News

Nadia was a guest on Dr Shane Huntington's show, Einstein a Go-Go on Triple R (Independent Radio station in Melbourne), together with her husband, theoretical physicist Dr Jayden Newstead, for a brief chat about their research. 

https://www.rrr.org.au/explore/programs/einstein-a-go-go/episodes/28351-einstein-a-go-go-25-february-2024

Cytochrome c oxidase (CcO) is a large membrane-bound hemeprotein that catalyzes the reduction of dioxygen to water. Unlike classical dioxygen binding hemeproteins with a heme b group in their active sites, CcO has a unique binuclear center (BNC) composed of a copper atom (CuB) and a heme a3 iron, where O2 binds and is reduced to water. CO is a versatile O2 surrogate in ligand binding and escape reactions. Previous time-resolved spectroscopic studies of the CO complexes of bovine CcO (bCcO) revealed that photolyzing CO from the heme a3 iron leads to a metastable intermediate (CuB-CO), where CO is bound to CuB, before it escapes out of the BNC. Here, with a pump-probe based time-resolved serial femtosecond X-ray crystallography, we detected a geminate photoproduct of the bCcO−CO complex, where CO is dissociated from the heme a3 iron and moved to a temporary binding site midway between the CuB and the heme a3 iron, while the locations of the two metal centers and the conformation of Helix-X, housing the proximal histidine ligand of the heme a3 iron, remain in the CO complex state. This new structure, combined with other reported structures of bCcO, allows for a clearer definition of the ligand dissociation trajectory as well as the associated protein dynamics.

Izumi Ishigami, Sergio Carbajo, Nadia Zatsepin et al., Denis L. Rousseau, and Syun-Ru Yeh. 2023. J. American Chem. Soc. 

September 2023

Nadia has been awarded an ARC Future Fellowship. 

This project aims to uncover the molecular structural dynamics of a bacterial enzyme responsible for protein folding in bacteria. This project expects to generate new knowledge to guide the development of a new type of antibacterial to circumvent antibiotic resistance. Expected outcomes of this project include new experimental, computational and simulation tools for dynamic X-ray crystallography including new capabilities at the Australian Synchrotron for very small microcrystals of any biomolecule. This would provide a powerful new tool for the Australian structural biology community that should accelerate fundamental discoveries, including facilitating high-resolution structure determination of membrane proteins and drug development.

Announced Sept 2022.

https://www.latrobe.edu.au/news/announcements/2022/arc-future-fellowship-2022

Nadia is on maternity leave, caring for the second tiny new human she created. 

2022

The increase in successful adaptations of serial crystallography at synchrotron radiation sources continues. To date, the number of serial synchrotron crystallography (SSX) experiments has grown exponentially, with over 40 experiments reported so far. In this work, we report the first SSX experiments with viscous jets conducted at ALBA beamline BL13-XALOC. Small crystals (15–30 mm) of five soluble proteins (lysozyme, proteinase K, phycocyanin, insulin and 􏰆-spectrin-SH3 domain) were suspended in lipidic cubic phase (LCP) and delivered to the X-ray beam with a high-viscosity injector developed at Arizona State University. Complete data sets were collected from all proteins and their high-resolution structures determined. The high quality of the diffraction data collected from all five samples, and the lack of specific radiation damage in the structures obtained in this study, confirm that the current capabilities at the beamline enables atomic resolution determination of protein structures from microcrystals as small as 15 mm using viscous jets at room temperature. Thus, BL13-XALOC can provide a feasible alternative to X-ray free-electron lasers when determining snapshots of macromolecular structures.

Martin-Garcia, J. M.   et al. 2022 J. Synchrotron Rad. 29, 896-907.

Big congratulations to Susannah Holmes on a successful PhD, including a first author Nature Communications paper! 

Dr Holmes is now a postdoctoral research fellow in the Centre for Bioimaging Science at the National University of Singapore, in the group of Assistant Prof Duane Loh.

