1
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Cai Y. Conjugation of primary amine groups in targeted proteomics. MASS SPECTROMETRY REVIEWS 2024. [PMID: 39229771 DOI: 10.1002/mas.21906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 03/21/2024] [Accepted: 08/12/2024] [Indexed: 09/05/2024]
Abstract
Primary amines, in the form of unmodified N-terminus of peptide/protein and unmodified lysine residue, are perhaps the most important functional groups that can serve as the starting points in proteomic analysis, especially via mass spectrometry-based approaches. A variety of multifunctional probes that conjugate primary amine groups through covalent bonds have been developed and employed to facilitate protein/protein complex characterization, including identification, quantification, structure and localization elucidation, protein-protein interaction investigation, and so forth. As an integral part of more accurate peptide quantification in targeted proteomics, isobaric stable isotope-coded primary amine labeling approaches eventually facilitated protein/peptide characterization at the single-cell level, paving the way for single-cell proteomics. The development and advances in the field can be reviewed in terms of key components of a multifunctional probe: functional groups and chemistry for primary amine conjugation; hetero-bifunctional moiety for separation/enrichment of conjugated protein/protein complex; and functionalized linker/spacer. Perspectives are primarily focused on optimizing primary amine conjugation under physiological conditions to improve characterization of native proteins, especially those associated with the surface of living cells/microorganisms.
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Affiliation(s)
- Yang Cai
- Department of Chemistry, University of New Orleans, New Orleans, Louisiana, USA
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2
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Ianni A, Ihling CH, Vranka T, Matoušek V, Sinz A, Iacobucci C. Evaluating Imide-Based Mass Spectrometry-Cleavable Cross-Linkers for Structural Proteomics Studies. JACS AU 2024; 4:2936-2943. [PMID: 39211594 PMCID: PMC11350583 DOI: 10.1021/jacsau.4c00282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 07/01/2024] [Accepted: 07/01/2024] [Indexed: 09/04/2024]
Abstract
Disuccinimidyl dibutyric urea (DSBU) is a mass spectrometry (MS)-cleavable cross-linker that has multiple applications in structural biology, ranging from isolated protein complexes to comprehensive system-wide interactomics. DSBU facilitates a rapid and reliable identification of cross-links through the dissociation of its urea group in the gas phase. In this study, we further advance the structural capabilities of DSBU by remodeling the urea group into an imide, thus introducing a novel class of cross-linkers. This modification preserves the MS cleavability of the amide bond, granted by the two acyl groups of the imide function. The central nitrogen atom enables the introduction of affinity purification tags. Here, we introduce disuccinimidyl disuccinic imide (DSSI) as a prototype of this class of cross-linkers. It features a phosphonate handle for immobilized metal ion affinity chromatography enrichment. We detail DSSI synthesis and describe its behavior in solution and in the gas phase while cross-linking isolated proteins and human cell lysates. DSSI and DSBU cross-links are compared at the same enrichment depth to bridge these two cross-linker classes. We validate DSSI cross-links by mapping them in high-resolution structures of large protein assemblies. The cross-links observed yield insights into the morphology of intrinsically disordered proteins and their complexes. The DSSI linker might spearhead a novel class of MS-cleavable and enrichable cross-linkers.
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Affiliation(s)
- Alessio
Di Ianni
- Department
of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, Halle/Saale D-01620, Germany
- Center
for Structural Mass Spectrometry, Martin
Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, Halle/Saale D-01620, Germany
| | - Christian H. Ihling
- Department
of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, Halle/Saale D-01620, Germany
- Center
for Structural Mass Spectrometry, Martin
Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, Halle/Saale D-01620, Germany
| | - Tomáš Vranka
- CF
Plus Chemicals s.r.o., Karásek 1767/1, Brno-Řečkovice 621 00, Czechia
| | - Václav Matoušek
- CF
Plus Chemicals s.r.o., Karásek 1767/1, Brno-Řečkovice 621 00, Czechia
| | - Andrea Sinz
- Department
of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, Halle/Saale D-01620, Germany
- Center
for Structural Mass Spectrometry, Martin
Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, Halle/Saale D-01620, Germany
| | - Claudio Iacobucci
- Department
of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, Halle/Saale D-01620, Germany
- Center
for Structural Mass Spectrometry, Martin
Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, Halle/Saale D-01620, Germany
- Department
of Physical and Chemical Sciences, University
of L’Aquila, Via Vetoio, Coppito II 67100, L’Aquila, Italy
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3
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Jiang Y, Rex DA, Schuster D, Neely BA, Rosano GL, Volkmar N, Momenzadeh A, Peters-Clarke TM, Egbert SB, Kreimer S, Doud EH, Crook OM, Yadav AK, Vanuopadath M, Hegeman AD, Mayta M, Duboff AG, Riley NM, Moritz RL, Meyer JG. Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry. ACS MEASUREMENT SCIENCE AU 2024; 4:338-417. [PMID: 39193565 PMCID: PMC11348894 DOI: 10.1021/acsmeasuresciau.3c00068] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 05/03/2024] [Accepted: 05/03/2024] [Indexed: 08/29/2024]
Abstract
Proteomics is the large scale study of protein structure and function from biological systems through protein identification and quantification. "Shotgun proteomics" or "bottom-up proteomics" is the prevailing strategy, in which proteins are hydrolyzed into peptides that are analyzed by mass spectrometry. Proteomics studies can be applied to diverse studies ranging from simple protein identification to studies of proteoforms, protein-protein interactions, protein structural alterations, absolute and relative protein quantification, post-translational modifications, and protein stability. To enable this range of different experiments, there are diverse strategies for proteome analysis. The nuances of how proteomic workflows differ may be challenging to understand for new practitioners. Here, we provide a comprehensive overview of different proteomics methods. We cover from biochemistry basics and protein extraction to biological interpretation and orthogonal validation. We expect this Review will serve as a handbook for researchers who are new to the field of bottom-up proteomics.
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Affiliation(s)
- Yuming Jiang
- Department
of Computational Biomedicine, Cedars Sinai
Medical Center, Los Angeles, California 90048, United States
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
| | - Devasahayam Arokia
Balaya Rex
- Center for
Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Dina Schuster
- Department
of Biology, Institute of Molecular Systems
Biology, ETH Zurich, Zurich 8093, Switzerland
- Department
of Biology, Institute of Molecular Biology
and Biophysics, ETH Zurich, Zurich 8093, Switzerland
- Laboratory
of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Benjamin A. Neely
- Chemical
Sciences Division, National Institute of
Standards and Technology, NIST, Charleston, South Carolina 29412, United States
| | - Germán L. Rosano
- Mass
Spectrometry
Unit, Institute of Molecular and Cellular
Biology of Rosario, Rosario, 2000 Argentina
| | - Norbert Volkmar
- Department
of Biology, Institute of Molecular Systems
Biology, ETH Zurich, Zurich 8093, Switzerland
| | - Amanda Momenzadeh
- Department
of Computational Biomedicine, Cedars Sinai
Medical Center, Los Angeles, California 90048, United States
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
| | - Trenton M. Peters-Clarke
- Department
of Pharmaceutical Chemistry, University
of California—San Francisco, San Francisco, California, 94158, United States
| | - Susan B. Egbert
- Department
of Chemistry, University of Manitoba, Winnipeg, Manitoba, R3T 2N2 Canada
| | - Simion Kreimer
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
| | - Emma H. Doud
- Center
for Proteome Analysis, Indiana University
School of Medicine, Indianapolis, Indiana, 46202-3082, United States
| | - Oliver M. Crook
- Oxford
Protein Informatics Group, Department of Statistics, University of Oxford, Oxford OX1 3LB, United
Kingdom
| | - Amit Kumar Yadav
- Translational
Health Science and Technology Institute, NCR Biotech Science Cluster 3rd Milestone Faridabad-Gurgaon
Expressway, Faridabad, Haryana 121001, India
| | | | - Adrian D. Hegeman
- Departments
of Horticultural Science and Plant and Microbial Biology, University of Minnesota, Twin Cities, Minnesota 55108, United States
| | - Martín
L. Mayta
- School
of Medicine and Health Sciences, Center for Health Sciences Research, Universidad Adventista del Plata, Libertador San Martin 3103, Argentina
- Molecular
Biology Department, School of Pharmacy and Biochemistry, Universidad Nacional de Rosario, Rosario 2000, Argentina
| | - Anna G. Duboff
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Nicholas M. Riley
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Robert L. Moritz
- Institute
for Systems biology, Seattle, Washington 98109, United States
| | - Jesse G. Meyer
- Department
of Computational Biomedicine, Cedars Sinai
Medical Center, Los Angeles, California 90048, United States
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
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4
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Inge MM, Miller R, Hook H, Bray D, Keenan JL, Zhao R, Gilmore TD, Siggers T. Rapid profiling of transcription factor-cofactor interaction networks reveals principles of epigenetic regulation. Nucleic Acids Res 2024:gkae706. [PMID: 39166482 DOI: 10.1093/nar/gkae706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 06/14/2024] [Accepted: 08/19/2024] [Indexed: 08/23/2024] Open
Abstract
Transcription factor (TF)-cofactor (COF) interactions define dynamic, cell-specific networks that govern gene expression; however, these networks are understudied due to a lack of methods for high-throughput profiling of DNA-bound TF-COF complexes. Here, we describe the Cofactor Recruitment (CoRec) method for rapid profiling of cell-specific TF-COF complexes. We define a lysine acetyltransferase (KAT)-TF network in resting and stimulated T cells. We find promiscuous recruitment of KATs for many TFs and that 35% of KAT-TF interactions are condition specific. KAT-TF interactions identify NF-κB as a primary regulator of acutely induced histone 3 lysine 27 acetylation (H3K27ac). Finally, we find that heterotypic clustering of CBP/P300-recruiting TFs is a strong predictor of total promoter H3K27ac. Our data support clustering of TF sites that broadly recruit KATs as a mechanism for widespread co-occurring histone acetylation marks. CoRec can be readily applied to different cell systems and provides a powerful approach to define TF-COF networks impacting chromatin state and gene regulation.
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Affiliation(s)
- Melissa M Inge
- Department of Biology, Boston University, Boston, MA 02215, USA
- Biological Design Center, Boston University, Boston, MA 02215, USA
| | - Rebekah Miller
- Department of Biology, Boston University, Boston, MA 02215, USA
- Biological Design Center, Boston University, Boston, MA 02215, USA
- Bioinformatics Program, Boston University, Boston, MA 02215, USA
| | - Heather Hook
- Department of Biology, Boston University, Boston, MA 02215, USA
| | - David Bray
- Department of Biology, Boston University, Boston, MA 02215, USA
- Bioinformatics Program, Boston University, Boston, MA 02215, USA
| | - Jessica L Keenan
- Department of Biology, Boston University, Boston, MA 02215, USA
- Bioinformatics Program, Boston University, Boston, MA 02215, USA
| | - Rose Zhao
- Department of Biology, Boston University, Boston, MA 02215, USA
| | | | - Trevor Siggers
- Department of Biology, Boston University, Boston, MA 02215, USA
- Biological Design Center, Boston University, Boston, MA 02215, USA
- Bioinformatics Program, Boston University, Boston, MA 02215, USA
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5
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Jiao F, Yu C, Wheat A, Chen L, Lih TSM, Zhang H, Huang L. DSBSO-Based XL-MS Analysis of Breast Cancer PDX Tissues to Delineate Protein Interaction Network in Clinical Samples. J Proteome Res 2024; 23:3269-3279. [PMID: 38334954 PMCID: PMC11296914 DOI: 10.1021/acs.jproteome.3c00832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
Protein-protein interactions (PPIs) are fundamental to understanding biological systems as protein complexes are the active molecular modules critical for carrying out cellular functions. Dysfunctional PPIs have been associated with various diseases including cancer. Systems-wide PPI analysis not only sheds light on pathological mechanisms, but also represents a paradigm in identifying potential therapeutic targets. In recent years, cross-linking mass spectrometry (XL-MS) has emerged as a powerful tool for defining endogenous PPIs of cellular networks. While proteome-wide studies have been performed in cell lysates, intact cells and tissues, applications of XL-MS in clinical samples have not been reported. In this study, we adopted a DSBSO-based in vivo XL-MS platform to map interaction landscapes from two breast cancer patient-derived xenograft (PDX) models. As a result, we have generated a PDX interaction network comprising 2,557 human proteins and identified interactions unique to breast cancer subtypes. Interestingly, most of the observed differences in PPIs correlated well with protein abundance changes determined by TMT-based proteome quantitation. Collectively, this work has demonstrated the feasibility of XL-MS analysis in clinical samples, and established an analytical workflow for tissue cross-linking that can be generalized for mapping PPIs from patient samples in the future to dissect disease-relevant cellular networks.
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Affiliation(s)
- Fenglong Jiao
- Department of Physiology and Biophysics, University of California, Irvine, CA 92697
| | - Clinton Yu
- Department of Physiology and Biophysics, University of California, Irvine, CA 92697
| | - Andrew Wheat
- Department of Physiology and Biophysics, University of California, Irvine, CA 92697
| | - Lijun Chen
- Department of Pathology and Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21231
| | - Tung-Shing Mamie Lih
- Department of Pathology and Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21231
| | - Hui Zhang
- Department of Pathology and Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21231
| | - Lan Huang
- Department of Physiology and Biophysics, University of California, Irvine, CA 92697
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6
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Kadavá T, Hevler JF, Kalaidopoulou Nteak S, Yin VC, Strasser J, Preiner J, Heck AJ. Higher-order structure and proteoforms of co-occurring C4b-binding protein assemblies in human serum. EMBO J 2024; 43:3009-3026. [PMID: 38811852 PMCID: PMC11251186 DOI: 10.1038/s44318-024-00128-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 05/03/2024] [Accepted: 05/08/2024] [Indexed: 05/31/2024] Open
Abstract
The complement is a conserved cascade that plays a central role in the innate immune system. To maintain a delicate equilibrium preventing excessive complement activation, complement inhibitors are essential. One of the major fluid-phase complement inhibitors is C4b-binding protein (C4BP). Human C4BP is a macromolecular glycoprotein composed of two distinct subunits, C4BPα and C4BPβ. These associate with vitamin K-dependent protein S (ProS) forming an ensemble of co-occurring higher-order structures. Here, we characterize these C4BP assemblies. We resolve and quantify isoforms of purified human serum C4BP using distinct single-particle detection techniques: charge detection mass spectrometry, and mass photometry accompanied by high-speed atomic force microscopy. Combining cross-linking mass spectrometry, glycoproteomics, and structural modeling, we report comprehensive glycoproteoform profiles and full-length structural models of the endogenous C4BP assemblies, expanding knowledge of this key complement inhibitor's structure and composition. Finally, we reveal that an increased C4BPα to C4BPβ ratio coincides with elevated C-reactive protein levels in patient plasma samples. This observation highlights C4BP isoform variation and affirms a distinct role of co-occurring C4BP assemblies upon acute phase inflammation.
