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BB101_Tutorial2

The document outlines a tutorial quiz for students, focusing on protein folding and Lennard-Jones potential energy functions. It includes specific questions about plotting free energy diagrams for proteins and calculating Coulomb energy for a three-charge protein on a 2D lattice. Additionally, it requires students to explore conformations and probabilities related to the protein's configuration, with a follow-up question regarding changes in energy constants.

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aagamkasliwal
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2 views

BB101_Tutorial2

The document outlines a tutorial quiz for students, focusing on protein folding and Lennard-Jones potential energy functions. It includes specific questions about plotting free energy diagrams for proteins and calculating Coulomb energy for a three-charge protein on a 2D lattice. Additionally, it requires students to explore conformations and probabilities related to the protein's configuration, with a follow-up question regarding changes in energy constants.

Uploaded by

aagamkasliwal
Copyright
© © All Rights Reserved
Available Formats
Download as PDF, TXT or read online on Scribd
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BB 101 Tutorial – 2

Quiz question.
Please write the answer on an A4 sheet and submit it at the end
of the tutorial class. Ensure your Roll number and name are on
the A4 sheet. You may prepare the answer even before coming to
the class.

1. Consider a protein folding in a free energy landscape (recall the folding


funnel discussed in the class). Plot the free energy diagram (2D) for
(a)Protein having one unique native structure.
(b)Protein having two native structures (states) with one is slightly
more probable than the other.
Plot the graphs separately.

2. The following Lennard-Jones (LJ) potential energy function is widely


used in biology as non-bonded interaction energy between two units of
bio-molecules:
"   6 #
σ 12 σ
U (r) = 4ϵ − (1)
r r

where U (r) is the potential energy, σ and ϵ are the two positive con-
stants representing the size of the unit and interaction energy strength,
respectively. r is the distance between two interacting units. Make a
rough sketch of the LJ potential function with σ=1 for two different
epsilon values: ϵ=1 and ϵ=2. Both should be plotted in the same graph
making it easy to compare.

(1+1 Marks)

(Please turn over to see tutorial questions)


Tutorial questions

1. Imagine a protein made of three connected positive charges; the bond


length is fixed as b=1nm. This three-charge protein is lying on a 3 × 3
square lattice in 2D (or a 2D grid connecting 9 vertices). The Coulomb
energy of the protein, in a conformation c is given by the typical formula
for energy,
i=2 X 3
X A
Ec =
i=1 j=i+1 rij
where rij is the distance between charges i and j. Assume A =
1kB Tr nm. Note that the charges can only lie on the vertices of the
lattice and the bonds on the edges, and Tr = 300K unless specified
otherwise. That is A = 1kB Tr nm ≈ 4 × 10−30 Jm, a constant. Also
note that the distance between any two adjacent vertices is b.

(a) What is the energy of a protein configuration (conformation) when


all the three charges on a straight line?
(b) What is the energy of a protein configuration that is bent (non-
straight; when one bond is making 90◦ with the other one)
(c) How many straight conformations are possible on this lattice?
(d) How many bent conformations are possible on this lattice?
(e) What is the probability that you will find the protein in a straight
configuration?
(f) What is the probability that you will find the protein in a bent
configuration?
(g) Did you expect this? Naively one would have expected that since
all 3 charges are positive, they will repel and protein will be less
likely to bend. Do you appreciate the role of entropy?
2. Repeat the same when A = 10kB Tr nm. Explain what is going on? (if
this part could not completed in class, you could take it as a homework)

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