Associate Research Prof. Jon Uranga

@article{funk-2024-multiple-redox-switches-of,
  title = {Multiple redox switches of the SARS-CoV-2 main protease in vitro provide opportunities for drug design},
  author = {Lisa-Marie Funk and Gereon Poschmann and Fabian Rabe von Pappenheim and Ashwin Chari and Kim M. Stegmann and Antje Dickmanns and Marie Wensien and Nora Eulig and Elham Paknia and Gabi Heyne and Elke Penka and Arwen R. Pearson and Carsten Berndt and Tobias Fritz and Sophia Bazzi and Jon Uranga and Ricardo A. Mata and Matthias Dobbelstein and Rolf Hilgenfeld and Ute Curth and Kai Tittmann},
  journal = {Nature Communications},
  year = {2024},
  volume = {15},
  number = {1},
  pages = {411},
  doi = {10.1038/s41467-023-44621-0},
  url = {https://doi.org/10.1038/s41467-023-44621-0},
}

@article{uranga-2023-the-catalytic-mechanism-of,
  title = {The Catalytic Mechanism of Acetoacetate Decarboxylase: A Detailed Study of Schiff Base Formation, Protonation States, and Their Impact on Catalysis},
  author = {Jon Uranga and Ricardo A. Mata},
  journal = {Journal of Chemical Information and Modeling},
  year = {2023},
  volume = {63},
  number = {10},
  pages = {3118-3127},
  doi = {10.1021/acs.jcim.3c00241},
  url = {https://doi.org/10.1021/acs.jcim.3c00241},
}

@article{10-1002-cphc-202300091,
  title = {One‐ and Two‐Electron Reductions in MiniSOG and their Implication in Catalysis**},
  author = {Oksana Azpitarte and Ane Zudaire and Jon Uranga and Xabier Lopez and Luca Salassa and Elena Formoso and Elixabete Rezabal},
  journal = {ChemPhysChem},
  year = {2023},
  volume = {24},
  number = {15},
  doi = {10.1002/cphc.202300091},
  url = {https://doi.org/10.1002/cphc.202300091},
}

@article{l-ce-2023-modulating-secondary-structure-motifs,
  title = {Modulating Secondary Structure Motifs Through Photo‐Labile Peptide Staples},
  author = {Ilze Lāce and Sophia Bazzi and Jon Uranga and Anastasiya Schirmacher and Ulf Diederichsen and Ricardo A. Mata and Nadja A. Simeth},
  journal = {ChemBioChem},
  year = {2023},
  volume = {24},
  number = {16},
  pages = {e202300270},
  doi = {10.1002/cbic.202300270},
  url = {https://doi.org/10.1002/cbic.202300270},
}

@article{ye-2023-mechanisms-of-cysteine-lysine,
  title = {Mechanisms of Cysteine‐Lysine Covalent Linkage—The Role of Reactive Oxygen Species and Competition with Disulfide Bonds**},
  author = {Jin Ye and Sophia Bazzi and Tobias Fritz and Kai Tittmann and Ricardo A. Mata and Jon Uranga},
  journal = {Angewandte Chemie International Edition},
  year = {2023},
  volume = {62},
  number = {36},
  pages = {e202304163},
  doi = {10.1002/anie.202304163},
  url = {https://doi.org/10.1002/anie.202304163},
}

@article{uranga-2023-dynamic-protonation-states-underlie,
  title = {Dynamic Protonation States Underlie Carbene Formation in ThDP-Dependent Enzymes: A Theoretical Study},
  author = {Jon Uranga and Fabian Rabe von Pappenheim and Kai Tittmann and Ricardo A. Mata},
  journal = {The Journal of Physical Chemistry B},
  year = {2023},
  volume = {127},
  number = {44},
  pages = {acs.jpcb.3c03137},
  doi = {10.1021/acs.jpcb.3c03137},
  url = {https://doi.org/10.1021/acs.jpcb.3c03137},
}

