Problem Set 2

Advice on rounding scientific numerical values

Before you begin this problem set, please read AND understand the following simple rules regarding the
rounding of scientific numerical values.

Imagine that you have the values that are 28.1, 28.2, 28.3 and 28.4. If you were to round these to JUST the
whole # (i.e.–excluding the decimal place), we would simply round EACH one of these values to 28. If you
would recall from your general chemistry courses, this is how rounding of numerical values was likely taught.
In other words, if the FIRST numerical digit in decimal place is either a 1,2, 3, or 4, you keep the whole # as is.
That is essentially what we have accomplished.

Now, instead, imagine if we had 28.5, 28.6, 28.7 28.8 and 28.9. What would be the result if we rounded these
five values to the nearest/closest whole #?
We would simply round each one of these values to 29. Why? Applying the rule students most often encounter
in an introductory chemistry (or physics) course, it states that IF the first numerical digit in (or within) the
decimal place is 5 or greater, the whole number you are trying to round to is increased EXACTLY by 1. This is
what we have done. Following the proper rules of rounding, we have rounded the value to 29.

1. Another octapeptide consists of His, Cys, Lys, 2Tyr, Gln, Asp and Arg
The following data was generated for the peptide
• One cycle of Edman sequencing yield PTH–Asp
• Use of chymotrypsin resulted in a dipeptide consisting of Asp and Tyr; a pentapeptide and a free His.
The pentapeptide is composed of Lys, Tyr, Gln, Cys and Arg.
• Use of trypsin resulted in a tetrapeptide consisting of Arg, Asp, Tyr and Cys AND two dipeptides. One
of the dipeptides consists of a Lys and Gln residue and another consists of a Tyr and His residue
• Based on this information, determine the sequence of this octapeptide

2. In another reaction, the sequence of an octapeptide comprising of Pro, Phe, Arg, Lys, Tyr, Ser, Gly
and Ala was subjected to a peptide sequencing reaction. In an attempt to sequence this peptide, the
following data was obtained:
• One round or cycle of Edman degradation resulted in the formation of a PTH-Gly derivative
• Treatment with Trypsin yielded two tetrapeptides. One of the tetrapeptides was comprised of Lys, Gly,
Ser and Tyr and the other tetrapeptide was comprised of Pro, Arg, Phe and Ala
• Treatment with chymotrypsin yields a dipeptide composed of Arg and Pro; another dipeptide
composed of Gly and Tyr and a tetrapeptide composed of Phe, Ala, Ser and Lys.
• Based on this information, please determine the sequence of the octapeptide

3. In the Ramachandran plot, which torsion angle combinations (please provide your response in terms of
+, +  coordinate) are largely forbidden for –helices and anti–parallel and parallel –strands? Which
combinations are allowed? Please note: You need NOT provide specific or approximate numerical
torsion angle values

4. Why are certain torsion angle combination largely disallowed or forbidden from the Ramachandran
plot? What would be the consequence if amino acid residues within a protein molecule began to adopt
those non-favorable torsion angles?

5. An –helix within a protein was found to be approximately 19 amino acid residues in length. Based on
this information, determine the number of approximate turns in this –helix. Please round your answer
to the NEAREST whole number value.

6. From the structure of a protein, it was discernible that a particular –helix had approximately eight
helical turns. Based on this information, please estimate the number of amino acid residues that would
be found within this helical sequence. Please round your result to the nearest plausible whole # value.

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 7. The association or interaction of two proteins known as EcfT and FolT, in part, is stabilized through an
interaction via the following residues as shown through their skeletal side chains. Each of these
residues is from an –helix within EcfT or FolT.
Based on this, what is the likely interaction that is stabilizing the interaction? Please briefly but clearly
explain your response.

8. In another study, researchers were studying the interaction between two proteins, Complexin and
Vamp. Specifically, they discovered that the side-chains of the residues Y and R from Complexin
interact with the side chain of a residue with the one–letter code, D from Vamp. Based on this,
please determine the type of interaction that is stabilizing the association of Vamp and
Complexin.

