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PS2 Spring2024

This document provides instructions for a problem set in biochemistry. It contains 5 questions related to analyzing peptide and protein structures using PyMOL. Students must work in groups of 3 and submit handwritten work by a deadline. The questions involve determining peptide sequences and structures, identifying hydrogen bonds, measuring torsion angles, predicting secondary structure, and performing thermodynamic calculations.

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Farah Abu Alshaar
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11 views2 pages

PS2 Spring2024

This document provides instructions for a problem set in biochemistry. It contains 5 questions related to analyzing peptide and protein structures using PyMOL. Students must work in groups of 3 and submit handwritten work by a deadline. The questions involve determining peptide sequences and structures, identifying hydrogen bonds, measuring torsion angles, predicting secondary structure, and performing thermodynamic calculations.

Uploaded by

Farah Abu Alshaar
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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Biochemistry (BT351)

Second Semester 2023/24


Problem Set II (Due on 06/05/2024 by 11:30 pm)

Important Notes:
• No late work will be accepted
• You should work the problem set as groups of THREE students
• Only hand-written and hard copies will be accepted
• You need to download PS1 pdp files folder
• You need to show all your calculations and units for all questions
• Good luck

Question 1
View the PyMOL peptide associated with your serial number. PSII pdp files

A) Write the correct sequence of your peptide.


B) Using the pKa values in table 4-1. Draw the titration curve for your peptide. Use equivalents for the x-axis.
C) Draw the structure of your peptide at pH 3, 8 and 12
D) Using arrows, indicate peptide bonds
E) Circle atom(s) that can act as hydrogen acceptor. Draw a water molecule forming a hydrogen bond with this
atom.
F) Circle atom(s) that can act as hydrogen donor. Draw a water molecule forming a hydrogen bond with this atom.

Question 2
Open the helix structure in file Helix.pdb. Show all the backbone hydrogen bonds (i.e. between C=O and H-N) and the
distances (dashes and numbers in black).
Change the lines to stick:
From H (Right menu), select lines then from S (Right menu) select sticks
Change the background to white:
From Display tab (Top menu), go to Background then select White
Finding and drawing the hydrogen bonds:
From Wizard tab select Measurements. Choose the first O (or H), and then select the H (or O). In PyMOL, nitrogen
is represented as blue and oxygen as red
Changing the color of dashed H-bond from yellow to black and hiding the distance:
Select from the right menu each measure (e.g measure01), from C (right menu) choose greys then black. Record all
distances from N- to C- terminal and from H (Right menu), select labels.

A) What is the type of this helix (α, π or 310)? Explain your answer.
B) Prepare a figure of this helix showing the H-bonds as dashed lines. Choose the best view that will show most of
the H-bonds and attach the figure to your answers.

Question 3
Open the structure in file Q3.pdb (PS1 pdp files). Answer the following questions.

A) This type of structure is called _____________and it’s composed of _____ chains.


B) Write down the amino acid sequence for each chain.
C) Determine the length of each chain.
D) Draw the helical wheel structure for residues 231-248 using the following website
(http://rzlab.ucr.edu/scripts/wheel/wheel.cgi?sequence=ABCDEFGHIJLKMNOP&subm).
Copy the One-letter amino acid sequence and paste it in the sequence box and hit submit. Include the generated
figure in your report and show the regions of the hydrophobic core, the hydrophilic surface and the ion pair.
Question 4
Open the structure in file Q4.pdb (PSII pdp files). Use PyMOL to determine Residue Phi (ϕ) Psi (ψ)
the phi and psi angles of residues 225-230 of the helix. 225
226
A) The phi and psi values. Make sure you are measuring angles for the 227
right residues. 228
229
Finding the dihedral angles Phi (ϕ) and Psi (ψ): 230
From Wizard tab select Measurements. Click Distance and select Dihedral. The phi angle for each residue is
measured by selecting atoms Ci-1 (carboxyl carbon), Ni (amino nitrogen), Ciα (chiral carbon), and Ci (carboxyl carbon of
the next residue). The psi angle for each residue is measured by selecting atoms Ni (amino nitrogen), Ciα (chiral carbon),
Ci (carboxyl carbon), and Ni+1 (amino nitrogen of the next residue). Both angles values will appear in yellow color.

B) Plot the phi and psi values for each residue to produce a Ramachandran plot (Use Excell). In which part of the
plot the residues cluster? Did the residues cluster in the part of the plot you expected? Explain why?

Question 5
The following peptide can fold to give a unique 3D structure.
SACVDVNPGSSKNAFEDVSKRFVDDNPGSRKVEFKYA

A) Use the following folding data for this peptide to determine Temperature (K) Fraction unfolded
DHo and DSo [Hint: Plot a van’t Hoff plot (ln(keq) vs 1/T)
290 0.01
295 0.05
B) Using the PSIPRED Protein Sequence Analysis 300 0.09
Workbench (Google it), predict the secondary and super- 305 0.19
secondary structure of this peptide. Draw the topology of this 310 0.38
peptide using the result obtained from PSIPRED.
315 0.57
1. Copy the peptide sequence to input sequence
2. Choose PSIPRED v3.3 (Predict Secondary Structure) 320 0.78
3. Fill the Short identifier for submission 325 0.87
4. Press Predict 330 0.94
5. You might have to wait for 30 minutes. 335 0.97
6. Choose the PSIPRED tap

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