المؤلفون: Dun, Chen, Pan, Qiutai, Jin, Shikai, Stevens, Ria, Miller, Mitchell D., Phillips, Jr., George N., Kyrillidis, Anastasios

مصطلحات موضوعية: Computer Science - Machine Learning

الوصف: Determining the structure of a protein has been a decades-long open question. A protein's three-dimensional structure often poses nontrivial computation costs, when classical simulation algorithms are utilized. Advances in the transformer neural network architecture -- such as AlphaFold2 -- achieve significant improvements for this problem, by learning from a large dataset of sequence information and corresponding protein structures. Yet, such methods only focus on sequence information; other available prior knowledge, such as protein crystallography and partial structure of amino acids, could be potentially utilized. To the best of our knowledge, we propose the first transformer-based model that directly utilizes protein crystallography and partial structure information to predict the electron density maps of proteins. Via two new datasets of peptide fragments (2-residue and 15-residue) , we demonstrate our method, dubbed \texttt{CrysFormer}, can achieve accurate predictions, based on a much smaller dataset size and with reduced computation costs.

الوصول الحر: http://arxiv.org/abs/2310.03899Test

المؤلفون: Alexander, Leila T, Durairaj, Janani, Kryshtafovych, Andriy, Abriata, Luciano A, Bayo, Yusupha, Bhabha, Gira, Breyton, Cécile, Caulton, Simon G, Chen, James, Degroux, Séraphine, Ekiert, Damian C, Erlandsen, Benedikte S, Freddolino, Peter L, Gilzer, Dominic, Greening, Chris, Grimes, Jonathan M, Grinter, Rhys, Gurusaran, Manickam, Hartmann, Marcus D, Hitchman, Charlie J, Keown, Jeremy R, Kropp, Ashleigh, Kursula, Petri, Lovering, Andrew L, Lemaitre, Bruno, Lia, Andrea, Liu, Shiheng, Logotheti, Maria, Lu, Shuze, Markússon, Sigurbjörn, Miller, Mitchell D, Minasov, George, Niemann, Hartmut H, Opazo, Felipe, Phillips, George N, Davies, Owen R, Rommelaere, Samuel, Rosas‐Lemus, Monica, Roversi, Pietro, Satchell, Karla, Smith, Nathan, Wilson, Mark A, Wu, Kuan‐Lin, Xia, Xian, Xiao, Han, Zhang, Wenhua, Zhou, Z Hong, Fidelis, Krzysztof, Topf, Maya, Moult, John, Schwede, Torsten

المصدر: Proteins Structure Function and Bioinformatics. 91(12)

مصطلحات موضوعية: Biochemistry and Cell Biology, Bioinformatics and Computational Biology, Biological Sciences, Protein Conformation, Models, Molecular, Computational Biology, Proteins, CASP, cryo-EM, protein structure prediction, X-ray crystallography, Mathematical Sciences, Information and Computing Sciences, Bioinformatics, Biological sciences, Mathematical sciences

الوصف: We present an in-depth analysis of selected CASP15 targets, focusing on their biological and functional significance. The authors of the structures identify and discuss key protein features and evaluate how effectively these aspects were captured in the submitted predictions. While the overall ability to predict three-dimensional protein structures continues to impress, reproducing uncommon features not previously observed in experimental structures is still a challenge. Furthermore, instances with conformational flexibility and large multimeric complexes highlight the need for novel scoring strategies to better emphasize biologically relevant structural regions. Looking ahead, closer integration of computational and experimental techniques will play a key role in determining the next challenges to be unraveled in the field of structural molecular biology.

