Review session: tonight at 7 pm in Lawrence 115

First midterm: next Wednesday (10/18) 7 pm in MacKenzie 240C

Midterm will cover up through the end of this week (lectures 1-9, homework 1-3, lab 1-3).

If you've talked to me about an alternate exam location/time, please talk to me after class

Protein recognition

2016-10-11


Conceptual goals

  • Proteins form specific interactions with molecular partners
  • Specificity is achieved by creating interactions that can only be fulfilled by one partner, not others
  • Interactions are "tuned" to affinities useful for the cell.

Skill goals

  • Use structure-based reasoning to predict relative affinities and specificities of different interactions.
  • Use $K_{D}$ to characterize the strength of interactions

Many animals exhibit sexual dimorphism

Wikimedia, mnn.com, zmescience
Testosterone
Estrogen
boundless.com

Estrogen and testosterone bind to different receptors, turning on different genes

  • Estrogen binds to the estrogen receptor
  • Testosterone binds to the androgen receptor

Receptors have almost identical steroid binding pockets

How do almost identical receptors distinguish between almost identical steroids?

Binding specificity is discrimination between steroids.

Specificity is determined by:

  • shape of the pocket
  • polar interactions

Biochemists use dissociation constants ($K_{D}$) to measure binding affinity

$ML \rightleftarrows M + L$

$M$ is macromolecule (protein)

$L$ is ligand (small molecule)


$K_{D} = \frac{[M][L]}{[ML]}$

We can measure $K_{D}$ by following $\theta$ versus $[L]$

$K_{D} = \frac{[M][L]}{[ML]}$

$[ML] \times K_{D} = [M][L]$

$[ML] = \frac{[M][L]}{K_{D}}$

$\theta = \frac{[ML]}{[M] + [ML]}$

$\theta = \frac{[M][L]/K_{D}}{[M] + [M][L]/K_{D}}$

$\theta = \frac{[L]/K_{D}}{1 + [L]/K_{D}}$

$\theta = \frac{1}{1 + K_{D}/[L]}$

The $K_{D}$ is the concentration of $L$ at which $\theta = 0.5$.

Chen et al. (2004) JBC 279(32):33855-33864

Steroids have only a small range of blood concentrations

Female
Male
Estrogen
$0.1-2.0\ nM$
$0.05-0.2\ nM$
Testosterone
$0.9-3\ nM$
$10-50\ nM$
wikipedia.org

ER responds to physiological concentrations of estrogen but not testosterone

Is one hydrogen bond, in principle, enough to explain the difference in bindng?

Summary

  • Proteins can bind to specific molecules in the cellular environment
  • Specificity is acheived by shape complementarity and polar contacs.
  • The strength of these interactions is quantified by the Dissociation constant ($K_{D}$)
  • $K_{D}$ is tuned to the concentration of the molecule in the cell

Review session: tonight at 7 pm in Lawrence 115

First midterm: next Wednesday (10/18) 7 pm in MacKenzie 240C

Midterm will cover up through the end of this week (lectures 1-9, homework 1-3, lab 1-3).

If you've talked to me about an alternate exam location/time, please talk to me after class