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2024 BioXFEL Summer Internship
Events 29 May 2024
May 29 2024
We are now accepting applications for the 2024 BioXFEL Summer Internship program that will occur May 29, 2024 - August 2, 2024.… Please email the BioXFEL Education and Diversity Director, Nicole Terranova, at nterranova@hwi.buffalo.edu if you have any questions. Click HERE to apply for the 2024 BioXFEL Summer Internship…
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News 18 Oct 2023
The 2024 BioXFEL Spring Symposium will be at Arizona State University from March 6 – 7, 2024.
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Events 6 Mar 2024
Mar 06 2024
The 2024 BioXFEL Spring Symposium will be at Arizona State University from March 6 – 7, 2024.
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Sequence-dependent conformational preferences of disordered single-stranded RNA
BioXFEL Publications 29 Oct 2024 Contributor(s): Lois Pollack
https://doi.org/10.1016/j.xcrp.2024.… , He, W., Pabit, S. A., Pollack, L., & Kirmizialtin, S. (2024).… Cell Reports Physical Science, 5(11), 102264. https://doi.org/10.1016/j.xcrp.2024.
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BioXFEL Publications 10 May 2024
http://dx.doi.org/10.1016/j.jbc.2024.… , Zhou, G., Lee Luo, C., Eleraky, S., Moradi, M., & Gao, Y. (2024).… Journal of Biological Chemistry, 300(6), 107361. https://doi.org/10.1016/j.jbc.2024.
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BioXFEL Publications 25 Mar 2024 Contributor(s): Jose Arcadio Rodriguez-Martinez
http://dx.doi.org/10.1016/j.jbc.2024.… , Peña-Martínez, E., & Rodriguez-Martinez, J. (2024).… Journal of Biological Chemistry, 300(3), 107071. https://doi.org/10.1016/j.jbc.2024.
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BPS2025 - Unraveling the catalytic mechanism of the SARS-CoV-2 macrodomain ADP-ribosylhydrolase
BioXFEL Publications 13 Feb 2025 Contributor(s): James Fraser
https://doi.org/10.1016/j.bpj.2024.… 2882 journal-article Mitra, R., Correy, G., & Fraser, J. (2025). BPS2025 - Unraveling the catalytic mechanism of the SARS-CoV-2 macrodomain ADP-ribosylhydrolase. Biophysical Journal, 124(3), 553a. https://doi.org/10.1016/j.bpj.2024.
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BioXFEL Publications 13 Feb 2025 Contributor(s): Lois Pollack
https://doi.org/10.1016/j.bpj.2024.… 476 journal-article Wang, T., Hu, Q., Fronhofer, S., & Pollack, L. (2025). BPS2025 - Disordered RNA conformations and nucleotide-specific dynamics within ribonucleoprotein condensates. Biophysical Journal, 124(3), 76a. https://doi.org/10.1016/j.bpj.2024.
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BioXFEL Publications 25 Mar 2024 Contributor(s): Jose Arcadio Rodriguez-Martinez
http://dx.doi.org/10.1016/j.jbc.2024.… , Pomales-Matos, D., Rivera-Madera, A., Messon-Bird, J., Medina-Feliciano, J., Sanabria-Alberto, L., Barreiro-Rosario, A., Rivera-Del Valle, J., & Rodríguez-Martínez, J. (2024).… Journal of Biological Chemistry, 300(3), 106540. https://doi.org/10.1016/j.jbc.2024.
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BPS2025 - Molecular simulation with 3D-RISM: Using hybrid Monte Carlo for efficient sampling
BioXFEL Publications 13 Feb 2025 Contributor(s): David Case
https://doi.org/10.1016/j.bpj.2024.… 1742 journal-article Pishaki, N. C., Luchko, T., & Case, D. A. (2025). BPS2025 - Molecular simulation with 3D-RISM: Using hybrid Monte Carlo for efficient sampling. Biophysical Journal, 124(3), 314a. https://doi.org/10.1016/j.bpj.2024.