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Affiliation(s)
- Tereza Kadavá
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht, 3584 CH, the Netherlands
- Netherlands Proteomics Center, Padualaan 8, Utrecht, 3584 CH, the Netherlands
| | - Johannes F Hevler
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht, 3584 CH, the Netherlands
- Netherlands Proteomics Center, Padualaan 8, Utrecht, 3584 CH, the Netherlands
| | - Sofia Kalaidopoulou Nteak
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht, 3584 CH, the Netherlands
- Netherlands Proteomics Center, Padualaan 8, Utrecht, 3584 CH, the Netherlands
| | - Victor C Yin
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht, 3584 CH, the Netherlands
- Netherlands Proteomics Center, Padualaan 8, Utrecht, 3584 CH, the Netherlands
| | - Juergen Strasser
- University of Applied Sciences Upper Austria, 4020, Linz, Austria
| | - Johannes Preiner
- University of Applied Sciences Upper Austria, 4020, Linz, Austria
| | - Albert Jr Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht, 3584 CH, the Netherlands.
- Netherlands Proteomics Center, Padualaan 8, Utrecht, 3584 CH, the Netherlands.
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7
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Liu DD, Ding W, Cheng JT, Wei Q, Lin Y, Zhu TY, Tian J, Sun K, Zhang L, Lu P, Yang F, Liu C, Tang S, Yang B. Characterize direct protein interactions with enrichable, cleavable and latent bioreactive unnatural amino acids. Nat Commun 2024; 15:5221. [PMID: 38890329 PMCID: PMC11189575 DOI: 10.1038/s41467-024-49517-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 06/10/2024] [Indexed: 06/20/2024] Open
Abstract
Latent bioreactive unnatural amino acids (Uaas) have been widely used in the development of covalent drugs and identification of protein interactors, such as proteins, DNA, RNA and carbohydrates. However, it is challenging to perform high-throughput identification of Uaa cross-linking products due to the complexities of protein samples and the data analysis processes. Enrichable Uaas can effectively reduce the complexities of protein samples and simplify data analysis, but few cross-linked peptides were identified from mammalian cell samples with these Uaas. Here we develop an enrichable and multiple amino acids reactive Uaa, eFSY, and demonstrate that eFSY is MS cleavable when eFSY-Lys and eFSY-His are the cross-linking products. An identification software, AixUaa is developed to decipher eFSY mass cleavable data. We systematically identify direct interactomes of Thioredoxin 1 (Trx1) and Selenoprotein M (SELM) with eFSY and AixUaa.
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Affiliation(s)
- Dan-Dan Liu
- Life Sciences Institute, Department of Medical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310058, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Wenlong Ding
- Life Sciences Institute, Department of Medical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310058, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Jin-Tao Cheng
- Life Sciences Institute, Department of Medical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310058, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Qiushi Wei
- School of Biological Science and Medical Engineering & School of Engineering Medicine, Beihang University, Beijing, 100191, China
| | - Yinuo Lin
- State Key Laboratory of Respiratory Disease, Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, 510530, China
| | - Tian-Yi Zhu
- Life Sciences Institute, Department of Medical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310058, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Jing Tian
- State Key Laboratory of Respiratory Disease, Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, 510530, China
| | - Ke Sun
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310030, China
| | - Long Zhang
- Life Sciences Institute, Department of Medical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Peilong Lu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310030, China
| | - Fan Yang
- Department of Biophysics, Kidney Disease Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, China
| | - Chao Liu
- School of Biological Science and Medical Engineering & School of Engineering Medicine, Beihang University, Beijing, 100191, China.
| | - Shibing Tang
- State Key Laboratory of Respiratory Disease, Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, 510530, China.
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou, 510530, China.
| | - Bing Yang
- Life Sciences Institute, Department of Medical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
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8
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Akkulak H, İnce HK, Goc G, Lebrilla CB, Kabasakal BV, Ozcan S. Structural proteomics of a bacterial mega membrane protein complex: FtsH-HflK-HflC. Int J Biol Macromol 2024; 269:131923. [PMID: 38697437 DOI: 10.1016/j.ijbiomac.2024.131923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/24/2024] [Accepted: 04/25/2024] [Indexed: 05/05/2024]
Abstract
Recent advances in mass spectrometry (MS) yielding sensitive and accurate measurements along with developments in software tools have enabled the characterization of complex systems routinely. Thus, structural proteomics and cross-linking mass spectrometry (XL-MS) have become a useful method for structural modeling of protein complexes. Here, we utilized commonly used XL-MS software tools to elucidate the protein interactions within a membrane protein complex containing FtsH, HflK, and HflC, over-expressed in E. coli. The MS data were processed using MaxLynx, MeroX, MS Annika, xiSEARCH, and XlinkX software tools. The number of identified inter- and intra-protein cross-links varied among software. Each interaction was manually checked using the raw MS and MS/MS data and distance restraints to verify inter- and intra-protein cross-links. A total of 37 inter-protein and 148 intra-protein cross-links were determined in the FtsH-HflK-HflC complex. The 59 of them were new interactions on the lacking region of recently published structures. These newly identified interactions, when combined with molecular docking and structural modeling, present opportunities for further investigation. The results provide valuable information regarding the complex structure and function to decipher the intricate molecular mechanisms underlying the FtsH-HflK-HflC complex.
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Affiliation(s)
- Hatice Akkulak
- Department of Chemistry, Middle East Technical University, Ankara 06800, Turkiye
| | - H Kerim İnce
- Department of Chemistry, Middle East Technical University, Ankara 06800, Turkiye
| | - Gunce Goc
- Turkish Accelerator and Radiation Laboratory (TARLA), Ankara 06830, Turkiye
| | - Carlito B Lebrilla
- Department of Chemistry, University of California, Davis, 95616, CA, USA
| | - Burak V Kabasakal
- Turkish Accelerator and Radiation Laboratory (TARLA), Ankara 06830, Turkiye; School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK.
| | - Sureyya Ozcan
- Department of Chemistry, Middle East Technical University, Ankara 06800, Turkiye; Cancer Systems Biology Laboratory (CanSyL), Middle East Technical University, 06800 Ankara, Turkiye
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9
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Rojas Echeverri JC, Hause F, Iacobucci C, Ihling CH, Tänzler D, Shulman N, Riffle M, MacLean BX, Sinz A. A Workflow for Improved Analysis of Cross-Linking Mass Spectrometry Data Integrating Parallel Accumulation-Serial Fragmentation with MeroX and Skyline. Anal Chem 2024; 96:7373-7379. [PMID: 38696819 PMCID: PMC11099889 DOI: 10.1021/acs.analchem.4c00829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/24/2024] [Accepted: 04/29/2024] [Indexed: 05/04/2024]
Abstract
Cross-linking mass spectrometry (XL-MS) has evolved into a pivotal technique for probing protein interactions. This study describes the implementation of Parallel Accumulation-Serial Fragmentation (PASEF) on timsTOF instruments, enhancing the detection and analysis of protein interactions by XL-MS. Addressing the challenges in XL-MS, such as the interpretation of complex spectra, low abundant cross-linked peptides, and a data acquisition bias, our current study integrates a peptide-centric approach for the analysis of XL-MS data and presents the foundation for integrating data-independent acquisition (DIA) in XL-MS with a vendor-neutral and open-source platform. A novel workflow is described for processing data-dependent acquisition (DDA) of PASEF-derived information. For this, software by Bruker Daltonics is used, enabling the conversion of these data into a format that is compatible with MeroX and Skyline software tools. Our approach significantly improves the identification of cross-linked products from complex mixtures, allowing the XL-MS community to overcome current analytical limitations.
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Affiliation(s)
- Juan Camilo Rojas Echeverri
- Department
of Pharmaceutical Chemistry and Bioanalytics, Martin-Luther-University Halle-Wittenberg, 06120 Halle, Germany
- Center
for Structural Mass Spectrometry, Martin-Luther-University
Halle-Wittenberg, 06120 Halle, Germany
| | - Frank Hause
- Department
of Pharmaceutical Chemistry and Bioanalytics, Martin-Luther-University Halle-Wittenberg, 06120 Halle, Germany
- Center
for Structural Mass Spectrometry, Martin-Luther-University
Halle-Wittenberg, 06120 Halle, Germany
- Institute
for Molecular Medicine, Martin-Luther-University
Halle-Wittenberg, 06120 Halle, Germany
| | - Claudio Iacobucci
- Department
of Pharmaceutical Chemistry and Bioanalytics, Martin-Luther-University Halle-Wittenberg, 06120 Halle, Germany
- Center
for Structural Mass Spectrometry, Martin-Luther-University
Halle-Wittenberg, 06120 Halle, Germany
- Department
of Physical and Chemical Sciences, University
of L’Aquila, 67100 L’Aquila, Italy
| | - Christian H. Ihling
- Department
of Pharmaceutical Chemistry and Bioanalytics, Martin-Luther-University Halle-Wittenberg, 06120 Halle, Germany
- Center
for Structural Mass Spectrometry, Martin-Luther-University
Halle-Wittenberg, 06120 Halle, Germany
| | - Dirk Tänzler
- Department
of Pharmaceutical Chemistry and Bioanalytics, Martin-Luther-University Halle-Wittenberg, 06120 Halle, Germany
- Center
for Structural Mass Spectrometry, Martin-Luther-University
Halle-Wittenberg, 06120 Halle, Germany
| | - Nicholas Shulman
- Department
of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Michael Riffle
- Department
of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - Brendan X. MacLean
- Department
of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Andrea Sinz
- Department
of Pharmaceutical Chemistry and Bioanalytics, Martin-Luther-University Halle-Wittenberg, 06120 Halle, Germany
- Center
for Structural Mass Spectrometry, Martin-Luther-University
Halle-Wittenberg, 06120 Halle, Germany
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10
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Liu X, Abad L, Chatterjee L, Cristea IM, Varjosalo M. Mapping protein-protein interactions by mass spectrometry. MASS SPECTROMETRY REVIEWS 2024. [PMID: 38742660 DOI: 10.1002/mas.21887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 04/22/2024] [Indexed: 05/16/2024]
Abstract
Protein-protein interactions (PPIs) are essential for numerous biological activities, including signal transduction, transcription control, and metabolism. They play a pivotal role in the organization and function of the proteome, and their perturbation is associated with various diseases, such as cancer, neurodegeneration, and infectious diseases. Recent advances in mass spectrometry (MS)-based protein interactomics have significantly expanded our understanding of the PPIs in cells, with techniques that continue to improve in terms of sensitivity, and specificity providing new opportunities for the study of PPIs in diverse biological systems. These techniques differ depending on the type of interaction being studied, with each approach having its set of advantages, disadvantages, and applicability. This review highlights recent advances in enrichment methodologies for interactomes before MS analysis and compares their unique features and specifications. It emphasizes prospects for further improvement and their potential applications in advancing our knowledge of PPIs in various biological contexts.
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Affiliation(s)
- Xiaonan Liu
- Department of Physiology, Faculty of Medical Sciences in Katowice, Medical University of Silesia in Katowice, Katowice, Poland
- Institute of Biotechnology, HiLIFE Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Lawrence Abad
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Lopamudra Chatterjee
- Institute of Biotechnology, HiLIFE Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Markku Varjosalo
- Institute of Biotechnology, HiLIFE Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
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11
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Liao QQ, Shu X, Sun W, Mandapaka H, Xie F, Zhang Z, Dai T, Wang S, Zhao J, Jiang H, Zhang L, Lin J, Li SW, Coin I, Yang F, Peng J, Li K, Wu H, Zhou F, Yang B. Capturing Protein-Protein Interactions with Acidic Amino Acids Reactive Cross-Linkers. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2308383. [PMID: 38073323 DOI: 10.1002/smll.202308383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/14/2023] [Indexed: 05/18/2024]
Abstract
Acidic residues (Asp and Glu) have a high prevalence on protein surfaces, but cross-linking reactions targeting these residues are limited. Existing methods either require high-concentration coupling reagents or have low structural compatibility. Here a previously reported "plant-and-cast" strategy is extended to develop heterobifunctional cross-linkers. These cross-linkers first react rapidly with Lys sidechains and then react with Asp and Glu sidechains, in a proximity-enhanced fashion. The cross-linking reaction proceeds at neutral pH and room temperature without coupling reagents. The efficiency and robustness of cross-linking using model proteins, ranging from small monomeric proteins to large protein complexes are demonstrated. Importantly, it is shown that this type of cross-linkers are efficient at identifying protein-protein interactions involving acidic domains. The Cross-linking mass spectrometry (XL-MS) study with p53 identified 87 putative binders of the C-terminal domain of p53. Among them, SARNP, ZRAB2, and WBP11 are shown to regulate the expression and alternative splicing of p53 target genes. Thus, these carboxylate-reactive cross-linkers will further expand the power of XL-MS in the analysis of protein structures and protein-protein interactions.
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Affiliation(s)
- Qing-Qing Liao
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute Cancer Center, Zhejiang University, Hangzhou, Zhejiang, 310058, China
- Institute of Biology and Medical Science, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Xin Shu
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute Cancer Center, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Wei Sun
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute Cancer Center, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Hyma Mandapaka
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, KS, 67260, USA
| | - Feng Xie
- Institute of Biology and Medical Science, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Zhengkui Zhang
- Institute of Biology and Medical Science, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Tong Dai
- Institute of Biology and Medical Science, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Shuai Wang
- Institute of Biology and Medical Science, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Jinghua Zhao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital Fudan University, Shanghai, 200438, China
| | - Hong Jiang
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, China
| | - Long Zhang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute Cancer Center, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Jinzhong Lin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital Fudan University, Shanghai, 200438, China
| | - Shu-Wei Li
- Nanjing Apollomics Biotech, Inc, Nanjing, Jiangsu, 210033, China
| | - Irene Coin
- Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, 04103, Leipzig, Germany
| | - Fan Yang
- Department of Biophysics, Kidney Disease Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Jinrong Peng
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Kui Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Haifan Wu
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, KS, 67260, USA
| | - Fangfang Zhou
- Institute of Biology and Medical Science, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Bing Yang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute Cancer Center, Zhejiang University, Hangzhou, Zhejiang, 310058, China
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12
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Inge MM, Miller R, Hook H, Bray D, Keenan JL, Zhao R, Gilmore TD, Siggers T. Rapid profiling of transcription factor-cofactor interaction networks reveals principles of epigenetic regulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.05.588333. [PMID: 38617258 PMCID: PMC11014505 DOI: 10.1101/2024.04.05.588333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Transcription factor (TF)-cofactor (COF) interactions define dynamic, cell-specific networks that govern gene expression; however, these networks are understudied due to a lack of methods for high-throughput profiling of DNA-bound TF-COF complexes. Here we describe the Cofactor Recruitment (CoRec) method for rapid profiling of cell-specific TF-COF complexes. We define a lysine acetyltransferase (KAT)-TF network in resting and stimulated T cells. We find promiscuous recruitment of KATs for many TFs and that 35% of KAT-TF interactions are condition specific. KAT-TF interactions identify NF-κB as a primary regulator of acutely induced H3K27ac. Finally, we find that heterotypic clustering of CBP/P300-recruiting TFs is a strong predictor of total promoter H3K27ac. Our data supports clustering of TF sites that broadly recruit KATs as a mechanism for widespread co-occurring histone acetylation marks. CoRec can be readily applied to different cell systems and provides a powerful approach to define TF-COF networks impacting chromatin state and gene regulation.