9. The purpose of this problem is to determine whether certain –helical segments can form into a
coiled–coil

a. The following sequence is known to form an –helix. Please determine whether this sequence
can form a coiled–coil type –helix

+1 –1
H3N … H H A E I A T F H L D R V L …COO

The following partial sequence is taken from a transcription factor known as GCN4 and it is likely
b.
to form into an –helical sequence. Please determine whether this sequence can form a coiled–
coil type –helix

+1 –1
H3N … M K Q L E D K V E E L L S K N Y H L E N E V A R L K K L V G E …COO

(Source: Biochemistry, 2012)

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c. The following partial sequence is taken from a mammalian protein known as BCR and it is likely
to form into an –helical sequence. Please determine whether this sequence can form a coiled–
coil type –helix
Source: Nature Structural and Molecular Biology

+1 –1
H3N …V G D I E Q E L E R C K A S I R R L E Q E V N Q E R F R M I Y L Q T L L…COO

10.

a. The sequence provided below is known to form into an α–helix. Determine whether it forms into
an amphipathic –helix.

H3N+1…R L F F K C I Y R F F E H G L K R G…COO–1

b. How many turns are in this –helix? Please round your answer to the nearest whole # using the
proper rules of rounding that we have discussed.

c. How many intrahelical hydrogen bonds are likely present in stabilizing this –helix?

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11.

a. The following sequence is taken from a rat protein known as ARF GAP1. Please determine if the
sequence below can form into an amphipathic –helix that can bend membranes.

H3N+1…F L N S A M S S L Y S G W S S F T T G A S K F A S…COO–1

b. How many turns are in this –helix? Please round your answer to the nearest whole # using the
proper rules of rounding that we have discussed.

c. How many intrahelical hydrogen bonds are likely present in stabilizing this –helix?

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12. Below, you have been provided models of actual –helices taken from different published protein
structures. Using the models, please determine the number of residues in each –helix (please
report values to the nearest whole #) as well as the number of intrahelical hydrogen bonds
stabilizing each –helix.

13.

a. An –helix has 25 hydrogen bonds. How many residues does it likely have?

b. An –helix has 25 amino acid residues. How many intrahelical hydrogen bonds are likely
contributing towards stabilizing this alpha helix?

14. Interpreting Ramachandran Plots

Does this Ramachandran plot represent a predominantly –helical or a

–strand structure? Please briefly but clearly explain your response.

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15.

Interpreting Ramachandran Plots

Does this Ramachandran plot represent a predominantly –helical

or a –strand structure? Please briefly but clearly explain your
response.

16. Interpreting one–dimensional and three–dimensional protein structures

Are the –strands present in this topology

diagram predominantly parallel or anti–
parallel? Please briefly explain your response.

17.

How many –helices and –strands are in this topology diagram?

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 18. Interpreting three-dimensional protein structures

a. How many beta strands and alpha helices are represented in this toplogy diagram?

b. Are the beta strands parallel or anti-parallel?

19. Drawing hydrogen bonds between amino acid side chains

Please assume that we are inside a cell at a pH of 7.40 and using the symbolism provided in the
table below, please determine the number of hydrogen bonds that can be drawn BETWEEN the
side chains of the following amino acids.
A note on symbolism: the respective amino acid is shown using the one–letter code and the
subscript denotes that the side chain is assuming/adopting a hydrogen bond acceptor (hence, the
A subscript) mode or a hydrogen bond donor mode (hence, the D subscript).
Some additional advice: please make sure to read each symbolism carefully and make sure to
neatly draw out the side chain with the lone pairs.

Side chains Number of hydrogen bonds that can be drawn BETWEEN them

YA: ND

SA: KD

DA: HD

EA: TD

SA: QD

20. Using your module 1 packet, please practice by drawing out the skeletal forms of the DESTY
HKR NQ side chains. Specifically, please determine the number of hydrogen bonding capacity of
each side chain. Please note that the hydrogen bonding capacity is defined as the number of
hydrogen bond donors and the number of hydrogen bond acceptors.

