BIO SEMINAR:Development of a DNA Origami platform for cryo-EM studies...

Speaker:Tural Aksel

Title: Development of a DNA Origami platform for cryo-EM studies of small proteins and nucleic acids

Date/Time: August 18,2023 11:40 A.M.

Place: FENS G032

The seminar will be held in person, however there will also be an option to attend online using the link below:

https://sabanciuniv.zoom.us/j/7260077994

Abstract: Correct reconstruction of macromolecular structure by cryo-electron microscopy (cryo-EM) relies on accurate determination of the orientation of single-particle images. For small (<100 kDa) proteins, obtaining particle images with sufficiently asymmetric features to correctly guide alignment is challenging. Here, we apply DNA origami to construct molecular goniometers—instruments that precisely orient objects—and use them to dock a DNA-binding protein on a double-helix stage that has user-programmable tilt and rotation angles. We construct goniometers with 14 different stage configurations to orient and visualize the protein just above the cryo-EM grid surface. Each goniometer has a distinct barcode pattern that we use during particle classification to assign angle priors to the bound protein. We use goniometers to obtain a 6.5-Å structure of BurrH, an 82-kDa DNA-binding protein whose helical pseudosymmetry prevents accurate image orientation using traditional cryo-EM. Our approach should be adaptable to other DNA-binding proteins as well as RNA and small proteins fused to DNA-binding domains. In this seminar, I will go through the challenges that were addressed in the process of developing this technology.

Bio:Tural Aksel is a Staff Scientist at Encodia, Inc., where he does protein engineering for a NextGen proteomics technology. He received his B.S. in Biological Sciences and Bioengineering from Sabanci University, Turkey in 2006. He received his Ph.D. in Biophysics from Johns Hopkins University in 2012. His Ph.D. studies were focused on repeat protein engineering and protein folding. He performed his postdoctoral work on the biomechanics of human cardiac myosin at Stanford University between 2013 and 2015. He was at the University of California, San Francisco as postdoctoral researcher and later as programmer between 2015 and 2020 to develop a DNA origami platform for cryo-EM. In 2020, he joined Nautilus Biotechnology, Inc. as the Lead Staff Scientist to develop DNA Origami reagents for a NextGen proteomics platform. In March 2023, he left Nautilus Biotechnology, Inc. to join Encodia, Inc. In San Diego. His research interests are centered around developing technologies using biomolecular design and scientific software development.