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BPS2025 - Automated, efficient, and rigorous absolute binding free energy calculations
BioXFEL Publications 13 Feb 2025 Contributor(s): David Case
https://doi.org/10.1016/j.bpj.2024.… 1764 journal-article Ayoub, S., Luchko, T., Barton, M., & Case, D. A. (2025). BPS2025 - Automated, efficient, and rigorous absolute binding free energy calculations. Biophysical Journal, 124(3), 318a–319a. https://doi.org/10.1016/j.bpj.2024.
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BioXFEL Publications 13 Feb 2025 Contributor(s): David Case
https://doi.org/10.1016/j.bpj.2024.… 509 journal-article Van Elslande, T. Y., Carvalho, F. S., Case, D., Cavagnero, S., & Luchko, T. (2025). BPS2025 - Computational modeling of magnesium ion solvation around Escherichia coli 70S ribosome using 3D reference interaction site model of molecular solvation. Biophysical Journal,…
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Extracting conformational heterogeneity from 2D and 3D cryo-EM data
BioXFEL Publications 8 Feb 2024 Contributor(s): James Fraser
http://dx.doi.org/10.1016/j.bpj.2023.11.376 journal-article Hoff, S., Bonomi, M., Fraser, J., & Greene, E. (2024).
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Visualizing the 3D Structures of Molecules Involved in Life's Processes UPR Workshop
News 18 Oct 2023
"Visualizing the 3D Structures of Molecules Involved in Life's Processes" Workshop Undergraduate students attending college in Puerto Rico are invited to participate in this two-day workshop. The workshop will be available in the following locations from 8am - 4pm each day: February 5th - 6th in Mayaguez February 7th - 8th in San…
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Role of conformational dynamics in the catalytic mechanism of viral macrodomains
BioXFEL Publications 8 Feb 2024 Contributor(s): James Fraser
https://doi.org/10.1016/j.bpj.2023.11.2156 journal-article Mitra, R., & Fraser, J. (2024).
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Sequence-dependent conformational preferences of disordered single-stranded RNA
BioXFEL Publications 8 Feb 2024 Contributor(s): Lois Pollack
http://dx.doi.org/10.1016/j.bpj.2023.11.2762 journal-article Wang, T., He, W., Pabit, S. A., Kirmizialtin, S., & Pollack, L. (2024).
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Computing a Bayesian multi-state model of a protein structure from an X-ray diffraction pattern
BioXFEL Publications 8 Feb 2024 Contributor(s): James Fraser
http://dx.doi.org/10.1016/j.bpj.2023.11.1276 journal-article Hancock, M. P., Fraser, J. S., & Sali, A. (2024).
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BioXFEL Publications 1 Mar 2024 Contributor(s): Jose Arcadio Rodriguez-Martinez
http://dx.doi.org/10.31083/j.fbs1601004 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Peña-Martínez, E. G., & Rodríguez-Martínez, J. A. (2024).
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Cation-induced intramolecular coil-to-globule transition in poly(ADP-ribose)
BioXFEL Publications 10 Sep 2024 Contributor(s): Lois Pollack
https://doi.org/10.1038/s41467-024-51972-9 journal-article Wang, T., Coshic, K., Badiee, M., McDonald, M. R., Aksimentiev, A., Pollack, L., & Leung, A. K. L. (2024).
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Author Correction: Cation-induced intramolecular coil-to-globule transition in poly(ADP-ribose)
BioXFEL Publications 4 Oct 2024 Contributor(s): Lois Pollack
https://doi.org/10.1038/s41467-024-52865-7 journal-article Wang, T., Coshic, K., Badiee, M., McDonald, M. R., Aksimentiev, A., Pollack, L., & Leung, A. K. L. (2024).
