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2,235 results on '"Sub NMR Spectroscopy"'

1. Unravelling potential reaction intermediates during catalytic pyrolysis of polypropylene with microscopy and spectroscopy

Author

NMR Spectroscopy, Sub Inorganic Chemistry and Catalysis, Sub NMR Spectroscopy, Inorganic Chemistry and Catalysis, Vollmer, Ina, Jenks, Michael J.F., Rejman, Sebastian, Meirer, Florian, Gurinov, Andrei, Baldus, Marc, Weckhuysen, Bert M., NMR Spectroscopy, Sub Inorganic Chemistry and Catalysis, Sub NMR Spectroscopy, Inorganic Chemistry and Catalysis, Vollmer, Ina, Jenks, Michael J.F., Rejman, Sebastian, Meirer, Florian, Gurinov, Andrei, Baldus, Marc, and Weckhuysen, Bert M.

Published
2024

2. Cooperative Gating of a K+ Channel by Unmodified Biological Anionic Lipids Viewed by Solid-State NMR Spectroscopy.

Author

Sub NMR Spectroscopy, Sub Membrane Biochemistry & Biophysics, Membrane Biochemistry and Biophysics, NMR Spectroscopy, Yekefallah, Maryam, van Aalst, Evan J, van Beekveld, Roy A M, Eason, Isaac R, Breukink, Eefjan, Weingarth, Markus, Wylie, Benjamin J, Sub NMR Spectroscopy, Sub Membrane Biochemistry & Biophysics, Membrane Biochemistry and Biophysics, NMR Spectroscopy, Yekefallah, Maryam, van Aalst, Evan J, van Beekveld, Roy A M, Eason, Isaac R, Breukink, Eefjan, Weingarth, Markus, and Wylie, Benjamin J

Published
2024

5. Correction: Unravelling potential reaction intermediates during catalytic pyrolysis of polypropylene with microscopy and spectroscopy

Author

Sub Inorganic Chemistry and Catalysis, Sub NMR Spectroscopy, Inorganic Chemistry and Catalysis, NMR Spectroscopy, Vollmer, I, Jenks, MJF, Rejman, S, Meirer, F, Gurinov, A, Baldus, M, Weckhuysen, BM, Sub Inorganic Chemistry and Catalysis, Sub NMR Spectroscopy, Inorganic Chemistry and Catalysis, NMR Spectroscopy, Vollmer, I, Jenks, MJF, Rejman, S, Meirer, F, Gurinov, A, Baldus, M, and Weckhuysen, BM

Published
2024

7. A structural and dynamic visualization of the interaction between MAP7 and microtubules

Author

NMR Spectroscopy, Sub NMR Spectroscopy, Sub Structural Biochemistry, Structural Biochemistry, Adler, Agnes, Bangera, Mamata, Beugelink, J Wouter, Bahri, Salima, van Ingen, Hugo, Moores, Carolyn A, Baldus, Marc, NMR Spectroscopy, Sub NMR Spectroscopy, Sub Structural Biochemistry, Structural Biochemistry, Adler, Agnes, Bangera, Mamata, Beugelink, J Wouter, Bahri, Salima, van Ingen, Hugo, Moores, Carolyn A, and Baldus, Marc

Published
2024

9. Teixobactin kills bacteria by a two-pronged attack on the cell envelope

Author

Shukla, Rhythm, Lavore, Francesca, Maity, Sourav, Derks, Maik G.N., Jones, Chelsea R., Vermeulen, Bram J.A., Melcrová, Adéla, Morris, Michael A., Becker, Lea Marie, Wang, Xiaoqi, Kumar, Raj, Medeiros-Silva, João, van Beekveld, Roy A.M., Bonvin, Alexandre M.J.J., Lorent, Joseph H., Lelli, Moreno, Nowick, James S., MacGillavry, Harold D., Peoples, Aaron J., Spoering, Amy L., Ling, Losee L., Hughes, Dallas E., Roos, Wouter H., Breukink, Eefjan, Lewis, Kim, Weingarth, Markus, Sub NMR Spectroscopy, Sub Membrane Biochemistry & Biophysics, Sub Cell Biology, NMR Spectroscopy, Celbiologie, Membrane Biochemistry and Biophysics, Sub NMR Spectroscopy, Sub Membrane Biochemistry & Biophysics, Sub Cell Biology, NMR Spectroscopy, Celbiologie, Membrane Biochemistry and Biophysics, and Molecular Biophysics

Subjects
Component, Target, Protein Structure, Secondary, Pyrrolidines, Nuclear Magnetic Resonance, Drug Resistance, Bacterial/drug effects, Drug Resistance, Anti-Bacterial Agents/chemistry, Bacteria/cytology, Lipids/chemistry, Microbial Sensitivity Tests, Molecular Dynamics Simulation, Microscopy, Atomic Force, Elucidation, Protein Structure, Secondary, Precursor lipid ii, Depsipeptides/chemistry, Cell Wall, Solid-state, Depsipeptides, Drug Resistance, Bacterial, Humans, Sugars/chemistry, Staphylococcus-aureus, General, Nuclear Magnetic Resonance, Biomolecular, Cell Wall/drug effects, Peptide antibiotics, Microscopy, Microbial Viability, Multidisciplinary, Bacteria, Cell Membrane/drug effects, Diphosphates/chemistry, Cell Membrane, Microbial Viability/drug effects, Bacterial/drug effects, Atomic Force, Enduracididine, Lipids, Nmr, Anti-Bacterial Agents, Diphosphates, Pyrrolidines/chemistry, Sugars, Analogs, Biomolecular
Abstract

Antibiotics that use novel mechanisms are needed to combat antimicrobial resistance1–3. Teixobactin4 represents a new class of antibiotics with a unique chemical scaffold and lack of detectable resistance. Teixobactin targets lipid II, a precursor of peptidoglycan5. Here we unravel the mechanism of teixobactin at the atomic level using a combination of solid-state NMR, microscopy, in vivo assays and molecular dynamics simulations. The unique enduracididine C-terminal headgroup of teixobactin specifically binds to the pyrophosphate-sugar moiety of lipid II, whereas the N terminus coordinates the pyrophosphate of another lipid II molecule. This configuration favours the formation of a β-sheet of teixobactins bound to the target, creating a supramolecular fibrillar structure. Specific binding to the conserved pyrophosphate-sugar moiety accounts for the lack of resistance to teixobactin4. The supramolecular structure compromises membrane integrity. Atomic force microscopy and molecular dynamics simulations show that the supramolecular structure displaces phospholipids, thinning the membrane. The long hydrophobic tails of lipid II concentrated within the supramolecular structure apparently contribute to membrane disruption. Teixobactin hijacks lipid II to help destroy the membrane. Known membrane-acting antibiotics also damage human cells, producing undesirable side effects. Teixobactin damages only membranes that contain lipid II, which is absent in eukaryotes, elegantly resolving the toxicity problem. The two-pronged action against cell wall synthesis and cytoplasmic membrane produces a highly effective compound targeting the bacterial cell envelope. Structural knowledge of the mechanism of teixobactin will enable the rational design of improved drug candidates.

Published
2022

10. The photochemical evolution of polycyclic aromatic hydrocarbons and nontronite clay on early Earth and Mars

Author

Kopacz, Nina, Corazzi, Maria Angela, Poggiali, Giovanni, von Essen, Ayla, Kofman, Vincent, Fornaro, Teresa, van Ingen, Hugo, Camprubi, Eloi, King, Helen E., Brucato, John, ten Kate, Inge Loes, Petrology, Sub NMR Spectroscopy, Petrology, and Sub NMR Spectroscopy

Subjects
Space and Planetary Science, Early Mars, Clays, Astronomy and Astrophysics, Polycyclic aromatic hydrocarbons
Abstract

The photochemical evolution of polycyclic aromatic hydrocarbons (PAHs), an abundant form of meteoritic organic carbon, is of great interest to early Earth and Mars origin-of-life studies and current organic molecule detection efforts on Mars. Fe-rich clay environments were abundant on early Earth and Mars, and may have played a role in prebiotic chemistry, catalyzing the breakdown of PAHs and freeing up carbon for subsequent chemical complexification. Current Mars is abundant in clay-rich environments, which are most promising for harboring organic molecules and have comprised the main studied features by the Curiosity rover in search of them. In this work we studied the photocatalytic effects of the Fe-rich clay nontronite on adsorbed PAHs. We tested the effect of ultraviolet radiation on pyrene, fluoranthene, perylene, triphenylene, and coronene adsorbed to nontronite using the spike technique, and in situ diffuse reflectance infrared Fourier transform (DRIFT) spectroscopy in a Mars simulation chamber. We studied the infrared vibrational PAH bands with first order reaction kinetics and observed an extensive decrease of bands of pyrene, fluoranthene, and perylene, accompanied by the formation of PAH cations, while triphenylene and coronene remained preserved. We further analyzed our irradiated samples with nuclear magnetic resonance (NMR). Our study showed certain PAHs to be degraded via the (photo)Fenton mechanism, even under a dry, hypoxic atmosphere. Using solar spectra representative of early Earth, early Mars, and current Mars surface illumination up to 400 nm, the processes occurring in our set up are indicative of the UV-induced photochemistry taking place in Fe-rich clay environments on early Earth and Mars.

