Xiao-chen Bai

Annotations

1. Ribosome structures to near-atomic resolution from thirty thousand cryo-EM particles

   Currently available detectors, combined with video processing algorithms like the one presented here, will result in higher-resolution cryo-EM structures for many more samples than those reported until now.

   This work makes an important contribution to the recent rapid progress of cryo-EM. Since then, many more structures have been determined to high resolution by cryo-EM, by following this approach and many other approaches developed by different labs.

2. Ribosome structures to near-atomic resolution from thirty thousand cryo-EM particles

   In addition, we noted a trend for particles that were calculated from later video frames to align less accurately, most likely as a result of accumulated radiation damage.

   Sjors Scheres, who is the correspondence author of this work, published another work, showing that the dose dependent radiation damage effect can be estimated by calculating the bfactor of the 3D reconstruction from each single movie frame. By downweighting the more damaged frames based their bfactor, the radiation damage effect can be reduced resulting in better 3D reconstruction. In the same paper, following this work, Sjors also described his newly developed method that can used to correct beam induced motion for small protein particles. Since then, many small proteins have been determined to high resolution with the help of this method, such as gamma secretase (XC Bai, et. al Nature 2015).

3. Ribosome structures to near-atomic resolution from thirty thousand cryo-EM particles

   we collected an entire data set as tilted pairs and used tilt-pair analysis to experimentally assess alignment errors for video frames

   Chris Russo from Lori Passmore lab published a paper in JSB systematically describe how to use tilt-pair method, which was originally developed by Richard Henderson and co-workers, to measure the alignment accuracy in single particle data processing. (C Russo, Lori Passmore. JSB 2014).

4. Ribosome structures to near-atomic resolution from thirty thousand cryo-EM particles

   Application of this procedure to a second, untilted data set of 80S S. cerevisiae ribosomes serves to illustrate the impact these detectors, combined with suitable video processing procedures, will have on the field of cryo-EM structure determination.

   After we published this work, there are many other work following this approach in order to determine the cryo-EM structures for large protein complex to near atomic resolution, such as, IS Fernandez et.al Science 2013; A Amunts et.al Science 2014; Z Yan et.al Nature 2015 and so on.

5. Ribosome structures to near-atomic resolution from thirty thousand cryo-EM particles

   Using a newly developed statistical movie processing approach to compensate for beam-induced movement, we show that ribosome reconstructions with unprecedented resolutions may be calculated from almost two orders of magnitude fewer particles than used previously.

   Hi eLife readers: I am Xiaochen Bai, an Assistant Professor from UT Southwestern Medical Center. I am the first author of this paper. The sentence I highlight is the key point in this research paper. By employing the recent developed direct electron detector that has fast read-out, we can realign the ribosome particles from each movie frame to correct the beam induced motion. As a result, the resolution improved significantly for both of 70S and 80S ribosome. 2 months later, Xueming Li from Yifan Cheng's lab published another fantastic paper describing how motion correction could help improve the resolution for 20S proteasome. There are some differences between our and Xueming's work. In our work, the motion for each particles are corrected individually, whereas in Xueming's work, the motion for each image is corrected as whole. Both approaches have advantages and disadvantages. Some later work showed that combining both approach can lead to the best cryo-EM reconstruction.