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Affiliation(s)
- M M Inge
- Department of Biology, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA, USA
- These authors contributed equally
| | - R Miller
- Department of Biology, Boston University, Boston, MA, USA
- Bioinformatics Program, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA, USA
- These authors contributed equally
| | - H Hook
- Department of Biology, Boston University, Boston, MA, USA
| | - D Bray
- Department of Biology, Boston University, Boston, MA, USA
- Bioinformatics Program, Boston University, Boston, MA, USA
| | - J L Keenan
- Department of Biology, Boston University, Boston, MA, USA
- Bioinformatics Program, Boston University, Boston, MA, USA
| | - R Zhao
- Department of Biology, Boston University, Boston, MA, USA
| | - T D Gilmore
- Department of Biology, Boston University, Boston, MA, USA
| | - T Siggers
- Department of Biology, Boston University, Boston, MA, USA
- Bioinformatics Program, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA, USA
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13
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Di Ianni A, Di Ianni A, Cowan K, Barbero LM, Sirtori FR. Leveraging Cross-Linking Mass Spectrometry for Modeling Antibody-Antigen Complexes. J Proteome Res 2024; 23:1049-1061. [PMID: 38372774 DOI: 10.1021/acs.jproteome.3c00816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Elucidating antibody-antigen complexes at the atomic level is of utmost interest for understanding immune responses and designing better therapies. Cross-linking mass spectrometry (XL-MS) has emerged as a powerful tool for mapping protein-protein interactions, suggesting valuable structural insights. However, the use of XL-MS studies to enable epitope/paratope mapping of antibody-antigen complexes is still limited up to now. XL-MS data can be used to drive integrative modeling of antibody-antigen complexes, where cross-links information serves as distance restraints for the precise determination of binding interfaces. In this approach, XL-MS data are employed to identify connections between binding interfaces of the antibody and the antigen, thus informing molecular modeling. Current literature provides minimal input about the impact of XL-MS data on the integrative modeling of antibody-antigen complexes. Here, we applied XL-MS to retrieve information about binding interfaces of three antibody-antigen complexes. We leveraged XL-MS data to perform integrative modeling using HADDOCK (active-passive residues and distance restraints strategies) and AlphaLink2. We then compared these three approaches with initial predictions of investigated antibody-antigen complexes by AlphaFold Multimer. This work emphasizes the importance of cross-linking data in resolving conformational dynamics of antibody-antigen complexes, ultimately enhancing the design of better protein therapeutics and vaccines.
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Affiliation(s)
- Andrea Di Ianni
- NBE-DMPK Innovative BioAnalytics, Merck Serono RBM S.p.A., an Affiliate of Merck KGaA, Darmstadt, Germany, Via Ribes 1, Colleretto Giacosa (TO) 10010, Italy
- University of Turin, Molecular Biotechnology Center, Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin 10126, Italy
| | - Alessio Di Ianni
- Martin Luther University Halle-Wittenberg, Department of Pharmaceutical Chemistry and Bioanalytics, Center for Structural Mass Spectrometry, Institute of Pharmacy, Kurt-Mothes-Str. 3, Halle/Saale D-06120, Germany
| | - Kyra Cowan
- New Biological Entities, Drug Metabolism and Pharmacokinetics (NBE-DMPK), Research and Development, Merck KGaA, Frankfurterstrasse 250, Darmstadt 64293, Germany
| | - Luca M Barbero
- NBE-DMPK Innovative BioAnalytics, Merck Serono RBM S.p.A., an Affiliate of Merck KGaA, Darmstadt, Germany, Via Ribes 1, Colleretto Giacosa (TO) 10010, Italy
| | - Federico Riccardi Sirtori
- NBE-DMPK Innovative BioAnalytics, Merck Serono RBM S.p.A., an Affiliate of Merck KGaA, Darmstadt, Germany, Via Ribes 1, Colleretto Giacosa (TO) 10010, Italy
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14
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Zhang Z, Zhao Q, Gong Z, Du R, Liu M, Zhang Y, Zhang L, Li C. Progress, Challenges and Opportunities of NMR and XL-MS for Cellular Structural Biology. JACS AU 2024; 4:369-383. [PMID: 38425916 PMCID: PMC10900494 DOI: 10.1021/jacsau.3c00712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/05/2024] [Accepted: 01/16/2024] [Indexed: 03/02/2024]
Abstract
The validity of protein structures and interactions, whether determined under ideal laboratory conditions or predicted by AI tools such as Alphafold2, to precisely reflect those found in living cells remains to be examined. Moreover, understanding the changes in protein structures and interactions in response to stimuli within living cells, under both normal and disease conditions, is key to grasping proteins' functionality and cellular processes. Nevertheless, achieving high-resolution identification of these protein structures and interactions within living cells presents a technical challenge. In this Perspective, we summarize the recent advancements in in-cell nuclear magnetic resonance (NMR) and in vivo cross-linking mass spectrometry (XL-MS) for studying protein structures and interactions within a cellular context. Additionally, we discuss the challenges, opportunities, and potential benefits of integrating in-cell NMR and in vivo XL-MS in future research to offer an exhaustive approach to studying proteins in their natural habitat.
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Affiliation(s)
- Zeting Zhang
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
National Center for Magnetic Resonance in Wuhan, Wuhan Institute of
Physics and Mathematics, Innovation Academy of Precision Measurement, Chinese Academy of Sciences, Wuhan 430071, China
| | - Qun Zhao
- CAS
Key Laboratory of Separation Science for Analytical Chemistry, National
Chromatographic R. & A. Center, State Key Laboratory of Medical
Proteomics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Zhou Gong
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
National Center for Magnetic Resonance in Wuhan, Wuhan Institute of
Physics and Mathematics, Innovation Academy of Precision Measurement, Chinese Academy of Sciences, Wuhan 430071, China
| | - Ruichen Du
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
National Center for Magnetic Resonance in Wuhan, Wuhan Institute of
Physics and Mathematics, Innovation Academy of Precision Measurement, Chinese Academy of Sciences, Wuhan 430071, China
- University
of Chinese Academy of Sciences, Beijing 10049, China
| | - Maili Liu
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
National Center for Magnetic Resonance in Wuhan, Wuhan Institute of
Physics and Mathematics, Innovation Academy of Precision Measurement, Chinese Academy of Sciences, Wuhan 430071, China
| | - Yukui Zhang
- CAS
Key Laboratory of Separation Science for Analytical Chemistry, National
Chromatographic R. & A. Center, State Key Laboratory of Medical
Proteomics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Lihua Zhang
- CAS
Key Laboratory of Separation Science for Analytical Chemistry, National
Chromatographic R. & A. Center, State Key Laboratory of Medical
Proteomics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Conggang Li
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
National Center for Magnetic Resonance in Wuhan, Wuhan Institute of
Physics and Mathematics, Innovation Academy of Precision Measurement, Chinese Academy of Sciences, Wuhan 430071, China
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15
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Hu H, Hu W, Guo AD, Zhai L, Ma S, Nie HJ, Zhou BS, Liu T, Jia X, Liu X, Yao X, Tan M, Chen XH. Spatiotemporal and direct capturing global substrates of lysine-modifying enzymes in living cells. Nat Commun 2024; 15:1465. [PMID: 38368419 PMCID: PMC10874396 DOI: 10.1038/s41467-024-45765-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 02/04/2024] [Indexed: 02/19/2024] Open
Abstract
Protein-modifying enzymes regulate the dynamics of myriad post-translational modification (PTM) substrates. Precise characterization of enzyme-substrate associations is essential for the molecular basis of cellular function and phenotype. Methods for direct capturing global substrates of protein-modifying enzymes in living cells are with many challenges, and yet largely unexplored. Here, we report a strategy to directly capture substrates of lysine-modifying enzymes via PTM-acceptor residue crosslinking in living cells, enabling global profiling of substrates of PTM-enzymes and validation of PTM-sites in a straightforward manner. By integrating enzymatic PTM-mechanisms, and genetically encoding residue-selective photo-crosslinker into PTM-enzymes, our strategy expands the substrate profiles of both bacterial and mammalian lysine acylation enzymes, including bacterial lysine acylases PatZ, YiaC, LplA, TmcA, and YjaB, as well as mammalian acyltransferases GCN5 and Tip60, leading to discovery of distinct yet functionally important substrates and acylation sites. The concept of direct capturing substrates of PTM-enzymes via residue crosslinking may extend to the other types of amino acid residues beyond lysine, which has the potential to facilitate the investigation of diverse types of PTMs and substrate-enzyme interactive proteomics.
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Affiliation(s)
- Hao Hu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Wei Hu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - An-Di Guo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Linhui Zhai
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- Translational Research Institute of Brain and Brain-Like Intelligence, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, 200434, China
| | - Song Ma
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Hui-Jun Nie
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Bin-Shan Zhou
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Tianxian Liu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Xinglong Jia
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Xing Liu
- MOE Key Laboratory for Cellular Dynamics and Hefei National Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, 230026, China
| | - Xuebiao Yao
- MOE Key Laboratory for Cellular Dynamics and Hefei National Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, 230026, China
| | - Minjia Tan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, Guangdong, 528400, China.
| | - Xiao-Hua Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China.
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16
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Nouchikian L, Fernandez-Martinez D, Renard PY, Sabot C, Duménil G, Rey M, Chamot-Rooke J. Do Not Waste Time─Ensure Success in Your Cross-Linking Mass Spectrometry Experiments before You Begin. Anal Chem 2024; 96:2506-2513. [PMID: 38294351 PMCID: PMC10867798 DOI: 10.1021/acs.analchem.3c04682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 01/09/2024] [Accepted: 01/19/2024] [Indexed: 02/01/2024]
Abstract
Cross-linking mass spectrometry (XL-MS) has become a very useful tool for studying protein complexes and interactions in living systems. It enables the investigation of many large and dynamic assemblies in their native state, providing an unbiased view of their protein interactions and restraints for integrative modeling. More researchers are turning toward trying XL-MS to probe their complexes of interest, especially in their native environments. However, due to the presence of other potentially higher abundant proteins, sufficient cross-links on a system of interest may not be reached to achieve satisfactory structural and interaction information. There are currently no rules for predicting whether XL-MS experiments are likely to work or not; in other words, if a protein complex of interest will lead to useful XL-MS data. Here, we show that a simple iBAQ (intensity-based absolute quantification) analysis performed from trypsin digest data can provide a good understanding of whether proteins of interest are abundant enough to achieve successful cross-linking data. Comparing our findings to large-scale data on diverse systems from several other groups, we show that proteins of interest should be at least in the top 20% abundance range to expect more than one cross-link found per protein. We foresee that this guideline is a good starting point for researchers who would like to use XL-MS to study their protein of interest and help ensure a successful cross-linking experiment from the beginning. Data are available via ProteomeXchange with identifier PXD045792.
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Affiliation(s)
- Lucienne Nouchikian
- Institut
Pasteur, Université Paris Cité, CNRS UAR 2024, Mass
Spectrometry for Biology Unit, Paris 75015, France
| | - David Fernandez-Martinez
- Institut
Pasteur, Université Paris Cité, INSERM UMR1225, Pathogenesis
of Vascular Infections Unit, Paris 75015, France
| | - Pierre-Yves Renard
- Univ
Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, COBRA
UMR 6014, INC3M FR 3038, Rouen F-76000, France
| | - Cyrille Sabot
- Univ
Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, COBRA
UMR 6014, INC3M FR 3038, Rouen F-76000, France
| | - Guillaume Duménil
- Institut
Pasteur, Université Paris Cité, INSERM UMR1225, Pathogenesis
of Vascular Infections Unit, Paris 75015, France
| | - Martial Rey
- Institut
Pasteur, Université Paris Cité, CNRS UAR 2024, Mass
Spectrometry for Biology Unit, Paris 75015, France
| | - Julia Chamot-Rooke
- Institut
Pasteur, Université Paris Cité, CNRS UAR 2024, Mass
Spectrometry for Biology Unit, Paris 75015, France
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17
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Zakopcanik M, Kavan D, Novak P, Loginov DS. Quantifying the Impact of the Peptide Identification Framework on the Results of Fast Photochemical Oxidation of Protein Analysis. J Proteome Res 2024; 23:609-617. [PMID: 38158558 PMCID: PMC10845142 DOI: 10.1021/acs.jproteome.3c00390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 10/17/2023] [Accepted: 12/06/2023] [Indexed: 01/03/2024]
Abstract
Fast Photochemical Oxidation of Proteins (FPOP) is a promising technique for studying protein structure and dynamics. The quality of insight provided by FPOP depends on the reliability of the determination of the modification site. This study investigates the performance of two search engines, Mascot and PEAKS, for the data processing of FPOP analyses. Comparison of Mascot and PEAKS of the hemoglobin--haptoglobin Bruker timsTOF data set (PXD021621) revealed greater consistency in the Mascot identification of modified peptides, with around 26% of the IDs being mutual for all three replicates, compared to approximately 22% for PEAKS. The intersection between Mascot and PEAKS results revealed a limited number (31%) of shared modified peptides. Principal Component Analysis (PCA) using the peptide-spectrum match (PSM) score, site probability, and peptide intensity was applied to evaluate the results, and the analyses revealed distinct clusters of modified peptides. Mascot showed the ability to assess confident site determination, even with lower PSM scores. However, high PSM scores from PEAKS did not guarantee a reliable determination of the modification site. Fragmentation coverage of the modification position played a crucial role in Mascot assignments, while the AScore localizations from PEAKS often become ambiguous because the software employs MS/MS merging.
