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Wakatsuki Laboratory

WELCOME

The Wakatsuki Laboratory investigates atomic, molecular, and cellular interactions of proteins and their complexes involved in post-translational modifications, membrane trafficking, signal transduction and metabolic pathways. We use a variety of structural biology methods such as x-ray crystallography, small angle x-ray scattering, and electron and optical microscopy. While continuing our original targets such as vesicle transport, ubiquitination and polyubiquitin recognition, as well as structure-based drug design, we are expanding our interests to environmental and biogeochemical microorganisms, for example, enzyme-driven nitrogen cycling by ammonia-oxidizing archaea. At the same time, we are pursuing development of new imaging methods using x-ray, electron and photon beams and aim to integrate these different modalities to understand these complex biological phenomena.

As a part of the new Biosciences Division at SLAC National Accelerator Laboratory, our group is involved in a number of new projects and initiatives. These include a new experimental station called Macromolecular Femtosecond Crystallography (MFX) at LCLS, the world’s first hard x-ray free electron laser as well as new modes of XFEL beams for experimental phasing and time-resolved crystallography. We are also involved in the installation of Stanford’s 300 keV cryo-electron microscope (cryoEM) instrument, an FEI Titan Krios, at SLAC and new Stanford/SLAC cryoEM initiatives. Additionally, we are pursuing high-throughput protein crystallization systems and developing biology programs at SLAC’s ultrafast electron diffraction facility.

 

NEWS

April 2022: We are pleased to share our recent manuscript entitled “Intersubunit Coupling Enables Fast CO2-Fixation by Reductive Carboxylases” published in ACS Central Science. Thr paper describes how an enzyme of soil bacterium fixes CO2 to create new C-C bonds for production of complex molecules for antibiotics and metabolites. The enzyme manages extremely fast reactions of CO2 fixation by swing and twist motions of their catalytic domains. Four enzymes form a pair of dimers, and their catalytic domains are “glued” between the pairs enabling the coupled swing-twist motions. We used synchrotron and XFEL X-ray protein crystallography, extensive classical and quantum mechanics simulations, as well as site-directed mutagenesis and enzyme activity assays. This is an international and interdisciplinary collaboration with Max Planck Institutes for Terrestrial Microbiology and Multidisciplinary Sciences (Germany), Universidad de Concepción (Chile), Koc University (Turkey), and DOE Joint Genome Institute (USA). Figure by Gregory M. Stewart, SLAC.

https://doi.org/10.1021/acscentsci.2c00057

https://www6.slac.stanford.edu/news/2022-04-29-how-soil-microbe-could-rev-artificial-photosynthesis.aspx

February 2022: Our new double-shell protein scaffold dessign for cryo-EM sigle particle analysis of small and flexible proteins enabling molecular therapeutics design against acute myeloid leukemia (AML) has been published in ACS Central Science. In this work, we used apoferritin as the inner shell and maltose binding protein as the outer shell to sandwich a protein of interest for cryo-EM structure determination. This also allows for in vitro fluorescene polarization assay to directly correlate the cryo-EM structure and the protein-protein or protein-small molecule interactions in solution. This is the result of an interdisciplinary collaboration with Kathy Sakamoto, Lucile Packard Children’s Hospital Stanford and Stanford University School of Medicine, Ron Dror, Stanford Computer Science, and Wah Chiu, SLAC and Stanford Bioengineering. We are continuing further development of this technology in search of promising protein-protein interaction inhibitors against AML, other cancers, and proteases relevant in SARS-COV2 infection.

https://doi.org/10.1021/acscentsci.1c01090

January 2022. Congratulations to Adriana Garcia, a graduate student in Daria Mochly-Rosen’s lab in Stanford’s Chemical Systems Biology Department for the publication of her work in Journal of Biological Chemistry!  Her thesis work has elucidated the mechanisms of tetramer stabilization of glucose 6-phosphate dehydrogenase mutant mimicking a post-translational acetylation of lysine at the structural NADP+ binding site. Her biochemical and biophysical work laid the foundation of the stabilization of tetramers. She then expanded her work to structural biology, and showed an elegant structural basis of the enzyme activity recovery of the acetylation-mimicking G6PD by stabilization of the tetramer interface in collaboration with Irimpan Mathews (X-ray crystallography) and Tsutomu Matsui (SEC-SAXS) of SSRL, and Naoki Horikoshi, a visiting assistant professor from University of Tsukuba and later University of Tokyo.

https://doi.org/10.1016/j.jbc.2022.101610

October 2021. Congratulations to Iyshwary Warren for receiving a poster award, the 2nd place in the third cycle of poster presentations of the LCLS Summer Internship, October 2021. Her poster Development of a Mutant Photoactivatable Active Site for Time-Resolved Crystallography”, mentored by Chris Kupitz, a sequel poster of the one by Jacob Summers.  Iyshwary is an undergraduate student at Stanford working with Jacob Summers and others at SLAC LCLS, SSRL and Stanford (see below). 