March 2022

Serial femtosecond crystallography (SFX) is a powerful technique that exploits X-ray free-electron lasers to determine the structure of macromolecules at room temperature. Despite the impressive exposition of structural details with this novel crystallographic approach, the methods currently available to introduce crystals into the path of the X-ray beam sometimes exhibit serious drawbacks. Samples requiring liquid injection of crystal slurries consume large quantities of crystals (at times up to a gram of protein per data set), may not be compatible with vacuum configurations on beamlines or provide a high background due to additional sheathing liquids present during the injection. Proposed and characterized here is the use of an immiscible inert oil phase to supplement the flow of sample in a hybrid microfluidic 3D-printed co-flow device. Co-flow generation is reported with sample and oil phases flowing in parallel, resulting in stable injection conditions for two different resin materials experimentally. A numerical model is presented that adequately predicts these flow-rate conditions. The co-flow generating devices reduce crystal clogging effects, have the potential to conserve protein crystal samples up to 95% and will allow degradation-free light-induced time-resolved SFX.

Doppler, D. et al.  2022. J. Appl. Cryst. 55 (1) 1-13. https://doi.org/10.1107/S1600576721011079

Abstract

MyD88 and MAL are Toll-like receptor (TLR) adaptors that signal to induce pro-inflammatory cytokine production. We previously observed that the TIR domain of MAL (MALTIR) forms filaments in vitro and induces formation of crystalline higher-order assemblies of the MyD88 TIR domain (MyD88TIR). These crystals are too small for conventional X-ray crystallography, but are ideally suited to structure determination by microcrystal electron diffraction (MicroED) and serial femtosecond crystallography (SFX). Here, we present MicroED and SFX structures of the MyD88TIR assembly, which reveal a two-stranded higher-order assembly arrangement of TIR domains analogous to that seen previously for MALTIR. We demonstrate via mutagenesis that the MyD88TIR assembly interfaces are critical for TLR4 signaling in vivo, and we show that MAL promotes unidirectional assembly of MyD88TIR. Collectively, our studies provide structural and mechanistic insight into TLR signal transduction and allow a direct comparison of the MicroED and SFX techniques.

Clabber, M.T.B, Holmes, S., Muusse, T. W., Vajjhala, P. R., Thygesen, S. J., Malde, A.K., Hunter, D.J.B., Croll, T.I., Flueckiger, L., Nanson, J.D., Rahaman, M.H., Aguila, A., Hunter, M.S., Liang, M., Yoon, C. H., Zhao, J., Zatsepin, N.A., Abbey, B., Sierecki, E., Gambin, Y., Stacey, K.J., Darmanin, Connie, Kobe, Bostjan., Xu, Hongyi, Ve, Thomas.

Nature Communications 12, 2578 (2021). 

Significance:

Light-driven rhodopsin proteins pump ions across cell membranes. They have applications in optogenetics and can potentially be used to develop solar energy–harvesting devices. A detailed understanding of rhodopsin dynamics and functions may therefore assist research in medicine, health, and clean energy. This time-resolved crystallography study carried out with X-ray free-electron lasers reveals detailed dynamics of chloride ion–pumping rhodopsin (ClR) within 100 ps of light activation. It shows the dissociation of Cl− from the Schiff base binding site upon light-triggered retinal isomerization. This Cl− dissociation is followed by diffusion toward the intracellular direction. The results hint at a common ion-pumping mechanism across rhodopsin families. 

Abstract

Chloride ion–pumping rhodopsin (ClR) in some marine bacteria utilizes light energy to actively transport Cl− into cells. How the ClR initiates the transport is elusive. Here, we show the dynamics of ion transport observed with time-resolved serial femtosecond (fs) crystallography using the Linac Coherent Light Source. X-ray pulses captured structural changes in ClR upon flash illumination with a 550 nm fs-pumping laser. High-resolution structures for five time points (dark to 100 ps after flashing) reveal complex and coordinated dynamics comprising retinal isomerization, water molecule rearrangement, and conformational changes of various residues. Combining data from time-resolved spectroscopy experiments and molecular dynamics simulations, this study reveals that the chloride ion close to the Schiff base undergoes a dissociation–diffusion process upon light-triggered retinal isomerization.