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/5122m3k6Test

المؤلفون: Liu, Zhiwen, Rivera, Sebastian, Newmister, Sean A, Sanders, Jacob N, Nie, Qiuyue, Liu, Shuai, Zhao, Fanglong, Ferrara, Joseph D, Shih, Hao-Wei, Patil, Siddhant, Xu, Weijun, Miller, Mitchell D, Phillips, George N, Houk, KN, Sherman, David H, Gao, Xue

المصدر: Nature Chemistry. 15(4)

مصطلحات موضوعية: Organic Chemistry, Chemical Sciences, Cycloaddition Reaction, Catalysis, Oxidoreductases, Chemistry Techniques, Synthetic, Oxidation-Reduction, Chemical sciences

الوصف: The Diels-Alder cycloaddition is one of the most powerful approaches in organic synthesis and is often used in the synthesis of important pharmaceuticals. Yet, strictly controlling the stereoselectivity of the Diels-Alder reactions is challenging, and great efforts are needed to construct complex molecules with desired chirality via organocatalysis or transition-metal strategies. Nature has evolved different types of enzymes to exquisitely control cyclization stereochemistry; however, most of the reported Diels-Alderases have been shown to only facilitate the energetically favourable diastereoselective cycloadditions. Here we report the discovery and characterization of CtdP, a member of a new class of bifunctional oxidoreductase/Diels-Alderase, which was previously annotated as an NmrA-like transcriptional regulator. We demonstrate that CtdP catalyses the inherently disfavoured cycloaddition to form the bicyclo[2.2.2]diazaoctane scaffold with a strict α-anti-selectivity. Guided by computational studies, we reveal a NADP+/NADPH-dependent redox mechanism for the CtdP-catalysed inverse electron demand Diels-Alder cycloaddition, which serves as the first example of a bifunctional Diels-Alderase that utilizes this mechanism.

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/19p1v1gxTest

المؤلفون: Pandey, Suraj, Calvey, George, Katz, Andrea M, Malla, Tek Narsingh, Koua, Faisal HM, Martin-Garcia, Jose M, Poudyal, Ishwor, Yang, Jay-How, Vakili, Mohammad, Yefanov, Oleksandr, Zielinski, Kara A, Bajt, Sasa, Awel, Salah, Doerner, Katarina, Frank, Matthias, Gelisio, Luca, Jernigan, Rebecca, Kirkwood, Henry, Kloos, Marco, Koliyadu, Jayanath, Mariani, Valerio, Miller, Mitchell D, Mills, Grant, Nelson, Garrett, Olmos, Jose L, Sadri, Alireza, Sato, Tokushi, Tolstikova, Alexandra, Xu, Weijun, Ourmazd, Abbas, Spence, John CH, Schwander, Peter, Barty, Anton, Chapman, Henry N, Fromme, Petra, Mancuso, Adrian P, Phillips, George N, Bean, Richard, Pollack, Lois, Schmidt, Marius

المصدر: IUCrJ. 8(Pt 6)

مصطلحات موضوعية: Tuberculosis, Rare Diseases, Good Health and Well Being, substrate diffusion in crystals, antibiotic resistance, beta-lactamases, enzyme kinetics, irreversible inhibition, mix-and-inject serial crystallography, serial femtosecond crystallography, European X-ray Free-Electron Laser, megahertz pulse-repetition rate, protein structure determination, drug discovery, ceftriaxone, sulbactam, X-ray crystallography, enzyme mechanisms, β-lactamases, Atomic, Molecular, Nuclear, Particle and Plasma Physics, Condensed Matter Physics, Physical Chemistry (incl. Structural)

الوصف: Here, we illustrate what happens inside the catalytic cleft of an enzyme when substrate or ligand binds on single-millisecond timescales. The initial phase of the enzymatic cycle is observed with near-atomic resolution using the most advanced X-ray source currently available: the European XFEL (EuXFEL). The high repetition rate of the EuXFEL combined with our mix-and-inject technology enables the initial phase of ceftriaxone binding to the Mycobacterium tuberculosis β-lactamase to be followed using time-resolved crystallography in real time. It is shown how a diffusion coefficient in enzyme crystals can be derived directly from the X-ray data, enabling the determination of ligand and enzyme-ligand concentrations at any position in the crystal volume as a function of time. In addition, the structure of the irreversible inhibitor sulbactam bound to the enzyme at a 66 ms time delay after mixing is described. This demonstrates that the EuXFEL can be used as an important tool for biomedically relevant research.