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Affiliation(s)
- Marek Zakopcanik
- Institute
of Microbiology, The Czech Academy of Sciences, 14220 Prague, Czech Republic
- Department
of Biochemistry, Faculty of Science, Charles
University, 12820 Prague, Czech Republic
| | - Daniel Kavan
- Institute
of Microbiology, The Czech Academy of Sciences, 14220 Prague, Czech Republic
| | - Petr Novak
- Institute
of Microbiology, The Czech Academy of Sciences, 14220 Prague, Czech Republic
| | - Dmitry S. Loginov
- Institute
of Microbiology, The Czech Academy of Sciences, 14220 Prague, Czech Republic
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18
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Mohr JP, Caudal A, Tian R, Bruce JE. Multidimensional Cross-Linking and Real-Time Informatics for Multiprotein Interaction Studies. J Proteome Res 2024; 23:107-116. [PMID: 38147001 PMCID: PMC10906106 DOI: 10.1021/acs.jproteome.3c00455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Chemical cross-linking combined with mass spectrometry is a technique used to study protein structures and identify protein complexes. Traditionally, chemical cross-linkers contain two reactive groups, allowing them to covalently bond a pair of proximal residues, either within a protein or between two proteins. The output of a cross-linking experiment is a list of interacting site pairs that provide structural constraints for modeling of new structures and complexes. Due to the binary reactive nature of cross-linking reagents, only pairs of interacting sites can be directly observed, and assembly of higher-order structures typically requires prior knowledge of complex composition or iterative docking to produce a putative model. Here, we describe a new tetrameric cross-linker bearing four amine-reactive groups, allowing it to covalently link up to four proteins simultaneously and a real-time instrument method to facilitate the identification of these tetrameric cross-links. We applied this new cross-linker to isolated mitochondria and identified a number of higher-order cross-links in various OXPHOS complexes and ATP synthase, demonstrating its utility in characterizing complex interfaces. We also show that higher-order cross-links can be used to effectively filter models of large protein assemblies generated by using Alphafold. Higher-dimensional cross-linking provides a new avenue for characterizing multiple protein interfaces, even in complex samples such as intact mitochondria.
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Affiliation(s)
- Jared P Mohr
- Department of Genome Sciences, University of Washington, Seattle, Washington 98105, United States
| | - Arianne Caudal
- Department of Biochemistry, University of Washington, Seattle, Washington 98105, United States
- Mitochondria and Metabolism Center, Department of Anesthesiology & Pain Medicine, University of Washington, Seattle, Washington 98109, United States
| | - Rong Tian
- Department of Biochemistry, University of Washington, Seattle, Washington 98105, United States
- Mitochondria and Metabolism Center, Department of Anesthesiology & Pain Medicine, University of Washington, Seattle, Washington 98109, United States
| | - James E Bruce
- Department of Genome Sciences, University of Washington, Seattle, Washington 98105, United States
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19
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Degliesposti G. Probing Protein Complexes Composition, Stoichiometry, and Interactions by Peptide-Based Mass Spectrometry. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 3234:41-57. [PMID: 38507199 DOI: 10.1007/978-3-031-52193-5_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
The characterization of a protein complex by mass spectrometry can be conducted at different levels. Initial steps regard the qualitative composition of the complex and subunit identification. After that, quantitative information such as stoichiometric ratios and copy numbers for each subunit in a complex or super-complex is acquired. Peptide-based LC-MS/MS offers a wide number of methods and protocols for the characterization of protein complexes. This chapter concentrates on the applications of peptide-based LC-MS/MS for the qualitative, quantitative, and structural characterization of protein complexes focusing on subunit identification, determination of stoichiometric ratio and number of subunits per complex as well as on cross-linking mass spectrometry and hydrogen/deuterium exchange as methods for the structural investigation of the biological assemblies.
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20
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Li X, Wei Y, Fei Q, Fu G, Gan Y, Shi C. TurboID-mediated proximity labeling for screening interacting proteins of FIP37 in Arabidopsis. PLANT DIRECT 2023; 7:e555. [PMID: 38111714 PMCID: PMC10727772 DOI: 10.1002/pld3.555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 11/22/2023] [Accepted: 11/25/2023] [Indexed: 12/20/2023]
Abstract
Proximity labeling was recently developed to detect protein-protein interactions and members of subcellular multiprotein structures in living cells. Proximity labeling is conducted by fusing an engineered enzyme with catalytic activity, such as biotin ligase, to a protein of interest (bait protein) to biotinylate adjacent proteins. The biotinylated protein can be purified by streptavidin beads, and identified by mass spectrometry (MS). TurboID is an engineered biotin ligase with high catalytic efficiency, which is used for proximity labeling. Although TurboID-based proximity labeling technology has been successfully established in mammals, its application in plant systems is limited. Here, we report the usage of TurboID for proximity labeling of FIP37, a core member of m6A methyltransferase complex, to identify FIP37 interacting proteins in Arabidopsis thaliana. By analyzing the MS data, we found 214 proteins biotinylated by GFP-TurboID-FIP37 fusion, including five components of m6A methyltransferase complex that have been previously confirmed. Therefore, the identified proteins may include potential proteins directly involved in the m6A pathway or functionally related to m6A-coupled mRNA processing due to spatial proximity. Moreover, we demonstrated the feasibility of proximity labeling technology in plant epitranscriptomics study, thereby expanding the application of this technology to more subjects of plant research.
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Affiliation(s)
- Xiaofang Li
- Shengzhou Research Base, State Key Laboratory of Cotton BiologyZhengzhou UniversityZhengzhouChina
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural ScienceShenzhenChina
| | - Yanping Wei
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural ScienceShenzhenChina
| | - Qili Fei
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural ScienceShenzhenChina
| | - Guilin Fu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural ScienceShenzhenChina
- College of AgricultureShanxi Agricultural UniversityTaiguChina
| | - Yu Gan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural ScienceShenzhenChina
- School of Life SciencesHenan UniversityKaifengChina
- Shenzhen Research Institute of Henan universityShenzhenChina
| | - Chuanlin Shi
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural ScienceShenzhenChina
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21
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Walia N, Murray DT, Garg Y, He H, Weiss KL, Nagy G, Elizabeth Stroupe M. Domain crossover in the reductase subunit of NADPH-dependent assimilatory sulfite reductase. J Struct Biol 2023; 215:108028. [PMID: 37704014 DOI: 10.1016/j.jsb.2023.108028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 09/08/2023] [Accepted: 09/10/2023] [Indexed: 09/15/2023]
Abstract
NADPH-dependent assimilatory sulfite reductase (SiR) from Escherichia coli performs a six-electron reduction of sulfite to the bioavailable sulfide. SiR is composed of a flavoprotein (SiRFP) reductase subunit and a hemoprotein (SiRHP) oxidase subunit. There is no known high-resolution structure of SiR or SiRFP, thus we do not yet fully understand how the subunits interact to perform their chemistry. Here, we used small-angle neutron scattering to understand the impact of conformationally restricting the highly mobile SiRFP octamer into an electron accepting (closed) or electron donating (open) conformation, showing that SiR remains active, flexible, and asymmetric even with these conformational restrictions. From these scattering data, we model the first solution structure of SiRFP. Further, computational modeling of the N-terminal 52 amino acids that are responsible for SiRFP oligomerization suggests an eight-helical bundle tethers together the SiRFP subunits to form the SiR core. Finally, mass spectrometry analysis of the closed SiRFP variant show that SiRFP is capable of inter-molecular domain crossover, in which the electron donating domain from one polypeptide is able to interact directly with the electron accepting domain of another polypeptide. This structural characterization suggests that SiR performs its high-volume electron transfer through both inter- and intramolecular pathways between SiRFP domains and, thus, cis or trans transfer from reductase to oxidase subunits. Such highly redundant potential for electron transfer makes this system a potential target for designing synthetic enzymes.
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Affiliation(s)
- Nidhi Walia
- Department of Biological Science, Florida State University, 91 Chieftain Way, Tallahassee, FL 32306, USA; Institute of Molecular Biophysics, Florida State University, 91 Chieftain Way, Tallahassee, FL 32306, USA
| | - Daniel T Murray
- Department of Biological Science, Florida State University, 91 Chieftain Way, Tallahassee, FL 32306, USA; Institute of Molecular Biophysics, Florida State University, 91 Chieftain Way, Tallahassee, FL 32306, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, USA(1)
| | - Yashika Garg
- Department of Biological Science, Florida State University, 91 Chieftain Way, Tallahassee, FL 32306, USA; Institute of Molecular Biophysics, Florida State University, 91 Chieftain Way, Tallahassee, FL 32306, USA
| | - Huan He
- Institute of Molecular Biophysics, Florida State University, 91 Chieftain Way, Tallahassee, FL 32306, USA; Translational Science Laboratory, College of Medicine, 1115 West Call Street, Tallahassee, FL 32306, USA
| | - Kevin L Weiss
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Gergely Nagy
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - M Elizabeth Stroupe
- Department of Biological Science, Florida State University, 91 Chieftain Way, Tallahassee, FL 32306, USA; Institute of Molecular Biophysics, Florida State University, 91 Chieftain Way, Tallahassee, FL 32306, USA.
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22
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Mandal K, Wicaksono G, Yu C, Adams JJ, Hoopmann MR, Temple WC, Izgutdina A, Escobar BP, Gorelik M, Ihling CH, Nix MA, Naik A, Xie WH, Hübner J, Rollins LA, Reid SM, Ramos E, Kasap C, Steri V, Serrano JAC, Salangsang F, Phojanakong P, McMillan M, Gavallos V, Leavitt AD, Logan AC, Rooney CM, Eyquem J, Sinz A, Huang BJ, Stieglitz E, Smith CC, Moritz RL, Sidhu SS, Huang L, Wiita AP. Structural surfaceomics reveals an AML-specific conformation of integrin β 2 as a CAR T cellular therapy target. NATURE CANCER 2023; 4:1592-1609. [PMID: 37904046 PMCID: PMC10663162 DOI: 10.1038/s43018-023-00652-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 09/12/2023] [Indexed: 11/01/2023]
Abstract
Safely expanding indications for cellular therapies has been challenging given a lack of highly cancer-specific surface markers. Here we explore the hypothesis that tumor cells express cancer-specific surface protein conformations that are invisible to standard target discovery pipelines evaluating gene or protein expression, and these conformations can be identified and immunotherapeutically targeted. We term this strategy integrating cross-linking mass spectrometry with glycoprotein surface capture 'structural surfaceomics'. As a proof of principle, we apply this technology to acute myeloid leukemia (AML), a hematologic malignancy with dismal outcomes and no known optimal immunotherapy target. We identify the activated conformation of integrin β2 as a structurally defined, widely expressed AML-specific target. We develop and characterize recombinant antibodies to this protein conformation and show that chimeric antigen receptor T cells eliminate AML cells and patient-derived xenografts without notable toxicity toward normal hematopoietic cells. Our findings validate an AML conformation-specific target antigen and demonstrate a tool kit for applying these strategies more broadly.
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Affiliation(s)
- Kamal Mandal
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Gianina Wicaksono
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Clinton Yu
- Department of Physiology and Biophysics, University of California Irvine, Irvine, CA, USA
| | - Jarrett J Adams
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- School of Pharmacy, University of Waterloo, Kitchener, Ontario, Canada
| | | | - William C Temple
- Department of Pediatrics, Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA
- Department of Pediatrics, Division of Allergy, Immunology, and Bone Marrow Transplantation, University of California San Francisco, San Francisco, CA, USA
| | - Adila Izgutdina
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Bonell Patiño Escobar
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Maryna Gorelik
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Christian H Ihling
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Halle, Germany
| | - Matthew A Nix
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Akul Naik
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - William H Xie
- UCSF/Gladstone Institute for Genomic Immunology, San Francisco, CA, USA
| | - Juwita Hübner
- Department of Pediatrics, Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Lisa A Rollins
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston Methodist Hospital-Texas Children's Hospital, Houston, TX, USA
| | - Sandy M Reid
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston Methodist Hospital-Texas Children's Hospital, Houston, TX, USA
| | - Emilio Ramos
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Corynn Kasap
- Department of Medicine, Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA
| | - Veronica Steri
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Juan Antonio Camara Serrano
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Fernando Salangsang
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Paul Phojanakong
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Melanie McMillan
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Victor Gavallos
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Andrew D Leavitt
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Aaron C Logan
- Department of Medicine, Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA
| | - Cliona M Rooney
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston Methodist Hospital-Texas Children's Hospital, Houston, TX, USA
| | - Justin Eyquem
- UCSF/Gladstone Institute for Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Halle, Germany
| | - Benjamin J Huang
- Department of Pediatrics, Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA
| | - Elliot Stieglitz
- Department of Pediatrics, Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Catherine C Smith
- Department of Medicine, Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA
| | | | - Sachdev S Sidhu
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- School of Pharmacy, University of Waterloo, Kitchener, Ontario, Canada
| | - Lan Huang
- Department of Physiology and Biophysics, University of California Irvine, Irvine, CA, USA
| | - Arun P Wiita
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub San Francisco, San Francisco, CA, USA.
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23
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KIM S, KAMARULZAMAN L, TANIGUCHI Y. Recent methodological advances towards single-cell proteomics. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2023; 99:306-327. [PMID: 37673661 PMCID: PMC10749393 DOI: 10.2183/pjab.99.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 07/20/2023] [Indexed: 09/08/2023]
Abstract
Studying the central dogma at the single-cell level has gained increasing attention to reveal hidden cell lineages and functions that cannot be studied using traditional bulk analyses. Nonetheless, most single-cell studies exploiting genomic and transcriptomic levels fail to address information on proteins that are central to many important biological processes. Single-cell proteomics enables understanding of the functional status of individual cells and is particularly crucial when the specimen is composed of heterogeneous entities of cells. With the growing importance of this field, significant methodological advancements have emerged recently. These include miniaturized and automated sample preparation, multi-omics analyses, and combined analyses of multiple techniques such as mass spectrometry and microscopy. Moreover, artificial intelligence and single-molecule detection technologies have advanced throughput and improved sensitivity limitations, respectively, over conventional methods. In this review, we summarize cutting-edge methodologies for single-cell proteomics and relevant emerging technologies that have been reported in the last 5 years, and provide an outlook on this research field.
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Affiliation(s)
- Sooyeon KIM
- Laboratory for Cell Systems Control, Center for Biosystems Dynamics Research, RIKEN, Suita, Osaka, Japan
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Latiefa KAMARULZAMAN
- Laboratory for Cell Systems Control, Center for Biosystems Dynamics Research, RIKEN, Suita, Osaka, Japan
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Yuichi TANIGUCHI
- Laboratory for Cell Systems Control, Center for Biosystems Dynamics Research, RIKEN, Suita, Osaka, Japan
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Sakyo-ku, Kyoto, Japan
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
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24
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Ruwolt M, Piazza I, Liu F. The potential of cross-linking mass spectrometry in the development of protein-protein interaction modulators. Curr Opin Struct Biol 2023; 82:102648. [PMID: 37423038 DOI: 10.1016/j.sbi.2023.102648] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/03/2023] [Accepted: 06/08/2023] [Indexed: 07/11/2023]
Abstract
Cross-linking mass spectrometry (XL-MS) can provide a wealth of information on endogenous protein-protein interaction (PPI) networks and protein binding interfaces. These features make XL-MS an attractive tool to support the development of PPI-targeting drugs. Though not yet widely used, applications of XL-MS to drug characterization are beginning to emerge. Here, we compare XL-MS to established structural proteomics methods in drug research, discuss the current state and remaining challenges of XL-MS technology, and provide a perspective on the future role XL-MS can play in drug development, with a particular emphasis on PPI modulators.
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Affiliation(s)
- Max Ruwolt
- Department of Structural Biology, Leibniz, Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10, 13125 Berlin, Germany. https://twitter.com/@MRuwolt
| | - Ilaria Piazza
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC Berlin), Berlin, Germany.
| | - Fan Liu
- Department of Structural Biology, Leibniz, Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10, 13125 Berlin, Germany; Charité - Universitätsmedizin Berlin, Charitépl. 1, 10117 Berlin, Germany.