Yun, J-H., Li, X., Yue, J. Park, J.-H., Jin, Z., Li, C., Hu, H. Shi, Y., Pandey, S., Carbajo, S., Boutet, S., Hunter, M.S., Liang, M., Sierra, R. G., Lane, T.J., Zhou, L., Weierstall, U., Zatsepin, N. A., Ohki, M., Tame, J. R. H., Park, S.-Y., Spence, J.C.H., Zhang, W., Schmidt, M., Lee, Weontae, and Liu, Haiguang. 

PNAS 118 (13), 2021. e2020486118. 

This work builds on our TR-SFX work (the first mixing-based time-resolved SFX) where we observed a large rotation of a molecular unit, which the crystals survived (!). This is a deep diver into the solid-solid phase transition we observed in adenine riboswitch aptamer RNA crystals. 

Abstract

Time-resolved studies of biomacromolecular crystals have been limited to systems involving only minute conformational changes within the same lattice. Ligand-induced changes greater than several angstroms, however, are likely to result in solid-solid phase transitions, which require a detailed understanding of the mechanistic interplay between conformational and lattice transitions. Here we report the synchronous behavior of the adenine riboswitch aptamer RNA in crystal during ligand-triggered isothermal phase transitions. Direct visualization using polarized video microscopy and atomic force microscopy shows that the RNA molecules undergo cooperative rearrangements that maintain lattice order, whose cell parameters change distinctly as a function of time. The bulk lattice order throughout the transition is further supported by time-resolved diffraction data from crystals using an X-ray free electron laser. The synchronous molecular rearrangements in crystal provide the physical basis for studying large conformational changes using time-resolved crystallography and micro/nanocrystals.

Ramakrishnan S, Stagno JR, Conrad CE, Ding J, Yu P, Bhandari YR, Lee Y-T, Pauly G, Yefanov O, Wiedorn MO, Knoska J, Oberthuer D, White TA, Barty A, Mariani V, Li C, Brehm W, Heinz WF, Magidson V, Lockett S, Hunter MS, Boutet S, Zatsepin NA, Zuo X, Grant TD, Pandey S, Schmidt M, Spence JCH, Chapman, Henry N., Wang Yun-Xing  

Nature Communications 12, 1762  (2021).

Accepted December 2020

Nadia is on maternity leave, caring for the tiny new human she created. 

September 2020.

Tiny human is now one year old and has thoroughly enjoyed having both mummy and daddy at home during the infamous local lockdowns. She has learned a lot about T cells!

Abstract

Serial femtosecond crystallography (SFX) with X-ray free electron lasers (XFELs) allows structure determination of membrane proteins and time-resolved crystallography. Common liquid sample delivery continuously jets the protein crystal suspension into the path of the XFEL, wasting a vast amount of sample due to the pulsed nature of all current XFEL sources. The European XFEL (EuXFEL) delivers femtosecond (fs) X-ray pulses in trains spaced 100 ms apart whereas pulses within trains are currently separated by 889 ns. Therefore, continuous sample delivery via fast jets wastes >99% of sample. Here, we introduce a microfluidic device delivering crystal laden droplets segmented with an immiscible oil reducing sample waste and demonstrate droplet injection at the EuXFEL compatible with high pressure liquid delivery of an SFX experiment. While achieving ~60% reduction in sample waste, we determine the structure of the enzyme 3-deoxy-D-manno-octulosonate-8-phosphate synthase from microcrystals delivered in droplets revealing distinct structural features not previously reported. 

Figure [left] taken from the publication. Led by Alexandra Ros' lab.

A. Echelmeier, J. C. Villarreal... et al., J. C. H. Spence, H. N. Chapman, N. Zatsepin, P. Fromme, R. A. Kirian and Alexandra Ros. Nature Communications 11 (4511), 2020. 

September 2020.