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/5tz658nrTest

المؤلفون: Burgie, E Sethe, Clinger, Jonathan A, Miller, Mitchell D, Brewster, Aaron S, Aller, Pierre, Butryn, Agata, Fuller, Franklin D, Gul, Sheraz, Young, Iris D, Pham, Cindy C, Kim, In-Sik, Bhowmick, Asmit, O'Riordan, Lee J, Sutherlin, Kyle D, Heinemann, Joshua V, Batyuk, Alexander, Alonso-Mori, Roberto, Hunter, Mark S, Koglin, Jason E, Yano, Junko, Yachandra, Vittal K, Sauter, Nicholas K, Cohen, Aina E, Kern, Jan, Orville, Allen M, Phillips, George N, Vierstra, Richard D

المصدر: Proceedings of the National Academy of Sciences of the United States of America. 117(1)

مصطلحات موضوعية: Inorganic Chemistry, Chemical Sciences, Adenylyl Cyclases, Crystallography, Crystallography, X-Ray, Cyanobacteria, Cyclic GMP, Light, Models, Molecular, Phosphoric Diester Hydrolases, Photoreceptor Cells, Phycobilins, Phycocyanin, Phytochrome, Protein Conformation, Protein Domains, Thermosynechococcus, Trans-Activators, phytochrome, photoreceptor, X-ray crystallography

الوصف: A major barrier to defining the structural intermediates that arise during the reversible photointerconversion of phytochromes between their biologically inactive and active states has been the lack of crystals that faithfully undergo this transition within the crystal lattice. Here, we describe a crystalline form of the cyclic GMP phosphodiesterases/adenylyl cyclase/FhlA (GAF) domain from the cyanobacteriochrome PixJ in Thermosynechococcus elongatus assembled with phycocyanobilin that permits reversible photoconversion between the blue light-absorbing Pb and green light-absorbing Pg states, as well as thermal reversion of Pg back to Pb. The X-ray crystallographic structure of Pb matches previous models, including autocatalytic conversion of phycocyanobilin to phycoviolobilin upon binding and its tandem thioether linkage to the GAF domain. Cryocrystallography at 150 K, which compared diffraction data from a single crystal as Pb or after irradiation with blue light, detected photoconversion product(s) based on Fobs - Fobs difference maps that were consistent with rotation of the bonds connecting pyrrole rings C and D. Further spectroscopic analyses showed that phycoviolobilin is susceptible to X-ray radiation damage, especially as Pg, during single-crystal X-ray diffraction analyses, which could complicate fine mapping of the various intermediate states. Fortunately, we found that PixJ crystals are amenable to serial femtosecond crystallography (SFX) analyses using X-ray free-electron lasers (XFELs). As proof of principle, we solved by room temperature SFX the GAF domain structure of Pb to 1.55-Å resolution, which was strongly congruent with synchrotron-based models. Analysis of these crystals by SFX should now enable structural characterization of the early events that drive phytochrome photoconversion.

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/0h74n8tpTest

المؤلفون: Olmos, Jose L, Pandey, Suraj, Martin-Garcia, Jose M, Calvey, George, Katz, Andrea, Knoska, Juraj, Kupitz, Christopher, Hunter, Mark S, Liang, Mengning, Oberthuer, Dominik, Yefanov, Oleksandr, Wiedorn, Max, Heyman, Michael, Holl, Mark, Pande, Kanupriya, Barty, Anton, Miller, Mitchell D, Stern, Stephan, Roy-Chowdhury, Shatabdi, Coe, Jesse, Nagaratnam, Nirupa, Zook, James, Verburgt, Jacob, Norwood, Tyler, Poudyal, Ishwor, Xu, David, Koglin, Jason, Seaberg, Matthew H, Zhao, Yun, Bajt, Saša, Grant, Thomas, Mariani, Valerio, Nelson, Garrett, Subramanian, Ganesh, Bae, Euiyoung, Fromme, Raimund, Fung, Russell, Schwander, Peter, Frank, Matthias, White, Thomas A, Weierstall, Uwe, Zatsepin, Nadia, Spence, John, Fromme, Petra, Chapman, Henry N, Pollack, Lois, Tremblay, Lee, Ourmazd, Abbas, Phillips, George N, Schmidt, Marius

