Stahl, K., Graziadei, A., Dau, T., Brock, O. & Rappsilber, J. Protein structure prediction with in-cell photo-crosslinking mass spectrometry and deep learning. Nat. Biotechnol. 41, 1810–1819 (2023).Lenz, S. et al. Reliable identification of protein-protein interactions by crosslinking mass spectrometry. Nat. Commun. 12, 3564 (2021).Article
ADS
CAS
PubMed
PubMed Central
Google Scholar
Bond, M. R., Zhang, H., Vu, P. D. & Kohler, J. J. Photocrosslinking of glycoconjugates using metabolically incorporated diazirine-containing sugars. Nat. Protoc. 4, 1044–1063 (2009).Article
CAS
PubMed
Google Scholar
Cuthbert, T. J. et al. Covalent functionalization of polypropylene filters with diazirine–photosensitizer conjugates producing visible light driven virus inactivating materials. Sci. Rep. 11, 19029 (2021).Article
ADS
CAS
PubMed
PubMed Central
Google Scholar
Manzi, L. et al. Carbene footprinting accurately maps binding sites in protein–ligand and protein–protein interactions. Nat. Commun. 7, 13288 (2016).Article
ADS
CAS
PubMed
PubMed Central
Google Scholar
Ahn, D.-S. et al. Mode-dependent fano resonances observed in the predissociation of diazirine in the S1 state. Angew. Chem. Int. Ed. 49, 1244–1247 (2010).Article
CAS
Google Scholar
Park, Y. C., An, H., Lee, Y. S. & Baeck, K. K. Dynamic Symmetry Breaking Hidden in Fano Resonance of a Molecule: S1 State of Diazirine Using Quantum Wave Packet Propagation. J. Phys. Chem. A 120, 932–938 (2016).Article
CAS
PubMed
Google Scholar
Yamamoto, N. et al. Mechanism of Carbene Formation from the Excited States of Diazirine and Diazomethane: An MC-SCF Study. J. Am. Chem. Soc. 116, 2064–2074 (1994).Article
CAS
Google Scholar
Procacci, B., Roy, S. S., Norcott, P., Turner, N. & Duckett, S. B. Unlocking a Diazirine Long-Lived Nuclear singlet state via photochemistry: NMR detection and lifetime of an unstabilized diazo-compound. J. Am. Chem. Soc. 140, 16855–16864 (2018).Article
CAS
PubMed
PubMed Central
Google Scholar
Ollevier, T. & Carreras, V. Emerging applications of aryl trifluoromethyl diazoalkanes and diazirines in synthetic transformations. ACS Org. Inorg. Au 2, 83–98 (2022).Article
CAS
PubMed
PubMed Central
Google Scholar
Li, M.-L., Yu, J.-H., Li, Y.-H., Zhu, S.-F. & Zhou, Q.-L. Highly enantioselective carbene insertion into N–H bonds of aliphatic amines. Science 366, 990–994 (2019).Article
ADS
CAS
PubMed
Google Scholar
Lepage, M. L. et al. A broadly applicable cross-linker for aliphatic polymers containing C–H bonds. Science 366, 875–878 (2019).Article
ADS
CAS
PubMed
Google Scholar
Suchanek, M., Radzikowska, A. & Thiele, C. Photo-leucine and photo-methionine allow identification of protein-protein interactions in living cells. Nat. Methods 2, 261–267 (2005).Article
CAS
PubMed
Google Scholar
Yang, T., Li, X.-M., Bao, X., Fung, Y. M. E. & Li, X. D. Photo-lysine captures proteins that bind lysine post-translational modifications. Nat. Chem. Biol. 12, 70–72 (2015).Article
PubMed
Google Scholar
Tanaka, Y. & Kohler, J. J. Photoactivatable crosslinking sugars for capturing glycoprotein interactions. J. Am. Chem. Soc. 130, 3278–3279 (2008).Article
CAS
PubMed
Google Scholar
Halloran, M. W. & Lumb, J. P. Recent applications of diazirines in chemical proteomics. Chem. Eur. J. 25, 4885–4898 (2019).Article
CAS
PubMed
Google Scholar
Das, J. Aliphatic diazirines as photoaffinity probes for proteins: recent developments. Chem. Rev. 111, 4405–4417 (2011).Article
CAS
PubMed
Google Scholar
Brunner, J., Senn, H. & Richards, F. M. 3-Trifluoromethyl-3-phenyldiazirine. A new carbene generating group for photolabeling reagents. J. Biol. Chem. 255, 3313–3318 (1980).Article
CAS
PubMed
Google Scholar
Musolino, S. F., Pei, Z., Bi, L., DiLabio, G. A. & Wulff, J. E. Structure-function relationships in aryl diazirines reveal optimal design features to maximize C-H insertion. Chem. Sci. 12, 12138–12148 (2021).Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang, M. et al. A genetically incorporated crosslinker reveals chaperone cooperation in acid resistance. Nat. Chem. Biol. 7, 671–677 (2011).Article