X-ray free-electron lasers (XFELs) produce uniquely brief (fs scale), transversely coherent X-ray pulses with about 10 orders of magnitude higher peak brightness than 3rdgeneration synchrotrons. In the decade since the first hard X-ray FEL came online, numerous unprecedented experimental modalities have emerged, particularly for time-resolved studies. Serial femtosecond crystallography (SFX) with XFELs has enabled high-resolution structure determination from solvated protein microcrystals at room temperature, without structure-altering radiation damage. A key advantage of time-resolved crystallography with XFELs is rapid reaction initiation using light or chemical mixing to probe protein dynamics on fs to second time scales. This talk will cover the latest developments in mix-and-inject serial fs crystallography with a focus on how it can help in understanding viral infection and antibiotic resistance.

https://monash.au.panopto.com/Panopto/Pages/Viewer.aspx?id=a9741da6-3f41-4758-a863-ac240000a3ae

Abstract

µNS is a 70 kDa major nonstructural protein of avian reoviruses, which cause significant economic losses in the poultry industry. They replicate inside viral factories in host cells, and the µNS protein has been suggested to be the minimal viral factor required for factory formation. Thus, determining the structure of µNS is of great importance for understanding its role in viral infection. In the study presented here, a fragment consisting of residues 448–605 of µNS was expressed as an EGFP fusion protein in Sf9 insect cells. EGFP-µNS(448–605) crystallization in Sf9 cells was monitored and verified by several imaging techniques. Cells infected with the EGFP-µNS(448–605) baculovirus formed rod- shaped microcrystals (5–15 mm in length) which were reconstituted in high- viscosity media (LCP and agarose) and investigated by serial femtosecond X-ray diffraction using viscous jets at an X-ray free-electron laser (XFEL). The crystals diffracted to 4.5 A ̊ resolution. A total of 4227 diffraction snapshots were successfully indexed into a hexagonal lattice with unit-cell parameters a = 109.29, b = 110.29, c = 324.97 A ̊ . The final data set was merged and refined to 7.0 A ̊ resolution. Preliminary electron-density maps were obtained. While more diffraction data are required to solve the structure of µNS(448–605), the current experimental strategy, which couples high-viscosity crystal delivery at an XFEL with in cellulo crystallization, paves the way towards structure determination of the µNS protein. 

Figure [left] taken from the publication.

N. Nagaratnam, Y. Tang, S. Botha, J. Saul, C. Li, H. Hu, S. Zaare, M. Hunter, D. Lowry, U. Weierstall, N. Zatsepin, J. C. H. Spence, J. Qiu, J. LaBaer, P. Fromme and J. M. Martin-Garcia. Acta Cryst. (2020) F76, 278-289. 

June 2020.

Highlights

• X-ray free-electron laser unveils alternative protein structure of lipoprotein

• Advanced molecular dynamics explore conformational space among solved structures

• Virtual ligand screening shows possible lead fragments for potential drug therapies

Figure [left] taken from the publication.

Zook, J.D., et al., Singharoy, A., Fromme, P., (2020). XFEL and NMR Structures of Francisella Lipoprotein Reveal Conformational Space of Drug Target against Tularemia. (2020) Structure 28, 1–8. 

Online March 2020.

Abstract:

Sleeping sickness is a fatal disease caused by the protozoan parasite Trypanosoma brucei (Tb). Inosine-5’-monophosphate dehydrogenase (IMPDH) has been proposed as a potential drug target, since it maintains the balance between guanylate deoxynucleotide and ribonucleotide levels that is pivotal for the parasite. Here we report the structure of TbIMPDH at room temperature utilizing free-electron laser radiation on crystals grown in living insect cells. The 2.80 Å resolution structure reveals the presence of ATP and GMP at the canonical sites of the Bateman domains, the latter in a so far unknown coordination mode. Consistent with previously reported IMPDH complexes harboring guanosine nucleotides at the second canonical site, TbIMPDH forms a compact oligomer structure, supporting a nucleotide-controlled conformational switch that allosterically modulates the catalytic activity. The oligomeric TbIMPDH structure we present here reveals the potential of in cellulo crystallization to identify genuine allosteric co-factors from a natural reservoir of specific compounds.Figure [left] taken from the publication.

