"It is like a cloud that gives you the volume within which you find 90 percent of all the electrons of the system," he said. The clouds capture the ribosome in action, but require computing to reveal chemical detail.
The researchers began by building computerized, atomic-scale models of the ribosome-protein complexes based on the crystal structures of the molecules, and then directed the computer to use this information to "fit" the structures into the electron clouds seen in cryo-EM studies. Simulations tracked the behavior of 2.7 million atoms in the SecY study, making it "the biggest, or one of the biggest, computer simulations to be published so far," Schulten said.
In the first study, the researchers were able to detect the precise molecular maneuvering that allows the ribosome and EF-Tu to recognize and interact with another molecule, transfer-RNA (tRNA). This interaction is key to the successful assembly of proteins because the ribosome and its partners must recognize the tRNA that carries the correct amino acid to be added to the growing protein chain.
The researchers on this study, led by Joachim Frank, of Columbia University (who also provided the cryo-EM data), found structural evidence that when the ribosome recognizes the correct tRNA it induces a change in the shape of EF-Tu. A gate in EF-Tu swings open, allowing a cascade of chemical interactions that lead to the addition of the amino acid to the protein.
The second study provided robust evidence that when the ribosome is translating a membrane protein, or a protein destined for excretion, it hooks up with a single SecY membrane channel shortly after protein translation begins.
The SecY binds to the ribosome by inserting two looped strands into the ribosome's exit channel. This interaction loosens a plug that normally seals the SecY channel. The plug moves out of the way, allowing the ribosome to funnel the growing protein through the membrane channel.
"We simulated the process of translocation of a (protein) out of the ribosome and into the SecY channel," said James (J.C.) Gumbart, a postdoctoral researcher at Illinois and first author on the Structure study. "And so we find that even though these loops are inserted into the (ribosome's) exit tunnel, they are not disturbed, nor do they get in the way of a nascent protein coming out."
Schulten directs the theoretical and computational biophysics group at the Beckman Institute for Advanced Science and Technology. He and his colleagues pioneered the MDFF approach and, thanks to support from the National Center for Research Resources at the National Institutes of Health, have made its software freely available to more than 160,000 users, he said.
Crystallographers and those doing cryo-EM are enthusiastically embracing MDFF, Schulten said, as this software can be used to tease out the elusive details of otherwise ambiguous data.
In these and other upcoming studies, Schulten and his colleagues are using the computer as a microscope to get a clearer picture of the dynamics of the ribosome, which is perhaps the cell's most essential, and most complex, molecular machine.
This movie depicts the simulated translocation of a growing protein (in green) from the ribosomal exit tunnel into the channel of SecY. The ribosome is pictured in blue. SecY is gray, orange and yellow.
(Photo Credit: Theoretical and Computational Biophysics Group, University of Illinois Beckman Insitute)
The SecY protein channel (grey, green, orange and brown) resides in the membrane.
(Photo Credit: Theoretical and Computational Biophysics Group, University of Illinois Beckman Institute.)