Reach Out Semi-finals

We are all very proud of our BioXFEL Scholar, Tek Narsigh Malla and our BioXFEL interns and UPR undergraduates Gabriela Díaz Figueroa and Ana Sofía Santiago-Russe for making it into the Semi-final round of the Reach Out Science Slam Competition. They gave wonderful presentations and  did an excellent job representing the BioXFEL Center.


BioXFEL Research Support Call for Proposals

Announcement of BioXFEL discretionary research support 

The NSF BioXFEL Science and Technology Center has funding intended to support research at US institutions. This support is for the application of X-ray free electron lasers to structural biology in collaboration with the BioXFEL STC. The aim is to foster collaboration with the BioXFEL Center and respond to current research needs and new directions. Applications should have direct relevance to the BioXFEL mission. 

Funding requests must be sponsored by a BioXFEL Center member and clearly identify that sponsor in the application.  Awardees will be granted a maximum of $90K in total costs for one year. Details of the BioXFEL mission and its members are provided at

How to Apply: Requests should include a cover sheet containing contact details, sponsor information, abstract, and the funding amount requested. The applicant should also have a letter from the sponsor (maximum of 2 pages). Proposals are limited to 5 pages excluding references. The proposal should describe the project and the potential for any BioXFEL funding to leverage further research efforts. A short budget justification should be included together with appropriate biosketches. The cover sheet, sponsor letter, budget justification, and biosketches do not count toward the 5 page limit. BioXFEL is NSF supported and proposals will be judged based on relevance and need to the BioXFEL program, the potential to leverage additional research efforts, and on the standard NSF criteria, intellectual merit and broader impact. The sponsor is excluded from the review process. Format criteria for standard NSF proposals (margin/font etc.) should be followed. Researchers who have applied previously for BioXFEL support, successful or not, are encouraged to apply.

All applications should be clearly identified and submitted electronically no later than April 26, 2021 to:

Erin Uppington, Managing Director

NSF BioXFEL Science and Technology Center 700 Ellicott Street Buffalo, NY  14203

This email address is being protected from spambots. You need JavaScript enabled to view it. 716-898-8610

Call for Papers on "Novel Structural Studies of Coronavirus Proteins"

Special Issue "Novel Structural Studies of Coronavirus Proteins"

A special issue of Crystals (ISSN 2073-4352). This special issue belongs to the section "Biomolecular Crystals".

Deadline for manuscript submissions: 20 December 2021.


The Z to E isomerization in Phytochromes revealed by Femtosecond X-ray Pulses from an X-ray Free Electron Laser

Phytochromes are the molecular eyes of plants and bacteria that regulate cellular response to light, an essential environmental signal. Upon light absorption, the phytochromes change their structures substantially from a conformation that absorbs in the red-light called Pr to another  conformation that absorbs in the far-red light called Pfr, respectively. These reversible changes are driven by a light triggered isomerization reaction of an open-chain tetrapyrrole chromophore. Phytochrome proteins are notoriously difficult to investigate because of their inherent flexibility that promotes structural change and is necessary for function. Phytochrome crystals can suffer from disorder that impairs the resolution of X-ray diffraction patterns collected from them. High resolution, however, is necessary to interpret subtle changes that occur during BV isomerization.

Phytochrome structures are diverse, but mostly follow a general blueprint. They consist of a photosensory core module (PCM) that perceives and processes the light input, and an effector domain, typically with enzymatic activity, that is covalently linked to the PCM. Most known phytochrome X-ray structures to date are PCM structures or structures of an even smaller fragment that only binds the chromophore.

Although first identified in plants and photosynthetic bacteria, phytochromes are also found in a variety of non-photosynthetic bacteria. In fact, the first X-ray structure of any phytochrome was solved from the eubacterium Deinococcus radiodurans. Bacteriophytochromes (BphP) contain biliverdin (BV) as central chromophores.  The myxobacterium Stigmatella aurantiaca also expresses BphPs. In the last few years, the structures of the two BphPs found in S. aurantiaca, SaBphP1 and SaBphP2, were determined. In particular, the SaBphP2-PCM forms exceptionally well diffracting crystals which scatter well beyond 1.6 Å, a record resolution so far for phytochrome PCM crystals. The myxobacterial phytochromes were first identified and characterized in the laboratory of Emina Stojković, Professor in the Department of Biology at Northeastern Illinois University (NEIU), Chicago, IL, who received discretionary funding from BioXFEL to pursue the determination of structure and function of these BphPs. NEIU is a public 4-year Hispanic Serving Institution (HSI), that is one of the most ethnically diverse universities in the Midwest and is, therefore, ideally aligned with the mission of BioXFEL.

An international team from the United States, Sweden and Japan followed, for the first time, the Z- to E isomerization of the central chromophore in any BphP in real time. The experiments were led by BioXFEL scientists Stojković and Schmidt and by University of Gothenburg investigator Westenhoff. For the experiments, trillions of microcrystals of the SaBphP2-PCM were produced and folded into a viscous carrier matrix consisting of nuclear grade grease also known as superlube. The isomerization of the BV and concomitant structural changes were determined with time-resolved femtosecond serial crystallography (TR-SFX) at a delay of 5 ns and 33 ms after light excitation at the free electron laser SACLA near Osaka in Japan. Strong difference electron density features in the chromophore pocket showed large chromophore displacements caused by the Z to E isomerization of BV ring D. Multiple structural details such as the photo-ejection of the so-called pyrrole water, and the separation of essential amino acids from the hydrogen bond network near the chromophore reveal a mechanism how the signal is transferred through the protein. This ground-breaking work is published in the journal Structure (


Our results on myxobacterial BphPs had profound consequences for the career path of several students at NEIU: Melissa, the lead author was a NEIU graduate student and moved to the Paul Scherrer Institute in Switzerland after being accepted to its PhD program. Juan Sanchez was also a NEIU graduate student, who is currently a PhD student at the University of Wisconsin-Madison. Undergraduate co-authors Luis Aldama and Moraima Noda were both part of the NIH-funded MARC scholars program at NEIU. Moraima is currently pursuing a PhD at Indiana University. Luis Aldama has been accepted to PhD programs at Harvard, Northwestern and the University of Chicago. Denisse Feliz is currently a graduate student in Chemistry at NEIU. She holds BA in Biology from NEIU. Melissa, Moraima and Juan all travelled to SACLA in Japan and participated in sample preparation and data collection for this publication. 


Full reference:

M. Carrillo, S. Pandey, J. Sanchez, M. Noda, I. Poudyal, L. Aldama, T. N. Malla, E. Claesson, W. Yuan Wahlgren, D. Feliz, V. Šrajer, M. Maj, L. Castillon, S. Iwata, E. Nango, R. Tanaka, T. Tanaka, L. Fangjia, K. Tono, S. Owada, S. Westenhoff, E. A. Stojković, M. Schmidt (2021)High-resolution Crystal Structures of Transient Intermediates in the Phytochrome Photocycle, Structure, published online March 22, 2021, DOI:

BioXFEL scientists make a molecular movie of a biological process to convert sunlight to chemical energy

Many organisms use sunlight to fuel cellular functions. But exactly how does this conversion of solar energy into chemical energy unfold?


ASU professor awarded top research prize

The Royal Swedish Academy of Sciences has awarded the prestigious Gregori Aminoff Crystallography Prize, one of the physics research community’s highest honors, to Arizona State University Regents Professor John Spence.