Karol Nass, Lars Redecke, et al. [...] C. Betzel, Nature Communications  11, 620 (2020).

30th January 2020

This was an epic effort and it's great to see it published!

Abstract:

The world’s first superconducting megahertz repetition rate hard X-ray free-electron laser (XFEL), the European XFEL, began operation in 2017, featuring a unique pulse train structure with 886 ns between pulses. With its rapid pulse rate, the European XFEL may alleviate some of the increasing demand for XFEL beamtime, particularly for membrane protein serial femtosecond crystallography (SFX), leveraging orders-of-magnitude faster data collection. Here, we report the first membrane protein megahertz SFX experiment, where we determined a 2.9 Å-resolution SFX structure of the large membrane protein complex, Photosystem I, a > 1 MDa complex containing 36 protein subunits and 381 cofactors. We address challenges to megahertz SFX for membrane protein complexes, including growth of large quantities of crystals and the large molecular and unit cell size that influence data collection and analysis. The results imply that megahertz crystallography could have an important impact on structure determination of large protein complexes with XFELs.

Figure [left] taken from the publication.

C. Gisriel, J. Coe, a great international team, P. Fromme and N. Zatsepin. 2019. Nature Communications 10 (5021).  

4 Nov 2019.

The DatView paper is now online: 

Natasha Stander, Petra Fromme, Nadia Zatsepin. 2019. J. Appl. Cryst. 52 (6), 1440-1448. 

Abstract:

DatView is a new graphical user interface (GUI) for plotting parameters to explore correlations, identify outliers and export subsets of data. It was designed to simplify and expedite analysis of very large unmerged serial femtosecond crystallography (SFX) data sets composed of indexing results from hundreds of thousands of microcrystal diffraction patterns. 

However, DatView works with any tabulated data, offering its functionality to many applications outside serial crystallography. In DatView's user-friendly GUI, selections are drawn onto plots and synchronized across all other plots, so correlations between multiple parameters in large multi-parameter data sets can be rapidly identified. It also includes an item viewer for displaying images in the current selection alongside the associated metadata. For serial crystallography data processed by indexamajig from CrystFEL.. 

DatView generates a table of parameters and metadata from stream files and, optionally, the associated HDF5 files. By combining the functionality of several commonly needed tools for SFX in a single GUI that operates on tabulated data, the time needed to load and calculate statistics from large data sets is reduced. This paper describes how DatView facilitates (i) efficient feedback during data collection by examining trends in time, sample position or any parameter, (ii) determination of optimal indexing and integration parameters via the comparison mode, (iii) identification of systematic errors in unmerged SFX data sets, and (iv) sorting and highly flexible data filtering (plot selections, Boolean filters and more), including direct export of subset CrystFEL stream files for further processing.

More details about DatView are available here:  https://zatsepinlab.atlassian.net/wiki/spaces/DAT/overview

Check out the tutorial to get started, and the manual for more details.

Online 31st October 2019. Open access.

In this work, led by Vadim Cherezov, we present a simple and efficient method, dubbed Complex-LCP (Crystallization of membrane proteins using transient ligand exchange in LCP), for structure determination of a target GPCR in complex with a panel of different ligands by taking advantage of the SFX method. This represents a major step towards high-throughput GPCR–ligand co-crystal structure determination. 

Online 24th October 2019. Open access.

Andrii Ishchenko, Benjamin Stauch, Gye Won Han, Alexander Batyuk, Anna Shiriaeva, Chufeng Li, Nadia Zatsepin, Uwe Weierstall, Wei Liu, Eriko Nango, Takanori Nakane, Rie Tanaka, Kensuke Tono, Yasumasa Joti, So Iwata, Isabel Moraes, Cornelius Gati and Vadim Cherezov. 2019.  IUCrJ 6(6). 