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21. Determining interactions within and amongst proteins.

a. An interaction facilitated between two –strands of the same protein was taking place as follows.
Based on this, please determine the type of interaction. Please also briefly explain your response.

b. An interaction between two proteins A and B was being facilitated by side chain of residue F
(from protein A) and side chain of residue L (from protein B). Based on this, what type of
interaction is stabilizing the association of protein A and B? Please briefly explain your response.

c. An interaction was observed within protein A, which entailed (involved) two –helices. For your
reference, the side chains from each –helix involved has been sketched below. Based on this,
please determine the type of interaction that is likely occurring and please make sure to explain
your response.

–helix 1 –helix 2

d. The following interaction has occurred. Based on this, please determine the type of interaction
and please make sure to explain your reasoning.

Protein A Protein B

22.
o An octapeptide is composed of Pro, Met, Trp., Tyr, Arg., Lys, Ser and Gln

o One cycle of Edman degradation yields PTH–Gln.

o Treatment with trypsin yields two tetrapeptides. One tetrapeptide was composed of Arg., Trp., Pro and
Gln and the other tetrapeptide was comprised of the remaining residues.

o Treatment with chymotrypsin yields a hexapeptide composed of Trp., Pro, Arg., Gln, Met and Tyr as
well as a dipeptide composed of Ser and Lys residues.

o Using cyanogen bromide yields a pentapeptide composed of Hsr, Gln, Pro, Trp. and Arg as well as a
tripeptide composed of Tyr, Lys and Ser.

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 o Based on these collective pieces of information, please determine the sequence of this octapeptide.
Please make sure to indicate the proper ends of the peptide.

o Please write the sequence in two ways: using the three–letter and the one–letter codes.

23.

o An octapeptide consists of 2 Arg., Pro., Tyr., Phe., Met, His and Ser.
o One cycle of Edman degradation yields a PTH–Arg derivative
o Treatment with trypsin yields a free Arg.; a tripeptide consisting of Arg, Pro and Tyr; and a tetrapeptide
consisting of Phe, Ser, Met and His
o Using cyanogen bromide on this peptide yields a pentapeptide containing Hsr, 2 Arg., Pro and Tyr as
well as a tripeptide consisting of His, Ser and Phe.
o Treatment with chymotrypsin yields a free His and a heptapeptide consisting of the remaining residues
2 Arg., Pro, Tyr, Phe, Met and Ser.
o Based on these pieces of information, please determine the correct sequence of the octapeptide.
Please make sure to indicate the proper ends of the peptide.
o Please write both the three–letter and the one–letter code.

Please also determine the number of cuts and subsequent fragments generated by trypsin and chymotrypsin

24. Consider the empty Ramachandran plot shown below.

In which quadrant, would we expect  –strands and the –helix

25. Consider the empty Ramachandran plot shown below. Which arrow points to a region where
there is likely to be minimal steric clash?

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 26.

a. A hypothetical protein has 8 cysteine residues. Please predict the exhaustive or maximal number
of disulfide bonds that can form in this protein. Please make sure to briefly explain your
reasoning.

b. What is the functional significance of having disulfide bonds in a protein?

c. Insulin is a peptide hormone that consists of two chains, named chain A and chain B whose
sequence has been provided for you below. Chain A and B are connected to each other through
disulfide bonds. Chain A is also known to contain disulfide bonds. Using the sequence of the
Chain A and chain B as a guide, please predict (without googling 😊), the number of disulfide
bonds in insulin

Chain A : GIVEQCCTSICSLYQLENYCN

Chain B: FVNQHLCGSHLVEALYLVCGERGFFYTPKA

27. Below, an alpha helix residue # is provided. Based on your knowledge of interpreting intrahelical
hydrogen bond network residue positions, please predict the # of the missing residue involved in
making the intrahelical hydrogen bond.

O N
|| -------- |
C H

13 __

__ 22

28. When we determine the three-dimensional shape of protein structures, why is it almost a non-
existent phenomenon to observe a single –strand. Rather, in every protein structure determined
that contains –strands, there appear to be at least two or more –strands. Please provide a
convincing explanation to this experimental observation.

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