CAS
PubMed
Google Scholar
Li, X.-M., Huang, S. & Li, X. D. Photo-ANA enables profiling of host–bacteria protein interactions during infection. Nat. Chem. Biol. 19, 614–623 (2023).Article
CAS
PubMed
Google Scholar
Ruoho, A. E., Kiefer, H., Roeder, P. E. & Singer, S. J. The mechanism of photoaffinity labeling. Proc. Natl. Acad. Sci. USA 70, 2567–2571 (1973).Article
ADS
CAS
PubMed
PubMed Central
Google Scholar
O’Brien, J. G. K., Jemas, A., Asare-Okai, P. N., Am Ende, C. W. & Fox, J. M. Probing the mechanism of photoaffinity labeling by dialkyldiazirines through bioorthogonal capture of diazoalkanes. Org. Lett. 22, 9415–9420 (2020).Article
PubMed
PubMed Central
Google Scholar
Dubinsky, L., Krom, B. P. & Meijler, M. M. Diazirine based photoaffinity labeling. Bioorg. Med. Chem. 20, 554–570 (2012).Article
CAS
PubMed
Google Scholar
Bayley, H. & Knowles, J. R. in Methods Enzymol. Vol. 46 69–114 (Academic Press, 1977).Müller, F., Graziadei, A. & Rappsilber, J. Quantitative photo-crosslinking mass spectrometry revealing protein structure response to environmental changes. Anal. Chem. 91, 9041–9048 (2019).Article
PubMed
PubMed Central
Google Scholar
Belsom, A., Schneider, M., Fischer, L., Brock, O. & Rappsilber, J. Serum albumin domain structures in human blood serum by mass spectrometry and computational biology. Mol. Cell. Proteomics 15, 1105–1116 (2016).Article
CAS
PubMed
Google Scholar
Brodie, N. I., Makepeace, K. A. T., Petrotchenko, E. V. & Borchers, C. H. Isotopically-coded short-range hetero-bifunctional photo-reactive crosslinkers for studying protein structure. J. Proteomics 118, 12–20 (2015).Article
CAS
PubMed
Google Scholar
Petrotchenko, E. V., Nascimento, E. M., Witt, J. M. & Borchers, C. H. Determination of protein monoclonal–antibody epitopes by a combination of structural proteomics methods. J. Proteome Res. 22, 3096–3102 (2023).Article
CAS
PubMed
PubMed Central
Google Scholar
Gong, Z. et al. Visualizing the ensemble structures of protein complexes using chemical cross-linking coupled with mass spectrometry. Biophys. Rep. 1, 127–138 (2015).Article
CAS
PubMed
Google Scholar
Zhang, W. et al. SpotLink enables sensitive and precise identification of site nonspecific cross-links at the proteome scale. Brief. Bioinform. 23, https://doi.org/10.1093/bib/bbac316 (2022).Chen, Z.-L. et al. A high-speed search engine pLink 2 with systematic evaluation for proteome-scale identification of cross-linked peptides. Nat. Commun. 10, 3404 (2019).Götze, M. et al. StavroX—A software for analyzing crosslinked products in protein interaction studies. J. Am. Soc. Mass Spectrom. 23, 76–87 (2012).Article
ADS
PubMed
Google Scholar
Rinner, O. et al. Identification of cross-linked peptides from large sequence databases. Nat. Methods 5, 315–318 (2008).Article
CAS
PubMed
PubMed Central
Google Scholar
Petrotchenko, E. V. & Borchers, C. H. Crosslinking combined with mass spectrometry for structural proteomics. Mass Spectrom. Rev. 29, 862–876 (2010).Article
ADS
CAS
PubMed
Google Scholar
Petrotchenko, E. V. & Borchers, C. H. Protein chemistry combined with mass spectrometry for protein structure determination. Chem. Rev. 122, 7488–7499 (2022).Article
CAS
PubMed
Google Scholar
Piersimoni, L., Kastritis, P. L., Arlt, C. & Sinz, A. Cross-linking mass spectrometry for investigating protein conformations and protein–protein interactions─A method for all seasons. Chem. Rev. 122, 7500–7531 (2021).Article
PubMed
Google Scholar
Wang, J.-H. et al. Characterization of protein unfolding by fast cross-linking mass spectrometry using di-ortho-phthalaldehyde cross-linkers. Nat. Commun. 13, 1468 (2022).Jian-Hua, W. et al. Fast cross-linking by DOPA2 promotes the capturing of a stereospecific protein complex over nonspecific encounter complexes. Biophys. Rep. 8, 239–252 (2022).Article
