Pset 7 Solution
a. k_on=0 is the appropriate rate constant to describe the Single Cycle Assay that the
authors were trying to model, which is described in the attached paper. Excess
competitor ligand in the assay media prevents any further binding of EPO
20.320 Spring 2004
1. Internalization is directly related to receptor-ligand binding since endocytosis occurs after
ligand binding at the surface. As given in class:
= kec Cs Ci = kec Cs dt = kec Cs dt .
Since we know Cs and
BE.320 Spring 2006
Problem Set 5
1. As discussed several times in class, epidermal growth factor receptor (EGFR) is a
receptor tyrosine kinase which will phosphorylate tyrosines on selected substrates.
EGFR (mol. wt ~180 kDa (180,000 g/mol)
Solution to problem 5.
Fractional saturation is most frequently defined as y = fraction of binding sites that are
occupied (number of sites bound/total number of sites). In this problem, the data was
created using this definition. In class we called = mol
The code is attached this code makes the plot below and outputs that the
maximum DP is 1.8858 g/L*hr and that the optimal D is 0.8593 hour^-1. These
values will differ slightly if you used a different number of x-axis points than I
Problem Set 9
1. Please code up the equations given in class on 5/8/06 for the continuous
well-stirred cell bioreactor, solving for C, S, and DP for a range of D values
from 0 to 1.5 hour^-1. Plot these quantities at each D value and find t
4/17/06 5:26 PM
C:\Documents and Settings\Craig Rothman\My Document.\problem2.m
%Problem 2, pset 5
Km = 17e-6;
N = 100;
Ki = linspace(10e-9, 10e-6, N);
S = linspace(0.1e-3, 5e-3, N);
olve for [I] where V = 1/2*Vmax
% V = (Vmax*[S]) / (K
3/2/06 8:29 PM
C:\Documents and Settings\Craig Rothman\My Documents\Coll.\hw3.m
%hw3 nlinfit example
%this code creates "experimental data" with error and then fits a model
%with 2 parameters to this data
global L0; %global parameter, passed into function
Problem Set 8
1. The enzyme luciferase is often used as a reporter to study delivery of transgenes
into cells, for instance in determining how effective delivery vectors (such as different
polymer formulations) might be in doing so. This is
Problem Set 3
1. From your ITC experiments, you have determined that a particular protein-small
molecule binding interaction has a DG of -10.49 kcal/mol (at 25C).
a. Using this information, calculate the off rate (koff) assuming that kon is 10
Problem Set 7
1. In pset6, you studied a hyperglycosylated version of EPO, NESP (Novel Erythropoiesisstimulating protein). It is often thought that tighter-binding drugs are always better than weakerbinding drugs, but NESP actually has great
Problem Set 4
1. Using multiple SPR measurements and evaluating tobs and koff, you have calculated
that kon for a given protein-protein interaction is 2 x 106 L.mol-1.sec-1 in 20 mM NaCl.
This same protein-protein interaction gives a kon of 1
Problem Set 2
1. A given protein-ligand interaction has a DG of -8.18 kcal/mole and a DS of 10
cal/mole.K. Calculate DH (at 25C) and use this value (assume it is DHapp) to calculate
the heat released by the 2nd injection of ligand (10 mL of a
20.320 Problem Set 1
1. In screening for small molecule drugs, often the first compound might have a KD of 10 nM.
Further elaborations may improve the binding affinity to 1 nM or 100 pM.
Calculate the free energy for each of these KDs.
20.320 Spring 2006
Problem Set 6
1. Despite many studies on the use of EGF in clinical wound healing and significant
commerical investment in R&D for use of EGF, there are yet no viable clinical products
using EGF for wound healing.