Published
2023

11. Highly bioresistant, hydrophilic and rigidly linked trityl-nitroxide biradicals for cellular high-field dynamic nuclear polarization

Author

Yao, Ru, Beriashvili, David, Zhang, Wenxiao, Li, Shuai, Safeer, Adil, Gurinov, Andrei, Rockenbauer, Antal, Yang, Yin, Song, Yuguang, Baldus, Marc, Liu, Yangping, Sub NMR Spectroscopy, NMR Spectroscopy, Sub NMR Spectroscopy, and NMR Spectroscopy

Subjects
Chemistry(all), General Chemistry
Abstract

Cellular dynamic nuclear polarization (DNP) has been an effective means of overcoming the intrinsic sensitivity limitations of solid-state nuclear magnetic resonance (ssNMR) spectroscopy, thus enabling atomic-level biomolecular characterization in native environments. Achieving DNP signal enhancement relies on doping biological preparations with biradical polarizing agents (PAs). Unfortunately, PA performance within cells is often limited by their sensitivity to the reductive nature of the cellular lumen. Herein, we report the synthesis and characterization of a highly bioresistant and hydrophilic PA (StaPol-1) comprising the trityl radical OX063 ligated to a gem-diethyl pyrroline nitroxide via a rigid piperazine linker. EPR experiments in the presence of reducing agents such as ascorbate and in HeLa cell lysates demonstrate the reduction resistance of StaPol-1. High DNP enhancements seen in small molecules, proteins and cell lysates at 18.8 T confirm that StaPol-1 is an excellent PA for DNP ssNMR investigations of biomolecular systems at high magnetic fields in reductive environments.

Published
2022

12. Cyclization and Docking Protocol for Cyclic Peptide–Protein Modeling Using HADDOCK2.4

Author

Charitou, Vicky, Van Keulen, Siri C., Bonvin, Alexandre M.J.J., Sub NMR Spectroscopy, and NMR Spectroscopy

Subjects
Molecular Docking Simulation, Cyclization, Protein Conformation, Proteins, Physical and Theoretical Chemistry, Peptides, Cyclic, Software, Protein Binding, Computer Science Applications
Abstract

An emerging class of therapeutic molecules are cyclic peptides with over 40 cyclic peptide drugs currently in clinical use. Their mode of action is, however, not fully understood, impeding rational drug design. Computational techniques could positively impact their design, but modeling them and their interactions remains challenging due to their cyclic nature and their flexibility. This study presents a step-by-step protocol for generating cyclic peptide conformations and docking them to their protein target using HADDOCK2.4. A dataset of 30 cyclic peptide-protein complexes was used to optimize both cyclization and docking protocols. It supports peptides cyclized via an N- and C-terminus peptide bond and/or a disulfide bond. An ensemble of cyclic peptide conformations is then used in HADDOCK to dock them onto their target protein using knowledge of the binding site on the protein side to drive the modeling. The presented protocol predicts at least one acceptable model according to the critical assessment of prediction of interaction criteria for each complex of the dataset when the top 10 HADDOCK-ranked single structures are considered (100% success rate top 10) both in the bound and unbound docking scenarios. Moreover, its performance in both bound and fully unbound docking is similar to the state-of-the-art software in the field, Autodock CrankPep. The presented cyclization and docking protocol should make HADDOCK a valuable tool for rational cyclic peptide-based drug design and high-throughput screening.

Published
2022

13. The photochemical evolution of polycyclic aromatic hydrocarbons and nontronite clay on early Earth and Mars

Author

Petrology, Sub NMR Spectroscopy, Kopacz, Nina, Corazzi, Maria Angela, Poggiali, Giovanni, von Essen, Ayla, Kofman, Vincent, Fornaro, Teresa, van Ingen, Hugo, Camprubi, Eloi, King, Helen E., Brucato, John, ten Kate, Inge Loes, Petrology, Sub NMR Spectroscopy, Kopacz, Nina, Corazzi, Maria Angela, Poggiali, Giovanni, von Essen, Ayla, Kofman, Vincent, Fornaro, Teresa, van Ingen, Hugo, Camprubi, Eloi, King, Helen E., Brucato, John, and ten Kate, Inge Loes

Published
2023

15. Probing Cell-Surface Interactions in Fungal Cell Walls by High-Resolution 1H-detected Solid-State NMR Spectroscopy

Author

Sub NMR Spectroscopy, Sub Molecular Microbiology, Immunologie, Molecular Microbiology, NMR Spectroscopy, Infectious Diseases and Immunology, Safeer, Adil, Kleijburg, Fleur, Bahri, Salima, Beriashvili, David, Veldhuizen, Edwin, van Neer, Jacq, Tegelaar, Martin, de Cock, Hans, Wösten, Han, Baldus, Marc, Sub NMR Spectroscopy, Sub Molecular Microbiology, Immunologie, Molecular Microbiology, NMR Spectroscopy, Infectious Diseases and Immunology, Safeer, Adil, Kleijburg, Fleur, Bahri, Salima, Beriashvili, David, Veldhuizen, Edwin, van Neer, Jacq, Tegelaar, Martin, de Cock, Hans, Wösten, Han, and Baldus, Marc

Published
2023

17. A new antibiotic from an uncultured bacterium binds to an immutable target

Author

NMR Spectroscopy, Membrane Biochemistry and Biophysics, Sub NMR Spectroscopy, Sub Membrane Biochemistry & Biophysics, Shukla, Rhythm, Peoples, Aaron J, Ludwig, Kevin C, Maity, Sourav, Derks, Maik G N, de Benedetti, Stefania, Krueger, Annika M, Vermeulen, Bram J A, Lavore, Francesca, Honorato, Rodrigo V, Grein, Fabian, Bonvin, Alexandre, Kubitscheck, Ulrich, Breukink, Eefjan, Achorn, Catherine, Nitti, Anthony, Schwalen, Christopher J, Spoering, Amy L, Ling, Losee Lucy, Hughes, Dallas, Lelli, Moreno, Roos, Wouter H, Lewis, Kim, Schneider, Tanja, Weingarth, Markus, NMR Spectroscopy, Membrane Biochemistry and Biophysics, Sub NMR Spectroscopy, Sub Membrane Biochemistry & Biophysics, Shukla, Rhythm, Peoples, Aaron J, Ludwig, Kevin C, Maity, Sourav, Derks, Maik G N, de Benedetti, Stefania, Krueger, Annika M, Vermeulen, Bram J A, Lavore, Francesca, Honorato, Rodrigo V, Grein, Fabian, Bonvin, Alexandre, Kubitscheck, Ulrich, Breukink, Eefjan, Achorn, Catherine, Nitti, Anthony, Schwalen, Christopher J, Spoering, Amy L, Ling, Losee Lucy, Hughes, Dallas, Lelli, Moreno, Roos, Wouter H, Lewis, Kim, Schneider, Tanja, and Weingarth, Markus

Published
2023

18. Full-Length Single-Molecule Protein Fingerprinting

Author

Afd Chemical Biology and Drug Discovery, Sub NMR Spectroscopy, Sub Chemical Biology and Drug Discovery, Chemical Biology and Drug Discovery, Filius, Mike, Wee, Raman van, Lannoy, Carlos de, Westerlaken, Ilja, Li, Zeshi, Kim, Sung Hyun, Pinto, Cecilia de Agrela, Wu, Yunfei, Boons, Geert-Jan, Pabst, Martin, Ridder, Dick de, Joo, Chirlmin, Afd Chemical Biology and Drug Discovery, Sub NMR Spectroscopy, Sub Chemical Biology and Drug Discovery, Chemical Biology and Drug Discovery, Filius, Mike, Wee, Raman van, Lannoy, Carlos de, Westerlaken, Ilja, Li, Zeshi, Kim, Sung Hyun, Pinto, Cecilia de Agrela, Wu, Yunfei, Boons, Geert-Jan, Pabst, Martin, Ridder, Dick de, and Joo, Chirlmin