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Product-stabilized filamentation by human glutamine synthetase allosterically tunes activity
BioXFEL Publications 8 Feb 2024 Contributor(s): James Fraser
http://dx.doi.org/10.1016/j.bpj.2023.11.2135 journal-article Greene, E. R., Muniz, R., Yamamura, H., Hoff, S., Arada, A., Bajaj, P., Chen, D., Lee, J. D., Bonomi, M., Kollman, J. M., & Fraser, J. (2024).
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DefNEtTrp: An Iron Dual Chelator Approach for Anticancer Application
BioXFEL Publications 4 Dec 2024 Contributor(s): Israel Rodriguez, Arthur Tinoco
https://doi.org/10.1021/jacsau.4c00774 journal-article Rodríguez, I., Acosta, C., Nieves-Escobar, C., Strangmark, E., Claudio-Ares, O., Vargas Figueroa, A. I., Soto-Millán, A. M., M. Orta-Rivera, A., Astashkin, A. V., & Tinoco, A. D. (2024).
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Single Particle cryoEM Structure Determination
News 28 Aug 2024
A group of BioXFEL researchers brought single particle cryoEM structure determination to BioXFEL. The research was spearheaded by Tek Malla, a BioXFEL graduate in the Schmidt lab. Using samples of a bacterial phytochrome prepared in the Stojkovic lab at Northeastern Illinois University, cryo-EM grids were prepared, and single particle cryo-EM…
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Biochemical and Structural Studies of the Carminomycin 4-O-Methyltransferase DnrK
BioXFEL Publications 27 Feb 2024 Contributor(s): Mitchell Miller, George Phillips
http://dx.doi.org/10.1021/acs.jnatprod.3c00947 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Jalali, E., Wang, F., Overbay, B. R., Miller, M. D., Shaaban, K. A., Ponomareva, L. V., Ye, Q., Saghaeiannejad-Esfahani, H., Bhardwaj, M., Steele, A. D., Teijaro, C. N., Shen, B., Van Lanen, S. G., She, Q.-B., Voss, S. R., Phillips, G.…
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Conformational dynamics of adenylate kinase in crystals
BioXFEL Publications 21 Feb 2024 Contributor(s): George Phillips
http://dx.doi.org/10.1063/4.0000205 Adenylate kinase is a ubiquitous enzyme in living systems and undergoes dramatic conformational changes during its catalytic cycle. For these reasons, it is widely studied by genetic, biochemical, and biophysical methods, both experimental and theoretical. We have determined the basic crystal structures of three…
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BioXFEL Publications 1 Jul 2024 Contributor(s): James Fraser
https://doi.org/10.1107/s2052252524005098 In the folded state, biomolecules exchange between multiple conformational states crucial for their function. However, most structural models derived from experiments and computational predictions only encode a single state. To represent biomolecules accurately, we must move towards modeling and predicting…
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Dynamics and Kinetics in Structural Biology
News 21 Nov 2023
Understand the latest experimental tools in structured biology with this pioneering work by Keith Moffat and Eaton E. Lattman. Structural biology seeks to understand the chemical mechanisms and functions of biological molecules based on their atomic structures. Until recently, these structures have been studied only statically. Dynamics and…
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BioXFEL Publications 24 May 2024 Contributor(s): James Fraser
http://dx.doi.org/10.1186/s13059-024-03279-7 AbstractDeep mutational scanning (DMS) measures the effects of thousands of genetic variants in a protein simultaneously. The small sample size renders classical statistical methods ineffective. For example, p-values cannot be correctly calibrated when treating variants independently. We propose , a…
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BioXFEL Publications 24 May 2024 Contributor(s): James Fraser
https://doi.org/10.1186/s13059-024-03279-7 AbstractDeep mutational scanning (DMS) measures the effects of thousands of genetic variants in a protein simultaneously. The small sample size renders classical statistical methods ineffective. For example, p-values cannot be correctly calibrated when treating variants independently. We propose , a…
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BioXFEL Publications 31 Jan 2024 Contributor(s): Marius Schmidt, Emina Stojkovic