@article{pappenheim-2022-widespread-occurrence-of-covalent,
  title = {Widespread occurrence of covalent lysine–cysteine redox switches in proteins},
  author = {Fabian Rabe von Pappenheim and Marie Wensien and Jin Ye and Jon Uranga and Iker Irisarri and Jan de Vries and Lisa-Marie Funk and Ricardo A. Mata and Kai Tittmann},
  journal = {Nature Chemical Biology},
  year = {2022},
  volume = {18},
  number = {4},
  pages = {368-375},
  doi = {10.1038/s41589-021-00966-5},
  url = {https://doi.org/10.1038/s41589-021-00966-5},
}

@article{funk-2022-redox-regulation-of-the,
  title = {Redox regulation of the SARS-CoV-2 main protease provides new opportunities for drug design},
  author = {Lisa-Marie Funk and Gereon Poschmann and Ashwin Chari and Fabian Rabe von Pappenheim and Kim-Maren Stegmann and Antje Dickmanns and Nora Eulig and Marie Wensien and Elham Paknia and Gabi Heyne and Elke Penka and Arwen R. Pearson and Carsten Berndt and Tobias Fritz and Sophia Bazzi and Jon Uranga and Ricardo A. Mata and Matthias Dobbelstein and Rolf Hilgenfeld and Ute Curth and Kai Tittmann},
  year = {2022},
  doi = {10.1101/2022.04.18.487732},
  url = {https://doi.org/10.1101/2022.04.18.487732},
}

@article{rindfleisch-2022-ground-state-destabilization-by,
  title = {Ground-state destabilization by electrostatic repulsion is not a driving force in orotidine-5′-monophosphate decarboxylase catalysis},
  author = {Sören Rindfleisch and Matthias Krull and Jon Uranga and Tobias Schmidt and Fabian Rabe von Pappenheim and Laura Liliana Kirck and Angeliki Balouri and Thomas Schneider and Ashwin Chari and Ronald Kluger and Gleb Bourenkov and Ulf Diederichsen and Ricardo A. Mata and Kai Tittmann},
  journal = {Nature Catalysis},
  year = {2022},
  volume = {5},
  number = {4},
  pages = {332-341},
  doi = {10.1038/s41929-022-00771-w},
  url = {https://doi.org/10.1038/s41929-022-00771-w},
}

@article{uranga-2021-theoretical-studies-of-the,
  title = {Theoretical Studies of the Acid–Base Equilibria in a Model Active Site of the Human 20S Proteasome},
  author = {Jon Uranga and Lukas Hasecke and Jonny Proppe and Jan Fingerhut and Ricardo A. Mata},
  journal = {Journal of Chemical Information and Modeling},
  year = {2021},
  volume = {61},
  number = {4},
  pages = {1942-1953},
  doi = {10.1021/acs.jcim.0c01459},
  url = {https://doi.org/10.1021/acs.jcim.0c01459},
}

@article{wensien-2021-a-lysine-cysteine-redox,
  title = {A lysine–cysteine redox switch with an NOS bridge regulates enzyme function},
  author = {Marie Wensien and Fabian Rabe von Pappenheim and Lisa-Marie Funk and Patrick Kloskowski and Ute Curth and Ulf Diederichsen and Jon Uranga and Jin Ye and Pan Fang and Kuan-Ting Pan and Henning Urlaub and Ricardo A. Mata and Viktor Sautner and Kai Tittmann},
  journal = {Nature},
  year = {2021},
  volume = {593},
  number = {7859},
  pages = {460-464},
  doi = {10.1038/s41586-021-03513-3},
  url = {https://doi.org/10.1038/s41586-021-03513-3},
}

@article{dai-2019-low-barrier-hydrogen-bonds,
  title = {Low-barrier hydrogen bonds in enzyme cooperativity},
  author = {Shaobo Dai and Lisa-Marie Funk and Fabian Rabe von Pappenheim and Viktor Sautner and Mirko Paulikat and Benjamin Schröder and Jon Uranga and Ricardo A. Mata and Kai Tittmann},
  journal = {Nature},
  year = {2019},
  volume = {573},
  number = {7775},
  pages = {609-613},
  doi = {10.1038/s41586-019-1581-9},
  url = {https://doi.org/10.1038/s41586-019-1581-9},
}