Published
2023

19. Information-Driven Antibody-Antigen Modelling with HADDOCK

Author

NMR Spectroscopy, Sub NMR Spectroscopy, Tsumoto, Kouhei, Kuroda, Daisuke, Ambrosetti, Francesco, Jandova, Zuzana, Bonvin, Alexandre M J J, NMR Spectroscopy, Sub NMR Spectroscopy, Tsumoto, Kouhei, Kuroda, Daisuke, Ambrosetti, Francesco, Jandova, Zuzana, and Bonvin, Alexandre M J J

Published
2023

24. Structural and Functional Characterization of the Newly Designed Antimicrobial Peptide Crabrolin21

Author

Sub NMR Spectroscopy, NMR Spectroscopy, Cantini, Francesca, Giannì, Paola, Bobone, Sara, Troiano, Cassandra, van Ingen, Hugo, Massoud, Renato, Perini, Nicoletta, Migliore, Luciana, Savarin, Philippe, Sanders, Charles, Stella, Lorenzo, Sette, Marco, Sub NMR Spectroscopy, NMR Spectroscopy, Cantini, Francesca, Giannì, Paola, Bobone, Sara, Troiano, Cassandra, van Ingen, Hugo, Massoud, Renato, Perini, Nicoletta, Migliore, Luciana, Savarin, Philippe, Sanders, Charles, Stella, Lorenzo, and Sette, Marco

Published
2023

25. Effects of Escherichia coli LPS Structure on Antibacterial and Anti-Endotoxin Activities of Host Defense Peptides.

Author

Immunologie, Sub NMR Spectroscopy, Afd Pharmacology, Infectious Diseases and Immunologie, Infectious Diseases and Immunology - Immunology, Research Department OH - Biomolecular Health Sciences, Javed, Ali, Balhuizen, Melanie D, Pannekoek, Arianne, Bikker, Floris J, Heesterbeek, Dani A C, Haagsman, Henk P, Broere, Femke, Weingarth, Markus, Veldhuizen, Edwin J A, Immunologie, Sub NMR Spectroscopy, Afd Pharmacology, Infectious Diseases and Immunologie, Infectious Diseases and Immunology - Immunology, Research Department OH - Biomolecular Health Sciences, Javed, Ali, Balhuizen, Melanie D, Pannekoek, Arianne, Bikker, Floris J, Heesterbeek, Dani A C, Haagsman, Henk P, Broere, Femke, Weingarth, Markus, and Veldhuizen, Edwin J A

Published
2023

26. Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment

Author

Sub NMR Spectroscopy, NMR Spectroscopy, Lensink, Marc F, Brysbaert, Guillaume, Raouraoua, Nessim, Bates, Paul A, Giulini, Marco, Honorato, Rodrigo V, van Noort, Charlotte, Teixeira, Joao M C, Bonvin, Alexandre M J J, Kong, Ren, Shi, Hang, Lu, Xufeng, Chang, Shan, Liu, Jian, Guo, Zhiye, Chen, Xiao, Morehead, Alex, Roy, Raj S, Wu, Tianqi, Giri, Nabin, Quadir, Farhan, Chen, Chen, Cheng, Jianlin, Del Carpio, Carlos A, Ichiishi, Eichiro, Rodriguez-Lumbreras, Luis A, Fernandez-Recio, Juan, Harmalkar, Ameya, Chu, Lee-Shin, Canner, Sam, Smanta, Rituparna, Gray, Jeffrey J, Li, Hao, Lin, Peicong, He, Jiahua, Tao, Huanyu, Huang, Sheng-You, Roel-Touris, Jorge, Jimenez-Garcia, Brian, Christoffer, Charles W, Jain, Anika J, Kagaya, Yuki, Kannan, Harini, Nakamura, Tsukasa, Terashi, Genki, Verburgt, Jacob C, Zhang, Yuanyuan, Zhang, Zicong, Fujuta, Hayato, Sekijima, Masakazu, Kihara, Daisuke, Khan, Omeir, Kotelnikov, Sergei, Ghani, Usman, Padhorny, Dzmitry, Beglov, Dmitri, Vajda, Sandor, Kozakov, Dima, Negi, Surendra S, Ricciardelli, Tiziana, Barradas-Bautista, Didier, Cao, Zhen, Chawla, Mohit, Cavallo, Luigi, Oliva, Romina, Yin, Rujie, Cheung, Melyssa, Guest, Johnathan D, Lee, Jessica, Pierce, Brian G, Shor, Ben, Cohen, Tomer, Halfon, Matan, Schneidman-Duhovny, Dina, Zhu, Shaowen, Sun, Yuanfei, Shen, Yang, Maszota-Zieleniak, Martyna, Bojarski, Krzysztof K, Lubecka, Emilia A, Marcisz, Mateusz, Danielsson, Annemarie, Dziadek, Lukasz, Gaardlos, Margrethe, Gieldon, Artur, Liwo, Adam, Samsonov, Sergey A, Slusarz, Rafal, Zieba, Karolina, Sieradzan, Adam K, Czaplewski, Cezary, Kobayashi, Shinpei, Miyakawa, Yuta, Kiyota, Yasuomi, Takeda-Shitaka, Mayuko, Olechnovic, Kliment, Valancauskas, Lukas, Dapkunas, Justas, Venclovas, Ceslovas, Wallner, Bjorn, Yang, Lin, Hou, Chengyu, He, Xiaodong, Guo, Shuai, Jiang, Shenda, Ma, Xiaoliang, Duan, Rui, Qui, Liming, Xu, Xianjin, Zou, Xiaoqin, Velankar, Sameer, Wodak, Shoshana J, Sub NMR Spectroscopy, NMR Spectroscopy, Lensink, Marc F, Brysbaert, Guillaume, Raouraoua, Nessim, Bates, Paul A, Giulini, Marco, Honorato, Rodrigo V, van Noort, Charlotte, Teixeira, Joao M C, Bonvin, Alexandre M J J, Kong, Ren, Shi, Hang, Lu, Xufeng, Chang, Shan, Liu, Jian, Guo, Zhiye, Chen, Xiao, Morehead, Alex, Roy, Raj S, Wu, Tianqi, Giri, Nabin, Quadir, Farhan, Chen, Chen, Cheng, Jianlin, Del Carpio, Carlos A, Ichiishi, Eichiro, Rodriguez-Lumbreras, Luis A, Fernandez-Recio, Juan, Harmalkar, Ameya, Chu, Lee-Shin, Canner, Sam, Smanta, Rituparna, Gray, Jeffrey J, Li, Hao, Lin, Peicong, He, Jiahua, Tao, Huanyu, Huang, Sheng-You, Roel-Touris, Jorge, Jimenez-Garcia, Brian, Christoffer, Charles W, Jain, Anika J, Kagaya, Yuki, Kannan, Harini, Nakamura, Tsukasa, Terashi, Genki, Verburgt, Jacob C, Zhang, Yuanyuan, Zhang, Zicong, Fujuta, Hayato, Sekijima, Masakazu, Kihara, Daisuke, Khan, Omeir, Kotelnikov, Sergei, Ghani, Usman, Padhorny, Dzmitry, Beglov, Dmitri, Vajda, Sandor, Kozakov, Dima, Negi, Surendra S, Ricciardelli, Tiziana, Barradas-Bautista, Didier, Cao, Zhen, Chawla, Mohit, Cavallo, Luigi, Oliva, Romina, Yin, Rujie, Cheung, Melyssa, Guest, Johnathan D, Lee, Jessica, Pierce, Brian G, Shor, Ben, Cohen, Tomer, Halfon, Matan, Schneidman-Duhovny, Dina, Zhu, Shaowen, Sun, Yuanfei, Shen, Yang, Maszota-Zieleniak, Martyna, Bojarski, Krzysztof K, Lubecka, Emilia A, Marcisz, Mateusz, Danielsson, Annemarie, Dziadek, Lukasz, Gaardlos, Margrethe, Gieldon, Artur, Liwo, Adam, Samsonov, Sergey A, Slusarz, Rafal, Zieba, Karolina, Sieradzan, Adam K, Czaplewski, Cezary, Kobayashi, Shinpei, Miyakawa, Yuta, Kiyota, Yasuomi, Takeda-Shitaka, Mayuko, Olechnovic, Kliment, Valancauskas, Lukas, Dapkunas, Justas, Venclovas, Ceslovas, Wallner, Bjorn, Yang, Lin, Hou, Chengyu, He, Xiaodong, Guo, Shuai, Jiang, Shenda, Ma, Xiaoliang, Duan, Rui, Qui, Liming, Xu, Xianjin, Zou, Xiaoqin, Velankar, Sameer, and Wodak, Shoshana J