Google Scholar
Kogut, M., Gong, Z., Tang, C. & Liwo, A. Pseudopotentials for coarse-grained cross-link-assisted modeling of protein structures. J. Comput. Chem. 42, 2054–2067 (2021).Article
CAS
PubMed
Google Scholar
Gong, Z., Ye, S.-X., Nie, Z.-F. & Tang, C. The conformational preference of chemical cross-linkers determines the cross-linking probability of reactive protein residues. J. Phys. Chem. B 124, 4446–4453 (2020).Article
CAS
PubMed
Google Scholar
Coffman, K. et al. Characterization of the raptor/4E-BP1 interaction by chemical cross-linking coupled with mass spectrometry Analysis *. J. Biol. Chem. 289, 4723–4734 (2014).Article
CAS
PubMed
PubMed Central
Google Scholar
Yan, X. et al. AI-empowered integrative structural characterization of m6A methyltransferase complex. Cell Res. 32, 1124–1127 (2022).Article
ADS
CAS
PubMed
PubMed Central
Google Scholar
Brodie, N. I., Petrotchenko, E. V. & Borchers, C. H. The novel isotopically coded short-range photo-reactive crosslinker 2,4,6-triazido-1,3,5-triazine (TATA) for studying protein structures. J. Proteomics 149, 69–76 (2016).Article
CAS
PubMed
Google Scholar
Wei, G. et al. Conformational ensemble of native α-synuclein in solution as determined by short-distance crosslinking constraint-guided discrete molecular dynamics simulations. PLoS Comput. Biol. 15, https://doi.org/10.1371/journal.pcbi.1006859 (2019).Ziemianowicz, D. S., Bomgarden, R., Etienne, C. & Schriemer, D. C. Amino acid insertion frequencies arising from photoproducts generated using aliphatic diazirines. J. Am. Soc. Mass Spectrom. 28, 2011–2021 (2017).Article
ADS
CAS
PubMed
Google Scholar
West, A. V. et al. Labeling preferences of diazirines with protein biomolecules. J. Am. Chem. Soc. 143, 6691–6700 (2021).Article
CAS
PubMed
Google Scholar
Iacobucci, C. et al. Carboxyl-photo-reactive MS-cleavable cross-linkers: unveiling a hidden aspect of diazirine-based reagents. Anal. Chem. 90, 2805–2809 (2018).Article
CAS
PubMed
Google Scholar
Gutierrez, C. et al. Enabling photoactivated cross-linking mass spectrometric analysis of protein complexes by novel MS-cleavable cross-linkers. Mol. Cell. Proteomics 20, https://doi.org/10.1016/j.mcpro.2021.100084 (2021).Hogan, J. M. et al. Residue-level characterization of antibody binding epitopes using carbene chemical footprinting. Anal. Chem. 95, 3922–3931 (2023).Article
CAS
PubMed
Google Scholar
Hashimoto, M. & Hatanaka, Y. Recent progress in diazirine-based photoaffinity labeling. Eur. J. Org. Chem. 2008, 2513–2523 (2008).Article
Google Scholar
Zhang, Y., Burdzinski, G., Kubicki, J. & Platz, M. S. Direct observation of carbene and diazo formation from aryldiazirines by ultrafast infrared spectroscopy. J. Am. Chem. Soc. 130, 16134–16135 (2008).Article
CAS
PubMed
Google Scholar
Admasu, A. et al. A laser flash photolysis study of p-tolyl(trifluoromethyl)carbene. J. Chem. Soc. Perkin Trans. 2, 1093–1100 (1998).Article
Google Scholar
Toscano, J. P., Platz, M. S. & Nikolaev, V. Lifetimes of simple ketocarbenes. J. Am. Chem. Soc. 117, 4712–4713 (1995).Article
CAS
Google Scholar
Mix, K. A., Aronoff, M. R. & Raines, R. T. Diazo compounds: versatile tools for chemical biology. ACS Chem. Biol. 11, 3233–3244 (2016).Article
CAS
PubMed
PubMed Central
Google Scholar
Cheng, S., Wu, Q., Xiao, H. & Chen, H. Online monitoring of enzymatic reactions using time-resolved desorption electrospray lonization mass spectrometry. Anal. Chem. 89, 2338–2344 (2017).Article
CAS
PubMed
Google Scholar
Fabry, D. C., Sugiono, E. & Rueping, M. Online monitoring and analysis for autonomous continuous flow self-optimizing reactor systems. React. Chem. Eng. 1, 129–133 (2016).Article
CAS
Google Scholar
Attwood, P. V. & Geeves, M. A. Kinetics of an enzyme-catalyzed reaction measured by electrospray ionization mass spectrometry using a simple rapid mixing attachment. Anal. Biochem. 334, 382–389 (2004).Article