المصدر: BMC Biology. 16(1)

مصطلحات موضوعية: Biochemistry and Cell Biology, Biological Sciences, Rare Diseases, Infectious Diseases, Good Health and Well Being, Anti-Bacterial Agents, Bacterial Proteins, Biocatalysis, Ceftriaxone, Cephalosporin Resistance, Crystallography, X-Ray, Kinetics, Lasers, Models, Molecular, Mycobacterium tuberculosis, Time Factors, beta-Lactamases, Developmental Biology

الوصف: BackgroundEver since the first atomic structure of an enzyme was solved, the discovery of the mechanism and dynamics of reactions catalyzed by biomolecules has been the key goal for the understanding of the molecular processes that drive life on earth. Despite a large number of successful methods for trapping reaction intermediates, the direct observation of an ongoing reaction has been possible only in rare and exceptional cases.ResultsHere, we demonstrate a general method for capturing enzyme catalysis "in action" by mix-and-inject serial crystallography (MISC). Specifically, we follow the catalytic reaction of the Mycobacterium tuberculosis β-lactamase with the third-generation antibiotic ceftriaxone by time-resolved serial femtosecond crystallography. The results reveal, in near atomic detail, antibiotic cleavage and inactivation from 30 ms to 2 s.ConclusionsMISC is a versatile and generally applicable method to investigate reactions of biological macromolecules, some of which are of immense biological significance and might be, in addition, important targets for structure-based drug design. With megahertz X-ray pulse rates expected at the Linac Coherent Light Source II and the European X-ray free-electron laser, multiple, finely spaced time delays can be collected rapidly, allowing a comprehensive description of biomolecular reactions in terms of structure and kinetics from the same set of X-ray data.

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/5vf7b95dTest

المؤلفون: Alexander, Leila T., Durairaj, Janani, Kryshtafovych, Andriy, Abriata, Luciano A., Bayo, Yusupha, Bhabha, Gira, Breyton, Cécile, Caulton, Simon G., Chen, James, Degroux, Séraphine, Ekiert, Damian C., Erlandsen, Benedikte S., Freddolino, Peter L., Gilzer, Dominic, Greening, Chris, Grimes, Jonathan M., Grinter, Rhys, Gurusaran, Manickam, Hartmann, Marcus D., Hitchman, Charlie J., Keown, Jeremy R., Kropp, Ashleigh, Kursula, Petri, Lovering, Andrew L., Lemaitre, Bruno, Lia, Andrea, Liu, Shiheng, Logotheti, Maria, Lu, Shuze, Markússon, Sigurbjörn, Miller, Mitchell D., Minasov, George, Niemann, Hartmut H., Opazo, Felipe, Phillips, George N., Davies, Owen R., Rommelaere, Samuel, Rosas-Lemus, Monica, Roversi, Pietro, Satchell, Karla, Smith, Nathan, Wilson, Mark A., Wu, Kuan-Lin, Xia, Xian, Xiao, Han, Zhang, Wenhua, Zhou, Z. Hong, Fidelis, Krzysztof, Topf, Maya, Moult, John, Schwede, Torsten

الوصف: We present an in-depth analysis of selected CASP15 targets, focusing on their biological and functional significance. The authors of the structures identify and discuss key protein features and evaluate how effectively these aspects were captured in the submitted predictions. While the overall ability to predict three-dimensional protein structures continues to impress, reproducing uncommon features not previously observed in experimental structures is still a challenge. Furthermore, instances with conformational flexibility and large multimeric complexes highlight the need for novel scoring strategies to better emphasize biologically relevant structural regions. Looking ahead, closer integration of computational and experimental techniques will play a key role in determining the next challenges to be unraveled in the field of structural molecular biology.

