Lesk: Introduction to Genomics 
Answers to end-of-chapter exercises
Figures from the bookLesk: Introduction to Genomics
Chapter 06
Please note: the filesize of some of the rotating structures is over 1MB and they may take a moment to view
Page 325, Fig 6.10
E. coli CheY protein. CheY is a bacterial signal-transduction protein involved in regulation of flagellar dynamics in chemotaxis. Activation of a receptor causes phosphorylation of CheY. Phosphorylated CheY interacts with flagellum protein
FliM to induce tumbling [3CHY].
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Page 326, Fig 6.11
Two related proteins that share the same general folding pattern, but differ in detail. Circles represent copper ions. (a) Spinach plastocyanin [1AG6], (b) cucumber stellacyanin [1JER]. Superposition showing (c) the entire structures and (d) only the well-fitting core (plastocyanin, green; stellacyanin, magenta). The main secondary structural elements of these proteins are two β-sheets packed face-to-face. It is seen in the superposition that several strands of β-sheet are conserved but displaced, and that the helix at the right of the cucumber stellacyanin structure has no counterpart in the spinach plastocyanin structure. Even the (relatively) well-fitting core shows the conservation of folding topology but nevertheless reveals considerable distortion.
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Page 328, Fig 6.12
Superposition of two conformational states of horseshoe crab arginine kinase
[1M15, 1M80]. The unligated state is shown in pink and purple; the ligated state in dark green
and cyan. The ligands, arginine and ADP, appear in the ligated structure only. There are steric
clashes between the ligands and the unligated structure in its position in the picture.
The nature of the conformational change has reminded many people of the Venus flytrap.
Regions of the structure have come together around the ligands. The motion of the small
domain at the top of the picture is primarily a 'hinge' motion the mobile domain moves almost
rigidly around an axis through the interdomain interface. The axis is approximately perpendicular to the page.
The parts of the structure at the lower right also deform. This protein is showing 'induced fit' - in response to ligation.
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Page 328, Fig 6.13
Superposition of two structures of ribose-binding protein [2DRI, 1URP]. The unligated
structure is shown in pink and cyan; the ligated structure is shown in dark green and purple. The
ribose, in yellow, appears only in the ligated structure.
Compared with arginine kinase (Figure 6.12), this is a more pure 'hinge' motion: the individual
domains remain nearly rigid. The conformational change is achieved by rotations about bonds in
only a few residues in the hinge region itself.
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Page 329, Fig 6.14
p21 Ras bound to GTP. Although an active GTPase, the system was stabilized for crystal-structure analysis by
cooling to 100 K [1QRA].
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Page 330, Fig 6.15
The conformational change in p21 Ras from the inactive GDP-binding conformation to the active GTPbinding
conformation primarily involves two regions (shown here in red) that form a patch on the molecular surface [1QRA, 1Q21].
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Page 332, Fig 6.17
The contraction of muscle is a transformation of chemical energy to mechanical
energy. It is carried out at the molecular level by a hinge motion in myosin, while myosin is
attached to an actin filament. The cycle of attach to actin-change conformation-release from
actin in a large number of individual myosin molecules creates a macroscopic force within the
muscle fibre. (a) The structure of myosin subfragment 1 from chicken. The active site binds and
hydrolyses ATP. ELC and RLC are the essential and regulatory light chains [2MYS]. (b) Hinge
motion in myosin. Comparison of parts of chicken myosin open form [2MYS] (no nucleotide bound)
and closed form binding the ATP analogue ADP•AlF−4 [1BR2]. This shows the segments of the
structure that surround the hinge region. (c) Model of the swinging of the long helical region in
myosin as a result of the hinge motion. The dashed line shows a model of the position that the
complete long helix would occupy in the closed form [2MYS] and [1BR1]. This conformational change
is coupled to hydrolysis of ATP. It takes place while myosin is bound to actin, providing the power
stroke for muscle contraction. In the context of the assembly and mechanism of function of a
muscle filament, it is arguable that one should regard the helix as fixed and the head as swinging.
However, this would not show the magnitude of the conformational change as dramatically.
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Page 337, Fig 6.20
Antithrombin III, a serine proteinase inhibitor.
(a) Native conformation;
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(b) latent conformation [1ATH]
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Page 340, Fig 6.21
(a) Aligned sequences and (b) superposed structures of two related proteins, hen
egg white lysozyme (black) [1AKI] and baboon α-lactalbumin (red) [1ALC]. The sequences are
related (37% identical residues in the aligned sequences) and the structures are very similar.
Each protein could serve as a good model for the other, at least as far as the course of the
mainchain is concerned.
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Page 344, Fig 6.22
Coiled-coil BZIP domain encoded byproto-oncogene c-jun [1JNM].
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Page 349, Fig 6.24
The sites of mutation in B. subtilis subtilisin E that produced a thermostable variant by directed evolution.
The sidechains shown are those of the final product.
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Page 353, Fig 6.25
The interface between phage M13 gene III protein (N-terminal domain) and E. coli protein TolA (C-terminal domain) [1TOL]. (a, b) Folding patterns and relative orientation of domains, viewed approximately (a,c) perpendicular and (b) parallel to the interface. Note the β-sheet formed from strands contributed by both partners. (c) Slice through the interface, with TolA shown in black, gene III protein in red, and water molecules in blue. It is possible that another water molecule sits next to the one inside the structure.
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Page 355, Fig 6.26
Interaction between PDZ domains in syntrophin (cyan) and neuronal nitric oxide synthas (magenta) [1QAV].
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