protein ligand interactions

what usually happens when a protein and ligand bind?

conformational change in protein

• makes site more complementary for protein (tighter fit)

induced fit

structural adaptation between protein and ligands in response to binding

conformation change in multi subunit proteins cause…

conformation changes in other subunits not just one

conformations of hemoglobin

r state- O2 has higher affinity hem

t state- more stable w/out O2

R state

when hemoglobin has higher affinity for O2

T state

when hemoglobin is more stable with/out O2

• deoxyhemoglobin is mostly in this state

How is the T state stablalized?

by a larger number of ion pairs

-many in the \alpha_1\beta_2 and a2b1 interface

when O2 binds to T state…

hemoglobin changes to R state

when T state —> R state

• 2 ab subunit pairs slide past eighother and rotate

• pocket between beta subunit narrows

• some stabilization ion pairs break (some new form)

myoglobin

• 1 O2 binding site

• distal His holding oxygen in place

• has an equation for binding that is a hyperbola (never fully gets to 1)

hemoglobin and binding

• 4 subunits

• 4 heme groups

• 4 O2 binding events

red curve (what state)

R-state (high affinity for O2) also hyperbolic shape

blue curve (state)

intermediate state (sigmoidal curve)

green curve

T-state (low affinity for O2)

why are the is there a shape change in protein-ligand binding?

to regulate the interactions

allosteric proteins

proteins where affinity can change

• ex. hemoglobin

modulators

ligands that bind at a separate site to change the binding at another site

• 2 types- homotropic and heterotropic

homotropic modulators

ligand that is binding affects the another binding site for the same type of ligand

ex. one ligand binds and makes it so no other of the same ligand can bind

heterotropic modulators

molecule other than the normal ligand that affects its binding

what does nL mean in the protein-ligand binding equation

There are more than one binding cite

what type of graph is made from a binding equation with more than one binding site?

sigmoidal graph

the hill equation

equation for cooperative binding (with logs)

hill coefficient

nH

• slope of line in hill graph

difference between n and nH

n is the number of binding sites

nH is how the binding at one site affects the binding at another site

nH=1

binding at different sites are independent of each other

• affinity state stays the same

nH>1

binding at one site helps binding at other sites

• low to high affinity

nH<1

binding at 1 site negatively impacts binding at another

• high to low affinity

dark orange type of curve

hyperbolic (nH=1)

red and black

• nH>1

• sigmoidal curve

yellow and orange

• nH<1

• hyperbolic

concerted model

-all subunits in same conformation R or T

-ligands bind more tightly in R state

Sequential model

• each subunit can be in either conformation

carbonic anhydrase

• takes CO2 released from respiration and turns it into a pronton and bicarbonate

• main buffer of blood

farther from the lungs there is ___ CO2 in our blood

more

Bohr effect

amount of CO2 and the pH have an affect on the binding and release of O2 by hemoglobin

when H+ and CO2 is bound to hemoglobin

it makes O2 less likely to bind

when O2 is high…

hemoglobin bind O2 and releases H+

when O2 is low…

hemoglobin releases O2 and bind H+

what does free CO2 do to hemoglobin?

• binds to the end terminal and kicks off a proton

• this makes it go to the tense state (to push off oxygen)

2,3-bisphosphoglycerate (BPG)

• regulates O2 binding to hemoglobin

• heterotropic modulater

• reduces affinity for oxygen

at high altitudes BPG…

increases so hemoglobin releases oxygen bc the body needs it

how does BPG work?

it binds hemoglobin between the beta subunits encouraging it to be in the tense state—> kicks off oxygen

fetal hemoglobin

• uses gamma instead of beta—> beta has higher affinity for O2

• baby needs oxygen more then mom’s blood does

in sickle cell anemia

hemoglobins clump together in a super low affinity tense state -> can’t grab oxygen

Kd

Dissociation constant

• low Kd—> higher affinity

• High Kd—> low affinity

Analog

Things that look the same and do the same things but have no shared ancestry

Paralogs

Similar because of shared ancestry