{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T14:07:08Z","timestamp":1790086028368,"version":"4.0.1"},"reference-count":73,"publisher":"American Chemical Society (ACS)","issue":"18","license":[{"start":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T00:00:00Z","timestamp":1788220800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001655","name":"Deutscher Akademischer Austauschdienst","doi-asserted-by":"publisher","award":["57814425"],"award-info":[{"award-number":["57814425"]}],"id":[{"id":"10.13039\/501100001655","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100010570","name":"Nieders?chsisches Ministerium f?r Wissenschaft und Kultur","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100010570","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["395940726 - SFB 1372"],"award-info":[{"award-number":["395940726 - SFB 1372"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["514664767 -  TRR386"],"award-info":[{"award-number":["514664767 -  TRR386"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["533653176 -  EXC-3051"],"award-info":[{"award-number":["533653176 -  EXC-3051"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["541484920"],"award-info":[{"award-number":["541484920"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,9,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Amino acid radicals play fundamental roles in many physiological processes ranging from DNA repair and synthesis to respiration and magnetoreception. In particular, tryptophan and tyrosine in their radical states often serve as key intermediates in electron transfer processes. Importantly, the radical states can be long-lived enough to trigger conformational changes in proteins that can be important for biomolecular signaling. Molecular dynamics (MD) simulations provide a perfect means to study the effects of tyrosine and tryptophan oxidation on the conformational dynamics of proteins and to reveal molecular mechanisms of their biological roles. However, a reliable application of MD simulations requires a comprehensive set of molecular mechanics parameters to describe amino acid residues in the radical states. Here, we present a complete set of molecular mechanics parameters for the radical states of tyrosine and tryptophan residues, developed within the framework of the CHARMM force field. Optimized to target a large body of quantum mechanical data, the parameters provide a robust description of the intramolecular energetics, interactions with water, and electrostatic properties of tyrosine and tryptophan in their radical states. The parameters were tested and validated through simulations of model protein systems including the \u03b13W protein, a \u03b2-hairpin maquette, and an avian cryptochrome. The simulation results demonstrate the effects of tyrosine and tryptophan oxidation on side-chain dynamics, conformational changes, and general biophysical properties of proteins. We expect that the presented set of force field parameters would be useful for the computational studies of various biological processes that involve oxidation of the tyrosine and tryptophan residues.<\/jats:p>","DOI":"10.1021\/acs.jctc.6c01280","type":"journal-article","created":{"date-parts":[[2026,9,3]],"date-time":"2026-09-03T10:34:09Z","timestamp":1788431649000},"page":"9790-9801","source":"Crossref","is-referenced-by-count":0,"title":["Developing CHARMM\nForce Field Parameters for the Radical\nStates of Tryptophan and Tyrosine"],"prefix":"10.1021","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5890-4123","authenticated-orcid":true,"given":"Andrei Y.","family":"Kostritski","sequence":"first","affiliation":[{"name":"Carl von Ossietzky Universita\u0308t Oldenburg , , Carl-von-Ossietzky Str. 9-11 , ,","place":["Oldenburg, Germany, 26111"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5128-263X","authenticated-orcid":true,"given":"Jonathan","family":"Hungerland","sequence":"additional","affiliation":[{"name":"Carl von Ossietzky Universita\u0308t Oldenburg , , Carl-von-Ossietzky Str. 9-11 , ,","place":["Oldenburg, Germany, 26111"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christian","family":"Schuster","sequence":"additional","affiliation":[{"name":"Carl von Ossietzky Universita\u0308t Oldenburg , , Carl-von-Ossietzky Str. 9-11 , ,","place":["Oldenburg, Germany, 26111"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8626-145X","authenticated-orcid":true,"given":"Ilia A.","family":"Solov\u2019yov","sequence":"additional","affiliation":[{"name":"Carl von Ossietzky Universita\u0308t Oldenburg , , Carl-von-Ossietzky Str. 9-11 , ,","place":["Oldenburg, Germany, 26111"]},{"name":"Carl von Ossietzky Universita\u0308t Oldenburg , , Carl-von-Ossietzky Str. 9-11 , ,","place":["Oldenburg, Germany, 26111"]},{"name":"Carl von Ossietzky Universita\u0308t Oldenburg , , ,","place":["Oldenburg, Germany, 26129"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,9,1]]},"reference":[{"key":"2026092209065934200_cit1","doi-asserted-by":"publisher","first-page":"453","DOI":"10.1146\/annurev-biophys-100521-103031","article-title":"Insights into\nthe Thermodynamics and Kinetics of Amino-Acid Radicals in Proteins","volume":"51","author":"Tommos","year":"2022","journal-title":"Annu. Rev. Biophys."