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AlphaCross-XL: A Seamless Tool for Automated and Proteome-Scale Mapping of Cross-Linked Peptides Onto 3D Protein Structures
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Abstract
Crosslinking mass spectrometry (XL-MS) is an exciting proteomics technology to capture native protein conformations in real time within biological systems. Historically, however, implementation of this technology has typically been limited to single purified recombinant proteins or in vitro-assembled protein complexes. These limitations are associated with inherent challenges in XL-MS analysis, including extremely low abundance of crosslinked (XL) peptides and complex deconvolution of XL peptide-derived spectral data. However, impressive recent developments in computation and instrumentation have now made it feasible to address biological questions using proteome-wide XL-MS analysis. Although some XL mapping software tools exist, these require manual input of specific Protein Data Bank structures at the single protein level and do not function at the high-throughput scale required to analyze datasets derived from thousands of proteins. To address this need, we therefore sought to develop a strategy enabling automated mapping of XL peptides onto the 3D structures of proteins, at a proteome-wide scale. Herein, we describe AlphaCross-XL, a first-in-class seamless computational tool for automated mapping of XL peptides onto the protein structures for intraprotein crosslinks and loop links. The AlphaCross-XL software first retrieves protein structures from the AlphaFold Protein Structure Database and maps all the identified crosslinks onto the 3D structure. It also calculates the Euclidian distance between the crosslinked residues and reports the violated and satisfied crosslink distances based on a user-defined distance threshold, which is visually discriminated by color in PyMOL. Last, the tool also supports further validation of user-submitted protein structures, which can include any computer-predicted protein structure and experimentally derived protein structures (i.e., from Protein Data Bank). AlphaCross-XL is available at https://github.com/sanjyotshenoy/alphacross-xl.
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Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764
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Research works printed but not linked: 33
- Mandal, 2023, Structural surfaceomics reveals an AML-specific conformation of integrin β2 as a CAR T cellular therapy target, Nat. Cancer, 4, 1592, 10.1038/s43018-023-00652-6 · DOI
- Gonzalez-Lozano, 2020, Stitching the synapse: cross-linking mass spectrometry into resolving synaptic protein interactions, Sci. Adv., 6, 1, 10.1126/sciadv.aax5783 · DOI
- Leitner, 2016, Crosslinking and mass spectrometry: an integrated technology to understand the structure and function of molecular machines, Trends Biochem. Sci., 41, 20, 10.1016/j.tibs.2015.10.008 · DOI
- Leitner, 2014, Lysine-specific chemical cross-linking of protein complexes and identification of cross-linking sites using LC-MS/MS and the xQuest/xProphet software pipeline, Nat. Protoc., 9, 120, 10.1038/nprot.2013.168 · DOI
- Kao, 2011, Development of a novel cross-linking strategy for fast and accurate identification of cross-linked peptides of protein complexes, Mol. Cell Proteomics, 10, 10.1074/mcp.M110.002212 · DOI
- Steigenberger, 2019, PhoX: an IMAC-enrichable cross-linking reagent, ACS Cent. Sci., 5, 1514, 10.1021/acscentsci.9b00416 · DOI
- Gutierrez, 2021, Enabling photoactivated cross-linking mass spectrometric analysis of protein complexes by novel MS-cleavable cross-linkers, Mol. Cell Proteomics, 20, 10.1016/j.mcpro.2021.100084 · DOI
- Faustino, 2023, Progress toward proteome-wide photo-cross-linking to enable residue-level visualization of protein structures and networks in vivo, Anal. Chem., 95, 10670, 10.1021/acs.analchem.3c01369 · DOI
- Ryl, 2020, In situ structural restraints from cross-linking mass spectrometry in human mitochondria, J. Proteome Res., 19, 327, 10.1021/acs.jproteome.9b00541 · DOI
- Chavez, 2018, Chemical crosslinking mass spectrometry analysis of protein conformations and supercomplexes in heart tissue, Cell Syst., 6, 136, 10.1016/j.cels.2017.10.017 · DOI
- Wheat, 2021, Protein interaction landscapes revealed by advanced in vivo cross-linking-mass spectrometry, Proc. Natl. Acad. Sci. U. S. A., 118, 10.1073/pnas.2023360118 · DOI
- Yu, 2018, Cross-linking mass spectrometry (XL-MS): an emerging technology for interactomics and structural biology, Anal. Chem., 90, 144, 10.1021/acs.analchem.7b04431 · DOI
- Varadi, 2022, AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models, Nucleic Acids Res., 50, D439, 10.1093/nar/gkab1061 · DOI · Paper page
