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Scaffold assembly equilibria.

Jérôme Feret, Walter Fontana


November 10, 2007

The simple“star” case: a central hub B with n binding sites for one type of ligand A

1. B is a scaffold with n sites, each of which can bind another protein - or ligand for short - of
just one type A. Bi is the number of cases in which B has i molecules of A bound to it.
2. The sites of B can be bound in any order.
Question: what is the equilibrium concentration of fully occupied B’s, Bn , as a function of B, the
total concentration of B in the mixture?
Let na be the number of binding sites available for binding an A molecule. nb is the number of
available binding sites that can bind a B. nab is the number of existing bonds between A’s and
B’s in the system. This is a local view in terms of sites, rather than agents bearing those sites.
With regard to agents, let A and B denote the total number of agents of type A and B,
respectively.
We have:

na nb = Kd nab (1)
nB = na + nab (2)
A = nb + nab (3)

with Kd = k−1 /k1 . The first equation is the equilibrium condition, the other two equations
express site conservation. This allows us to express nab as a function of Kd , A, B, n. In addition,
from ligand binding equilibria calculations (see pertinent handout), we have (using current
notation):
 n
Bn nb
= . (4)
B K d + nb

nb – the number of free sites (in equilibrium) available for binding to B – is the same as S in the
lecture slides or the ligand binding handout of lecture 9.
Combining equations (3) and (4), we obtain:
 n
A − nab
Bn = B . (5)
Kd + A − nab

Now we need to get nab . Substituting nb from equation (3) into equation (2), we express na in

1
500

400

300
Bn

200

100

0
0 1000 2000 3000 4000

Figure 1: Star equilibrium. n = 2, A = 1000, Kd = 1. Red: analytical [equations (5) with (8)],
black: simulation

terms of nab and constants:


nab
na = Kd . (6)
A − nab

Substituting (6) into (3) yields a quadratic equation for nab :

0 = n2ab − nab (Kd + A + nB) + nAB, (7)

with solution
1 p 
nab = (Kd + A + nB) − (Kd + A + nB)2 − 4nAB . (8)
2
The other solution is physically meaningless, because it violates site conservation.
Using (8) in (5) yields the solution, whose graph is the solid line in Figure 1. The wiggly line is
made of equilibrium ”measurements” of Bn from stochastic simulations (using the KappaFactory).