وصف الملف: application/pdf

العلاقة: https://edoc.unibas.ch/95444/1/Proteins%20-%202023%20-%20Alexander.pdfTest; Alexander, Leila T. and Durairaj, Janani and Kryshtafovych, Andriy and Abriata, Luciano A. and Bayo, Yusupha and Bhabha, Gira and Breyton, Cécile and Caulton, Simon G. and Chen, James and Degroux, Séraphine and Ekiert, Damian C. and Erlandsen, Benedikte S. and Freddolino, Peter L. and Gilzer, Dominic and Greening, Chris and Grimes, Jonathan M. and Grinter, Rhys and Gurusaran, Manickam and Hartmann, Marcus D. and Hitchman, Charlie J. and Keown, Jeremy R. and Kropp, Ashleigh and Kursula, Petri and Lovering, Andrew L. and Lemaitre, Bruno and Lia, Andrea and Liu, Shiheng and Logotheti, Maria and Lu, Shuze and Markússon, Sigurbjörn and Miller, Mitchell D. and Minasov, George and Niemann, Hartmut H. and Opazo, Felipe and Phillips, George N. and Davies, Owen R. and Rommelaere, Samuel and Rosas-Lemus, Monica and Roversi, Pietro and Satchell, Karla and Smith, Nathan and Wilson, Mark A. and Wu, Kuan-Lin and Xia, Xian and Xiao, Han and Zhang, Wenhua and Zhou, Z. Hong and Fidelis, Krzysztof and Topf, Maya and Moult, John and Schwede, Torsten. (2023) Protein target highlights in CASP15: Analysis of models by structure providers. Proteins: Structure, Function, and Bioinformatics . Online ahead of print.; info:pmid/37493353; urn:ISSN:0887-3585; urn:ISSN:1097-0134

الإتاحة: https://doi.org/10.1002/prot.26545Test
https://edoc.unibas.ch/95444Test/
https://edoc.unibas.ch/95444/1/Proteins%20-%202023%20-%20Alexander.pdfTest

المؤلفون: Kupitz, Christopher, Olmos, Jose L, Holl, Mark, Tremblay, Lee, Pande, Kanupriya, Pandey, Suraj, Oberthür, Dominik, Hunter, Mark, Liang, Mengning, Aquila, Andrew, Tenboer, Jason, Calvey, George, Katz, Andrea, Chen, Yujie, Wiedorn, Max O, Knoska, Juraj, Meents, Alke, Majriani, Valerio, Norwood, Tyler, Poudyal, Ishwor, Grant, Thomas, Miller, Mitchell D, Xu, Weijun, Tolstikova, Aleksandra, Morgan, Andrew, Metz, Markus, Martin-Garcia, Jose M, Zook, James D, Roy-Chowdhury, Shatabdi, Coe, Jesse, Nagaratnam, Nirupa, Meza, Domingo, Fromme, Raimund, Basu, Shibom, Frank, Matthias, White, Thomas, Barty, Anton, Bajt, Sasa, Yefanov, Oleksandr, Chapman, Henry N, Zatsepin, Nadia, Nelson, Garrett, Weierstall, Uwe, Spence, John, Schwander, Peter, Pollack, Lois, Fromme, Petra, Ourmazd, Abbas, Phillips, George N, Schmidt, Marius

المصدر: Structural Dynamics. 4(4)

مصطلحات موضوعية: Inorganic Chemistry, Chemical Sciences, Physical Sciences, Infectious Diseases, Good Health and Well Being, Physical chemistry, Condensed matter physics, Particle and high energy physics

الوصف: Mix-and-inject serial crystallography (MISC) is a technique designed to image enzyme catalyzed reactions in which small protein crystals are mixed with a substrate just prior to being probed by an X-ray pulse. This approach offers several advantages over flow cell studies. It provides (i) room temperature structures at near atomic resolution, (ii) time resolution ranging from microseconds to seconds, and (iii) convenient reaction initiation. It outruns radiation damage by using femtosecond X-ray pulses allowing damage and chemistry to be separated. Here, we demonstrate that MISC is feasible at an X-ray free electron laser by studying the reaction of M. tuberculosis ß-lactamase microcrystals with ceftriaxone antibiotic solution. Electron density maps of the apo-ß-lactamase and of the ceftriaxone bound form were obtained at 2.8 Å and 2.4 Å resolution, respectively. These results pave the way to study cyclic and non-cyclic reactions and represent a new field of time-resolved structural dynamics for numerous substrate-triggered biological reactions.

