Visualizing Biological Molecules at Atomic Resolution: Advances in Cryo-EM
Tiffany Zhou | May 9th, 2023
The Discovery Lecture Series, a year-long event hosted by the Vanderbilt University Medical Center since 2006, features talks from globally prominent scientists. Typically around five lectures are given each year, during which students and faculty have the opportunity to listen to perspectives from researchers and policy-makers working on the cutting-edge of current scientific and medical issues. So far this year, the series has featured Ruth Lehmann, PhD, a renowned germ cell biologist, and Sir Paul Nurse, PhD, a geneticist who discovered key components of the eukaryotic cell cycle. The lecture on April 6th, 2023 will feature Kunle Odunsi, MD, PhD, a gynecologic oncologist who studies immunotherapy treatments for ovarian cancer. Before that, however, the Discovery Lecture for March was presented by Yifan Cheng, PhD, a biophysicist and structural biologist who has been a major pioneer in the field of single particle cryo-EM (cryogenic electron microscopy).
About the Speaker
Dr. Cheng is currently a Professor of Biochemistry and Biophysics at the University of California, San Francisco. He is an Investigator of the Howard Hughes Medical Institute (HMMI), a biomedical research philanthropy dedicated to supporting discovery science. He is also a member of the National Academy of Sciences. Initially trained in solid-state physics for his undergraduate and graduate degrees, he transitioned to studying cryo-EM after his postdoctoral fellowship, a field where his lab has discovered exciting new methodologies.
Highlights from the Lecture
History of cryo-EM in structural biology
Protein structure is the main focus of structural biologists. Knowing the structure of a protein is key to understanding its function, mechanisms, and possible interactions. The main tools at a structural biologist’s disposal typically include X-ray crystallography, nuclear magnetic resonance spectroscopy (NMR), and electron microscopy. These tools help researchers in the field determine 3D structures of biological molecules, such as the SARS-CoV-2 spike protein.
Since its advent in the 1970s, cryo-EM has been a powerful tool for visualizing protein structures while bypassing the need for crystallization of proteins, which presents a technical challenge in the laboratory. Cheng, in particular, spoke about the major breakthroughs which have brought 3D visualizations closer to atomic resolution than ever before.
For example, one of the most important relevant innovations in hardware was the introduction of the electron counting camera in 2013. These new cameras essentially reduced noise and improved the clarity of images. Additionally, correction of beam-induced motion during microscopy further increased the resolution and reduced blurriness of images.
Cheng also elaborated on the breakthrough in software, in which the maximum likelihood approach, based on probability, refined analysis. Cheng spoke about his optimism for the field: “We are already way past the time where we are simply trying to determine the structure. We are really trying to understand the mechanism by looking at all the intermediate states, and the transition between the states to understand the whole biological process. That, I think, is the next stage for single particle cryo-EM.”
At its inception, cryo-EM was only used for determining a protein’s structure. Now, the technique has enabled structural biologists to track conformational changes and monitor protein dynamics at a macromolecular level. In 2013, Cheng’s lab published a groundbreaking structure determination of a TRP ion channel, a type of mammalian receptor responsible for detecting environmental stimuli like heat and the spiciness of capsaicin, a chemical found in chili peppers. These images were produced at atomic resolution without the need for crystallization, showing the power and potential of single-particle cryo-EM.
“We are already way past the time where we are simply trying to determine the structure. We are really trying to understand the mechanism by looking at all the intermediate states, and the transition between the states to understand the whole biological process. That, I think, is the next stage for single particle cryo-EM.” – Yifan Cheng, PhD
Current research
Currently, some of the research done in the Cheng Lab is focused on dynamic processes of genome packaging that affect gene expression. Genes that are more tightly packaged in a heterochromatin form have suppressed transcription, so these genes are typically off. Genes that are unwound in a euchromatin form have more transcription activity, so these genes are typically on and active. Nucleosomes, as well as hexosomes, are subunits of wrapped DNA. Chromatin remodelers are proteins that interact with nucleosomes to facilitate access to DNA by transcription factors, proteins that enable gene expression.
During his talk, Cheng discussed his work with UCSF collaborators on defining the interactions between a chromatin remodeler (INO80), nucleosomes, and hexasomes, to determine DNA availability. Structures from electron microscopy helped them better understand site-binding interactions during chromatin remodeling and modification. Although it is still a work in progress to fully elucidate the mechanisms behind this process, Cheng and his team have faith that single particle cryo-EM will be the key to unraveling this biological puzzle.
In Dr. Yifan Cheng’s Discovery Lecture at the VUMC, he discussed the history of cryo-EM, current advances, and the progress of his research on genome packaging. His research with fellow collaborators will set the stage for the new era of visualizing biological mechanisms, not only structure, with single-particle cryo-EM.
Image Credits
“Cartoon representation of Arabidopsis DCL1 in complex with pri-miRNA 166f (elucidated by Cryo-EM in Wei X. et al. Nat. Plants. 2021)” by AimerD is licensed under CC BY-SA 4.0. To view a copy of this license, visit https://creativecommons.org/licenses/by-sa/4.0/?ref=openverse.