Zooming In On The Protein-conducting Channel

Howard Hughes Medical Institute investigator Joachim Frank at the Wadsworth Center and his colleagues reported their detailed study of the translocon's core, called the protein-conducting channel (PCC), in an article published in the November 17, 2005, issue of the journal Nature. Co-lead authors on the paper were Kakoli Mitra in Frank's laboratory and Christiane Schaffitzel of the Eidgenössische Technische Hochschule Hönggerberg in Switzerland, who is in the laboratory of the other senior author, Nenad Ban. Other co-authors were from the Scripps Research Institute and the State University of New York at Albany.

The researchers studied the PCC, which grabs newly made protein as it is extruded from the ribosome's protein synthesis machinery. The PCC then opens either a pore that is perpendicular or lateral to the cell membrane to feed the new protein either across or into the membrane.

For the studies, the Swiss researchers created a complex comprising the PCC from E. coli attached to a ribosome that contained a newly forming protein segment. The ribosome is the massive protein-RNA complex that constitutes the cell's protein-making machinery.

Mitra explored the structure of this PCC-ribosome complex using three-dimensional cryogenic electron microscopy (cryo-EM), as well as computational methods. Three-dimensional cryo-EM is one of the few techniques capable of visualizing large, dynamic molecules.

In preparing for cryo-EM, researchers immersed the PCC-containing complex in water and then abruptly froze it in supercold liquid ethane. The rapid freezing imprisoned the complex in vitreous ice, a glassy non-crystalline form of ice, thus preserving its native structure. Using an electron microscope with a low-intensity beam to avoid damaging the molecules, scientists then obtained images of thousands of captive protein complexes. Next, they used computer image analysis to produce detailed, three-dimensional maps of the complex in two different states from the low-contrast, noisy images produced by the electron microscope.

“What we have achieved is a huge jump in resolution of this complex,” said Frank. “Even so, this resolution would not allow us to study the complex in atomic detail, or even see individual helices.” He said the results from the cryo-EM analysis were informed by detailed x-ray crystallographic data on the PCC structure done by other researchers. In x-ray crystallography, an x-ray beam is directed through crystals of a target protein. As the x-rays pass through the crystal, they are diffracted. Researchers can then analyze the diffraction pattern to determine the atomic structure of the protein.

The analysis by Frank and his colleagues revealed that each channel consists of two PCC subunits joined in a clamshell arrangement. The cryo-EM data also revealed two different arrangements of the PCC — one that was apparently in the functional, or “translocating” state, and one in a non-translocating state.

X-ray crystallography data from the lab of HHMI investigator Tom A. Rappaport suggested that the halves of the PCC clamshell were joined in a back-to-back arrangement. However, said Frank, x-ray crystallographic structures often do not represent the arrangements of proteins in their native functional state.

Thus, he and his colleagues applied a computational analytical method called “normal mode-based flexible fitting” (NMFF) to model how well the two possible channel structures could explain the structural data from cryo-EM. The NMFF method was developed and applied by co-authors Florence Tama and Charles Brooks of the Scripps Research Institute. The technique provides dynamic information on the multitude of vibrations and motions that complex molecules preferentially undergo.

NMFF analysis revealed that the cryo-EM data were best explained by a model in which the two PCC clamshells were joined in a “front-to-front” arrangement. This arrangement yielded significant insight into how the channel functions to translocate proteins across or into membranes, said Frank.

“Now that we have these new insights into the architecture of the PCC in its translocating, and possibly non-translocating state, we can explore the mechanisms of perpendicular versus lateral transport,” Frank said.