August 2021. Congratulations to Jacob Summers for receiving a poster award, the 3rd place in the second cycle of poster presentations of the LCLS Summer Internship, August 2021. His poster title was “Development of a Mutant Photoactivatable Active Site for Time-Resolved Crystallography” mentored by Chris Kupitz, LCLS in collaboration with our group. His project aims to develop photoactivatable mutants of SARS-COV2 proteases for uniform and fast initiation of decaging of photo-caged active sites, and follow the kinetics using room temperature femto-second serial crystallography at LCLS. Jacob is collaborating with Chris Kupitz and Frank Moss of LCLS, Irimpan Mathews of SSRL, and Mikhail Hameedi and others in our lab to prepare photoactivatable active site in the SARS-COV2 proteases. 

March 2021: Congratulations to Andew for the submission of a manuscript entiled "An image-incorporated immersed boundary method for diffusion equation" to an archive and a journal. Andrew's work extends the most advanced numerical estimation method of complex boundary condition calculations to with an extremely robust algorithm.  This paves the way for simulating and estimating diffusion of substrates or macromolecules in micron sized holes in cryoEM grids in preparation of time-resolved cryoEM experiments.

arXiv:2103.17256 

https://arxiv.org/pdf/2103.17256.pdf

 

 

January 2021: Congratulations to Naoki and all the collaborators for the work on the mechanism of the loss of activity of the most severe patient-derived mutants of glucose-6-phosphate dehydrogenase (G6PD) deficiency, one of the most prevalent enzymopathy diseases, publication on January 19, 2021 in the Proceedings of the National Academy of Sciences of the United States of America. This is a culmination of several years of efforts in collaboration with Prof. Daria Mochly-Rosen of Chemical and Systems Biology Department, Stanford School of Medicine, and Prof. Esteban Vohringer-Martinez of Universidad de Concepción, Chile, and Prof. Naoki Horikoshi, University of Tsukuba, Japan. Many intern studnets including 3 high school students have contributed to this work. 

PNAS January 26, 2021, 118 (4) e2022790118; https://doi.org/10.1073/pnas.2022790118

See also SLAC News January 19, 2021

December 20129: Congratulations to Cornelius for staring his new job as an assistant professor in University of Souther California!  Cornelius   He joined the Wakatsuki lab in 2017 from MRC, Cambrige, UK.  He was subsequently awarded with a Panofsky Fellowship at SLAC National Accelerator Laboratory in 2018, workin on various technology development projects in XFEL and cryoEM while making seminal contributions on GPCR and other membrane proteins. He moved to USC in Los Angels in December 2020 to start a new research group. We wish you a phenomenal success in his new place!!

Please visit his website at USC.

June 2019: Congratulations to Hasan for assuming a new assistant professor position in the Koc University, Turkey! He will continue working with our group, Prof. Chris Francis, Stanford Environmental Systems Science, and Dr. Yasuo Yoshikuni, Joint Genome Institute, LBNL on C- and N-cycling pathways using ambient temperature and time-resolved crystallography. His group is the first fully fledged protein crystallography group in Turkey. He has already attracted a cohort of young talents in Turkey, and expects to establish and expand his research portofolio in the new reserach environment. 

Please visit Hasan's website in Koc University

June 2019: Congratulations to Hasan and Yash for their collaborative publication with the Tobias Erb laboratory at the Max Planck Institute.