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25
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Hao Y, Chen M, Huang X, Xu H, Wu P, Chen S. 4D-diaXLMS: Proteome-wide Four-Dimensional Data-Independent Acquisition Workflow for Cross-Linking Mass Spectrometry. Anal Chem 2023; 95:14077-14085. [PMID: 37691250 DOI: 10.1021/acs.analchem.3c02824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Cross-linking mass spectrometry (XL-MS) is a powerful tool for examining protein structures and interactions. Nevertheless, analysis of low-abundance cross-linked peptides is often limited in the data-dependent acquisition (DDA) mode due to its semistochastic nature. To address this issue, we introduced a workflow called 4D-diaXLMS, representing the first-ever application of four-dimensional data-independent acquisition for proteome-wide cross-linking analysis. Cross-linking studies of the HeLa cell proteome were evaluated using the classical cross-linker disuccinimidyl suberate as an example. Compared with the DDA analysis, 4D-diaXLMS exhibited marked improvement in the identification coverage of cross-linked peptides, with a total increase of 36% in single-shot analysis across all 16 SCX fractions. This advantage was further amplified when reducing the fraction number to 8 and 4, resulting in 125 and 149% improvements, respectively. Using 4D-diaXLMS, up to 83% of the cross-linked peptides were repeatedly identified in three replicates, more than twice the 38% in the DDA mode. Furthermore, 4D-diaXLMS showed good performance in the quantitative analysis of yeast cross-linked peptides even in a 15-fold excess amount of HeLa cell matrix, with a low coefficient of variation and high quantitative accuracies in all concentrations. Overall, 4D-diaXLMS was proven to have high coverage, good reproducibility, and accurate quantification for in-depth XL-MS analysis in complex samples, demonstrating its immense potential for advances in the field.
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Affiliation(s)
- Yanhong Hao
- The Institute for Advanced Studies, Wuhan University, Wuhan, Hubei 430072, China
| | - Moran Chen
- The Institute for Advanced Studies, Wuhan University, Wuhan, Hubei 430072, China
| | - Xiao Huang
- The Institute for Advanced Studies, Wuhan University, Wuhan, Hubei 430072, China
| | - Hui Xu
- The Institute for Advanced Studies, Wuhan University, Wuhan, Hubei 430072, China
| | - Pengfei Wu
- The Institute for Advanced Studies, Wuhan University, Wuhan, Hubei 430072, China
| | - Suming Chen
- The Institute for Advanced Studies, Wuhan University, Wuhan, Hubei 430072, China
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26
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Garcia-Del Rio DF, Fournier I, Cardon T, Salzet M. Protocol to identify human subcellular alternative protein interactions using cross-linking mass spectrometry. STAR Protoc 2023; 4:102380. [PMID: 37384523 PMCID: PMC10511867 DOI: 10.1016/j.xpro.2023.102380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 05/04/2023] [Accepted: 05/24/2023] [Indexed: 07/01/2023] Open
Abstract
Since the start of mass-spectrometry-based proteomics, proteins from non-referenced open reading frames or alternative proteins (AltProts) have been overlooked. Here, we present a protocol to identify human subcellular AltProt and decipher some interactions using cross-linking mass spectrometry. We describe steps for cell culture, in cellulo cross-link, subcellular extraction, and sequential digestion. We then detail both liquid chromatography-tandem mass spectrometry and cross-link data analyses. The implementation of a single workflow allows the non-targeted identification of signaling pathways involving AltProts. For complete details on the use and execution of this protocol, please refer to Garcia-del Rio et al.1.
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Affiliation(s)
- Diego Fernando Garcia-Del Rio
- Université de Lille, Univ. Lille, CHU Lille, Inserm U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000 Lille, France; VIB Center for Medical Biotechnology, VIB, Ghent 9052, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent 9052, Belgium
| | - Isabelle Fournier
- Université de Lille, Univ. Lille, CHU Lille, Inserm U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000 Lille, France.
| | - Tristan Cardon
- Université de Lille, Univ. Lille, CHU Lille, Inserm U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000 Lille, France.
| | - Michel Salzet
- Université de Lille, Univ. Lille, CHU Lille, Inserm U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000 Lille, France
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27
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Nie M, Li H. Innovation in Cross-Linking Mass Spectrometry Workflows: Toward a Comprehensive, Flexible, and Customizable Data Analysis Platform. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:1949-1956. [PMID: 37537999 DOI: 10.1021/jasms.3c00123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
Cross-linking mass spectrometry (XL-MS) is widely used in the analysis of protein structure and protein-protein interactions (PPIs). Throughout the entire workflow, the utilization of cross-linkers and the interpretation of cross-linking data are the core steps. In recent years, the development of cross-linkers and analytical software mostly follow up on the classical models of non-cleavable cross-linkers such as BS3/DSS and MS-cleavable cross-linkers such as DSSO. Although such a paradigm promotes the maturity and robustness of the XL-MS field, it confines the innovation and flexibility of new cross-linkers and analytical software. This critical insight will discuss the classification, advantages, and disadvantages of existing data analysis search engines. Take the new platinum-based metal cross-linker as an example, potential pitfalls in characterization of cross-linked peptides using existing software are discussed. Finally, ideas on developing more flexible, comprehensive, and user-friendly cross-linkers and software tools are proposed.
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Affiliation(s)
- Minhan Nie
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Huilin Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
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28
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Cohen S, Schneidman-Duhovny D. A deep learning model for predicting optimal distance range in crosslinking mass spectrometry data. Proteomics 2023; 23:e2200341. [PMID: 37070547 DOI: 10.1002/pmic.202200341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 04/02/2023] [Accepted: 04/03/2023] [Indexed: 04/19/2023]
Abstract
Macromolecular assemblies play an important role in all cellular processes. While there has recently been significant progress in protein structure prediction based on deep learning, large protein complexes cannot be predicted with these approaches. The integrative structure modeling approach characterizes multi-subunit complexes by computational integration of data from fast and accessible experimental techniques. Crosslinking mass spectrometry is one such technique that provides spatial information about the proximity of crosslinked residues. One of the challenges in interpreting crosslinking datasets is designing a scoring function that, given a structure, can quantify how well it fits the data. Most approaches set an upper bound on the distance between Cα atoms of crosslinked residues and calculate a fraction of satisfied crosslinks. However, the distance spanned by the crosslinker greatly depends on the neighborhood of the crosslinked residues. Here, we design a deep learning model for predicting the optimal distance range for a crosslinked residue pair based on the structures of their neighborhoods. We find that our model can predict the distance range with the area under the receiver-operator curve of 0.86 and 0.7 for intra- and inter-protein crosslinks, respectively. Our deep scoring function can be used in a range of structure modeling applications.
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Affiliation(s)
- Shon Cohen
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Dina Schneidman-Duhovny
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
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29
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Cao Y, Liu XT, Mao PZ, Chen ZL, Tarn C, Dong MQ. Comparative Analysis of Chemical Cross-Linking Mass Spectrometry Data Indicates That Protein STY Residues Rarely React with N-Hydroxysuccinimide Ester Cross-Linkers. J Proteome Res 2023; 22:2593-2607. [PMID: 37494005 DOI: 10.1021/acs.jproteome.3c00037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
When it comes to mass spectrometry data analysis for identification of peptide pairs linked by N-hydroxysuccinimide (NHS) ester cross-linkers, search engines bifurcate in their setting of cross-linkable sites. Some restrict NHS ester cross-linkable sites to lysine (K) and protein N-terminus, referred to as K only for short, whereas others additionally include serine (S), threonine (T), and tyrosine (Y) by default. Here, by setting amino acids with chemically inert side chains such as glycine (G), valine (V), and leucine (L) as cross-linkable sites, which serves as a negative control, we show that software-identified STY-cross-links are only as reliable as GVL-cross-links. This is true across different NHS ester cross-linkers including DSS, DSSO, and DSBU, and across different search engines including MeroX, xiSearch, and pLink. Using a published data set originated from synthetic peptides, we demonstrate that STY-cross-links indeed have a high false discovery rate. Further analysis revealed that depending on the data and the search engine used to analyze the data, up to 65% of the STY-cross-links identified are actually K-K cross-links of the same peptide pairs, up to 61% are actually K-mono-links, and the rest tend to contain short peptides at high risk of false identification.
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Affiliation(s)
- Yong Cao
- National Institute of Biological Sciences, Beijing, Beijing 102206, China
| | - Xin-Tong Liu
- National Institute of Biological Sciences, Beijing, Beijing 102206, China
| | - Peng-Zhi Mao
- Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen-Lin Chen
- Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ching Tarn
- Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
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30
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Burnap SA, Ortega-Prieto AM, Jimenez-Guardeño JM, Ali H, Takov K, Fish M, Shankar-Hari M, Giacca M, Malim MH, Mayr M. Cross-Linking Mass Spectrometry Uncovers Interactions Between High-Density Lipoproteins and the SARS-CoV-2 Spike Glycoprotein. Mol Cell Proteomics 2023; 22:100600. [PMID: 37343697 PMCID: PMC10279469 DOI: 10.1016/j.mcpro.2023.100600] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 06/23/2023] Open
Abstract
High-density lipoprotein (HDL) levels are reduced in patients with coronavirus disease 2019 (COVID-19), and the extent of this reduction is associated with poor clinical outcomes. While lipoproteins are known to play a key role during the life cycle of the hepatitis C virus, their influence on coronavirus (CoV) infections is poorly understood. In this study, we utilize cross-linking mass spectrometry (XL-MS) to determine circulating protein interactors of the severe acute respiratory syndrome (SARS)-CoV-2 spike glycoprotein. XL-MS of plasma isolated from patients with COVID-19 uncovered HDL protein interaction networks, dominated by acute-phase serum amyloid proteins, whereby serum amyloid A2 was shown to bind to apolipoprotein (Apo) D. XL-MS on isolated HDL confirmed ApoD to interact with SARS-CoV-2 spike but not SARS-CoV-1 spike. Other direct interactions of SARS-CoV-2 spike upon HDL included ApoA1 and ApoC3. The interaction between ApoD and spike was further validated in cells using immunoprecipitation-MS, which uncovered a novel interaction between both ApoD and spike with membrane-associated progesterone receptor component 1. Mechanistically, XL-MS coupled with data-driven structural modeling determined that ApoD may interact within the receptor-binding domain of the spike. However, ApoD overexpression in multiple cell-based assays had no effect upon viral replication or infectivity. Thus, SARS-CoV-2 spike can bind to apolipoproteins on HDL, but these interactions do not appear to alter infectivity.
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Affiliation(s)
- Sean A Burnap
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK; The Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, Oxford, UK; King's College London British Heart Foundation Centre, School of Cardiovascular Medicine and Sciences, London, UK.
| | - Ana Maria Ortega-Prieto
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Jose M Jimenez-Guardeño
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Hashim Ali
- King's College London British Heart Foundation Centre, School of Cardiovascular Medicine and Sciences, London, UK; Division of Virology, Department of Pathology, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK
| | - Kaloyan Takov
- King's College London British Heart Foundation Centre, School of Cardiovascular Medicine and Sciences, London, UK
| | - Matthew Fish
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK; Department of Intensive Care Medicine, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Manu Shankar-Hari
- Centre for Inflammation Research, Institute of Regeneration and Repair, University of Edinburgh, Edinburgh, UK; Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, UK
| | - Mauro Giacca
- King's College London British Heart Foundation Centre, School of Cardiovascular Medicine and Sciences, London, UK
| | - Michael H Malim
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Manuel Mayr
- King's College London British Heart Foundation Centre, School of Cardiovascular Medicine and Sciences, London, UK.
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31
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Faustino AM, Sharma P, Manriquez-Sandoval E, Yadav D, Fried SD. Progress toward Proteome-Wide Photo-Cross-Linking to Enable Residue-Level Visualization of Protein Structures and Networks In Vivo. Anal Chem 2023; 95:10670-10685. [PMID: 37341467 DOI: 10.1021/acs.analchem.3c01369] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2023]
Abstract
Cross-linking mass spectrometry (XL-MS) is emerging as a method at the crossroads of structural and cellular biology, uniquely capable of identifying protein-protein interactions with residue-level resolution and on the proteome-wide scale. With the development of cross-linkers that can form linkages inside cells and easily cleave during fragmentation on the mass spectrometer (MS-cleavable cross-links), it has become increasingly facile to identify contacts between any two proteins in complex samples, including in live cells or tissues. Photo-cross-linkers possess the advantages of high temporal resolution and high reactivity, thereby engaging all residue-types (rather than just lysine); nevertheless, photo-cross-linkers have not enjoyed widespread use and are yet to be employed for proteome-wide studies because their products are challenging to identify. Here, we demonstrate the synthesis and application of two heterobifunctional photo-cross-linkers that feature diazirines and N-hydroxy-succinimidyl carbamate groups, the latter of which unveil doubly fissile MS-cleavable linkages upon acyl transfer to protein targets. Moreover, these cross-linkers demonstrate high water-solubility and cell-permeability. Using these compounds, we demonstrate the feasibility of proteome-wide photo-cross-linking in cellulo. These studies elucidate a small portion of Escherichia coli's interaction network, albeit with residue-level resolution. With further optimization, these methods will enable the detection of protein quinary interaction networks in their native environment at residue-level resolution, and we expect that they will prove useful toward the effort to explore the molecular sociology of the cell.
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Affiliation(s)
- Anneliese M Faustino
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Piyoosh Sharma
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Edgar Manriquez-Sandoval
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Divya Yadav
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Stephen D Fried
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
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32
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Abendstein L, Dijkstra DJ, Tjokrodirijo RTN, van Veelen PA, Trouw LA, Hensbergen PJ, Sharp TH. Complement is activated by elevated IgG3 hexameric platforms and deposits C4b onto distinct antibody domains. Nat Commun 2023; 14:4027. [PMID: 37419978 PMCID: PMC10328927 DOI: 10.1038/s41467-023-39788-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 06/29/2023] [Indexed: 07/09/2023] Open
Abstract
IgG3 is unique among the IgG subclasses due to its extended hinge, allotypic diversity and enhanced effector functions, including highly efficient pathogen neutralisation and complement activation. It is also underrepresented as an immunotherapeutic candidate, partly due to a lack of structural information. Here, we use cryoEM to solve structures of antigen-bound IgG3 alone and in complex with complement components. These structures reveal a propensity for IgG3-Fab clustering, which is possible due to the IgG3-specific flexible upper hinge region and may maximise pathogen neutralisation by forming high-density antibody arrays. IgG3 forms elevated hexameric Fc platforms that extend above the protein corona to maximise binding to receptors and the complement C1 complex, which here adopts a unique protease conformation that may precede C1 activation. Mass spectrometry reveals that C1 deposits C4b directly onto specific IgG3 residues proximal to the Fab domains. Structural analysis shows this to be caused by the height of the C1-IgG3 complex. Together, these data provide structural insights into the role of the unique IgG3 extended hinge, which will aid the development and design of upcoming immunotherapeutics based on IgG3.
