{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T12:54:48Z","timestamp":1791291288694,"version":"4.3.0"},"reference-count":57,"publisher":"American Chemical Society (ACS)","issue":"19","license":[{"start":{"date-parts":[[2026,9,8]],"date-time":"2026-09-08T00:00:00Z","timestamp":1788825600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2026,9,8]],"date-time":"2026-09-08T00:00:00Z","timestamp":1788825600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2026,9,8]],"date-time":"2026-09-08T00:00:00Z","timestamp":1788825600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-045"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["2041692"],"award-info":[{"award-number":["2041692"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000052","name":"NIH Office of the Director","doi-asserted-by":"publisher","award":["S10OD032175"],"award-info":[{"award-number":["S10OD032175"]}],"id":[{"id":"10.13039\/100000052","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["P20GM130422"],"award-info":[{"award-number":["P20GM130422"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["R35GM156443"],"award-info":[{"award-number":["R35GM156443"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000066","name":"National Institute of Environmental Health Sciences","doi-asserted-by":"publisher","award":["P30ES032755"],"award-info":[{"award-number":["P30ES032755"]}],"id":[{"id":"10.13039\/100000066","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,10,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Cross-linking mass spectrometry (XL-MS) with photoactivatable reagents has been increasingly applied to probe protein conformational dynamics; however, its sensitivity to shifts in conformational equilibrium involving transient, sparsely populated docked states within multidomain proteins remains largely unexplored. Mammalian nitric oxide synthase (NOS), a family of modular redox enzymes, relies on large-amplitude FMN domain swinging motions and local, dynamic interdomain FMN\u2013heme docking to function. This makes it a stringent test case for evaluating how sensitive photoactivated XL-MS is to shifts in the docking equilbrium. In our previous work, quantitative XL-MS using the primarily lysine-reactive homobifunctional cross-linker DSBU revealed E546N mutation-induced decreases in specific intersubunit FMN\u2013heme cross-links in an oxygenase\/FMN construct of human inducible NOS (iNOS). Here, we extended these XL-MS studies to sulfo-SDA, a heterobifunctional, photoactivatable cross-linker with ultrafast reactivity and broad residue specificity. SDA captured interdomain FMN\u2013heme cross-links at the docking interfaces but, unlike DSBU, did not reveal statistically robust changes in the abundances of these cross-links between wild-type and E546N mutant. SDA produced a higher proportion of dead-end labeling products for iNOS oxyFMN proteins, particularly the E546N mutant, than for the conformationally stable protein BSA. Moreover, the SDA cross-link distance restraints were largely satisfied by a minimal subset of docked states with distinct FMN domain orientations, whereas DSBU cross-links require a combination of docked and undocked conformations for optimal restraint satisfaction. These findings reflect the short effective distance range and near-instantaneous reactivity of SDA, which restrict FMN\u2013heme cross-link formation to a narrow subset of transient docking states. Taken together, these results underscore the importance of selecting appropriate cross-linking reagents and employing complementary cross-linkers to define the conformational landscapes of dynamic multidomain proteins.<\/jats:p>","DOI":"10.1021\/acs.biochem.6c00511","type":"journal-article","created":{"date-parts":[[2026,9,8]],"date-time":"2026-09-08T19:01:53Z","timestamp":1788894113000},"page":"2986-3002","source":"Crossref","is-referenced-by-count":0,"title":["Photoactivated\nCross-Linking Mass Spectrometry for\nProbing Multidomain Protein Dynamics in Inducible Nitric Oxide Synthase"],"prefix":"10.1021","volume":"65","author":[{"given":"Ting","family":"Jiang","sequence":"first","affiliation":[{"name":"University of New Mexico , , , ,","place":["Albuquerque, New Mexico, United States, 87131"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haikun","family":"Zhang","sequence":"additional","affiliation":[{"name":"University of New Mexico , , , ,","place":["Albuquerque, New Mexico, United States, 87131"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yadav