This work combined high-resolution x-ray crystal structures with computer simulations to reveal the molecular basis for CO2 binding by enoyl-CoA carboxylases/reductases.

 https://doi.org/10.1073/pnas.1901471116

June 2019: Congratulations to Jonathan for his new published paper in Nature communications. This interdisciplinary study examined the formation of the surface layer in the bacterium Caulobacter crescentus.

https://rdcu.be/bHo1i

You can also find the press release from SLAC here:

https://www6.slac.stanford.edu/news/2019-06-21-scientists-make-first-high-res-movies-proteins-forming-crystals-living-cell.aspx

Artist:Greg Stewart/SLAC

May 2019: EMBL-Stanford workshop

First EMBL-Stanford worshop on structural biology was held on May 2-3, 2019, at EMBL Hamburg Outstation where esearchers from Stanford joined colleagues from EMBL’s sites to discuss cutting-edge research and technology, and how they can work together to advance their field. Read more 

April 2019, Congratulation Naoki!

Naoki, a post doc in the Wakatsuki lab is joining the University of Tsukuba as an Assistant Professor. He will continue his work at Stanford/SLAC as a Visiting Assistant Professor for the following year. 

March 2019, Congratulation Jonathan!

Jonathan received a Student Research Achievement Award from the Cryo-EM subgroup at the Biophysical Society annual meeting (BPS19) at Baltimore, Maryland on his work on the S-Layer protein. 

He also received another poster award on his work early Feb 2019 during the Bio-X Symposium.  

 

January 2019: Visit to Chapman University

Dr. Wakatsuki was invited for a talk and meeting with faculty and staff at Chapman University where he is an external advisor for Dr. Rahighi’s lab. Dr. Simin Rahighi was a postdoctoral fellow in the Wakatsuki lab before joining Chapman University as an assistant professor. 

January 2019: Welcome Lynnette!

We are pleased to have Lynnette, first year Structural Biology PhD student, joining our lab as a rotating student for Winter 2019. 

December 2018: Congratulations Josh!

Josh, our summer intern from The Harker High school, was accepted to Carleton college in Minnesota majoring in Biology. Good luck to you Josh in all your endeavors. 

November 2018: Good luck Jonathan and Colin!

Jonathan and Colin's (WE Moerner Lab) in vivo work on S-layer assembly is scheduled for a talk at 63rd Biophysical Society Meeting in March at Baltimore, Maryland. 

Stanford-SLAC Cryo-EM Facilities

The Stanford-SLAC Cryo-EM Facility is equipped with three 300 kV and one 200 kV electron microscopes (FEI Krios and Talos-Arctica), with phase plates, energy filters, and direct electron detector technologies. Read More

 

 

 

June  2018: Congratulations, Po-Nan!

Po-Nan's paper published in the ISME Journal. An interdisciplinary study of the ammonia-oxidizing archaea and how they keep the global nitrogen cycle in check. Find the press release from SLAC here:

https://www6.slac.stanford.edu/news/2018-06-13-slac-stanford-scientists-discover-how-hardy-microbe’s-crystalline-shell-helps-it

June 2018: Welcome back Rosie

It is our pleasure to have Rosie join our group once again for this summer. Rosie, an assistant professor at university of Gutenberg, spent a year of sabbatical last year at Wakatsuki lab helping and guiding through different projects.

 

August 2017: Congratulations, Cornelius!

Cornelius Gati has been awarded a 2017 Panofsky Fellowship by the Department of Energy’s SLAC National Accelerator Laboratory.

https://www6.slac.stanford.edu/news/2017-08-02-franklin-fuller-and-cornelius-gati-named-2017-panofsky-fellows-slac.aspx

 

May 2017: Congratulations, Jonathan!

Jonathan's recent paper published in Biophysical journal from which the Caulobactor surface layer illustration has been selected as the cover picture on the May issue of Biophysical Journal.

http://www.cell.com/biophysj/fulltext/S0006-3495(17)30390-9

 

Artist:Greg Stewart/SLAC

Please join us for JST-Bay Area Structural Biology workshop

WHERE:  LiKa Shing Center, Paul Berg Hall A

WHEN:  Monday, January 23, 2017 to Tuesday, January 24, 2017

See attached program

August 2016: Congratulations, Jonathan!

Jonathan received a poster award at BSR 2016 conference at SLAC on his work on the S-Layer protein. 

April 2016: Congratulations, Jonathan!

It is with great pleasure to announce that Jonathan Herrmann has been selected to receive the U.S. Department of Energy (DOE) Office of Science Graduate Student Research (SCGSR) award.

http://science.energy.gov/wdts/scgsr

March 2016: Congratulations, Simin!

Simin's recent paper has been selected as a featured article in March issue of the Structure journal. 

http://www.cell.com/structure/fulltext/S0969-2126(16)00015-0