http://dx.doi.org/10.1063/4.0000233 Time-resolved crystallography (TRX) is a method designed to investigate functional motions of biological macromolecules on all time scales. Originally a synchrotron-based method, TRX is enabled by the development of TR Laue crystallography (TRLX). TR serial crystallography (TR-SX) is an extension of TRLX. As the…
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BioXFEL Publications 31 Jan 2024 Contributor(s): Marius Schmidt, Emina Stojkovic
https://doi.org/10.1063/4.0000233 Time-resolved crystallography (TRX) is a method designed to investigate functional motions of biological macromolecules on all time scales. Originally a synchrotron-based method, TRX is enabled by the development of TR Laue crystallography (TRLX). TR serial crystallography (TR-SX) is an extension of TRLX. As the…
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BioXFEL Publications 26 Nov 2024 Contributor(s): Konstantinos Karpos, Diandra Doppler, Reza Nazari, Alexandra Ros, Richard Kirian
https://doi.org/10.1063/4.0000262 We introduce a hardware–software system for rapidly characterizing liquid microjets for x-ray diffraction experiments. An open-source python-based software package allows for programmatic and automated data collection and analysis. We show how jet speed, length, and diameter are influenced by nozzle geometry, gas…
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"Visualizing the 3D Structures of Molecules Involved in Life's Processes" Workshop
Events 5 Feb 2024
Feb 05 2024
"Visualizing the 3D Structures of Molecules Involved in Life's Processes" Workshop Undergraduate students attending college in Puerto Rico are invited to participate in this two-day workshop. The workshop will be available in the following locations from 8am - 4pm each day: February 5th - 6th in Mayaguez February 7th - 8th in San…
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Crystal structure of the 4-hydroxybutyryl-CoA synthetase (ADP-forming) from nitrosopumilus maritimus
BioXFEL Publications 21 Oct 2024 Contributor(s): Hasan Demirci
https://doi.org/10.1038/s42003-024-06432-x AbstractThe 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) cycle from ammonia-oxidizing Thaumarchaeota is currently considered the most energy-efficient aerobic carbon fixation pathway. The Nitrosopumilus maritimus 4-hydroxybutyryl-CoA synthetase (ADP-forming; Nmar_0206) represents one of several enzymes…
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BioXFEL Publications 14 Aug 2024 Contributor(s): Mitchell Miller, George Phillips
https://doi.org/10.1063/4.0000252 Determining the atomic-level structure of a protein has been a decades-long challenge. However, recent advances in transformers and related neural network architectures have enabled researchers to significantly improve solutions to this problem. These methods use large datasets of sequence information and…
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BioXFEL Publications 12 Feb 2024 Contributor(s): Gihan Kaushylal Ketawala, Petra Fromme, Sabine Botha
http://dx.doi.org/10.1107/s1600576724000116 Data collection at X-ray free electron lasers has particular experimental challenges, such as continuous sample delivery or the use of novel ultrafast high-dynamic-range gain-switching X-ray detectors. This can result in a multitude of data artefacts, which can be detrimental to accurately determining…
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Scaling and merging time-resolved pink-beam diffraction with variational inference
BioXFEL Publications 8 Nov 2024 Contributor(s): Kara Zielinski, Lois Pollack
https://doi.org/10.1063/4.0000269 Time-resolved x-ray crystallography (TR-X) at synchrotrons and free electron lasers is a promising technique for recording dynamics of molecules at atomic resolution. While experimental methods for TR-X have proliferated and matured, data analysis is often difficult. Extracting small, time-dependent changes in…
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BioXFEL Publications 13 Sep 2024 Contributor(s): James Fraser
https://doi.org/10.7554/elife.91619.3 MET is a receptor tyrosine kinase (RTK) responsible for initiating signaling pathways involved in development and wound repair. MET activation relies on ligand binding to the extracellular receptor, which prompts dimerization, intracellular phosphorylation, and recruitment of associated signaling proteins.…