Prasad","family":"Gyawali","sequence":"additional","affiliation":[{"name":"University of New Mexico , , , ,","place":["Albuquerque, New Mexico, United States, 87131"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rebecca","family":"Owopetu","sequence":"additional","affiliation":[{"name":"University of New Mexico , , , ,","place":["Albuquerque, New Mexico, United States, 87131"]},{"name":"University of New Mexico , , , ,","place":["Albuquerque, New Mexico, United States, 87131"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kanghyun","family":"Lee","sequence":"additional","affiliation":[{"name":"University of California, San Francisco , , , ,","place":["San Francisco, California, United States, 94158"]},{"name":"University of California, San Francisco , , , ,","place":["San Francisco, California, United States, 94158"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4542-6497","authenticated-orcid":true,"given":"Changjian","family":"Feng","sequence":"additional","affiliation":[{"name":"University of New Mexico , , , ,","place":["Albuquerque, New Mexico, United States, 87131"]},{"name":"University of New Mexico , , , ,","place":["Albuquerque, New Mexico, United States, 87131"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,9,8]]},"reference":[{"key":"2026100608071763600_cit1","doi-asserted-by":"publisher","first-page":"1000","DOI":"10.1038\/s41594-018-0147-0","article-title":"Cross-linking mass spectrometry: methods and applications\nin structural, molecular and systems biology","volume":"25","author":"O\u2019Reilly","year":"2018","journal-title":"Nat. Struct. Mol. Biol."},{"key":"2026100608071763600_cit2","doi-asserted-by":"publisher","first-page":"583","DOI":"10.1038\/s41586-021-03819-2","article-title":"Highly accurate protein\nstructure prediction with AlphaFold","volume":"596","author":"Jumper","year":"2021","journal-title":"Nature"},{"key":"2026100608071763600_cit3","doi-asserted-by":"publisher","first-page":"2232","DOI":"10.1021\/acs.biochem.3c00245","article-title":"Probing protein dynamics\nin neuronal nitric oxide synthase by quantitative\ncross-linking mass spectrometry","volume":"62","author":"Jiang","year":"2023","journal-title":"Biochemistry"},{"key":"2026100608071763600_cit4","doi-asserted-by":"publisher","first-page":"1395","DOI":"10.1021\/acs.biochem.4c00157","article-title":"Mapping the Intersubunit\nInterdomain FMN-Heme Interactions in Neuronal\nNitric Oxide Synthase by Targeted Quantitative Cross-Linking Mass\nSpectrometry","volume":"63","author":"Jiang","year":"2024","journal-title":"Biochemistry"},{"key":"2026100608071763600_cit5","doi-asserted-by":"publisher","first-page":"110673","DOI":"10.1016\/j.jbc.2025.110673","article-title":"Deciphering\nmutational effects on inducible NO synthase conformational dynamics\nvia quantitative cross-linking mass spectrometry and AlphaFold2 subsampling","volume":"301","author":"Jiang","year":"2025","journal-title":"J. Biol. Chem."},{"key":"2026100608071763600_cit6","doi-asserted-by":"publisher","first-page":"887","DOI":"10.1016\/j.str.2026.05.001","article-title":"Cross-linking with diazirines: Bright\nsides and blind spots","volume":"34","author":"Sinz","year":"2026","journal-title":"Structure"},{"key":"2026100608071763600_cit7","doi-asserted-by":"publisher","first-page":"103102","DOI":"10.1016\/j.sbi.2025.103102","article-title":"Photo-crosslinkers\nboost structural information from\ncrosslinking mass spectrometry","volume":"93","author":"Ciancone","year":"2025","journal-title":"Curr. Opin.\nStruct. Biol."},{"key":"2026100608071763600_cit8","doi-asserted-by":"publisher","DOI":"10.1083\/jcb.202507084","article-title":"A Rab1 interactome\nilluminates a dual role in autophagy and membrane trafficking","volume":"225","author":"van Vliet","year":"2026","journal-title":"J. Cell Biol."},{"key":"2026100608071763600_cit9","doi-asserted-by":"publisher","first-page":"63","DOI":"10.1038\/s41594-025-01688-1","article-title":"Phosphorylation-dependent\ntuning of mRNA deadenylation rates","volume":"33","author":"Stowell","year":"2026","journal-title":"Nat. Struct.\nMol. Biol."},{"key":"2026100608071763600_cit10","doi-asserted-by":"publisher","first-page":"108445","DOI":"10.1016\/j.jbc.2025.108445","article-title":"Determining T-cell receptor binding orientation and\nPeptide-HLA interactions using cross-linking mass spectrometry","volume":"301","author":"Powell","year":"2025","journal-title":"J. Biol. Chem."