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Protein FOlding 2

The document outlines 9 problems related to forces and interactions between molecules based on a lecture about Van der Waals interactions, electrostatic interactions, solvation energies, entropy, and protein folding thermodynamics. The problems ask the student to calculate interaction energies, sketch interaction energy plots, determine changes in free energy and equilibrium constants, and calculate temperatures related to protein folding using given thermodynamic values.

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Darius Mills
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6 views2 pages

Protein FOlding 2

The document outlines 9 problems related to forces and interactions between molecules based on a lecture about Van der Waals interactions, electrostatic interactions, solvation energies, entropy, and protein folding thermodynamics. The problems ask the student to calculate interaction energies, sketch interaction energy plots, determine changes in free energy and equilibrium constants, and calculate temperatures related to protein folding using given thermodynamic values.

Uploaded by

Darius Mills
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PDF, TXT or read online on Scribd
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BIOC530: Homework 1

Due 10/17
Contact information:
Name: __________________ Department_______________
Student #________________ Email address_____________

The following problems are based on David Baker’s lectures of forces. When numerical
values are not specified, you should be able to find appropriate values in lecture notes.

1. What is the Van der Waal’s interaction energy between a nitrogen atom and the
oxygen in a carbonyl group 6 Å apart? Use the parameter table from the lecture notes.

2. Sketch out or plot the attractive and repulsive contributions (and their sum) to the
interaction energy of these atoms (from question 1) as a function of distance.

3. What is the electrostatic interaction energy of a lysine nitrogen and a glutamate


oxygen when they are separated by 6Å (Assume the charge on the nitrogen is +1 and the
charge on the oxygen is -1.)
(1) in water?
(2) in the protein interior (assumed to be a homogeneous medium with dielectric
constant 4)?
(3) What is the change in energy when the two atoms are moved from 6Å to 3Å apart
in water?
(4) What is the change in energy when the two atoms are moved from 6Å to 3Å apart
in the protein interior?

4. Calculate the G for moving two charges (+1 and -1) from an organic solvent with
dielectric constant 1 into water, keeping their distance fixed at:
a) rij=4Å
b) rij=7.5Å
Be sure to include both the Coulombic interaction term and the solvation energy!
For these charges, use ri=rj=1.6 Å (the distance from the center of the ion to the solvent)

5. An arginine side-chain on the protein surface can adopt one of 81 possible rotamer
conformations with equal probabilities. When the protein forms a complex with anther
protein, only one rotamer is possible (the others would bump into the other protein). What
is the free energy loss associated with the entropy at room temperature?

6. In mass spectrometers, proteins are dispersed into the gas phase. Would you expect
proteins to be more or less stable in the gas phase? (Answer this by listing how the
contributions to protein stability of each of the major forces would change for a protein in
gas phase compared to a protein in water.)

7. If the free energy difference between unfolded state and folded state of protein X is
6.2 kcal/mol, what is the ratio of the two populations (the equilibrium constant) at 300K?

8. A small protein has a H of folding=6 kcal/mol and S of folding=31 cal/K mol.


(1) Calculate the temperature at which the ratio of folded to unfolded protein is 10:1;
(2) Calculate the melting temperature (the temperature at which half the protein will
be folded and half will be unfolded).

9. Problem from class:


Suppose a protein has three states:
(1) Unfolded state: 1000 different conformations, each with no specific interactions;
(2) Intermediate state: 10 different conformations, each with two hydrogen bonds
worth 1 kcal/mole;
(3) Native state: 1 conformation, with twenty hydrogen bonds worth 1 kcal/mole
Question: What is the fraction of the protein which is folded as a function of temperature?

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