We present a brief overview of two complementary techniques for high-resolution structure determination from micro and nanocrystals of biological samples. Both fields of SFX and MicroED move fast, so updates in brief review journals like COSB are a great way to highlight key papers and progress in the fields. 

Zatsepin, N., Chufeng Li, Paige Colasurd and Brent Nannenga, "The complementarity of serial femtosecond crystallography and MicroED for structure determination from microcrystals", 2019. Current Opinion in Structural Biology, Vol 58, 286-293. 

October 2019.

It was a great PhD defence summarizing interesting and difficult work. Congratulations are also due for the recent acceptance of Natasha's first-author paper on DatView, coming soon to the Journal of Applied Crystallography. 

DatView: https://zatsepinlab.atlassian.net/wiki/spaces/DAT/overview  with code at https://github.com/nstander/DatView

September 2019

Sabine Botha presented our work at FMX, NSLS-II, in her talk, "Single-wavelength anomalous dispersion phasing for Serial Millisecond Snapshot Crystallography" in Session 3.2.1: Application of anomalous techniques in macromolecular crystallography, Tuesday 23rd July @ 4:30 PM  at the American Crystallographic Association 2019 Meeting in Cincinnati. 

Nadia spoke about the need for standards and best practices for data sharing & optimizing data quality in serial (snapshot) millisecond crystallography at the TA.1: Transactions—Data Best Practices: Current State and Future Needs Session on Sunday 22nd July. There'll be a transactions paper to follow soon.

July 2019

After 8+ years at ASU, Nadia and her husband moved home to Melbourne, Australia. Nadia has joined the Australian Research Council's Center of Excellence in Advanced Molecular Imaging. She will now be at the La Trobe Institute for Molecular Sciences (LIMS), working with the groups of Assoc. Profs. Connie Darmanin and Brian Abbey on XFEL and synchrotron serial crystallography and other time-resolved methods. The Imaging CoE includes and collaborates with researchers at  Uni Melbourne, RMIT, Monash University, CFEL at DESY, and ASU. 

New PhD and masters students are welcome! We'll be looking for postdocs in the future too. Email  n.zatsepin { at } latrobe edu au  if interested in joining as a student. 

Does down under seem too far?? Melbourne is frequently voted the world's most livable city, and sprouted Profs John Spence, Anton Barty, Henry Chapman, Adrian Mancuso and many other fun people you might know. It's where the Braggs wished they'd lived instead of Adelaide :) and it's in the country of excellent coffee, bread, cheese, wine, beaches, drop bears, little penguins in little jumpers, avian dinosaurs that want small government, and X-ray science. 

Exciting times ahead for the previous Zatsepin lab members at ASU:

Chufeng Li is moving to Henry Chapman's group at CFEL, DESY. Congratulations on the new position! 

Sabine Botha is continuing her postdoc at ASU as a BioXFEL postdoc at ASU in Prof. John Spence's lab. She is independently running the crystallization lab she single-handedly set up, funded by the Zatsepin lab, in the ASU BioXFEL labs (PSF275)! 

Natasha Stander is going to defend her PhD dissertation in early September 2019!

Rick Hewitt is doing the BioXFEL summer internship, supervised by Nadia Zatsepin remotely and Rick Kirian at ASU. He has accepted a STEM teaching position at a high school! He may return to research in the future and we support either path - they can both be very rewarding and valuable. 

Bye sunny Arizona, hello lush green yummy Melbourne.

June 2019.

The 2019 NSLS-II and CFS Users' Meeting AT Brookhaven National Lab included a workshop on "Macromolecular Serial Crystallography with an LCP Jet Injector" organized by our collaborators Martin Fuchs (BNL), Wuxian Shi (BNL) and Jose Martin-Garcia (ASU). Chufeng presented SMX data analysis tools including the EZ hit finder, which he wrote at NSLS-II in March 2019 and how to interface the Dozor/DIALS hit finding output (in house at FMX, NSLS-II) with DatView, developed by Natasha Stander.   Sabine presented a novel heavy-atom soaking-in-LCP method and results from phasing Hg-SAD LCP-SMX data. This is part of a 3-year partnership between ASU and NSLS-II to establish LCP-SMX at the FMX beamline. 