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Affiliation(s)
- Leoni Abendstein
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
| | - Douwe J Dijkstra
- Department of Immunology, Leiden University Medical Center, 2333 ZA, Leiden, The Netherlands
| | - Rayman T N Tjokrodirijo
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333 ZA, Leiden, The Netherlands
| | - Peter A van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333 ZA, Leiden, The Netherlands
| | - Leendert A Trouw
- Department of Immunology, Leiden University Medical Center, 2333 ZA, Leiden, The Netherlands
| | - Paul J Hensbergen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333 ZA, Leiden, The Netherlands
| | - Thomas H Sharp
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands.
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33
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Blueggel M, Kroening A, Kracht M, van den Boom J, Dabisch M, Goehring A, Kaschani F, Kaiser M, Bayer P, Meyer H, Beuck C. The UBX domain in UBXD1 organizes ubiquitin binding at the C-terminus of the VCP/p97 AAA-ATPase. Nat Commun 2023; 14:3258. [PMID: 37277335 DOI: 10.1038/s41467-023-38604-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 05/09/2023] [Indexed: 06/07/2023] Open
Abstract
The AAA+ ATPase p97/VCP together with different sets of substrate-delivery adapters and accessory cofactor proteins unfolds ubiquitinated substrates to facilitate degradation by the proteasome. The UBXD1 cofactor is connected to p97-associated multisystem proteinopathy but its biochemical function and structural organization on p97 has remained largely elusive. Using a combination of crosslinking mass spectrometry and biochemical assays, we identify an extended UBX (eUBX) module in UBXD1 related to a lariat in another cofactor, ASPL. Of note, the UBXD1-eUBX intramolecularly associates with the PUB domain in UBXD1 close to the substrate exit pore of p97. The UBXD1 PUB domain can also bind the proteasomal shuttling factor HR23b via its UBL domain. We further show that the eUBX domain has ubiquitin binding activity and that UBXD1 associates with an active p97-adapter complex during substrate unfolding. Our findings suggest that the UBXD1-eUBX module receives unfolded ubiquitinated substrates after they exit the p97 channel and before hand-over to the proteasome. The interplay of full-length UBXD1 and HR23b and their function in the context of an active p97:UBXD1 unfolding complex remains to be studied in future work.
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Affiliation(s)
- Mike Blueggel
- Structural and Medicinal Biochemistry, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Alexander Kroening
- Molecular Biology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Matthias Kracht
- Molecular Biology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | | | - Matthias Dabisch
- Structural and Medicinal Biochemistry, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Anna Goehring
- Structural and Medicinal Biochemistry, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Farnusch Kaschani
- Chemical Biology and ACE Analytical Core Facility Essen, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Markus Kaiser
- Chemical Biology and ACE Analytical Core Facility Essen, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Peter Bayer
- Structural and Medicinal Biochemistry, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Hemmo Meyer
- Molecular Biology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Christine Beuck
- Structural and Medicinal Biochemistry, Faculty of Biology, University of Duisburg-Essen, Essen, Germany.
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34
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Dai S, Liu S, Zhou C, Yu F, Zhu G, Zhang W, Deng H, Burlingame A, Yu W, Wang T, Li N. Capturing the hierarchically assorted modules of protein-protein interactions in the organized nucleome. MOLECULAR PLANT 2023; 16:930-961. [PMID: 36960533 DOI: 10.1016/j.molp.2023.03.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 02/16/2023] [Accepted: 03/21/2023] [Indexed: 05/04/2023]
Abstract
Nuclear proteins are major constituents and key regulators of nucleome topological organization and manipulators of nuclear events. To decipher the global connectivity of nuclear proteins and the hierarchically organized modules of their interactions, we conducted two rounds of cross-linking mass spectrometry (XL-MS) analysis, one of which followed a quantitative double chemical cross-linking mass spectrometry (in vivoqXL-MS) workflow, and identified 24,140 unique crosslinks in total from the nuclei of soybean seedlings. This in vivo quantitative interactomics enabled the identification of 5340 crosslinks that can be converted into 1297 nuclear protein-protein interactions (PPIs), 1220 (94%) of which were non-confirmative (or novel) nuclear PPIs compared with those in repositories. There were 250 and 26 novel interactors of histones and the nucleolar box C/D small nucleolar ribonucleoprotein complex, respectively. Modulomic analysis of orthologous Arabidopsis PPIs produced 27 and 24 master nuclear PPI modules (NPIMs) that contain the condensate-forming protein(s) and the intrinsically disordered region-containing proteins, respectively. These NPIMs successfully captured previously reported nuclear protein complexes and nuclear bodies in the nucleus. Surprisingly, these NPIMs were hierarchically assorted into four higher-order communities in a nucleomic graph, including genome and nucleolus communities. This combinatorial pipeline of 4C quantitative interactomics and PPI network modularization revealed 17 ethylene-specific module variants that participate in a broad range of nuclear events. The pipeline was able to capture both nuclear protein complexes and nuclear bodies, construct the topological architectures of PPI modules and module variants in the nucleome, and probably map the protein compositions of biomolecular condensates.
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Affiliation(s)
- Shuaijian Dai
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Shichang Liu
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Chen Zhou
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Fengchao Yu
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Guang Zhu
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Wenhao Zhang
- Tsinghua-Peking Joint Centre for Life Sciences, Centre for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China
| | - Haiteng Deng
- Tsinghua-Peking Joint Centre for Life Sciences, Centre for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China
| | - Al Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Weichuan Yu
- The HKUST Shenzhen-Hong Kong Collaborative Innovation Research Institute, Futian, Shenzhen, Guangdong 518057, China; Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China.
| | - Tingliang Wang
- Tsinghua-Peking Joint Centre for Life Sciences, Centre for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China.
| | - Ning Li
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China; Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Hong Kong, China; The HKUST Shenzhen-Hong Kong Collaborative Innovation Research Institute, Futian, Shenzhen, Guangdong 518057, China.
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35
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Ruwolt M, He Y, Borges Lima D, Barshop W, Broichhagen J, Huguet R, Viner R, Liu F. Real-Time Library Search Increases Cross-Link Identification Depth across All Levels of Sample Complexity. Anal Chem 2023; 95:5248-5255. [PMID: 36926872 PMCID: PMC10061366 DOI: 10.1021/acs.analchem.2c05141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Cross-linking mass spectrometry (XL-MS) is a universal tool for probing structural dynamics and protein-protein interactions in vitro and in vivo. Although cross-linked peptides are naturally less abundant than their unlinked counterparts, recent experimental advances improved cross-link identification by enriching the cross-linker-modified peptides chemically with the use of enrichable cross-linkers. However, mono-links (i.e., peptides modified with a hydrolyzed cross-linker) still hinder efficient cross-link identification since a large proportion of measurement time is spent on their MS2 acquisition. Currently, cross-links and mono-links cannot be separated by sample preparation techniques or chromatography because they are chemically almost identical. Here, we found that based on the intensity ratios of four diagnostic peaks when using PhoX/tBu-PhoX cross-linkers, cross-links and mono-links can be partially distinguished. Harnessing their characteristic intensity ratios for real-time library search (RTLS)-based triggering of high-resolution MS2 scans increased the number of cross-link identifications from both single protein samples and intact E. coli cells. Specifically, RTLS improves cross-link identification from unenriched samples and short gradients, emphasizing its advantages in high-throughput approaches and when instrument time or sample amount is limited.
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Affiliation(s)
- Max Ruwolt
- Department of Structural Biology, Leibniz─Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10, Berlin 13125, Germany
| | - Yi He
- Thermo Fisher Scientific, 355 River Oaks Pkwy, San Jose, California 95134, United States
| | - Diogo Borges Lima
- Department of Structural Biology, Leibniz─Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10, Berlin 13125, Germany
| | - William Barshop
- Thermo Fisher Scientific, 355 River Oaks Pkwy, San Jose, California 95134, United States
| | - Johannes Broichhagen
- Department of Chemical Biology, Leibniz─Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10, Berlin 13125, Germany
| | - Romain Huguet
- Thermo Fisher Scientific, 355 River Oaks Pkwy, San Jose, California 95134, United States
| | - Rosa Viner
- Thermo Fisher Scientific, 355 River Oaks Pkwy, San Jose, California 95134, United States
| | - Fan Liu
- Department of Structural Biology, Leibniz─Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10, Berlin 13125, Germany.,Charité─Universitätsmedizin Berlin, Charitépl. 1, Berlin 10117, Germany
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36
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Malinovska L, Cappelletti V, Kohler D, Piazza I, Tsai TH, Pepelnjak M, Stalder P, Dörig C, Sesterhenn F, Elsässer F, Kralickova L, Beaton N, Reiter L, de Souza N, Vitek O, Picotti P. Proteome-wide structural changes measured with limited proteolysis-mass spectrometry: an advanced protocol for high-throughput applications. Nat Protoc 2023; 18:659-682. [PMID: 36526727 DOI: 10.1038/s41596-022-00771-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 07/08/2022] [Indexed: 12/23/2022]
Abstract
Proteins regulate biological processes by changing their structure or abundance to accomplish a specific function. In response to a perturbation, protein structure may be altered by various molecular events, such as post-translational modifications, protein-protein interactions, aggregation, allostery or binding to other molecules. The ability to probe these structural changes in thousands of proteins simultaneously in cells or tissues can provide valuable information about the functional state of biological processes and pathways. Here, we present an updated protocol for LiP-MS, a proteomics technique combining limited proteolysis with mass spectrometry, to detect protein structural alterations in complex backgrounds and on a proteome-wide scale. In LiP-MS, proteins undergo a brief proteolysis in native conditions followed by complete digestion in denaturing conditions, to generate structurally informative proteolytic fragments that are analyzed by mass spectrometry. We describe advances in the throughput and robustness of the LiP-MS workflow and implementation of data-independent acquisition-based mass spectrometry, which together achieve high reproducibility and sensitivity, even on large sample sizes. We introduce MSstatsLiP, an R package dedicated to the analysis of LiP-MS data for the identification of structurally altered peptides and differentially abundant proteins. The experimental procedures take 3 d, mass spectrometric measurement time and data processing depend on sample number and statistical analysis typically requires ~1 d. These improvements expand the adaptability of LiP-MS and enable wide use in functional proteomics and translational applications.
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Affiliation(s)
- Liliana Malinovska
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Valentina Cappelletti
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Devon Kohler
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
| | - Ilaria Piazza
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC Berlin), Berlin, Germany
| | - Tsung-Heng Tsai
- Department of Mathematical Sciences, Kent State University, Kent, OH, USA
| | - Monika Pepelnjak
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Patrick Stalder
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Christian Dörig
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Fabian Sesterhenn
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Franziska Elsässer
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Lucie Kralickova
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | | | | | - Natalie de Souza
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Olga Vitek
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA.
| | - Paola Picotti
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland.
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37
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Robinson NA, Robledo D, Sveen L, Daniels RR, Krasnov A, Coates A, Jin YH, Barrett LT, Lillehammer M, Kettunen AH, Phillips BL, Dempster T, Doeschl‐Wilson A, Samsing F, Difford G, Salisbury S, Gjerde B, Haugen J, Burgerhout E, Dagnachew BS, Kurian D, Fast MD, Rye M, Salazar M, Bron JE, Monaghan SJ, Jacq C, Birkett M, Browman HI, Skiftesvik AB, Fields DM, Selander E, Bui S, Sonesson A, Skugor S, Østbye TK, Houston RD. Applying genetic technologies to combat infectious diseases in aquaculture. REVIEWS IN AQUACULTURE 2023; 15:491-535. [PMID: 38504717 PMCID: PMC10946606 DOI: 10.1111/raq.12733] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 07/24/2022] [Accepted: 08/16/2022] [Indexed: 03/21/2024]
Abstract
Disease and parasitism cause major welfare, environmental and economic concerns for global aquaculture. In this review, we examine the status and potential of technologies that exploit genetic variation in host resistance to tackle this problem. We argue that there is an urgent need to improve understanding of the genetic mechanisms involved, leading to the development of tools that can be applied to boost host resistance and reduce the disease burden. We draw on two pressing global disease problems as case studies-sea lice infestations in salmonids and white spot syndrome in shrimp. We review how the latest genetic technologies can be capitalised upon to determine the mechanisms underlying inter- and intra-species variation in pathogen/parasite resistance, and how the derived knowledge could be applied to boost disease resistance using selective breeding, gene editing and/or with targeted feed treatments and vaccines. Gene editing brings novel opportunities, but also implementation and dissemination challenges, and necessitates new protocols to integrate the technology into aquaculture breeding programmes. There is also an ongoing need to minimise risks of disease agents evolving to overcome genetic improvements to host resistance, and insights from epidemiological and evolutionary models of pathogen infestation in wild and cultured host populations are explored. Ethical issues around the different approaches for achieving genetic resistance are discussed. Application of genetic technologies and approaches has potential to improve fundamental knowledge of mechanisms affecting genetic resistance and provide effective pathways for implementation that could lead to more resistant aquaculture stocks, transforming global aquaculture.
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Affiliation(s)
- Nicholas A. Robinson
- Nofima ASTromsøNorway
- Sustainable Aquaculture Laboratory—Temperate and Tropical (SALTT)School of BioSciences, The University of MelbourneMelbourneVictoriaAustralia
| | - Diego Robledo
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghEdinburghUK
| | | | - Rose Ruiz Daniels
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghEdinburghUK
| | | | - Andrew Coates
- Sustainable Aquaculture Laboratory—Temperate and Tropical (SALTT)School of BioSciences, The University of MelbourneMelbourneVictoriaAustralia
| | - Ye Hwa Jin
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghEdinburghUK
| | - Luke T. Barrett
- Sustainable Aquaculture Laboratory—Temperate and Tropical (SALTT)School of BioSciences, The University of MelbourneMelbourneVictoriaAustralia
- Institute of Marine Research, Matre Research StationMatredalNorway
| | | | | | - Ben L. Phillips
- Sustainable Aquaculture Laboratory—Temperate and Tropical (SALTT)School of BioSciences, The University of MelbourneMelbourneVictoriaAustralia
| | - Tim Dempster
- Sustainable Aquaculture Laboratory—Temperate and Tropical (SALTT)School of BioSciences, The University of MelbourneMelbourneVictoriaAustralia
| | - Andrea Doeschl‐Wilson
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghEdinburghUK
| | - Francisca Samsing
- Sydney School of Veterinary ScienceThe University of SydneyCamdenAustralia
| | | | - Sarah Salisbury
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghEdinburghUK
| | | | | | | | | | - Dominic Kurian
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghEdinburghUK
| | - Mark D. Fast
- Atlantic Veterinary CollegeThe University of Prince Edward IslandCharlottetownPrince Edward IslandCanada
| | | | | | - James E. Bron
- Institute of AquacultureUniversity of StirlingStirlingScotlandUK
| | - Sean J. Monaghan
- Institute of AquacultureUniversity of StirlingStirlingScotlandUK
| | - Celeste Jacq
- Blue Analytics, Kong Christian Frederiks Plass 3BergenNorway
| | | | - Howard I. Browman
- Institute of Marine Research, Austevoll Research Station, Ecosystem Acoustics GroupTromsøNorway
| | - Anne Berit Skiftesvik
- Institute of Marine Research, Austevoll Research Station, Ecosystem Acoustics GroupTromsøNorway
| | | | - Erik Selander
- Department of Marine SciencesUniversity of GothenburgGothenburgSweden
| | - Samantha Bui
- Institute of Marine Research, Matre Research StationMatredalNorway
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Cross-linking mass spectrometry for mapping protein complex topologies in situ. Essays Biochem 2023; 67:215-228. [PMID: 36734207 PMCID: PMC10070479 DOI: 10.1042/ebc20220168] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 01/03/2023] [Accepted: 01/05/2023] [Indexed: 02/04/2023]
Abstract
Cross-linking mass spectrometry has become an established technology to provide structural information on the topology and dynamics of protein complexes. Readily accessible workflows can provide detailed data on simplified systems, such as purified complexes. However, using this technology to study the structure of protein complexes in situ, such as in organelles, cells, and even tissues, is still a technological frontier. The complexity of these systems remains a considerable challenge, but there have been dramatic improvements in sample handling, data acquisition, and data processing. Here, we summarise these developments and describe the paths towards comprehensive and comparative structural interactomes by cross-linking mass spectrometry.
