT ln K_a  = RT ln K_d 

strong interactions

• Kd < 10nM

weak interactions

• Kd > 10nM

lock and key model

high specificity binding model

based on the complementary of the binding site and the ligand, complementary surfaces are preformed

• size

• shape

• charge

• hydrophobicity

discovered by Emil Fisher in 1894