},{"key":"2026092209065934200_cit2","doi-asserted-by":"publisher","first-page":"13463","DOI":"10.1021\/jacs.1c05952","article-title":"Radicals in Biology:\nYour Life Is in Their Hands","volume":"143","author":"Stubbe","year":"2021","journal-title":"J. Am. Chem. Soc."},{"key":"2026092209065934200_cit3","doi-asserted-by":"publisher","first-page":"514","DOI":"10.1126\/science.6306767","article-title":"Ribonucleotide\nReductase\u2013a Radical Enzyme","volume":"221","author":"Reichard","year":"1983","journal-title":"Science"},{"key":"2026092209065934200_cit4","doi-asserted-by":"publisher","first-page":"5694","DOI":"10.1021\/bi00476a008","article-title":"Excited-state\nproperties of Escherichia coli DNA\nphotolyase in the picosecond\nto millisecond time scale","volume":"29","author":"Heelis","year":"1990","journal-title":"Biochemistry"},{"key":"2026092209065934200_cit5","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1111\/php.12197","article-title":"Formation and Direct Repair of UV\u2013induced Dimeric\nDNA Pyrimidine Lesions","volume":"90","author":"Kneuttinger","year":"2014","journal-title":"Photochem. Photobiol."},{"key":"2026092209065934200_cit6","doi-asserted-by":"publisher","first-page":"7099","DOI":"10.1073\/pnas.84.20.7099","article-title":"Tyrosine radicals\nare involved in the photosynthetic\noxygen-evolving system","volume":"84","author":"Barry","year":"1987","journal-title":"Proc. Natl. Acad. Sci.\nU. S. A."},{"key":"2026092209065934200_cit7","doi-asserted-by":"publisher","first-page":"217","DOI":"10.1016\/j.bbabio.2003.09.015","article-title":"Photosynthetic water oxidation: the\nrole of tyrosine radicals","volume":"1655","author":"Nugent","year":"2004","journal-title":"Biochim. 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Biochem."},{"key":"2026092209065934200_cit13","doi-asserted-by":"publisher","first-page":"586","DOI":"10.1038\/35014644","article-title":"Intraprotein\nradical transfer during photoactivation of DNA photolyase","volume":"405","author":"Aubert","year":"2000","journal-title":"Nature"},{"key":"2026092209065934200_cit14","doi-asserted-by":"publisher","first-page":"20210601","DOI":"10.1098\/rsif.2021.0601","article-title":"Cryptochrome magnetoreception:\nfour tryptophans could be better than three","volume":"18","author":"Wong","year":"2021","journal-title":"J. R. Soc. Interface"},{"key":"2026092209065934200_cit15","doi-asserted-by":"publisher","first-page":"4393","DOI":"10.1021\/ja068805f","article-title":"Proton-Coupled Electron\nTransfer in a Biomimetic Peptide\nas a Model of Enzyme Regulatory Mechanisms","volume":"129","author":"Sibert","year":"2007","journal-title":"J. Am. Chem. 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Lett."},{"key":"2026092209065934200_cit21","doi-asserted-by":"publisher","first-page":"11550","DOI":"10.1021\/jacs.0c04655","article-title":"Proton-Coupled Electron\nTransfer\nfrom Tyrosine in the Interior of a de novo Protein: Mechanisms and\nPrimary Proton Acceptor","volume":"142","author":"Nilsen-Moe","year":"2020","journal-title":"J. Am. Chem. Soc."},{"key":"2026092209065934200_cit22","doi-asserted-by":"publisher","first-page":"3536","DOI":"10.1021\/acs.jpcb.6b09481","article-title":"Redox-Driven Conformational\nDynamics in a Photosystem-II-Inspired \u03b2-Hairpin\nMaquette Determined through Spectroscopy and Simulation","volume":"121","author":"Hwang","year":"2017","journal-title":"J. Phys. Chem. 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Theory Comput."},{"key":"2026092209065934200_cit32","doi-asserted-by":"publisher","first-page":"3586","DOI":"10.1021\/jp973084f","article-title":"All-Atom Empirical\nPotential for Molecular Modeling\nand Dynamics Studies of Proteins","volume":"102","author":"MacKerell","year":"1998","journal-title":"J. Phys. Chem.\nB"},{"key":"2026092209065934200_cit33","doi-asserted-by":"publisher","first-page":"19449","DOI":"10.1073\/pnas.1907875116","article-title":"Chemical and structural analysis of a photoactive vertebrate\ncryptochrome from pigeon","volume":"116","author":"Zoltowski","year":"2019","journal-title":"Proc. Natl. Acad.\nSci. U. S. A."},{"key":"2026092209065934200_cit34","doi-asserted-by":"publisher","first-page":"3543","DOI":"10.1021\/ct4003477","article-title":"Automated Force Field Parameterization for Nonpolarizable and Polarizable\nAtomic Models Based on Ab Initio Target Data","volume":"9","author":"Huang","year":"2013","journal-title":"J. Chem. 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