Download 462a Reading and Homework Assignment 3

462aH Homework Assignment 3
Homework (10 points). For numerical questions, please show your work.
(1) Draw the dipeptide Gly-Ala with a trans peptide bond and showing all atoms in their correct
ionic state at pH 7.0. Indicate on your drawing:
(a) The atoms that are restrained to be planar with the peptide bond.
(b) Rotations about which angles are designated phi and psi.
(c) The dipole moment for the peptide bond.
(d) The hydrogen bonding groups that are used in forming  helices and  sheets.

 sheets
psi
+
phi
psi
can H-bond in
 helices and  sheets
phi
(2) Could the amino acid sequence listed below be used to form an amphipathic alpha helix?
Use a helical wheel* to justify your answer.
AFNSVLQDINQFMSCAQSLVK
8Asp
19Leu
1Ala 12Phe
5Val
15Cys
16Ala
4Ser
11Gln
9Ile
18Ser
20Val
2Phe
13Met
7Gln
6Leu
14Ser
3Gln
21Lys
10Asn
17Gln
The hydrophobic amino acids (shown in bold) clearly lie on one face of this helix. The polar
or charged amino acid lie on the other face. Therefore this is an amphipathic helix. Residues
19-21 are slightly offset to make them visible.
(3). Given the following peptides:
i) Lys-Glu-Ala-Trp
ii) Ile-Arg-His-Ser
iii) Gly-Phe-Lys-Tyr
iv) Leu-Lys-Gln-Pro
(a) What is the overall charge on each peptide at pH 3, 7 and 11?
pH 3 pH 7 pH 11
i)
+1
0
-2
ii)
+2
+1
0
iii)
+1
+1
-2
iv)
+1
+1
-1
(b)Predict the direction of migration (i.e., stationary, towards the positive electrode, or
toward the negative electrode) of the peptides during electrophoresis at pH 3, 7, and 11
pH 3 pH 7 pH 11
i)
0
+
ii)
0
iii)
+
iv)
+
(4) Both cis and trans peptide bonds gain about 85 kJ/mol resonance energy when planar
(through  orbital alignment). Why are cis peptide bonds rarely seen in proteins? Why are
cis peptide bonds more common for prolines than for other amino acids?
Steric clash limits cis peptide bonds in most amino acids. In prolines, there is less difference in
terms of cis and trans conformations, since both result in some degree of clash.
(5) Obtain file 1G6S from the PDB database and display it with RasMol. What is the name of
this protein? Describe the secondary structure of the protein (how many and what kind of
elements are present). Describe the tertiary and quaternary structures of the protein.
This is the protein Epsp synthase. Secondary structure: 6 mixed beta sheets (24 strands), and 14
alpha helices. The tertiary structure is a mixed alpha/beta structure with two domains. As it
is a monomer, it has no quaternary structure.
(6) Obtain from the class web page the PDB file for triose phosphate isomerase (TIM). The PDB
file can also be obtained from the PDB (file name 2ypi). (a) Using RasMol, determine the
sequence number of the histidine that is hydrogen bonded to the inhibitor in the TIM
complex. The following RasMol commands may prove helpful:
cpk off
cartoons off
restrict within (8.0,*249a)
** Note: use the decimal, that is 8.0, not 8
wireframe .2
center *249a
select his
color cyan
The histidine that is hydrogen bonded to the inhibitor in the TIM complex is residue number 95.
(b) What is the three-letter group name (that is, the “residue” name) for the inhibitor, 2phosphoglycolate, bound to TIM in this structure? (Hint: click on the inhibitor).
PGA
(7) Examine the two Ramachandran diagrams, each of which corresponds to one of the two
proteins shown below. (Two views of protein 2 are shown so that its structure is more
apparent.)
a. For each diagram, what are the predominant secondary structures?
For diagram A, the predominant secondary structure is - helix. There are only about 20
residues with ,  angles characteristic of -sheet.
For diagram B, both -helix and -sheet are well represented, and has a few residues in
the region of left-handed -helix.
b. What would you surmise about the majority of the bonds where ,  angles are in
“highly unfavorable” regions?
Most of the residues with “unfavorable” ,  angles probably involve glycine residues.
c. Which of the two Ramachandran diagrams corresponds to which of the two
proteins shown below? Explain.
Protein 1 (Ramachandran plot A) is T4 lysozyme, which is almost all -helical.
Protein 2 (Ramachandran plot B) is TATA binding protein, which has a lot of both helix and -sheet.
*How to draw a helical wheel. A helical wheel is a two-dimensional representation of a helix
obtained by projecting the helix down its central axis. Since an alpha helix contains 3.6 residues
per turn, each amino acid in the helix lies 100o around the helix axis from the previous amino
acid [(360o /turn) / (3.6 residues / turn) = 100o / residue). To draw a helical wheel, start by
drawing a vertical line (0o). The bottom end of the line will represent the helix axis, and the top
end the side chain for the first amino acid in the helix. Draw a second line rotated clockwise
1000 from the first line such that one end is on the helix axis, and the other end labeled amino
acid number 2. Draw a third line 1000 from the second, etc., until sufficient lines for all amino
acids in the helix are in place. Note: after 5 turns around the helix, the pattern will repeat (i.e.
residue number 19 will lie on top of residue number 1 in the projection). Thus, an 18 amino acid
helix will have a helical wheel with lines separated by 200.