20 May 2019

Nadia joined the Integrative Structural Biology working group on "Time-resolved structural biology - new possibilities in a time of new facilities", run by LINXS - Lund Institute of Advanced Neutron and X-ray Science. 

May 2019

This paper reveals the structural basis of melatonin receptor subtype selectivity to help drive the development of a new generation of highly selective pharmacological tools and new therapies aimed at treating type 2 diabetes, cancer and sleep disorders. We report high-resolution structures of the human MT2 receptor in complex with two agonists (which bind to receptors to yield a biological response) and two function-related mutants also in complex with one of the agonists. 

The human MT1 and MT2 melatonin receptors are G-protein-coupled receptors that help to regulate circadian rhythm and sleep patterns. Drug development efforts have targeted both receptors for the treatment of insomnia, circadian rhythm and mood disorders, and cancer, and MT2 has also been implicated in type 2 diabetes.

Figure & abstract quote are from the full paper: Johansson et al. (Cherezov Lab, USC), Nature, April 2019. and PDB entries: 6ME6, 6ME7, 6ME8, 6ME9. 

 Chufeng Li contributed to the determination of this biomedically important macromolecular complex from XFEL femtosecond crystallography data collected at LCLS. 

For more context, see: https://www.eurekalert.org/pub_releases/2019-04/uosc-agn042319.php 

April 2019 - online. Due to appear in print in Nature on May 9 2019.

Pink beam crystallography enables faster collection of data, which is crucial for room-temperature time-resolved studies from microcrystals using synchrotron sources. We report the first structures determined from from soluble and membrane protein microcrystals delivered in serial (snapshot) millisecond crystallography (SMX) with a viscous-medium injector (LCP-SMX). 

Figure taken from paper - click here for details; 

PDB entries 6mh6, 6mh8

Martin-Garcia, J.M., Zhu, L., Mendez, D., Lee, M.-Y., Chun, E., Li, C., Hu, H., Subramanian, G., Kissick, D., Ogata, C., Henning, R., Ishchenko, A., Dobson, Z., Zhang, S., Weierstall, U., Spence, J.C.H., Fromme, P., Zatsepin, N.A., Fischetti, R.F., Vadim Cherezov, Liu, W. (2019). High-viscosity injector-based pink beam serial crystallography of micro-crystals at a synchrotron radiation source. IUCrJ 6, 1-14 

April 2019

Congratulations to undergraduate research student Rick Hewitt for being recognized for his work on "Simulations of kilohertz serial femtosecond crystallography with a compact X-ray light source"!

Rick is doing great work on microcrystal diffraction simulations for a new X-ray source being built at ASU in the Graves Lab (Physics & Biodesign Center for Applied Structural Biology) - the Compact X-ray Light Source, and (in the future), the Compact X-ray free-electron Laser. 

This prize is well deserved!

Izumi Ishigami, Ariel Lewis-Ballester, Austin Echelmeier, Gerrit Brehm, Nadia A. Zatsepin, Thomas D. Grant, Jesse D. Coe, Stella Lisova, Garrett Nelson, Shangji Zhang, Zachary F. Dobson, Sébastien Boutet, Raymond G. Sierra, Alexander Batyuk, Petra Fromme, Raimund Fromme, John C. H. Spence, Alexandra Ros, Syun-Ru Yeh, and Denis L. Rousseau. PNAS February 26, 2019 116 (9) 3572-3577.