CAS
PubMed
Google Scholar
Beck, D. A. C., Alonso, D. O. V., Inoyama, D. & Daggett, V. The intrinsic conformational propensities of the 20 naturally occurring amino acids and reflection of these propensities in proteins. Proc. Natl. Acad. Sci. USA 105, 12259–12264 (2008).Article
ADS
CAS
PubMed
PubMed Central
Google Scholar
Rosenberg, A. A., Yehishalom, N., Marx, A. & Bronstein, A. M. An amino-domino model described by a cross-peptide-bond Ramachandran plot defines amino acid pairs as local structural units. Proc. Natl. Acad. Sci. USA 120, e2301064120 (2023).Article
CAS
PubMed
PubMed Central
Google Scholar
Belsom, A., Mudd, G., Giese, S., Auer, M. & Rappsilber, J. Complementary benzophenone cross-linking/mass spectrometry Photochemistry. Anal. Chem. 89, 5319–5324 (2017).Article
CAS
PubMed
PubMed Central
Google Scholar
Iyer, L. K., Moorthy, B. S. & Topp, E. M. Photolytic cross-linking to probe protein–protein and protein–matrix interactions inlyophilized Powders. Mol. Pharm. 12, 3237–3249 (2015).Article
CAS
PubMed
PubMed Central
Google Scholar
Guangcan, S. et al. How to use open-pFind in deep proteomics data analysis?— A protocol for rigorous identification and quantitation of peptides and proteins from mass spectrometry data. Biophys. Rep. 7, 207–226 (2021).Article
Google Scholar
Gong, Z., Gu, X.-H., Guo, D.-C., Wang, J. & Tang, C. Protein structural ensembles visualized by solvent paramagnetic relaxation enhancement. Angew. Chem. Int. Ed. 56, 1002–1006 (2017).Article
CAS
Google Scholar
Zhang, B. et al. Decoding protein dynamics in cells using chemical cross-linking and hierarchical analysis**. Angew. Chem. Int. Ed. 62, e202301345 (2023).Article
CAS
Google Scholar
Abramson, J. et al. Accurate structure prediction of biomolecular interactions with AlphaFold 3. Nature 630, 493–500 (2024).Pei, H.-H. et al. The δ subunit and NTPase HelD institute a two-pronged mechanism for RNA polymerase recycling. Nat. Commun. 11, 6418 (2020).Article
ADS
CAS
PubMed
PubMed Central
Google Scholar
Walzthoeni, T. et al. xTract: software for characterizing conformational changes of protein complexes by quantitative cross-linking mass spectrometry. Nat. Methods 12, 1185–1190 (2015).Article
CAS
PubMed
PubMed Central
Google Scholar
Ding, Y.-H. et al. Modeling protein excited-state structures from “over-length” chemical cross-links. J. Biol. Chem. 292, 1187–1196 (2017).Article
CAS
PubMed
Google Scholar
Jin, Z. et al. Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors. Nature 582, 289–293 (2020).Article
ADS
CAS
PubMed
Google Scholar
Campos-Olivas, R., Newman, J. L. & Summers, M. F. Solution structure and dynamics of the Rous sarcoma virus capsid protein and comparison with capsid proteins of other retroviruses11Edited by P. E. Wright. J. Mol. Biol. 296, 633–649 (2000).Article
CAS
PubMed
Google Scholar
Scott, D. J. et al. A novel ultra-stable, monomeric green fluorescent protein for direct volumetric imaging of whole organs using CLARITY. Sci. Rep. 8, 667 (2018).Article
ADS
PubMed
PubMed Central
Google Scholar
Chen, X., Lee, B.-H., Finley, D. & Walters, K. J. Structure of proteasome ubiquitin receptor hRpn13 and Its activation by the scaffolding protein hRpn2. Mol. Cell 38, 404–415 (2010).Article
CAS
PubMed
PubMed Central
Google Scholar
Liu, Z. et al. Structural basis for the recognition of K48-linked Ub chain by proteasomal receptor Rpn13. Cell Discovery 5, 19 (2019).Article
PubMed
PubMed Central
Google Scholar
Bjorndahl, T. C., Andrew, L. C., Semenchenko, V. & Wishart, D. S. NMR Solution structures of the apo and peptide-inhibited human rhinovirus 3C protease (Serotype 14): structural and dynamic comparison. Biochemistry 46, 12945–12958 (2007).Article
CAS
PubMed
Google Scholar
Mitternacht, S. FreeSASA: An open source C library for solvent accessible surface area calculations. F1000Res. 5, https://doi.org/10.12688/f1000research.7931.1 (2016).