Published
2023

27. An antibiotic from an uncultured bacterium binds to an immutable target

Author

Sub NMR Spectroscopy, Sub Membrane Biochemistry & Biophysics, NMR Spectroscopy, Membrane Biochemistry and Biophysics, Shukla, Rhythm, Peoples, Aaron J, Ludwig, Kevin C, Maity, Sourav, Derks, Maik G N, De Benedetti, Stefania, Krueger, Annika M, Vermeulen, Bram J A, Harbig, Theresa, Lavore, Francesca, Kumar, Raj, Honorato, Rodrigo V, Grein, Fabian, Nieselt, Kay, Liu, Yangping, Bonvin, Alexandre M J J, Baldus, Marc, Kubitscheck, Ulrich, Breukink, Eefjan, Achorn, Catherine, Nitti, Anthony, Schwalen, Christopher J, Spoering, Amy L, Ling, Losee Lucy, Hughes, Dallas, Lelli, Moreno, Roos, Wouter H, Lewis, Kim, Schneider, Tanja, Weingarth, Markus, Sub NMR Spectroscopy, Sub Membrane Biochemistry & Biophysics, NMR Spectroscopy, Membrane Biochemistry and Biophysics, Shukla, Rhythm, Peoples, Aaron J, Ludwig, Kevin C, Maity, Sourav, Derks, Maik G N, De Benedetti, Stefania, Krueger, Annika M, Vermeulen, Bram J A, Harbig, Theresa, Lavore, Francesca, Kumar, Raj, Honorato, Rodrigo V, Grein, Fabian, Nieselt, Kay, Liu, Yangping, Bonvin, Alexandre M J J, Baldus, Marc, Kubitscheck, Ulrich, Breukink, Eefjan, Achorn, Catherine, Nitti, Anthony, Schwalen, Christopher J, Spoering, Amy L, Ling, Losee Lucy, Hughes, Dallas, Lelli, Moreno, Roos, Wouter H, Lewis, Kim, Schneider, Tanja, and Weingarth, Markus

Published
2023

28. Designing Highly Conductive Sodium-Based Metal Hydride Nanocomposites: Interplay between Hydride and Oxide Properties

Author

Sub Materials Chemistry and Catalysis, Sub NMR Spectroscopy, NMR Spectroscopy, Materials Chemistry and Catalysis, de Kort, Laura M., Brandt Corstius, Oscar E., Gulino, Valerio, Gurinov, Andrei, Baldus, Marc, Ngene, Peter, Sub Materials Chemistry and Catalysis, Sub NMR Spectroscopy, NMR Spectroscopy, Materials Chemistry and Catalysis, de Kort, Laura M., Brandt Corstius, Oscar E., Gulino, Valerio, Gurinov, Andrei, Baldus, Marc, and Ngene, Peter

Published
2023

30. The complex structure of Fomes fomentarius represents an architectural design for high-performance ultralightweight materials

Author

Sub NMR Spectroscopy, NMR Spectroscopy, Pylkkänen, Robert, Werner, Daniel, Bishoyi, Ajit, Weil, Dominik, Scoppola, Ernesto, Wagermaier, Wolfgang, Safeer, Adil, Bahri, Salima, Baldus, Marc, Paananen, Arja, Penttilä, Merja, Szilvay, Géza R., Mohammadi, Pezhman, Sub NMR Spectroscopy, NMR Spectroscopy, Pylkkänen, Robert, Werner, Daniel, Bishoyi, Ajit, Weil, Dominik, Scoppola, Ernesto, Wagermaier, Wolfgang, Safeer, Adil, Bahri, Salima, Baldus, Marc, Paananen, Arja, Penttilä, Merja, Szilvay, Géza R., and Mohammadi, Pezhman

Published
2023

31. A high-field cellular DNP-supported solid-state NMR approach to study proteins with sub-cellular specificity

Author

NMR Spectroscopy, Sub NMR Spectroscopy, Beriashvili, David, Yao, Ru, D'Amico, Francesca, Krafčíková, Michaela, Gurinov, Andrei, Safeer, Adil, Cai, Xinyi, Mulder, Monique P C, Liu, Yangping, Folkers, Gert E, Baldus, Marc, NMR Spectroscopy, Sub NMR Spectroscopy, Beriashvili, David, Yao, Ru, D'Amico, Francesca, Krafčíková, Michaela, Gurinov, Andrei, Safeer, Adil, Cai, Xinyi, Mulder, Monique P C, Liu, Yangping, Folkers, Gert E, and Baldus, Marc

Published
2023

33. Discriminating physiological from non-physiological interfaces in structures of protein complexes: A community-wide study

Author

Sub NMR Spectroscopy, NMR Spectroscopy, Schweke, Hugo, Xu, Qifang, Tauriello, Gerardo, Pantolini, Lorenzo, Schwede, Torsten, Cazals, Frédéric, Lhéritier, Alix, Fernandez-Recio, Juan, Rodríguez-Lumbreras, Luis Angel, Schueler-Furman, Ora, Varga, Julia K., Jiménez-García, Brian, Réau, Manon F., Bonvin, Alexandre M.J.J., Savojardo, Castrense, Martelli, Pier Luigi, Casadio, Rita, Tubiana, Jérôme, Wolfson, Haim J., Oliva, Romina, Barradas-Bautista, Didier, Ricciardelli, Tiziana, Cavallo, Luigi, Venclovas, Česlovas, Olechnovič, Kliment, Guerois, Raphael, Andreani, Jessica, Martin, Juliette, Wang, Xiao, Terashi, Genki, Sarkar, Daipayan, Christoffer, Charles, Aderinwale, Tunde, Verburgt, Jacob, Kihara, Daisuke, Marchand, Anthony, Correia, Bruno E., Duan, Rui, Qiu, Liming, Xu, Xianjin, Zhang, Shuang, Zou, Xiaoqin, Dey, Sucharita, Dunbrack, Roland L., Levy, Emmanuel D., Wodak, Shoshana J., Sub NMR Spectroscopy, NMR Spectroscopy, Schweke, Hugo, Xu, Qifang, Tauriello, Gerardo, Pantolini, Lorenzo, Schwede, Torsten, Cazals, Frédéric, Lhéritier, Alix, Fernandez-Recio, Juan, Rodríguez-Lumbreras, Luis Angel, Schueler-Furman, Ora, Varga, Julia K., Jiménez-García, Brian, Réau, Manon F., Bonvin, Alexandre M.J.J., Savojardo, Castrense, Martelli, Pier Luigi, Casadio, Rita, Tubiana, Jérôme, Wolfson, Haim J., Oliva, Romina, Barradas-Bautista, Didier, Ricciardelli, Tiziana, Cavallo, Luigi, Venclovas, Česlovas, Olechnovič, Kliment, Guerois, Raphael, Andreani, Jessica, Martin, Juliette, Wang, Xiao, Terashi, Genki, Sarkar, Daipayan, Christoffer, Charles, Aderinwale, Tunde, Verburgt, Jacob, Kihara, Daisuke, Marchand, Anthony, Correia, Bruno E., Duan, Rui, Qiu, Liming, Xu, Xianjin, Zhang, Shuang, Zou, Xiaoqin, Dey, Sucharita, Dunbrack, Roland L., Levy, Emmanuel D., and Wodak, Shoshana J.