February 2019

Press release: https://www.eurekalert.org/pub_releases/2019-02/asu-xls021019.php

This work is a follow-up paper from

Crystal structure of CO-bound cytochrome coxidase determined by serial femtosecond X-ray crystallography at room temperature. Izumi Ishigami, Nadia A. Zatsepin, Masahide Hikita, Chelsie E. Conrad, Garrett Nelson, Jesse D. Coe, Shibom Basu, Thomas D. Grant, Matthew H. Seaberg, Raymond G. Sierra, Mark S. Hunter, Petra Fromme, Raimund Fromme, Syun-Ru Yeh, and Denis L. Rousseau. PNAS July 25, 2017 114 (30) 8011-8016. 

Non-cryogenic structure of a chloride pump provides crucial clues to temperature-dependent channel transport efficiency 

Ji-Hye Yuna1, Xuanxuan Libc1, Jae-Hyun Parka, Yang Wangb, Mio Ohkid, Zeyu Jina, Wonbin Leea, Sam- Yong Parkd, Hao Hue, Chufeng Lie, Nadia Zatsepine, Mark S. Hunterf, Raymond G. Sierraf, Jake Koralekf, Chun Hong Yoonf, Hyun-Soo Chog, Uwe Weierstalle, Leihan Tangb, Haiguang Liub* and Weontae Leea* 

J. Biol. Chem. (2019) 294(3) 794 –804 

January 2019

As part of the BioXFEL 6th Annual International Conference in Feb 2019, we hosted an informal mini-workshop focused on sample delivery options for XFEL experiments (crystallography and single particle imaging, including GDVNs, double-flow focusing liquid jets, various ultrafast mixing jets, sheet jets, acoustic drop-on-demand delivery systems, fixed targets, tape drives, and of course, the LCP injector and other high-viscosity injection systems. 

This was held on day 3 of the  BioXFEL 6th Annual International Conference on Feb 12-14th in San Diego, CA, USA. 

February 2018  

(photo on the left may be from our 2014 data analysis workshop at Berkeley Nat. Lab, and that may be James Holton speaking to the panel of XFEL and synchrotron crystallography analysis experts)

As part of a large international collaboration of 100+ researchers, we report the first experiments from the European XFEL - the first superconducting linac-based XFEL. 

• Europe's new X-ray laser reveals structure of antibiotic-disabling enzyme, October 2, 2018

"Megahertz serial crystallography"; Max O. Wiedorn, et al. Anton Barty ; Nature Communications, 2018; DOI: 10.1038/s41467-018-06156-7

We are excited to welcome Dr. Sabine Botha, who recently graduated from University of Hamburg, to the Zatsepin lab.  

December 2018

Are you struggling to index your snapshot serial crystallography data? Do you have too few peaks for the usual pundits (MOSFLM & DirAx) to deal with? Come try our new auto-indexing software, SPIND.

SPIND (sparse-pattern indexing) is an auto-indexing algorithm for sparse snapshot diffraction patterns (`stills') that requires the positions of only five Bragg peaks in a single pattern, when provided with unit-cell parameters. The capability of SPIND is demonstrated for the orientation determination of sparse diffraction patterns using simulated data from microcrystals of a small inorganic molecule, I3C, which is challenging for commonly used indexing algorithms. SPIND, integrated with CrystFEL is shown to improve the indexing rate and quality of merged serial femtosecond crystallography data from two membrane proteins, the human δ-opioid receptor (DOR) in complex with a bi-functional peptide ligand DIPP-NH2 (data available publicly through the link) and the NTQ chloride-pumping rhodopsin (CIR). 

The study demonstrates the suitability of SPIND for indexing sparse inorganic crystal data with smaller unit cells, and for improving the quality of serial femtosecond protein crystallography data, significantly reducing the amount of sample and beam time required by making better use of limited data sets. SPIND is written in Python and is publicly available under the GNU General Public License from https://github.com/LiuLab-CSRC/SPIND.

Chufeng Li, Xuanxuan Li, Richard Kirian, John Spence, Haiguang Liu and Nadia Zatsepin.  IUCrJ 6 (1), 2019. 

For details, click here.  

December 2018

Published by the Royal Society of Chemistry. 

https://pubs.rsc.org/en/content/ebook/978-1-78262-728-9

August 2018