BT3020 Jan-May 2024 Structural Biology Problem Set 1

Instructions: Handwrite the answers. Use all available resources and peer group learning. Deadline to
submit online is March 10th 2024. Use your smail id to login into the google form
https://forms.gle/tSyF3zUbJnNZdBza9

1) There is only one standard amino-acid ‘alphabet’ used by most of living beings on earth. Which
of these 20 standard amino acids is most similar to Phe in the covalent structure? Next, download and
examine the standard genetic code. What other amino acids can you make from the Phe codons using a
single-base change at the third position (genetic-code neighbor)? What physicochemical properties does
the amino acid share with Phe? What is the % prevalence of these amino acids in natural proteins.?
Given all this data, do you think that the earliest genetic code of the life encoded all 20 amino acids?

2) Oxytocin is a peptide hormone and neuropeptide normally produced in the hypothalamus and
released by the posterior pituitary. It plays a role in social bonding, reproduction, childbirth, and the
period after childbirth and is also called the love hormone. The sequence of oxytocin is shown below.
a) Draw the structure of this peptide where all peptides are in the trans conformation.
b) Draw the structure of the dipeptide region Cys-Pro where the Pro is in the cis conformation.
Remember that the cis peptide always occurs with the Pro at the C-terminal end.
c) What is the net charge of this peptide at i) pH 2.0, ii) pH 7.0, ii) pH 11.0?
d) Will the pH affect the formation of a disulphide bond in this peptide?

Cys – Tyr – Ile – Gln – Asn – Cys – Pro – Leu – Gly – NH2

3) Calculate the pKa of water in aqueous phase. The enzyme carbonic anhydrase catalyzes the reaction
HCO3- + H+ ⇋ CO2 + H2O in the blood and its primary function in animals including humans is to
maintain the acid-base balance in blood and other tissues, and to help transport carbon dioxide out of
tissues. The structure of the active site of this protein contains a zinc ion that coordinates with the water
molecule to carry out the reaction (see figure). What will be the effect of the Zn ion on the pKa of this
water molecule in this enzyme? Will it affect the normal functioning of the enzyme?

4) Read through the given research article summarizing pKa values of ionizable groups in protein
structures.
a) What techniques are used to measure pKa values of sidechains in a protein?
b) In Table I, pKa values of the sidechains measured within proteins and those measured for the same
sidechain in alanine pentapeptides are given. Which amino acid shows the largest difference between
the two values? Are pKa values measured from peptides similar to those measured in real proteins?
c) For the pKa measurements of amino acids obtained from the peptide titration studies, what is the
rationale for the choice of an alanine pentapeptide? Why not a di-, tri- or tetrapeptide? Why is alanine
chosen for these peptides?
d) Columns 4 and 5 list the lowest and highest values of pKa reported for each sidechain in proteins.
Which amino acid has the most deviation from the average value? Give an explanation for why the
same amino acid displays such divergent values when measured in proteins.

5) a) Draw the ionic and tautomeric states of the histidine side chain.
b) Consider a His residue on a protein surface that makes no interactions with any other amino acid.
What fraction of the histidine side chains will be charged at pH 9.0? Use the pKa value from the
previous question.