},{"key":"2026100608071763600_cit11","doi-asserted-by":"publisher","first-page":"6060","DOI":"10.1038\/s41467-024-50315-y","article-title":"Dissecting diazirine\nphoto-reaction mechanism for protein residue-specific cross-linking\nand distance mapping","volume":"15","author":"Jiang","year":"2024","journal-title":"Nat. Commun."},{"key":"2026100608071763600_cit12","doi-asserted-by":"publisher","first-page":"881","DOI":"10.1038\/s41594-022-00820-9","article-title":"The DNA-damage kinase\nATR activates the FANCD2-FANCI clamp by priming it for ubiquitination","volume":"29","author":"Sijacki","year":"2022","journal-title":"Nat. Struct. Mol. Biol."},{"key":"2026100608071763600_cit13","doi-asserted-by":"publisher","first-page":"593","DOI":"10.1042\/bj3570593","article-title":"Nitric oxide synthases:\nstructure,\nfunction and inhibition","volume":"357","author":"Alderton","year":"2001","journal-title":"Biochem. J."},{"key":"2026100608071763600_cit14","doi-asserted-by":"publisher","first-page":"108282","DOI":"10.1016\/j.jbc.2025.108282","article-title":"Emerging approaches\nto investigating\nfunctional protein dynamics in modular redox enzymes: Nitric oxide\nsynthase as a model system","volume":"301","author":"Jiang","year":"2025","journal-title":"J. Biol. 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Chem."},{"key":"2026100608071763600_cit27","doi-asserted-by":"publisher","first-page":"6940","DOI":"10.1021\/ja902141v","article-title":"Mutations in the FMN\ndomain modulate MCD spectra of the heme site in the oxygenase domain\nof inducible nitric oxide synthase","volume":"131","author":"Sempombe","year":"2009","journal-title":"J. Am. Chem.\nSoc."},{"key":"2026100608071763600_cit28","doi-asserted-by":"publisher","first-page":"6859","DOI":"10.1021\/ic200952c","article-title":"Mutation in the flavin\nmononucleotide domain modulates magnetic circular dichroism spectra\nof the iNOS ferric cyano complex in a substrate-specific manner","volume":"50","author":"Sempombe","year":"2011","journal-title":"Inorg. Chem."},{"key":"2026100608071763600_cit29","doi-asserted-by":"publisher","first-page":"4795","DOI":"10.1021\/ic3020892","article-title":"Regulatory role of\nGlu546 in flavin mononucleotide\u2500heme electron transfer in human\ninducible nitric oxide synthase","volume":"52","author":"Li","year":"2013","journal-title":"Inorg. Chem."},{"key":"2026100608071763600_cit30","doi-asserted-by":"publisher","first-page":"4335","DOI":"10.1016\/j.febslet.2010.09.028","article-title":"Electron transfer\nin a human inducible nitric oxide synthase oxygenase\/FMN construct\nco-expressed with the N-terminal globular domain of calmodulin","volume":"584","author":"Feng","year":"2010","journal-title":"FEBS Lett."},{"key":"2026100608071763600_cit31","doi-asserted-by":"publisher","DOI":"10.15252\/msb.20198994","article-title":"An integrated\nworkflow for crosslinking\nmass spectrometry","volume":"15","author":"Mendes","year":"2019","journal-title":"Mol. Syst. Biol."},{"key":"2026100608071763600_cit32","doi-asserted-by":"publisher","first-page":"966","DOI":"10.1093\/bioinformatics\/btq054","article-title":"Skyline: an open source document editor for creating\nand analyzing targeted proteomics experiments","volume":"26","author":"MacLean","year":"2010","journal-title":"Bioinformatics"},{"key":"2026100608071763600_cit33","first-page":"659707","article-title":"Boltz-2: Towards Accurate and Efficient Binding Affinity\nPrediction","author":"Passaro","year":"2025","journal-title":"bioRxiv"},{"key":"2026100608071763600_cit34","doi-asserted-by":"publisher","first-page":"7866","DOI":"10.1038\/s41467-024-51771-2","article-title":"Modelling protein complexes with crosslinking mass\nspectrometry and deep learning","volume":"15","author":"Stahl","year":"2024","journal-title":"Nat. Commun."},{"key":"2026100608071763600_cit35","first-page":"502811","article-title":"Uni-Fold: An Open-Source Platform for Developing Protein\nFolding\nModels beyond AlphaFold","author":"Li","year":"2022","journal-title":"bioRxiv"},{"key":"2026100608071763600_cit36","doi-asserted-by":"publisher","first-page":"168656","DOI":"10.1016\/j.jmb.2024.168656","article-title":"xiVIEW: Visualisation\nof Crosslinking Mass Spectrometry Data","volume":"436","author":"Combe","year":"2024","journal-title":"J. Mol.\nBiol."},{"key":"2026100608071763600_cit37","doi-asserted-by":"publisher","first-page":"3498","DOI":"10.1021\/acs.jpca.5c00801","article-title":"Photodissociation\nDynamics of the Simplest Diazirine:\nCyclo-CH2N2 \u2192 CH2 + N2","volume":"129","author":"Datta","year":"2025","journal-title":"J. Phys. Chem.