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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.2024.11.2882 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.2024.11.2882 Rishav Mitra and Galen Correy and James Fraser
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BioXFEL Publications 13 Feb 2025 Contributor(s): Lois Pollack
https://doi.org/10.1016/j.bpj.2024.11.476 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.2024.11.476 Tong Wang and Qingyue Hu and Scout Fronhofer and…
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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.2024.102264 journal-article Wang, T., He, W., Pabit, S. A., Pollack, L., & Kirmizialtin, S. (2024). Sequence-dependent conformational preferences of disordered single-stranded RNA. Cell Reports Physical Science, 5(11), 102264. https://doi.org/10.1016/j.xcrp.2024.102264 Tong Wang and Weiwei He and Suzette A. Pabit…
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BioXFEL Publications 10 May 2024
http://dx.doi.org/10.1016/j.jbc.2024.107361 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Chang, C., Zhou, G., Lee Luo, C., Eleraky, S., Moradi, M., & Gao, Y. (2024). Sugar ring alignment and dynamics underline cytarabine and gemcitabine inhibition on Pol η catalyzed DNA synthesis. Journal of Biological Chemistry, 300(6),…
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BioXFEL Publications 25 Mar 2024 Contributor(s): Jose Arcadio Rodriguez-Martinez
http://dx.doi.org/10.1016/j.jbc.2024.107071 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Rivera-Madera, A., Peña-Martínez, E., & Rodriguez-Martinez, J. (2024). Abstract 2307 Evaluating the thermal stability of congenital heart diseases-associated TBX5 missense mutants. Journal of Biological Chemistry, 300(3), 107071.…
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BioXFEL Publications 25 Mar 2024 Contributor(s): Jose Arcadio Rodriguez-Martinez
http://dx.doi.org/10.1016/j.jbc.2024.106540 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Peña-Martínez, E., 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). Abstract 1473 Integrating Machine Learning…
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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). Extracting conformational heterogeneity from 2D and 3D cryo-EM data. Biophysical Journal, 123(3), 50a–51a. https://doi.org/10.1016/j.bpj.2023.11.376 Samuel Hoff and Massimiliano Bonomi and James Fraser and Eric Greene
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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). Role of conformational dynamics in the catalytic mechanism of viral macrodomains. Biophysical Journal, 123(3), 356a–357a. https://doi.org/10.1016/j.bpj.2023.11.2156 Rishav Mitra and James Fraser
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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). Sequence-dependent conformational preferences of disordered single-stranded RNA. Biophysical Journal, 123(3), 453a–454a. https://doi.org/10.1016/j.bpj.2023.11.2762 Tong Wang and Weiwei He and Suzette A. Pabit and…
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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). Computing a Bayesian multi-state model of a protein structure from an X-ray diffraction pattern. Biophysical Journal, 123(3), 200a–201a. https://doi.org/10.1016/j.bpj.2023.11.1276 Matthew P. Hancock and James S. Fraser and Andrej Sali
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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). Decoding Non-coding Variants: Recent Approaches to Studying Their Role in Gene Regulation and Human Diseases. Frontiers in Bioscience-Scholar, 16(1), 4.…
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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). Cation-induced intramolecular coil-to-globule transition in poly(ADP-ribose). Nature Communications, 15(1). https://doi.org/10.1038/s41467-024-51972-9 Tong Wang and Kush Coshic and…
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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). Author Correction: Cation-induced intramolecular coil-to-globule transition in poly(ADP-ribose). Nature Communications, 15(1). https://doi.org/10.1038/s41467-024-52865-7 Tong Wang…
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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). Product-stabilized filamentation by human glutamine synthetase allosterically tunes activity. Biophysical Journal, 123(3), 352a.…
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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). DefNEtTrp: An Iron Dual Chelator Approach for Anticancer Application. JACS Au, 4(12), 4799–4808.…
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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 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 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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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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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 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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BioXFEL Publications 10 Jan 2025 Contributor(s): Kara Zielinski, Lois Pollack
https://doi.org/10.1063/5.0218572 X-ray spectroscopies are uniquely poised to describe the geometric and electronic structure of metalloenzyme active sites under a wide variety of sample conditions. UV/Vis (ultraviolet/visible) spectroscopy is a similarly well-established technique that can identify and quantify catalytic intermediates. The work…
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Exploiting fourth-generation synchrotron radiation for enzyme and photoreceptor characterization
BioXFEL Publications 22 Nov 2024 Contributor(s): Tek Narsingh Malla, SRINIVASAN MUNIYAPPAN, Emina Stojkovic, Shibom Basu, Marius Schmidt
https://doi.org/10.1107/s2052252524010868 The upgrade of the European Synchrotron Radiation Facility (ESRF) in Grenoble, France to an Extremely Brilliant Source (EBS) is expected to enable time-resolved synchrotron serial crystallography (SSX) experiments with sub-millisecond time resolution. ID29 is a new beamline dedicated to SSX experiments at…
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Filling data analysis gaps in time-resolved crystallography by machine learning
BioXFEL Publications 21 Jan 2025 Contributor(s): Russell Fung, Peter Schwander, Ahmad Hosseinizadeh
https://doi.org/10.1063/4.0000280 There is a growing understanding of the structural dynamics of biological molecules fueled by x-ray crystallography experiments. Time-resolved serial femtosecond crystallography (TR-SFX) with x-ray Free Electron Lasers allows the measurement of ultrafast structural changes in proteins. Nevertheless, this technique…