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Coronavirus M Protein Trafficking in Epithelial Cells Utilizes a Myosin Vb Splice Variant and Rab10
BioXFEL Publications 10 Jan 2024 Contributor(s): Brenda Hogue
http://dx.doi.org/10.3390/cells13020126 The membrane (M) glycoprotein of coronaviruses (CoVs) serves as the nidus for virion assembly. Using a yeast two-hybrid screen, we identified the interaction of the cytosolic tail of Murine Hepatitis Virus (MHV-CoV) M protein with Myosin Vb (MYO5B), specifically with the alternative splice variant of cellular…
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Time-resolved cryogenic electron tomography for the study of transient cellular processes
BioXFEL Publications 8 May 2024 Contributor(s): Kara Zielinski, Christopher Kupitz, Mark S. Hunter, Lois Pollack
https://doi.org/10.1091/mbc.e24-01-0042 Cryogenic electron tomography (cryo-ET) is the highest resolution imaging technique applicable to the life sciences, enabling subnanometer visualization of specimens preserved in their near native states. The rapid plunge freezing process used to prepare samples lends itself to time-resolved studies, which…
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Time-resolved cryogenic electron tomography for the study of transient cellular processes
BioXFEL Publications 8 May 2024 Contributor(s): Kara Zielinski, Christopher Kupitz, Mark S. Hunter, Lois Pollack
http://dx.doi.org/10.1091/mbc.e24-01-0042 Cryogenic electron tomography (cryo-ET) is the highest resolution imaging technique applicable to the life sciences, enabling subnanometer visualization of specimens preserved in their near native states. The rapid plunge freezing process used to prepare samples lends itself to time-resolved studies, which…
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BioXFEL Publications 17 Jun 2024 Contributor(s): Iris Diane Young, Michael Thompson, James Fraser
http://dx.doi.org/10.7554/elife.89918.3 Chitin is an abundant biopolymer and pathogen-associated molecular pattern that stimulates a host innate immune response. Mammals express chitin-binding and chitin-degrading proteins to remove chitin from the body. One of these proteins, Acidic Mammalian Chitinase (AMCase), is an enzyme known for its ability…
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BioXFEL Publications 17 Jun 2024 Contributor(s): Iris Diane Young, Michael Thompson, James Fraser
https://doi.org/10.7554/elife.89918.3 Chitin is an abundant biopolymer and pathogen-associated molecular pattern that stimulates a host innate immune response. Mammals express chitin-binding and chitin-degrading proteins to remove chitin from the body. One of these proteins, Acidic Mammalian Chitinase (AMCase), is an enzyme known for its ability to…
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BioXFEL Publications 13 Aug 2024 Contributor(s): Kara Zielinski, Lois Pollack
https://doi.org/10.1038/s42003-024-06672-x AbstractTransglutaminase 2 (TG2) is a GTP-binding, protein-crosslinking enzyme that has been investigated as a therapeutic target for Celiac disease, neurological disorders, and aggressive cancers. TG2 has been suggested to adopt two conformational states that regulate its functions: a GTP-bound, closed…
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BioXFEL Publications 25 Sep 2024 Contributor(s): Kevin Gu, Megan Shelby, SRINIVASAN MUNIYAPPAN, Marius Schmidt, Sankar Raju Narayanasamy, Matthew Coleman, Matthias Frank
https://doi.org/10.1107/s1600576724007544 Compared with batch and vapor diffusion methods, counter diffusion can generate larger and higher-quality protein crystals yielding improved diffraction data and higher-resolution structures. Typically, counter-diffusion experiments are conducted in elongated chambers, such as glass capillaries, and the…
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Graduated BioXFEL Summer Interns
Education 18 Oct 2016
BioXFEL is committed to ensuring a quality experience for all interns both during and after their internships. We frequently follow up with interns after they have graduated, track their progression through their scientific careers and provide extended support. Some interns choose to reapply to BioXFEL for a second summer, while others move to…