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Jiao F, Salituro LJ, Yu C, Gutierrez CB, Rychnovsky SD, Huang L. Exploring an Alternative Cysteine-Reactive Chemistry to Enable Proteome-Wide PPI Analysis by Cross-Linking Mass Spectrometry. Anal Chem 2023; 95:2532-2539. [PMID: 36652389 DOI: 10.1021/acs.analchem.2c04986] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The development of MS-cleavable cross-linking mass spectrometry (XL-MS) has enabled the effective capture and identification of endogenous protein-protein interactions (PPIs) and their residue contacts at the global scale without cell engineering. So far, only lysine-reactive cross-linkers have been successfully applied for proteome-wide PPI profiling. However, lysine cross-linkers alone cannot uncover the complete PPI map in cells. Previously, we have developed a maleimide-based cysteine-reactive MS-cleavable cross-linker (bismaleimide sulfoxide (BMSO)) that is effective for mapping PPIs of protein complexes to yield interaction contacts complementary to lysine-reactive reagents. While successful, the hydrolysis and limited selectivity of maleimides at physiological pH make their applications in proteome-wide XL-MS challenging. To enable global PPI mapping, we have explored an alternative cysteine-labeling chemistry and thus designed and synthesized a sulfoxide-containing MS-cleavable haloacetamide-based cross-linker, Dibromoacetamide sulfoxide (DBrASO). Our results have demonstrated that DBrASO cross-linked peptides display the same fragmentation characteristics as other sulfoxide-containing MS-cleavable cross-linkers, permitting their unambiguous identification by MSn. In combination with a newly developed two-dimensional peptide fractionation method, we have successfully performed DBrASO-based XL-MS analysis of HEK293 cell lysates and demonstrated its capability to complement lysine-reactive reagents and expand PPI coverage at the systems-level.
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Affiliation(s)
- Fenglong Jiao
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, California 92697, United States
| | - Leah J Salituro
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Clinton Yu
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, California 92697, United States
| | - Craig B Gutierrez
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, California 92697, United States
| | - Scott D Rychnovsky
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Lan Huang
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, California 92697, United States
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40
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Shcherbakova L, Pardo M, Roumeliotis T, Choudhary J. Identifying and characterising Thrap3, Bclaf1 and Erh interactions using cross-linking mass spectrometry. Wellcome Open Res 2023; 6:260. [PMID: 35865489 PMCID: PMC9270653 DOI: 10.12688/wellcomeopenres.17160.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/24/2021] [Indexed: 01/11/2023] Open
Abstract
Background: Cross-linking mass spectrometry (XL-MS) is a powerful technology capable of yielding structural insights across the complex cellular protein interaction network. However, up to date most of the studies utilising XL-MS to characterise individual protein complexes' topology have been carried out on over-expressed or recombinant proteins, which might not accurately represent native cellular conditions. Methods: We performed XL-MS using MS-cleavable crosslinker disuccinimidyl sulfoxide (DSSO) after immunoprecipitation of endogenous BRG/Brahma-associated factors (BAF) complex and co-purifying proteins. Data are available via ProteomeXchange with identifier PXD027611. Results: Although we did not detect the expected enrichment of crosslinks within the BAF complex, we identified numerous crosslinks between three co-purifying proteins, namely Thrap3, Bclaf1 and Erh. Thrap3 and Bclaf1 are mostly disordered proteins for which no 3D structure is available. The XL data allowed us to map interaction surfaces on these proteins, which overlap with the non-disordered portions of both proteins. The identified XLs are in agreement with homology-modelled structures suggesting that the interaction surfaces are globular. Conclusions: Our data shows that MS-cleavable crosslinker DSSO can be used to characterise in detail the topology and interaction surfaces of endogenous protein complexes without the need for overexpression. We demonstrate that Bclaf1, Erh and Thrap3 interact closely with each other, suggesting they might form a novel complex, hereby referred to as BET complex. This data can be exploited for modelling protein-protein docking to characterise the three-dimensional structure of the complex. Endogenous XL-MS might be challenging due to crosslinker accessibility, protein complex abundance or isolation efficiency, and require further optimisation for some complexes like the BAF complex to detect a substantial number of crosslinks.
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Affiliation(s)
| | - Mercedes Pardo
- Cancer Biology, Institute of Cancer Research, UK, London, UK
| | | | - Jyoti Choudhary
- Cancer Biology, Institute of Cancer Research, UK, London, UK,
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41
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Zhou C, Dai S, Lin Y, Lian S, Fan X, Li N, Yu W. Exhaustive Cross-Linking Search with Protein Feedback. J Proteome Res 2023; 22:101-113. [PMID: 36480279 DOI: 10.1021/acs.jproteome.2c00500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Improving the sensitivity of protein-protein interaction detection and protein structure probing is a principal challenge in cross-linking mass spectrometry (XL-MS) data analysis. In this paper, we propose an exhaustive cross-linking search method with protein feedback (ECL-PF) for cleavable XL-MS data analysis. ECL-PF adopts an optimized α/β mass detection scheme and establishes protein-peptide association during the identification of cross-linked peptides. Existing major scoring functions can all benefit from the ECL-PF workflow to a great extent. In comparisons using synthetic data sets and hybrid simulated data sets, ECL-PF achieved 3-fold higher sensitivity over standard techniques. In experiments using real data sets, it also identified 65.6% more cross-link spectrum matches and 48.7% more unique cross-links.
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Affiliation(s)
- Chen Zhou
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong 999077, China
| | - Shuaijian Dai
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong 999077, China
| | - Yuanqiao Lin
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong 999077, China
| | - Sheng Lian
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong 999077, China
| | - Xiaodan Fan
- Department of Statistics, The Chinese University of Hong Kong, Hong Kong 999077, China
| | - Ning Li
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong 999077, China.,HKUST Shenzhen-Hong Kong Collaborative Innovation Research Institute, Futian, Shenzhen, 518000, China
| | - Weichuan Yu
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong 999077, China.,HKUST Shenzhen-Hong Kong Collaborative Innovation Research Institute, Futian, Shenzhen, 518000, China
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42
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Shcherbakova L, Pardo M, Roumeliotis T, Choudhary J. Identifying and characterising Thrap3, Bclaf1 and Erh interactions using cross-linking mass spectrometry. Wellcome Open Res 2023; 6:260. [PMID: 35865489 PMCID: PMC9270653 DOI: 10.12688/wellcomeopenres.17160.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2022] [Indexed: 01/09/2023] Open
Abstract
Background: Cross-linking mass spectrometry (XL-MS) is a powerful technology capable of yielding structural insights across the complex cellular protein interaction network. However, up to date most of the studies utilising XL-MS to characterise individual protein complexes' topology have been carried out on over-expressed or recombinant proteins, which might not accurately represent native cellular conditions. Methods: We performed XL-MS using MS-cleavable crosslinker disuccinimidyl sulfoxide (DSSO) after immunoprecipitation of endogenous BRG/Brahma-associated factors (BAF) complex and co-purifying proteins. Data are available via ProteomeXchange with identifier PXD027611. Results: Although we did not detect the expected enrichment of crosslinks within the BAF complex, we identified numerous crosslinks between three co-purifying proteins, namely Thrap3, Bclaf1 and Erh. Thrap3 and Bclaf1 are mostly disordered proteins for which no 3D structure is available. The XL data allowed us to map interaction surfaces on these proteins, which overlap with the non-disordered portions of both proteins. The identified XLs are in agreement with homology-modelled structures suggesting that the interaction surfaces are globular. Conclusions: Our data shows that MS-cleavable crosslinker DSSO can be used to characterise in detail the topology and interaction surfaces of endogenous protein complexes without the need for overexpression. We demonstrate that Bclaf1, Erh and Thrap3 interact closely with each other, suggesting they might form a novel complex, hereby referred to as TEB complex. This data can be exploited for modelling protein-protein docking to characterise the three-dimensional structure of the complex. Endogenous XL-MS might be challenging due to crosslinker accessibility, protein complex abundance or isolation efficiency, and require further optimisation for some complexes like the BAF complex to detect a substantial number of crosslinks.
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Affiliation(s)
| | - Mercedes Pardo
- Cancer Biology, Institute of Cancer Research, UK, London, UK
| | | | - Jyoti Choudhary
- Cancer Biology, Institute of Cancer Research, UK, London, UK,
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43
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Employing non-targeted interactomics approach and subcellular fractionation to increase our understanding of the ghost proteome. iScience 2023; 26:105943. [PMID: 36866041 PMCID: PMC9971881 DOI: 10.1016/j.isci.2023.105943] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/07/2022] [Accepted: 01/04/2023] [Indexed: 01/09/2023] Open
Abstract
Eukaryotic mRNA has long been considered monocistronic, but nowadays, alternative proteins (AltProts) challenge this tenet. The alternative or ghost proteome has largely been neglected and the involvement of AltProts in biological processes. Here, we used subcellular fractionation to increase the information about AltProts and facilitate the detection of protein-protein interactions by the identification of crosslinked peptides. In total, 112 unique AltProts were identified, and we were able to identify 220 crosslinks without peptide enrichment. Among these, 16 crosslinks between AltProts and Referenced Proteins (RefProts) were identified. We further focused on specific examples such as the interaction between IP_2292176 (AltFAM227B) and HLA-B, in which this protein could be a potential new immunopeptide, and the interactions between HIST1H4F and several AltProts which can play a role in mRNA transcription. Thanks to the study of the interactome and the localization of AltProts, we can reveal more of the importance of the ghost proteome.
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44
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Chen X, Sailer C, Kammer KM, Fürsch J, Eisele MR, Sakata E, Pellarin R, Stengel F. Mono- and Intralink Filter (Mi-Filter) To Reduce False Identifications in Cross-Linking Mass Spectrometry Data. Anal Chem 2022; 94:17751-17756. [PMID: 36510358 PMCID: PMC9798375 DOI: 10.1021/acs.analchem.2c00494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Cross-linking mass spectrometry (XL-MS) has become an indispensable tool for the emerging field of systems structural biology over the recent years. However, the confidence in individual protein-protein interactions (PPIs) depends on the correct assessment of individual inter-protein cross-links. In this article, we describe a mono- and intralink filter (mi-filter) that is applicable to any kind of cross-linking data and workflow. It stipulates that only proteins for which at least one monolink or intra-protein cross-link has been identified within a given data set are considered for an inter-protein cross-link and therefore participate in a PPI. We show that this simple and intuitive filter has a dramatic effect on different types of cross-linking data ranging from individual protein complexes over medium-complexity affinity enrichments to proteome-wide cell lysates and significantly reduces the number of false-positive identifications for inter-protein links in all these types of XL-MS data.
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Affiliation(s)
- Xingyu Chen
- Department
of Biology, University of Konstanz, Universitätsstrasse 10, Konstanz 78457, Germany,Konstanz
Research School Chemical Biology, University
of Konstanz, Universitätsstrasse 10, Konstanz 78457, Germany
| | - Carolin Sailer
- Department
of Biology, University of Konstanz, Universitätsstrasse 10, Konstanz 78457, Germany,Konstanz
Research School Chemical Biology, University
of Konstanz, Universitätsstrasse 10, Konstanz 78457, Germany
| | - Kai Michael Kammer
- Department
of Biology, University of Konstanz, Universitätsstrasse 10, Konstanz 78457, Germany,Konstanz
Research School Chemical Biology, University
of Konstanz, Universitätsstrasse 10, Konstanz 78457, Germany
| | - Julius Fürsch
- Department
of Biology, University of Konstanz, Universitätsstrasse 10, Konstanz 78457, Germany,Konstanz
Research School Chemical Biology, University
of Konstanz, Universitätsstrasse 10, Konstanz 78457, Germany
| | - Markus R. Eisele
- Department
of Molecular Structural Biology, Max Planck
Institute of Biochemistry, Martinsried 82152, Germany
| | - Eri Sakata
- Department
of Molecular Structural Biology, Max Planck
Institute of Biochemistry, Martinsried 82152, Germany,Institute
for Auditory Neuroscience, University Medical
Center Göttingen, Göttingen 37077, Germany
| | - Riccardo Pellarin
- Structural
Bioinformatics Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR 3528, 28 rue du Docteur Roux, Paris 75015, France
| | - Florian Stengel
- Department
of Biology, University of Konstanz, Universitätsstrasse 10, Konstanz 78457, Germany,Konstanz
Research School Chemical Biology, University
of Konstanz, Universitätsstrasse 10, Konstanz 78457, Germany,
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45
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Yadav R, Courouble VV, Dey SK, Harrison JJE, Timm J, Hopkins JB, Slack RL, Sarafianos SG, Ruiz FX, Griffin PR, Arnold E. Biochemical and structural insights into SARS-CoV-2 polyprotein processing by Mpro. SCIENCE ADVANCES 2022; 8:eadd2191. [PMID: 36490335 PMCID: PMC9733933 DOI: 10.1126/sciadv.add2191] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 11/02/2022] [Indexed: 06/17/2023]
Abstract
SARS-CoV-2, a human coronavirus, is the causative agent of the COVID-19 pandemic. Its genome is translated into two large polyproteins subsequently cleaved by viral papain-like protease and main protease (Mpro). Polyprotein processing is essential yet incompletely understood. We studied Mpro-mediated processing of the nsp7-11 polyprotein, whose mature products include cofactors of the viral replicase, and identified the order of cleavages. Integrative modeling based on mass spectrometry (including hydrogen-deuterium exchange and cross-linking) and x-ray scattering yielded a nsp7-11 structural ensemble, demonstrating shared secondary structural elements with individual nsps. The pattern of cross-links and HDX footprint of the C145A Mpro and nsp7-11 complex demonstrate preferential binding of the enzyme active site to the polyprotein junction sites and additional transient contacts to help orient the enzyme on its substrate for cleavage. Last, proteolysis assays were used to characterize the effect of inhibitors/binders on Mpro processing/inhibition using the nsp7-11 polyprotein as substrate.
