Scientists have made enormous strides in the field of structural biology, looking into the activities of nature at the smallest scale. Such analyses are crucial for plotting the behavior of key macromolecules and interpreting their critical role in living organisms.
Abhishek Singharoy is a researcher in the Biodesign Center for Applied Structural Discovery and ASU’s School of Molecular Sciences. Image Credit: Arizona State University.
Scientists from the Biodesign Center for Applied Structural Discovery and Arizona State University’s School of Molecular Sciences have adopted a new method to investigate the molecules of life, analyzing their static structures at high resolution and also examining the all-important dynamic movements of these molecules as they perform biological functions.
In the new technique, data acquired through an innovative method called cryogenic electron microscopy (cryo-EM), is aggressively reprocessed. In this case, molecules meant for analysis are flash-frozen in a thin membrane of ice and then subjected to electron microscopy. An unlimited number of still images are obtained and subsequently reorganized using computer.
The method provides a strong alternative to X-ray crystallography for studying the molecular world in more detail. Undoubtedly, cryo-EM excels in the fields of study that are most difficult for X-ray crystallography—the imaging of huge protein complexes impervious to traditional crystallization techniques.
While early iterations of cryo-EM strived to compete with the intense image resolution characteristic of X-ray crystallography, rapid advancements in the field currently allow cryo-EM to generate incredible macromolecular pictures at near-atomic-resolution.
In the latest study, Abhishek Singharoy and his collaborators showed that the cryo-EM method can be pushed to even greater extremes of clarity, by acquiring valuable data that was formerly hidden in the reams of cryo-EM information.
Now, we can actually see minimum free-energy pathways image-by-image during a simulation. It was impossible to see energetically feasible molecular movies before. Now cryo-EM, machine learning and molecular dynamics simulations have got us there.”
Abhishek Singharoy, Researcher, Arizona State University
Singharoy is joined by the study’s joint first authors Ali Dashti and Ghoncheh Mashayekhi from the Department of Physics at the University of Wisconsin Milwaukee and by Arizona State University researcher Mrinal Shekhar.
The new study is the outcome of an association between five teams: Abbas Ourmazd’s group and Peter Schwander’s group from the University of Wisconsin in Milwaukee, Joachim Frank’s group from Columbia Medical Center, Amedee des Georges at CUNY, and Singharoy from Arizona State University.
The new findings were reported in the latest issue of the Nature Communications journal.
By using the new approach developed by the study’s co-authors Abbas Ourmazd and 2017 Chemistry Nobel Laureate Joachim Frank, which involves mathematical methods of geometric machine learning integrated with definitive molecular dynamics simulations, scientists were able to record the brief movements of ryanodine receptor type 1, a crucial calcium channel that can attach other molecules.
Slight conformational modifications of the receptor play a vital role in the contraction of heart muscles and skeletal muscles, after the receptor has been activated by a particular binding molecule.
Though single-particle cryo-EM, the team successfully constructed impressive molecular movies of the continuous conformational changes of the ryanodine receptor type 1, constructed from about 800,000 cryo-EM pictures of molecules confined in ice, similar to insects buried in amber.
Integrating pictures that were intermediary between the fully open and closed conformations allowed the team to capture the structural shape-shifting behavior of the receptor both before and after binding by activating molecules.
The novel method will be an advantage in practical fields, specifically, drug discovery, while helping scientists to solve the foundational problems in molecular biology.
Dashti, A., et al. (2020) Retrieving functional pathways of biomolecules from single-particle snapshots. Nature Communications. doi.org/10.1038/s41467-020-18403-x.