Published
2023

35. A novel antifolate suppresses growth of FPGS-deficient cells and overcomes methotrexate resistance

Author

Sub NMR Spectroscopy, Immunologie, Interne geneeskunde GD, CS_Cancer, Sub Biomol.Mass Spectrometry & Proteom., Infectious Diseases and Immunology - Immunology, van der Krift, Felix, Zijlmans, Dick W, Shukla, Rhythm, Javed, Ali, Koukos, Panagiotis I, Schwarz, Laura LE, Timmermans-Sprang, Elpetra Pm, Maas, Peter Em, Gahtory, Digvijay, van den Nieuwboer, Maurits, Mol, Jan A, Strous, Ger J, Bonvin, Alexandre Mjj, van der Stelt, Mario, Veldhuizen, Edwin Ja, Weingarth, Markus, Vermeulen, Michiel, Klumperman, Judith, Maurice, Madelon M, Sub NMR Spectroscopy, Immunologie, Interne geneeskunde GD, CS_Cancer, Sub Biomol.Mass Spectrometry & Proteom., Infectious Diseases and Immunology - Immunology, van der Krift, Felix, Zijlmans, Dick W, Shukla, Rhythm, Javed, Ali, Koukos, Panagiotis I, Schwarz, Laura LE, Timmermans-Sprang, Elpetra Pm, Maas, Peter Em, Gahtory, Digvijay, van den Nieuwboer, Maurits, Mol, Jan A, Strous, Ger J, Bonvin, Alexandre Mjj, van der Stelt, Mario, Veldhuizen, Edwin Ja, Weingarth, Markus, Vermeulen, Michiel, Klumperman, Judith, and Maurice, Madelon M

Published
2023

36. Binding of micro-nutrients to the cell wall of the fungus Schizophyllum commune

Author

Sub Molecular Microbiology, Sub NMR Spectroscopy, Molecular Microbiology, NMR Spectroscopy, Kleijburg, Fleur E.L., Safeer, Adil A., Baldus, Marc, Wösten, Han A.B., Sub Molecular Microbiology, Sub NMR Spectroscopy, Molecular Microbiology, NMR Spectroscopy, Kleijburg, Fleur E.L., Safeer, Adil A., Baldus, Marc, and Wösten, Han A.B.

Published
2023

37. Chimeric Peptidomimetic Antibiotic Efficiently Neutralizes Lipopolysaccharides (LPS) and Bacteria-Induced Activation of RAW Macrophages

Author

Immunologie, Sub NMR Spectroscopy, Interne geneeskunde GD, CS_Welfare & emerging diseases, Infectious Diseases and Immunology - Immunology, Javed, Ali, Slingerland, Cornelis J, Wood, Thomas M, Martin, Nathaniel I, Broere, Femke, Weingarth, Markus H, Veldhuizen, Edwin J A, Immunologie, Sub NMR Spectroscopy, Interne geneeskunde GD, CS_Welfare & emerging diseases, Infectious Diseases and Immunology - Immunology, Javed, Ali, Slingerland, Cornelis J, Wood, Thomas M, Martin, Nathaniel I, Broere, Femke, Weingarth, Markus H, and Veldhuizen, Edwin J A

Published
2023

38. Impact of AlphaFold on Structure Prediction of Protein Complexes: The CASP15-CAPRI Experiment

Author

NMR Spectroscopy, Sub NMR Spectroscopy, Lensink, Marc, Brysbaert, Guillaume, Raouraoua, Nessim, Bates, Paul, Giulini, Marco, Honorato, Rodrigo Vargas, Noort, Charlotte van, Teixeira, João, Bonvin, Alexandre M.J.J., Kong, Ren, Shi, Hang, Lu, Xufeng, Chang, Shan, Liu, Jian, Guo, Zhiye, Chen, Xiao, Morehead, Alex, Roy, Raj, Wu, Tianqi, Giri, Nabin, Quadir, Farhan, Chen, Chen, Cheng, Jianlin, Carpio, Carlos Del, Ichiishi, Eichiro, Luis, Rodriguez-Lumbreras A, Fernández-Recio, Juan, Harmalkar, Ameya, Chu, Lee-Shin, Canner, Sam, Smanta, Rituparna, Gray, Jeffrey, Li, Hao, Lin, Peicong, He, Jiahua, Tao, Huanyu, Huang, Shengyou, Roel, Jorge, Jimenez-Garcia, Brian, Christoffer, Charles, Anika, Jain J, Kagaya, Yuki, Kannan, Harini, Nakamura, Tsukasa, Terashi, Genki, Verburgt, Jacob, Zhang, Yuanyuan, Zhang, Zicong, Fujuta, Hayato, Sekijima, Masakazu, Kihara, Daisuke, Khan, Omeir, Kotelnikov, Sergei, Ghani, Usman, Padhorny, Dzmitry, Beglov, Dmitri, Vajda, Sandor, Kozakov, Dima, Surendra, Negi S, Ricciardelli, Tiziana, Barradas-Bautista, Didier, Cao, Zhen, Chawla, Mohit, Cavallo, Luigi, Oliva, Romina, Yin, Rujie, Cheung, Melyssa, Guest, Johnathan, Lee, Jessica, Pierce, Brian, Shor, Ben, Cohen, Tomer, Halfon, Matan, Schneidman-Duhovny, Dina, Zhu, Shaowen, Sun, Yuanfei, Shen, Yang, Maszota-Zieleniak, Martyna, Krzysztof, Bojarski K, Lubecka, Emilia, Marcisz, Mateusz, Danielsson, Annemarie, Dziadek, Lukasz, Gaardlos, Margrethe, Giełdoń, Artur, Liwo, Jozef, Samsonov, Sergey, Slusarz, Rafal, Zieba, Karolina, Sieradzan, Adam, Czaplewski, Cezary, Kobayashi, Shinpei, Miyakawa, Yuta, Kiyota, Yasuomi, Takeda-Shitaka, Mayuko, Olechnovič, Kliment, Valančauskas, Lukas, Dapkūnas, Justas, Venclovas, Ceslovas, Wallner, Björn, Yang, Lin, Hou, Chengyu, He, Xiaodong, Guo, Shuai, Jiang, Shenda, Ma, Xiaoliang, Duan, Rui, Qiu, Liming, Xu, Xianjin, Zou, Xiaoqin, Velankar, Sameer, Shoshana, Wodak J, NMR Spectroscopy, Sub NMR Spectroscopy, Lensink, Marc, Brysbaert, Guillaume, Raouraoua, Nessim, Bates, Paul, Giulini, Marco, Honorato, Rodrigo Vargas, Noort, Charlotte van, Teixeira, João, Bonvin, Alexandre M.J.J., Kong, Ren, Shi, Hang, Lu, Xufeng, Chang, Shan, Liu, Jian, Guo, Zhiye, Chen, Xiao, Morehead, Alex, Roy, Raj, Wu, Tianqi, Giri, Nabin, Quadir, Farhan, Chen, Chen, Cheng, Jianlin, Carpio, Carlos Del, Ichiishi, Eichiro, Luis, Rodriguez-Lumbreras A, Fernández-Recio, Juan, Harmalkar, Ameya, Chu, Lee-Shin, Canner, Sam, Smanta, Rituparna, Gray, Jeffrey, Li, Hao, Lin, Peicong, He, Jiahua, Tao, Huanyu, Huang, Shengyou, Roel, Jorge, Jimenez-Garcia, Brian, Christoffer, Charles, Anika, Jain J, Kagaya, Yuki, Kannan, Harini, Nakamura, Tsukasa, Terashi, Genki, Verburgt, Jacob, Zhang, Yuanyuan, Zhang, Zicong, Fujuta, Hayato, Sekijima, Masakazu, Kihara, Daisuke, Khan, Omeir, Kotelnikov, Sergei, Ghani, Usman, Padhorny, Dzmitry, Beglov, Dmitri, Vajda, Sandor, Kozakov, Dima, Surendra, Negi S, Ricciardelli, Tiziana, Barradas-Bautista, Didier, Cao, Zhen, Chawla, Mohit, Cavallo, Luigi, Oliva, Romina, Yin, Rujie, Cheung, Melyssa, Guest, Johnathan, Lee, Jessica, Pierce, Brian, Shor, Ben, Cohen, Tomer, Halfon, Matan, Schneidman-Duhovny, Dina, Zhu, Shaowen, Sun, Yuanfei, Shen, Yang, Maszota-Zieleniak, Martyna, Krzysztof, Bojarski K, Lubecka, Emilia, Marcisz, Mateusz, Danielsson, Annemarie, Dziadek, Lukasz, Gaardlos, Margrethe, Giełdoń, Artur, Liwo, Jozef, Samsonov, Sergey, Slusarz, Rafal, Zieba, Karolina, Sieradzan, Adam, Czaplewski, Cezary, Kobayashi, Shinpei, Miyakawa, Yuta, Kiyota, Yasuomi, Takeda-Shitaka, Mayuko, Olechnovič, Kliment, Valančauskas, Lukas, Dapkūnas, Justas, Venclovas, Ceslovas, Wallner, Björn, Yang, Lin, Hou, Chengyu, He, Xiaodong, Guo, Shuai, Jiang, Shenda, Ma, Xiaoliang, Duan, Rui, Qiu, Liming, Xu, Xianjin, Zou, Xiaoqin, Velankar, Sameer, and Shoshana, Wodak J

