332 Chapter 9. Cooperative transitions in macromolecules[[Student version, January 17, 2003]]
Figure 9.11:(Image reconstructed from electron microscopy data.) Direct visualization of an allosteric change.
The four panels show three-dimensional maps of a molecular motor (kinesin) attached to a microtubule. In each
frame the microtubule is in the background, running vertically and directed upward. A gold particle was attached to
the neck linker region of the motor, enabling the microscope to show changes in the linker’s position when the motor
binds a small molecule. Dotted circles draw attention to the significant differences between the frames. (a)Here
the motor has not bound any nucleotide in its catalytic domain; its neck linker flops between two positions (circles).
(b,c)Here the motor has bound an ATP-like molecule (respectively AMP-PNP and ADP-AlF 4 −in the two frames).
The position of the neck linker has changed. (d)When the motor has bound ADP, its conformation is much the
same as in the unbound state (a). Each of the images shown was reconstructed from data taken on 10 000–20 000
individual molecules. [From Rice et al., 1999.]
ical linkage, and in general manipulated by the protein in all the ways familiar to us from
macroscopic machinery.- Distortions transmitted to a distant binding site in this way can alter its local geometry, and
hence its affinity for its own target molecule.
Although this a purely mechanical picture of allosteric interactions is highly idealized, it has proven
quite useful in understanding the mechanisms of motor proteins. More generally, we should view
the mechanical elements in the above picture (forces, linkages) as metaphors also representing more
chemical elements (such as charge rearrangements).
9.6.3 Vista: Protein substates
This chapter has emphasized the role of cooperative, weak interactions in giving macromolecules
definite structures. Actually, though, it’s an oversimplification to say that a protein has a unique
native conformation. Though the native state is much more restricted than a random coil, never-
theless it consists of a very large number of closely-related conformations.
Figure 9.12 summarizes one key experiment by R. Austin and coauthors on the structure of
myoglobin. Myoglobin (abbreviated Mb) is a globular protein consisting of about 150 amino acids.
Like hemoglobin, myoglobin has a “prosthetic group” containing an iron atom, which can bind either
oxygen (O 2 )orcarbon monoxide (CO). The native conformation has a “pocket” region surrounding
the binding site. To study the dynamics of CO binding, the experimenters took a sample of Mb·CO
and suddenly dissociated all the carbon monoxide with an intense flash of light. At temperatures
below about 200K,the CO molecule remains in the protein’s pocket, close to the binding site.
Monitoring the optical absorption spectrum of the sample then let the experimenters measure the
fractionN(t)ofmyoglobin molecules that had re-bound their CO, as a function of time.