\nA"},{"key":"2026100608071763600_cit38","doi-asserted-by":"publisher","DOI":"10.1002\/chem.202500414","article-title":"The Versatility of Diazirines: Properties, Synthetic and Modern Applications","volume":"31","author":"Lepage","year":"2025","journal-title":"Chem. A Euro. J."},{"key":"2026100608071763600_cit39","doi-asserted-by":"publisher","first-page":"6153","DOI":"10.1002\/ejoc.201100224","article-title":"Valence\nIsomerization between Diazo Compounds and Diazirines","volume":"2011","author":"Korneev","year":"2011","journal-title":"Eur. J. Org. Chem."},{"key":"2026100608071763600_cit40","doi-asserted-by":"publisher","first-page":"828","DOI":"10.1016\/S0009-2614(98)00370-4","article-title":"Direct\nformation of CH2 (b\u0303 1B1) in the near-UV photodissociation of\ndiazirine","volume":"288","author":"Lim","year":"1998","journal-title":"Chem. Phys. Lett."},{"key":"2026100608071763600_cit41","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1313331110","article-title":"Nitric\noxide synthase domain interfaces regulate electron transfer and calmodulin\nactivation","volume":"110","author":"Smith","year":"2013","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"2026100608071763600_cit42","doi-asserted-by":"publisher","first-page":"30708","DOI":"10.1074\/jbc.M109.031682","article-title":"Regulation of\ninterdomain interactions by calmodulin in inducible nitric oxide synthase","volume":"284","author":"Xia","year":"2009","journal-title":"J. Biol. Chem."},{"key":"2026100608071763600_cit43","doi-asserted-by":"publisher","first-page":"12059","DOI":"10.1021\/ja104461p","article-title":"Pulsed EPR determination of the distance between heme iron and FMN\ncenters in a human inducible nitric oxide synthase","volume":"132","author":"Astashkin","year":"2010","journal-title":"J. Am. Chem. Soc."},{"key":"2026100608071763600_cit44","doi-asserted-by":"publisher","first-page":"1109","DOI":"10.1038\/s41592-022-01585-1","article-title":"US-align: universal\nstructure alignments of proteins, nucleic acids, and macromolecular\ncomplexes","volume":"19","author":"Zhang","year":"2022","journal-title":"Nat. Methods"},{"key":"2026100608071763600_cit45","doi-asserted-by":"publisher","first-page":"bbac316","DOI":"10.1093\/bib\/bbac316","article-title":"SpotLink enables\nsensitive and precise identification of site nonspecific cross-links\nat the proteome scale","volume":"23","author":"Zhang","year":"2022","journal-title":"Brief Bioinform"},{"key":"2026100608071763600_cit46","doi-asserted-by":"publisher","first-page":"6558","DOI":"10.1038\/s41467-026-73272-0","article-title":"Inherent MS-cleavability of diazirine\nphoto-cross-links enables residue-level structural analysis","volume":"17","author":"Jiang","year":"2026","journal-title":"Nat. Commun."},{"key":"2026100608071763600_cit47","doi-asserted-by":"publisher","first-page":"128","DOI":"10.1038\/s42003-025-09407-8","article-title":"Towards a universal\ncross-linking mass spectrometry approach for protein structure analysis\nwith homo-bi-functional photo-activatable cross-linkers","volume":"9","author":"Ser","year":"2025","journal-title":"Commun. Biol."},{"key":"2026100608071763600_cit48","doi-asserted-by":"crossref","DOI":"10.1002\/pro.4792","article-title":"UCSF ChimeraX:\nTools for structure\nbuilding and analysis","volume":"32","author":"Meng","year":"2023","journal-title":"Protein Sci."},{"key":"2026100608071763600_cit49","doi-asserted-by":"publisher","first-page":"1810","DOI":"10.1038\/s41587-023-01704-z","article-title":"Protein structure\nprediction with in-cell photo-crosslinking mass spectrometry and deep\nlearning","volume":"41","author":"Stahl","year":"2023","journal-title":"Nat. Biotechnol."},{"key":"2026100608071763600_cit50","doi-asserted-by":"publisher","first-page":"146","DOI":"10.1016\/j.jinorgbio.2018.03.012","article-title":"A docked state conformational\ndynamics model to explain the ionic strength dependence of FMN \u2013\nheme electron transfer in nitric oxide synthase","volume":"184","author":"Astashkin","year":"2018","journal-title":"J. Inorg. Biochem."},{"key":"2026100608071763600_cit51","doi-asserted-by":"publisher","first-page":"611","DOI":"10.1007\/s00775-024-02068-8","article-title":"Analyzing\nthe FMN\u2500heme interdomain docking interactions in neuronal and\ninducible NOS isoforms by pulsed EPR experiments and conformational\ndistribution modeling","volume":"29","author":"Astashkin","year":"2024","journal-title":"JBIC, J. Biol. 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