Published
2023

39. Biological solid-state NMR: Integrative across different scientific disciplines

Author

Baldus, Marc, Sub NMR Spectroscopy, NMR Spectroscopy, Sub NMR Spectroscopy, and NMR Spectroscopy

Subjects
Structural Biology
Abstract

For almost five decades, solid-state NMR (ssNMR) has been used to study complex biomolecular systems. This article gives a view on how ssNMR methods and applications have evolved during this time period in a broader structural biology context. It also discusses possible directions for additional developments and the future role of ssNMR in a life science context and beyond.

Published
2022

40. Chaperoning of the histone octamer by the acidic domain of DNA repair factor APLF

Author

Corbeski, Ivan, Guo, Xiaohu, Eckhardt, Bruna V, Fasci, Domenico, Wiegant, Wouter, Graewert, Melissa A, Vreeken, Kees, Wienk, Hans, Svergun, Dmitri I, Heck, Albert J R, van Attikum, Haico, Boelens, Rolf, Sixma, Titia K, Mattiroli, Francesca, van Ingen, Hugo, Sub NMR Spectroscopy, Sub Biomol.Mass Spectrometry & Proteom., Afd Biomol.Mass Spect. and Proteomics, NMR Spectroscopy, Biomolecular Mass Spectrometry and Proteomics, Hubrecht Institute for Developmental Biology and Stem Cell Research, Sub NMR Spectroscopy, Sub Biomol.Mass Spectrometry & Proteom., Afd Biomol.Mass Spect. and Proteomics, NMR Spectroscopy, and Biomolecular Mass Spectrometry and Proteomics

Subjects
Histones, Histone Chaperones/genetics, Multidisciplinary, DNA Repair, Histones/metabolism, Histone Chaperones, ddc:500, DNA, Molecular Chaperones/genetics, DNA/chemistry, Molecular Chaperones, Nucleosomes
Abstract

Science advances 8(30), eabo0517 (2022). doi:10.1126/sciadv.abo0517, Nucleosome assembly requires the coordinated deposition of histone complexes H3-H4 and H2A-H2B to form a histone octamer on DNA. In the current paradigm, specific histone chaperones guide the deposition of first H3-H4 and then H2A-H2B. Here, we show that the acidic domain of DNA repair factor APLF (APLF$^{AD}$) can assemble the histone octamer in a single step and deposit it on DNA to form nucleosomes. The crystal structure of the APLF$^{AD}$-histone octamer complex shows that APLF$^{AD}$ tethers the histones in their nucleosomal conformation. Mutations of key aromatic anchor residues in APLF$^{AD}$ affect chaperone activity in vitro and in cells. Together, we propose that chaperoning of the histone octamer is a mechanism for histone chaperone function at sites where chromatin is temporarily disrupted., Published by Assoc., Washington, DC [u.a.]

Published
2022

41. Probing Cell-Surface Interactions in Fungal Cell Walls by High-Resolution 1H-detected Solid-State NMR Spectroscopy

Author

Safeer, Adil, Kleijburg, Fleur, Bahri, Salima, Beriashvili, David, Veldhuizen, Edwin, van Neer, Jacq, Tegelaar, Martin, de Cock, Hans, Wösten, Han, Baldus, Marc, Sub NMR Spectroscopy, Sub Molecular Microbiology, Immunologie, Molecular Microbiology, NMR Spectroscopy, and Infectious Diseases and Immunology

Subjects
NMR spectroscopy, proton detection, Organic Chemistry, cell wall, General Chemistry, peptide, Catalysis, schizophyllum commune
Abstract

Solid-state NMR (ssNMR) spectroscopy facilitates the non-destructive characterization of structurally heterogeneous biomolecules in their native setting, for example, comprising proteins, lipids and polysaccharides. Here we demonstrate the utility of high and ultra-high field 1 H-detected fast MAS ssNMR spectroscopy, which exhibits increased sensitivity and spectral resolution, to further elucidate the atomic-level composition and structural arrangement of the cell wall of Schizophyllum commune, a mushroom-forming fungus from the Basidiomycota phylum. These advancements allowed us to reveal that Cu(II) ions and the antifungal peptide Cathelicidin-2 mainly bind to cell wall proteins at low concentrations while glucans are targeted at high metal ion concentrations. In addition, our data suggest the presence of polysaccharides containing N-acetyl galactosamine (GalNAc) and proteins, including the hydrophobin proteins SC3, shedding more light on the molecular make-up of cells wall as well as the positioning of the polypeptide layer. Obtaining such information may be of critical relevance for future research into fungi in material science and biomedical contexts.

Published
2023

42. DeepRank-GNN: a graph neural network framework to learn patterns in protein-protein interfaces

Author

Réau, Manon, Renaud, Nicolas, Xue, Li C, Bonvin, Alexandre M J J, Sub NMR Spectroscopy, and NMR Spectroscopy

Subjects
Statistics and Probability, Computational Mathematics, All institutes and research themes of the Radboud University Medical Center, Complexes, Computational Theory and Mathematics, Cancer development and immune defence Radboud Institute for Molecular Life Sciences [Radboudumc 2], Benchmark, Molecular Biology, Biochemistry, Docking, Computer Science Applications
Abstract

Motivation Gaining structural insights into the protein–protein interactome is essential to understand biological phenomena and extract knowledge for rational drug design or protein engineering. We have previously developed DeepRank, a deep-learning framework to facilitate pattern learning from protein–protein interfaces using convolutional neural network (CNN) approaches. However, CNN is not rotation invariant and data augmentation is required to desensitize the network to the input data orientation which dramatically impairs the computation performance. Representing protein–protein complexes as atomic- or residue-scale rotation invariant graphs instead enables using graph neural networks (GNN) approaches, bypassing those limitations. Results We have developed DeepRank-GNN, a framework that converts protein–protein interfaces from PDB 3D coordinates files into graphs that are further provided to a pre-defined or user-defined GNN architecture to learn problem-specific interaction patterns. DeepRank-GNN is designed to be highly modularizable, easily customized and is wrapped into a user-friendly python3 package. Here, we showcase DeepRank-GNN’s performance on two applications using a dedicated graph interaction neural network: (i) the scoring of docking poses and (ii) the discriminating of biological and crystal interfaces. In addition to the highly competitive performance obtained in those tasks as compared to state-of-the-art methods, we show a significant improvement in speed and storage requirement using DeepRank-GNN as compared to DeepRank. Availability and implementation DeepRank-GNN is freely available from https://github.com/DeepRank/DeepRank-GNN. Supplementary information Supplementary data are available at Bioinformatics online.