@article{10-1021-acs-jpcb-7b12450,
  title = {Oxidation of Acid, Base, and Amide Side-Chain Amino Acid Derivatives via Hydroxyl Radical},
  author = {J. Uranga and J. I. Mujika and R. Grande-Aztatzi and J. M. Matxain},
  journal = {Journal of Physical Chemistry B},
  year = {2018},
  volume = {122},
  number = {19},
  pages = {4956-4971},
  doi = {10.1021/acs.jpcb.7b12450},
  url = {https://doi.org/10.1021/acs.jpcb.7b12450},
}

@article{10-1039-c7cp03319b,
  title = {Photosensitization mechanism of Cu(II) porphyrinst},
  author = {Jon Uranga and Jon M. Matxain and Xabier Lopez and Jesus M. Ugalde and David Casanova},
  journal = {PHYSICAL CHEMISTRY CHEMICAL PHYSICS},
  year = {2017},
  volume = {19},
  number = {31},
  pages = {20533-20540},
  doi = {10.1039/c7cp03319b},
  url = {https://doi.org/10.1039/c7cp03319b},
}

@article{manzoni-2017-can-system-truncation-speed,
  title = {Can System Truncation Speed up Ligand-Binding Calculations with Periodic Free-Energy Simulations?},
  author = {Francesco Manzoni and Jon Uranga and Samuel Genheden and Ulf Ryde},
  journal = {Journal of Chemical Information and Modeling},
  year = {2017},
  volume = {57},
  number = {11},
  pages = {2865-2873},
  doi = {10.1021/acs.jcim.7b00324},
  url = {https://doi.org/10.1021/acs.jcim.7b00324},
}

@article{10-1039-c6cp06529e,
  title = {A computational study of radical initiated protein backbone homolytic dissociation on all natural amino acids},
  author = {J. Uranga and O. Lakuntza and E. Ramos-Cordoba and J. M. Matxain and J. I. Mujika},
  journal = {Physical Chemistry Chemical Physics},
  year = {2016},
  volume = {18},
  number = {45},
  pages = {30972-30981},
  doi = {10.1039/c6cp06529e},
  url = {https://doi.org/10.1039/c6cp06529e},
}

@article{10-1021-acs-jpcb-5b09825,
  title = {center dot OH Oxidation Toward S- and OH-Containing Amino Acids},
  author = {J. Uranga and J. I. Mujika and J. M. Matxain},
  journal = {Journal of Physical Chemistry B},
  year = {2015},
  volume = {119},
  number = {50},
  pages = {15430-15442},
  doi = {10.1021/acs.jpcb.5b09825},
  url = {https://doi.org/10.1021/acs.jpcb.5b09825},
}

@article{10-1002-chem-201203862,
  title = {Computational Study on the Attack of (OH)-O-center dot Radicals on Aromatic Amino Acids},
  author = {J. I. Mujika and J. Uranga and J. M. Matxain},
  journal = {Chemistry-a European Journal},
  year = {2013},
  volume = {19},
  number = {21},
  pages = {6862-6873},
  doi = {10.1002/chem.201203862},
  url = {https://doi.org/10.1002/chem.201203862},
}

@article{10-1002-cphc-201200205,
  title = {The Nature of Chemical Bonds from PNOF5 Calculations},
  author = {J. M. Matxain and M. Piris and J. Uranga and X. Lopez and G. Merino and J. M. Ugalde},
  journal = {Chemphyschem},
  year = {2012},
  volume = {13},
  number = {9},
  pages = {2297-2303},
  doi = {10.1002/cphc.201200205},
  url = {https://doi.org/10.1002/cphc.201200205},
}