- Chen, 2019, A high-speed search engine pLink 2 with systematic evaluation for proteome-scale identification of cross-linked peptides, Nat. Commun., 10, 3404, 10.1038/s41467-019-11337-z · DOI
- Hoopmann, 2015, Kojak: efficient analysis of chemically cross-linked protein complexes, J. Proteome Res., 14, 2190, 10.1021/pr501321h · DOI
- Clasen, 2024, Proteome-scale recombinant standards and a robust high-speed search engine to advance cross-linking MS-based interactomics, Nat. Methods, 21, 2327, 10.1038/s41592-024-02478-1 · DOI
- Mendes, 2019, An integrated workflow for crosslinking mass spectrometry, Mol. Syst. Biol., 15, 10.15252/msb.20198994 · DOI
- Rey, 2014, Mass Spec Studio for integrative structural biology, Structure, 22, 1538, 10.1016/j.str.2014.08.013 · DOI
- Ruwolt, 2023, Real-time library search increases cross-link identification depth across all levels of sample complexity, Anal. Chem., 95, 5248, 10.1021/acs.analchem.2c05141 · DOI
- Wollscheid, 2009, Mass-spectrometric identification and relative quantification of N-linked cell surface glycoproteins, Nat. Biotechnol., 27, 378, 10.1038/nbt.1532 · DOI · Paper page
- Jiao, 2022, Two-dimensional fractionation method for proteome-wide cross-linking mass spectrometry analysis, Anal. Chem., 94, 4236, 10.1021/acs.analchem.1c04485 · DOI
- Bakan, 2011, ProDy: protein dynamics inferred from theory and experiments, Bioinformatics, 27, 1575, 10.1093/bioinformatics/btr168 · DOI
- Du, 2021, Pyfastx: a robust Python package for fast random access to sequences from plain and gzipped FASTA/Q files, Brief Bioinform., 22, 10.1093/bib/bbaa368 · DOI
- Berman, 2000, The protein Data Bank, Nucleic Acids Res., 28, 235, 10.1093/nar/28.1.235 · DOI · Paper page
- Piersimoni, 2022, Cross-linking mass spectrometry for investigating protein conformations and protein-protein Interactions─A method for all Seasons, Chem. Rev., 122, 7500, 10.1021/acs.chemrev.1c00786 · DOI
- Leitner, 2012, Expanding the chemical cross-linking toolbox by the use of multiple proteases and enrichment by size exclusion chromatography, Mol. Cell Proteomics, 11, 10.1074/mcp.M111.014126 · DOI
- Stahl, 2023, Protein structure prediction with in-cell photo-crosslinking mass spectrometry and deep learning, Nat. Biotechnol., 41, 1810, 10.1038/s41587-023-01704-z · DOI
- Manalastas-Cantos, 2024, Modeling flexible protein structure with AlphaFold2 and crosslinking mass spectrometry, Mol. Cell Proteomics, 23, 100724, 10.1016/j.mcpro.2024.100724 · DOI
- Combe, 2024, xiVIEW: Visualisation of crosslinking mass spectrometry data, J. Mol. Biol., 436, 168656, 10.1016/j.jmb.2024.168656 · DOI
- Schiffrin, 2020, PyXlinkViewer: a flexible tool for visualization of protein chemical crosslinking data within the PyMOL molecular graphics system, Protein Sci., 29, 1851, 10.1002/pro.3902 · DOI
- Lima, 2021, XlinkCyNET: a cytoscape application for visualization of protein interaction networks based on cross-linking mass spectrometry identifications, J. Proteome Res., 20, 1943, 10.1021/acs.jproteome.0c00957 · DOI
- Khanppnavar, 2024, Regulatory sites of CaM-sensitive adenylyl cyclase AC8 revealed by cryo-EM and structural proteomics, EMBO Rep., 25, 1513, 10.1038/s44319-024-00076-y · DOI
- Datler, 2024, Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores, Nat. Struct. Mol. Biol., 31, 1114, 10.1038/s41594-023-01201-6 · DOI · Paper page
Metadata
- Authors
- Shenoy, S. V., Biswas, D., Zalevsky, A., Kishishita, A., Verma, A., Upadhay, I., He, Y., Sali, A., Viner, R., Mandal, K., Srivastava, S., & Wiita, A. P.
- Affiliations
- Indian Institute of Technology Bombay (IN)
- University of California, San Francisco (US)
- Thermo Fisher Scientific (United States) (US)
- Corresponding author
- Mandal, Kamal
- Srivastava, Sanjeeva
- Wiita, Arun P.
- ORCID
- Venue
- Molecular & Cellular Proteomics
- Publisher
- Elsevier BV
- Published
- 2025-10
- Volume
- 24
- Issue
- 10
- Pages
- 101057
- ISSN
- 1535-9476 (ISSN-L)
- PMC
- PMC12509755
- OpenAlex
- W4413324451
- Cited by
- 5
- References
- 1
- Citations by year
- 2026: 5
- FWCI
- 1.27
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Molecular & Cellular Proteomics (publishedVersion, cc-by-nc-nd)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- PubMed Central (publishedVersion, cc-by-nc-nd)
- Funders
- Indian Institute of Technology Bombay (BT/PR13114/INF/22/206/2015)
- National Institutes of Health
- National Institutes of Health National Cancer Institute (R01 CA290875, R21 CA263299)
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Keywords
- cross-linking mass spectrometry, AlphaFold structures, protein structure validation, proteome-wide analysis, native protein conformation
- MeSH terms
- Cross-Linking Reagents, Humans, Peptides, Protein Conformation, Software, Mass Spectrometry, Proteome, Proteomics
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