Published
2023

43. E‐selective Semi‐hydrogenation of Alkynes under Mild Conditions by a Diruthenium Hydride Complex

Author

Van beek, Cody B., Killian, Lars, Lutz, Martin, Weingarth, Markus, Asundi, Arun S., Sarangi, Ritimukta, Klein gebbink, Robertus J. M., Broere, Daniël L. J., Sub Organic Chemistry and Catalysis, Sub Structural Biochemistry, Sub NMR Spectroscopy, Faculteit Betawetenschappen, Structural Biochemistry, Organic Chemistry and Catalysis, and NMR Spectroscopy

Subjects
bimetallic compounds, expanded pincer ligands, polyhydride complex, Organic Chemistry, General Chemistry, metal-ligand cooperativity, alkyne semi-hydrogenation, Catalysis
Abstract

The synthesis, characterization and catalytic activity of a new class of diruthenium hydrido carbonyl complexes bound to the tBuPNNP expanded pincer ligand is described. Reacting tBuPNNP with two equiv of RuHCl(PPh3)3(CO) at 140 °C produces an insoluble air-stable complex, which was structurally characterized as [Ru2(tBuPNNP)H(μ-H)Cl(μ-Cl)(CO)2] (1) using solid-state NMR, IR and X-ray absorption spectroscopies and follow-up reactivity. A reaction with KOtBu results in deprotonation of a methylene linker to produce [Ru2(tBuPNNP*)H(μ-H)(μ-OtBu)(CO)2] (3) featuring a partially dearomatized naphthyridine core. This enables metal-ligand cooperative activation of H2 analogous to the mononuclear analogue, [Ru(tBuPNP*)H(CO)]. In contrast to the mononuclear system, the bimetallic analogue 3 catalyzes the E-selective semi-hydrogenation of alkynes at ambient temperature and atmospheric H2 pressure with good functional group tolerance. Monitoring the semi-hydrogenation of diphenylacetylene by 1H NMR spectroscopy shows the intermediacy of Z-stilbene, which is subsequently isomerized to the E-isomer. Initial findings into the mode of action of this system are provided, including the spectroscopic characterization of a polyhydride intermediate and the isolation of a deactivated species with a partially hydrogenated naphthyridine backbone.

Published
2022

44. Characterization of nucleosome sediments for protein interaction studies by solid-state NMR spectroscopy

Author

le Paige, Ulric B., Xiang, ShengQi, Hendrix, Marco M. R. M., Zhang, Yi, Folkers, Gert E., Weingarth, Markus, Bonvin, Alexandre M. J. J., Kutateladze, Tatiana G., Voets, Ilja K., Baldus, Marc, van Ingen, Hugo, NMR Spectroscopy, Sub NMR Spectroscopy, Self-Organizing Soft Matter, NMR Spectroscopy, and Sub NMR Spectroscopy

Subjects
QC501-766, 0303 health sciences, Precipitation (chemistry), Chemistry, Small-angle X-ray scattering, Nuclear magnetic resonance spectroscopy, 010402 general chemistry, 01 natural sciences, 0104 chemical sciences, Electricity and magnetism, 03 medical and health sciences, Solid-state nuclear magnetic resonance, Chemical physics, Phase (matter), Magic angle spinning, Nucleosome, Spectroscopy, 030304 developmental biology
Abstract

Regulation of DNA-templated processes such as gene transcription and DNA repair depend on the interaction of a wide range of proteins with the nucleosome, the fundamental building block of chromatin. Both solution and solid-state NMR spectroscopy have become an attractive approach to study the dynamics and interactions of nucleosomes, despite their high molecular weight of ∼200 kDa. For solid-state NMR (ssNMR) studies, dilute solutions of nucleosomes are converted to a dense phase by sedimentation or precipitation. Since nucleosomes are known to self-associate, these dense phases may induce extensive interactions between nucleosomes, which could interfere with protein-binding studies. Here, we characterized the packing of nucleosomes in the dense phase created by sedimentation using NMR and small-angle X-ray scattering (SAXS) experiments. We found that nucleosome sediments are gels with variable degrees of solidity, have nucleosome concentration close to that found in crystals, and are stable for weeks under high-speed magic angle spinning (MAS). Furthermore, SAXS data recorded on recovered sediments indicate that there is no pronounced long-range ordering of nucleosomes in the sediment. Finally, we show that the sedimentation approach can also be used to study low-affinity protein interactions with the nucleosome. Together, our results give new insights into the sample characteristics of nucleosome sediments for ssNMR studies and illustrate the broad applicability of sedimentation-based NMR studies.

Published
2021

45. Molecular Insights Into Binding and Activation of the Human KCNQ2 Channel by Retigabine

Author

Garofalo, Barbara, Bonvin, Alexandre M.J.J., Bosin, Andrea, Di Giorgio, Francesco P., Ombrato, Rosella, Vargiu, Attilio V., Sub NMR Spectroscopy, NMR Spectroscopy, Sub NMR Spectroscopy, and NMR Spectroscopy

Subjects
Kv7.2, voltage-gated potassium channels, docking, retigabine, Genetics and Molecular Biology (miscellaneous), Biochemistry, Genetics and Molecular Biology (miscellaneous), Molecular Biology, Biochemistry, homology modelling, molecular dynamics
Abstract

Voltage-gated potassium channels of the Kv7.x family are involved in a plethora of biological processes across many tissues in animals, and their misfunctioning could lead to several pathologies ranging from diseases caused by neuronal hyperexcitability, such as epilepsy, or traumatic injuries and painful diabetic neuropathy to autoimmune disorders. Among the members of this family, the Kv7.2 channel can form hetero-tetramers together with Kv7.3, forming the so-called M-channels, which are primary regulators of intrinsic electrical properties of neurons and of their responsiveness to synaptic inputs. Here, prompted by the similarity between the M-current and that in Kv7.2 alone, we perform a computational-based characterization of this channel in its different conformational states and in complex with the modulator retigabine. After validation of the structural models of the channel by comparison with experimental data, we investigate the effect of retigabine binding on the two extreme states of Kv7.2 (resting-closed and activated-open). Our results suggest that binding, so far structurally characterized only in the intermediate activated-closed state, is possible also in the other two functional states. Moreover, we show that some effects of this binding, such as increased flexibility of voltage sensing domains and propensity of the pore for open conformations, are virtually independent on the conformational state of the protein. Overall, our results provide new structural and dynamic insights into the functioning and the modulation of Kv7.2 and related channels.

Published
2022
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46. Divide and Conquer: A Tailored Solid-state NMR Approach to Study Large Membrane Protein Complexes

Author

Xiang, Sheng Qi, Pinto, Cecilia, Baldus, Marc, Sub NMR Spectroscopy, NMR Spectroscopy, Sub NMR Spectroscopy, and NMR Spectroscopy

Subjects
Protein Folding, Chemistry(all), Escherichia coli Proteins, Lipoproteins, Lipid Bilayers, Membrane Protein Complex, Membrane Proteins, Proton Detection, General Medicine, General Chemistry, NMR Spectroscopy, Catalysis, Isotopic Labelling, BAM Complex, Lipid-Linked Proteins
Abstract

Membrane proteins are known to exert many essential biological functions by forming complexes in cell membranes. An example refers to the β-barrel assembly machinery (BAM), a 200 kDa pentameric complex containing BAM proteins A–E that catalyzes the essential process of protein insertion into the outer membrane of gram-negative bacteria. While progress has been made in capturing three-dimensional structural snapshots of the BAM complex, the role of the lipoprotein BamC in the complex assembly in functional lipid bilayers has remained unclear. We have devised a component-selective preparation scheme to directly study BamC as part of the entire BAM complex in lipid bilayers. Combination with proton-detected solid-state NMR methods allowed us to probe the structure, dynamics, and supramolecular topology of full-length BamC embedded in the entire complex in lipid bilayers. Our approach may help decipher how individual proteins contribute to the dynamic formation and functioning of membrane protein complexes in membranes.

Published
2022

47. Using machine-learning-driven approaches to boost hot-spot's knowledge

Author

Rosário-Ferreira, Nícia, Bonvin, Alexandre M.J.J., Moreira, Irina S., Sub NMR Spectroscopy, and NMR Spectroscopy

Subjects
computational alanine scanning mutagenesis, Computational Mathematics, binding hot-spots, Taverne, Materials Chemistry, interaction energetics, protein–protein interactions, Physical and Theoretical Chemistry, Biochemistry, machine-learning algorithms, Computer Science Applications
Abstract

Understanding protein–protein interactions (PPIs) is fundamental to describe and to characterize the formation of biomolecular assemblies, and to establish the energetic principles underlying biological networks. One key aspect of these interfaces is the existence and prevalence of hot-spots (HS) residues that, upon mutation to alanine, negatively impact the formation of such protein–protein complexes. HS have been widely considered in research, both in case studies and in a few large-scale predictive approaches. This review aims to present the current knowledge on PPIs, providing a detailed understanding of the microspecifications of the residues involved in those interactions and the characteristics of those defined as HS through a thorough assessment of related field-specific methodologies. We explore recent accurate artificial intelligence-based techniques, which are progressively replacing well-established classical energy-based methodologies. This article is categorized under: Data Science > Databases and Expert Systems Structure and Mechanism > Computational Biochemistry and Biophysics Molecular and Statistical Mechanics > Molecular Interactions.