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Affiliation(s)
- Ruchi Yadav
- Center for Advanced Biotechnology and Medicine (CABM), Rutgers University, Piscataway, NJ, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, USA
| | - Valentine V. Courouble
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, USA
- Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, Jupiter, FL, USA
| | - Sanjay K. Dey
- Center for Advanced Biotechnology and Medicine (CABM), Rutgers University, Piscataway, NJ, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, USA
| | | | - Jennifer Timm
- Center for Advanced Biotechnology and Medicine (CABM), Rutgers University, Piscataway, NJ, USA
| | - Jesse B. Hopkins
- BioCAT, Department of Physics, Illinois Institute of Technology, Chicago, IL, USA
| | - Ryan L. Slack
- Division of Laboratory of Biochemical Pharmacology and Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Stefan G. Sarafianos
- Division of Laboratory of Biochemical Pharmacology and Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Children’s Healthcare of Atlanta, Atlanta, GA, USA
| | - Francesc X. Ruiz
- Center for Advanced Biotechnology and Medicine (CABM), Rutgers University, Piscataway, NJ, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, USA
| | - Patrick R. Griffin
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, USA
- Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, Jupiter, FL, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL, USA
- Department of Molecular Medicine, UF Scripps Biomedical Research, University of Florida, Jupiter, FL, USA
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine (CABM), Rutgers University, Piscataway, NJ, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, USA
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46
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Santorelli L, Caterino M, Costanzo M. Dynamic Interactomics by Cross-Linking Mass Spectrometry: Mapping the Daily Cell Life in Postgenomic Era. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2022; 26:633-649. [PMID: 36445175 DOI: 10.1089/omi.2022.0137] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The majority of processes that occur in daily cell life are modulated by hundreds to thousands of dynamic protein-protein interactions (PPI). The resulting protein complexes constitute a tangled network that, with its continuous remodeling, builds up highly organized functional units. Thus, defining the dynamic interactome of one or more proteins allows determining the full range of biological activities these proteins are capable of. This conceptual approach is poised to gain further traction and significance in the current postgenomic era wherein the treatment of severe diseases needs to be tackled at both genomic and PPI levels. This also holds true for COVID-19, a multisystemic disease affecting biological networks across the biological hierarchy from genome to proteome to metabolome. In this overarching context and the current historical moment of the COVID-19 pandemic where systems biology increasingly comes to the fore, cross-linking mass spectrometry (XL-MS) has become highly relevant, emerging as a powerful tool for PPI discovery and characterization. This expert review highlights the advanced XL-MS approaches that provide in vivo insights into the three-dimensional protein complexes, overcoming the static nature of common interactomics data and embracing the dynamics of the cell proteome landscape. Many XL-MS applications based on the use of diverse cross-linkers, MS detection methods, and predictive bioinformatic tools for single proteins or proteome-wide interactions were shown. We conclude with a future outlook on XL-MS applications in the field of structural proteomics and ways to sustain the remarkable flexibility of XL-MS for dynamic interactomics and structural studies in systems biology and planetary health.
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Affiliation(s)
- Lucia Santorelli
- Department of Oncology and Hematology-Oncology, University of Milano, Milan, Italy.,IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Marianna Caterino
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy.,CEINGE-Biotecnologie Avanzate s.c.ar.l., Naples, Italy
| | - Michele Costanzo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy.,CEINGE-Biotecnologie Avanzate s.c.ar.l., Naples, Italy
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47
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Singh J, Elhabashy H, Muthukottiappan P, Stepath M, Eisenacher M, Kohlbacher O, Gieselmann V, Winter D. Cross-linking of the endolysosomal system reveals potential flotillin structures and cargo. Nat Commun 2022; 13:6212. [PMID: 36266287 PMCID: PMC9584938 DOI: 10.1038/s41467-022-33951-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 10/06/2022] [Indexed: 12/24/2022] Open
Abstract
Lysosomes are well-established as the main cellular organelles for the degradation of macromolecules and emerging as regulatory centers of metabolism. They are of crucial importance for cellular homeostasis, which is exemplified by a plethora of disorders related to alterations in lysosomal function. In this context, protein complexes play a decisive role, regulating not only metabolic lysosomal processes but also lysosome biogenesis, transport, and interaction with other organelles. Using cross-linking mass spectrometry, we analyze lysosomes and early endosomes. Based on the identification of 5376 cross-links, we investigate protein-protein interactions and structures of lysosome- and endosome-related proteins. In particular, we present evidence for a tetrameric assembly of the lysosomal hydrolase PPT1 and a heterodimeric structure of FLOT1/FLOT2 at lysosomes and early endosomes. For FLOT1-/FLOT2-positive early endosomes, we identify >300 putative cargo proteins and confirm eleven substrates for flotillin-dependent endocytosis, including the latrophilin family of adhesion G protein-coupled receptors.
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Affiliation(s)
- Jasjot Singh
- Institute for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, 53115, Bonn, Germany
| | - Hadeer Elhabashy
- Department of Protein Evolution, Max-Planck-Institute for Developmental Biology, 72076, Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, 72076, Tübingen, Germany
- Department of Computer Science, University of Tübingen, 72076, Tübingen, Germany
| | - Pathma Muthukottiappan
- Institute for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, 53115, Bonn, Germany
| | - Markus Stepath
- Medical Proteome-Center, Medical Faculty, Ruhr-University Bochum, 48801, Bochum, Germany
- Medical Proteome Analysis, Center for Protein Diagnostics, Ruhr-University Bochum, 48801, Bochum, Germany
| | - Martin Eisenacher
- Medical Proteome-Center, Medical Faculty, Ruhr-University Bochum, 48801, Bochum, Germany
- Medical Proteome Analysis, Center for Protein Diagnostics, Ruhr-University Bochum, 48801, Bochum, Germany
| | - Oliver Kohlbacher
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, 72076, Tübingen, Germany
- Department of Computer Science, University of Tübingen, 72076, Tübingen, Germany
- Institute for Translational Bioinformatics, University Hospital Tübingen, 72076, Tübingen, Germany
| | - Volkmar Gieselmann
- Institute for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, 53115, Bonn, Germany
| | - Dominic Winter
- Institute for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, 53115, Bonn, Germany.
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48
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Hallal S, Tűzesi Á, Grau GE, Buckland ME, Alexander KL. Understanding the extracellular vesicle surface for clinical molecular biology. J Extracell Vesicles 2022; 11:e12260. [PMID: 36239734 PMCID: PMC9563386 DOI: 10.1002/jev2.12260] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 07/26/2022] [Accepted: 07/26/2022] [Indexed: 12/17/2022] Open
Abstract
Extracellular vesicles (EVs) are lipid-membrane enclosed nanoparticles that play significant roles in health and disease. EVs are abundant in body fluids and carry an array of molecules (proteins, lipids, nucleic acids and glycans) that reflect the identity and activity of their cell-of-origin. While the advent of high throughput omics technologies has allowed in-depth characterisation of EV compositions, how these molecular species are spatially distributed within EV structures is not well appreciated. This is particularly true of the EV surface where a plethora of molecules are reported to be both integral and peripherally associated to the EV membrane. This coronal layer or 'atmosphere' that surrounds the EV membrane contributes to a large, highly interactive and dynamic surface area that is responsible for facilitating EV interactions with the extracellular environment. The EV coronal layer harbours surface molecules that reflect the identity of parent cells, which is likely a highly valuable property in the context of diagnostic liquid biopsies. In this review, we describe the current understanding of the mechanical, electrostatic and molecular properties of the EV surface that offer significant biomarker potential and contribute to a highly dynamic interactome.
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Affiliation(s)
- Susannah Hallal
- Neurosurgery DepartmentChris O'Brien LifehouseCamperdownNSWAustralia,Brainstorm Brain Cancer Research, Brain and Mind CentreThe University of SydneyNSWAustralia,Neuropathology DepartmentRoyal Prince Alfred HospitalCamperdownNSWAustralia
| | - Ágota Tűzesi
- Brainstorm Brain Cancer Research, Brain and Mind CentreThe University of SydneyNSWAustralia,Neuropathology DepartmentRoyal Prince Alfred HospitalCamperdownNSWAustralia,School of Medical SciencesFaculty of Medicine & HealthThe University of SydneyCamperdownNSWAustralia
| | - Georges E. Grau
- School of Medical SciencesFaculty of Medicine & HealthThe University of SydneyCamperdownNSWAustralia
| | - Michael E. Buckland
- Brainstorm Brain Cancer Research, Brain and Mind CentreThe University of SydneyNSWAustralia,Neuropathology DepartmentRoyal Prince Alfred HospitalCamperdownNSWAustralia,School of Medical SciencesFaculty of Medicine & HealthThe University of SydneyCamperdownNSWAustralia
| | - Kimberley L. Alexander
- Neurosurgery DepartmentChris O'Brien LifehouseCamperdownNSWAustralia,Brainstorm Brain Cancer Research, Brain and Mind CentreThe University of SydneyNSWAustralia,Neuropathology DepartmentRoyal Prince Alfred HospitalCamperdownNSWAustralia,School of Medical SciencesFaculty of Medicine & HealthThe University of SydneyCamperdownNSWAustralia
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Nitika, Zheng B, Ruan L, Kline JT, Omkar S, Sikora J, Texeira Torres M, Wang Y, Takakuwa JE, Huguet R, Klemm C, Segarra VA, Winters MJ, Pryciak PM, Thorpe PH, Tatebayashi K, Li R, Fornelli L, Truman AW. Comprehensive characterization of the Hsp70 interactome reveals novel client proteins and interactions mediated by posttranslational modifications. PLoS Biol 2022; 20:e3001839. [PMID: 36269765 PMCID: PMC9629621 DOI: 10.1371/journal.pbio.3001839] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 11/02/2022] [Accepted: 09/21/2022] [Indexed: 01/06/2023] Open
Abstract
Hsp70 interactions are critical for cellular viability and the response to stress. Previous attempts to characterize Hsp70 interactions have been limited by their transient nature and the inability of current technologies to distinguish direct versus bridged interactions. We report the novel use of cross-linking mass spectrometry (XL-MS) to comprehensively characterize the Saccharomyces cerevisiae (budding yeast) Hsp70 protein interactome. Using this approach, we have gained fundamental new insights into Hsp70 function, including definitive evidence of Hsp70 self-association as well as multipoint interaction with its client proteins. In addition to identifying a novel set of direct Hsp70 interactors that can be used to probe chaperone function in cells, we have also identified a suite of posttranslational modification (PTM)-associated Hsp70 interactions. The majority of these PTMs have not been previously reported and appear to be critical in the regulation of client protein function. These data indicate that one of the mechanisms by which PTMs contribute to protein function is by facilitating interaction with chaperones. Taken together, we propose that XL-MS analysis of chaperone complexes may be used as a unique way to identify biologically important PTMs on client proteins.
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Affiliation(s)
- Nitika
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, North Carolina, United States America
| | - Bo Zheng
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, North Carolina, United States America
| | - Linhao Ruan
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States America
- Biochemistry, Cellular and Molecular Biology (BCMB) Graduate Program, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States America
| | - Jake T. Kline
- Department of Biology, University of Oklahoma, Norman, Oklahoma, United States America
| | - Siddhi Omkar
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, North Carolina, United States America
| | - Jacek Sikora
- Department of Molecular Biosciences, Department of Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, Illinois, United States America
| | - Mara Texeira Torres
- School of Biological and Chemical Sciences, Queen Mary University, London, United Kingdom
| | - Yuhao Wang
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States America
- Biochemistry, Cellular and Molecular Biology (BCMB) Graduate Program, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States America
| | - Jade E. Takakuwa
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, North Carolina, United States America
| | - Romain Huguet
- Thermo Scientific, San Jose, California, United States America
| | - Cinzia Klemm
- School of Biological and Chemical Sciences, Queen Mary University, London, United Kingdom
| | - Verónica A. Segarra
- Departments of Biological Sciences and Chemistry, Goucher College, Baltimore, Maryland, United States America
| | - Matthew J. Winters
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States America
| | - Peter M. Pryciak
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States America
| | - Peter H. Thorpe
- School of Biological and Chemical Sciences, Queen Mary University, London, United Kingdom
| | - Kazuo Tatebayashi
- Laboratory of Molecular Genetics, Frontier Research Unit, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Rong Li
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States America
- Biochemistry, Cellular and Molecular Biology (BCMB) Graduate Program, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States America
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, Singapore
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland, United States America
| | - Luca Fornelli
- Department of Biology, University of Oklahoma, Norman, Oklahoma, United States America
| | - Andrew W. Truman
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, North Carolina, United States America
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Renzone G, Arena S, Scaloni A. Cross-linking reactions in food proteins and proteomic approaches for their detection. MASS SPECTROMETRY REVIEWS 2022; 41:861-898. [PMID: 34250627 DOI: 10.1002/mas.21717] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 06/29/2021] [Accepted: 06/29/2021] [Indexed: 06/13/2023]
Abstract
Various protein cross-linking reactions leading to molecular polymerization and covalent aggregates have been described in processed foods. They are an undesired side effect of processes designed to reduce bacterial load, extend shelf life, and modify technological properties, as well as being an expected result of treatments designed to modify raw material texture and function. Although the formation of these products is known to affect the sensory and technological properties of foods, the corresponding cross-linking reactions and resulting protein polymers have not yet undergone detailed molecular characterization. This is essential for describing how their generation can be related to food processing conditions and quality parameters. Due to the complex structure of cross-linked species, bottom-up proteomic procedures developed to characterize various amino acid modifications associated with food processing conditions currently offer a limited molecular description of bridged peptide structures. Recent progress in cross-linking mass spectrometry for the topological characterization of protein complexes has facilitated the development of various proteomic methods and bioinformatic tools for unveiling bridged species, which can now also be used for the detailed molecular characterization of polymeric cross-linked products in processed foods. We here examine their benefits and limitations in terms of evaluating cross-linked food proteins and propose future scenarios for application in foodomics. They offer potential for understanding the protein cross-linking formation mechanisms in processed foods, and how the inherent beneficial properties of treated foodstuffs can be preserved or enhanced.
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Affiliation(s)
- Giovanni Renzone
- Proteomics and Mass Spectrometry Laboratory, ISPAAM, National Research Council, Naples, Italy
| | - Simona Arena
- Proteomics and Mass Spectrometry Laboratory, ISPAAM, National Research Council, Naples, Italy
| | - Andrea Scaloni
- Proteomics and Mass Spectrometry Laboratory, ISPAAM, National Research Council, Naples, Italy
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