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/4bd673qnTest

المؤلفون: Fuller, Franklin D, Gul, Sheraz, Chatterjee, Ruchira, Burgie, E Sethe, Young, Iris D, Lebrette, Hugo, Srinivas, Vivek, Brewster, Aaron S, Michels-Clark, Tara, Clinger, Jonathan A, Andi, Babak, Ibrahim, Mohamed, Pastor, Ernest, de Lichtenberg, Casper, Hussein, Rana, Pollock, Christopher J, Zhang, Miao, Stan, Claudiu A, Kroll, Thomas, Fransson, Thomas, Weninger, Clemens, Kubin, Markus, Aller, Pierre, Lassalle, Louise, Bräuer, Philipp, Miller, Mitchell D, Amin, Muhamed, Koroidov, Sergey, Roessler, Christian G, Allaire, Marc, Sierra, Raymond G, Docker, Peter T, Glownia, James M, Nelson, Silke, Koglin, Jason E, Zhu, Diling, Chollet, Matthieu, Song, Sanghoon, Lemke, Henrik, Liang, Mengning, Sokaras, Dimosthenis, Alonso-Mori, Roberto, Zouni, Athina, Messinger, Johannes, Bergmann, Uwe, Boal, Amie K, Bollinger, J Martin, Krebs, Carsten, Högbom, Martin, Phillips, George N, Vierstra, Richard D, Sauter, Nicholas K, Orville, Allen M, Kern, Jan, Yachandra, Vittal K, Yano, Junko

المصدر: Nature methods. 14(4)

مصطلحات موضوعية: Photosystem II Protein Complex, Ribonucleotide Reductases, Phytochrome, Crystallography, X-Ray, Spectrometry, X-Ray Emission, Lasers, Acoustics, Crystallography, X-Ray, Spectrometry, X-Ray Emission, Developmental Biology, Biological Sciences, Technology, Medical and Health Sciences

الوصف: X-ray crystallography at X-ray free-electron laser sources is a powerful method for studying macromolecules at biologically relevant temperatures. Moreover, when combined with complementary techniques like X-ray emission spectroscopy, both global structures and chemical properties of metalloenzymes can be obtained concurrently, providing insights into the interplay between the protein structure and dynamics and the chemistry at an active site. The implementation of such a multimodal approach can be compromised by conflicting requirements to optimize each individual method. In particular, the method used for sample delivery greatly affects the data quality. We present here a robust way of delivering controlled sample amounts on demand using acoustic droplet ejection coupled with a conveyor belt drive that is optimized for crystallography and spectroscopy measurements of photochemical and chemical reactions over a wide range of time scales. Studies with photosystem II, the phytochrome photoreceptor, and ribonucleotide reductase R2 illustrate the power and versatility of this method.

الوصول الحر: https://escholarship.org/uc/item/5b33q2r1Test

المؤلفون: Jalali, Elnaz, Wang, Fengbin, Overbay, Brooke R., Miller, Mitchell D., Shaaban, Khaled A., Ponomareva, Larissa V., Ye, Qing, Saghaeiannejad-Esfahani, Hoda, Bhardwaj, Minakshi, Steele, Andrew D., Teijaro, Christiana N., Shen, Ben, Van Lanen, Steven G., She, Qing-Bai, Voss, S. Randal, Phillips, George N., Thorson, Jon S.

المساهمون: National Center for Advancing Translational Sciences, National Cancer Institute, Division of Biological Infrastructure, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institute of General Medical Sciences, College of Pharmacy, University of Kentucky

المصدر: Journal of Natural Products ; volume 87, issue 4, page 798-809 ; ISSN 0163-3864 1520-6025

الإتاحة: https://doi.org/10.1021/acs.jnatprod.3c00947Test