Published
2022

48. Matrix Effects in a Fluid Catalytic Cracking Catalyst Particle: Influence on Structure, Acidity, and Accessibility

Author

Velthoen, Marjolein E.Z., Lucini Paioni, Alessandra, Teune, Iris E., Baldus, Marc, Weckhuysen, Bert M., Sub Inorganic Chemistry and Catalysis, Sub NMR Spectroscopy, Inorganic Chemistry and Catalysis, NMR Spectroscopy, Sub Inorganic Chemistry and Catalysis, Sub NMR Spectroscopy, Inorganic Chemistry and Catalysis, and NMR Spectroscopy

Subjects
Boehmite, spectroscopy, Full Paper, 010405 organic chemistry, Chemistry, Organic Chemistry, Infrared spectroscopy, fluid catalytic cracking, General Chemistry, matrix effects, Full Papers, 010402 general chemistry, Fluid catalytic cracking, 01 natural sciences, Catalysis, 0104 chemical sciences, Zeolites | Hot Paper, Physisorption, Chemical engineering, Desorption, Zeolite, Brønsted–Lowry acid–base theory, acidity, binder effects
Abstract

Matrix effects in a fluid catalytic cracking (FCC) catalyst have been studied in terms of structure, accessibility, and acidity. An extensive characterization study into the structural and acidic properties of a FCC catalyst, its individual components (i.e., zeolite H‐Y, binder (boehmite/silica) and kaolin clay), and two model FCC catalyst samples containing only two components (i.e., zeolite‐binder and binder‐clay) was performed at relevant conditions. This allowed the drawing of conclusions about the role of each individual component, describing their mutual physicochemical interactions, establishing structure‐acidity relationships, and determining matrix effects in FCC catalyst materials. This has been made possible by using a wide variety of characterization techniques, including temperature‐programmed desorption of ammonia, infrared spectroscopy in combination with CO as probe molecule, transmission electron microscopy, X‐ray diffraction, Ar physisorption, and advanced nuclear magnetic resonance. By doing so it was, for example, revealed that a freshly prepared spray‐dried FCC catalyst appears as a physical mixture of its individual components, but under typical riser reactor conditions, the interaction between zeolite H‐Y and binder material is significant and mobile aluminum migrates and inserts from the binder into the defects of the zeolite framework, thereby creating additional Brønsted acid sites and restoring the framework structure., On the interplay between matrix and catalyst: A combination of advanced characterization techniques reveals that while a freshly prepared spray‐dried fluid catalytic cracking catalyst appears as a physical mixture of its individual components, significant matrix effects actually come into play under industrial riser reactor conditions, leading to changing Brønsted and Lewis acidity, pore accessibility as well as various structural changes.

Published
2020

49. Mode of action of teixobactins in cellular membranes

Author

Shukla, Rhythm, Medeiros-Silva, João, Parmar, Anish, Vermeulen, Bram J A, Das, Sanjit, Paioni, Alessandra Lucini, Jekhmane, Shehrazade, Lorent, Joseph, Bonvin, Alexandre M J J, Baldus, Marc, Lelli, Moreno, Veldhuizen, Edwin J A, Breukink, Eefjan, Singh, Ishwar, Weingarth, Markus, Sub NMR Spectroscopy, Sub Membrane Biochemistry & Biophysics, Moleculaire afweer, dI&I I&I-3, Sub NMR Spectroscopy, Sub Membrane Biochemistry & Biophysics, Moleculaire afweer, and dI&I I&I-3

Subjects
0301 basic medicine, Magnetic Resonance Spectroscopy, Science, Teixobactin, General Physics and Astronomy, 010402 general chemistry, medicine.disease_cause, Solid-state NMR, 01 natural sciences, Article, General Biochemistry, Genetics and Molecular Biology, Cell wall, Structure-Activity Relationship, 03 medical and health sciences, teixobactins, antibiotics, NMR, cellular membrane, Lipid II, Antibiotics, Cell Wall, Depsipeptides, medicine, Structure–activity relationship, Drug discovery and development, lcsh:Science, Mode of action, Multidisciplinary, Molecular Structure, biology, Lipid II, Chemistry, Cell Membrane, Pathogenic bacteria, General Chemistry, biology.organism_classification, Uridine Diphosphate N-Acetylmuramic Acid, Anti-Bacterial Agents, 3. Good health, 0104 chemical sciences, 030104 developmental biology, Membrane, Microscopy, Fluorescence, Liposomes, Biophysics, lcsh:Q, Bacterial infection, Bacteria
Abstract

The natural antibiotic teixobactin kills pathogenic bacteria without detectable resistance. The difficult synthesis and unfavourable solubility of teixobactin require modifications, yet insufficient knowledge on its binding mode impedes the hunt for superior analogues. Thus far, teixobactins are assumed to kill bacteria by binding to cognate cell wall precursors (Lipid II and III). Here we present the binding mode of teixobactins in cellular membranes using solid-state NMR, microscopy, and affinity assays. We solve the structure of the complex formed by an improved teixobactin-analogue and Lipid II and reveal how teixobactins recognize a broad spectrum of targets. Unexpectedly, we find that teixobactins only weakly bind to Lipid II in cellular membranes, implying the direct interaction with cell wall precursors is not the sole killing mechanism. Our data suggest an additional mechanism affords the excellent activity of teixobactins, which can block the cell wall biosynthesis by capturing precursors in massive clusters on membranes., The natural antibiotic teixobactin kills bacteria by direct binding to their cognate cell wall precursors (Lipid II and III). Here authors use solid-state NMR to reveal the native binding mode of teixobactins and show that teixobactins only weakly bind to Lipid II in anionic cellular membranes.

Published
2020

50. Direct observation of dynamic protein interactions involving human microtubules using solid-state NMR spectroscopy

Author

Luo, Yanzhang, Xiang, ShengQi, Hooikaas, Peter Jan, van Bezouwen, Laura, Jijumon, A S, Janke, Carsten, Förster, Friedrich, Akhmanova, Anna, Baldus, Marc, NMR Spectroscopy, Cryo-EM, Sub NMR Spectroscopy, Sub Cell Biology, Sub Cryo - EM, Celbiologie, Utrecht University [Utrecht], Intégrité du génome, ARN et cancer, Institut Curie [Paris]-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut Curie, Laboratoire Raymond Latarjet, Orsay, Institut Curie [Paris], NMR Spectroscopy, Cryo-EM, Sub NMR Spectroscopy, Sub Cell Biology, Sub Cryo - EM, and Celbiologie

Subjects
0301 basic medicine, Magnetic Resonance Spectroscopy, Science, Protein domain, General Physics and Astronomy, Total internal reflection microscopy, 010402 general chemistry, 01 natural sciences, Solid-state NMR, Microtubules, General Biochemistry, Genetics and Molecular Biology, Article, Protein–protein interaction, 03 medical and health sciences, Protein Domains, Microtubule, Tubulin, Electron microscopy, Humans, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], lcsh:Science, Cytoskeleton, Carbon Isotopes, Multidisciplinary, Binding Sites, biology, Nitrogen Isotopes, Chemistry, Protein dynamics, General Chemistry, 0104 chemical sciences, 3. Good health, Cytoskeletal proteins, 030104 developmental biology, Solid-state nuclear magnetic resonance, biology.protein, Biophysics, lcsh:Q, Microtubule-Associated Proteins, Post-translational modifications, HeLa Cells
Abstract

Microtubules are important components of the eukaryotic cytoskeleton. Their structural organization is regulated by nucleotide binding and many microtubule-associated proteins (MAPs). While cryo-EM and X-ray crystallography have provided detailed views of interactions between MAPs with the microtubule lattice, little is known about how MAPs and their intrinsically disordered regions interact with the dynamic microtubule surface. NMR carries the potential to directly probe such interactions but so far has been precluded by the low tubulin yield. We present a protocol to produce [13C, 15N]-labeled, functional microtubules (MTs) from human cells for solid-state NMR studies. This approach allowed us to demonstrate that MAPs can differently modulate the fast time-scale dynamics of C-terminal tubulin tails, suggesting distinct interaction modes. Our results pave the way for in-depth NMR studies of protein dynamics involved in MT assembly and their interactions with other cellular components., Microtubule (MT) organization is regulated by many microtubule-associated proteins (MAPs) that contain intrinsically disordered regions. Here authors produce [13C, 15N] labeled, functional microtubules from human cells for solid-state NMR which allows studying MAP-MT interactions.

Published
2020

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