1
|
Cheng J, Wang H, Zhang Y, Wang X, Liu G. Advances in crosslinking chemistry and proximity-enabled strategies: deciphering protein complexes and interactions. Org Biomol Chem 2024; 22:7549-7559. [PMID: 39192765 DOI: 10.1039/d4ob01058b] [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: 08/29/2024]
Abstract
Mass spectrometry, coupled with innovative crosslinking techniques to decode protein conformations and interactions through uninterrupted signal connections, has undergone remarkable progress in recent years. It is crucial to develop selective crosslinking reagents that minimally disrupt protein structure and dynamics, providing insights into protein network regulation and biological functions. Compared to traditional crosslinkers, new bifunctional chemical crosslinkers exhibit high selectivity and specificity in connecting proximal amino acid residues, resulting in stable molecular crosslinked products. The conjugation with specific amino acid residues like lysine, cysteine, arginine and tyrosine expands the XL-MS toolbox, enabling more precise modeling of target substrates and leading to improved data quality and reliability. Another emerging crosslinking method utilizes unnatural amino acids (UAAs) derived from proximity-enabled reactivity with specific amino acids or sulfur-fluoride exchange (SuFEx) reactions with nucleophilic residues. These UAAs are genetically encoded into proteins for the formation of specific covalent bonds. This technique combines the benefits of genetic encoding for live cell compatibility with chemical crosslinking, providing a valuable method for capturing transient and weak protein-protein interactions (PPIs) for mapping PPI coordinates and improving the pharmacological properties of proteins. With continued advancements in technology and applications, crosslinking mass spectrometry is poised to play an increasingly significant role in guiding our understanding of protein dynamics and function in the future.
Collapse
Affiliation(s)
- Jiongjia Cheng
- Key Laboratory of Advanced Functional Materials of Nanjing, School of Environmental Science, Nanjing Xiaozhuang University, Nanjing, 211171, China.
| | - Haiying Wang
- Key Laboratory of Advanced Functional Materials of Nanjing, School of Environmental Science, Nanjing Xiaozhuang University, Nanjing, 211171, China.
| | - Yuchi Zhang
- Key Laboratory of Advanced Functional Materials of Nanjing, School of Environmental Science, Nanjing Xiaozhuang University, Nanjing, 211171, China.
| | - Xiaofeng Wang
- Key Laboratory of Advanced Functional Materials of Nanjing, School of Environmental Science, Nanjing Xiaozhuang University, Nanjing, 211171, China.
| | - Guangxiang Liu
- Key Laboratory of Advanced Functional Materials of Nanjing, School of Environmental Science, Nanjing Xiaozhuang University, Nanjing, 211171, China.
| |
Collapse
|
2
|
Kim D, Nita-Lazar A. Progress in mass spectrometry approaches to profiling protein-protein interactions in the studies of the innate immune system. JOURNAL OF PROTEINS AND PROTEOMICS 2024; 15:545-559. [PMID: 39380887 PMCID: PMC11460538 DOI: 10.1007/s42485-024-00156-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 06/04/2024] [Accepted: 06/24/2024] [Indexed: 10/10/2024]
Abstract
Understanding protein-protein interactions (PPIs) is pivotal for deciphering the intricacies of biological processes. Dysregulation of PPIs underlies a spectrum of diseases, including cancer, neurodegenerative disorders, and autoimmune conditions, highlighting the imperative of investigating these interactions for therapeutic advancements. This review delves into the realm of mass spectrometry-based techniques for elucidating PPIs and their profound implications in biological research. Mass spectrometry in the PPI research field not only facilitates the evaluation of protein-protein interaction modulators but also discovers unclear molecular mechanisms and sheds light on both on- and off-target effects, thus aiding in drug development. Our discussion navigates through six pivotal techniques: affinity purification mass spectrometry (AP-MS), proximity labeling mass spectrometry (PL-MS), cross-linking mass spectrometry (XL-MS), size exclusion chromatography coupled with mass spectrometry (SEC-MS), limited proteolysis-coupled mass spectrometry (LiP-MS), and thermal proteome profiling (TPP).
Collapse
Affiliation(s)
- Doeun Kim
- Functional Cellular Networks Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-1892, USA
| | - Aleksandra Nita-Lazar
- Functional Cellular Networks Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-1892, USA
| |
Collapse
|
3
|
Yu C, Novitsky E, Wang X, Echeverria I, Rychnovsky S, Huang L. Trioxane-based MS-cleavable Cross-linking Mass Spectrometry for Profiling Multimeric Interactions of Cellular Networks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.06.606913. [PMID: 39211111 PMCID: PMC11360931 DOI: 10.1101/2024.08.06.606913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Cross-linking mass spectrometry (XL-MS) is a powerful technology for mapping protein-protein interactions (PPIs) at the systems-level. By covalently connecting pairs of proximal residues, cross-linking reagents provide distance restraints to infer protein conformations and interaction interfaces. While binary cross-links have been remarkably informative, multimeric cross-links can offer enhanced spatial resolution to facilitate the characterization of dynamic and heterogeneous protein complexes. However, the identification of multimeric cross-links remains extremely challenging due to fragmentation complexity and the vast expansion of database search space. Here, we present a novel trioxane-based MS-cleavable homotrifunctional cross-linker TSTO, which can target three proximal lysine residues simultaneously. Owing to its unique structure and MS-cleavability, TSTO enables fast and unambiguous identification of cross-linked peptides using LC-MS n analysis. Importantly, we have demonstrated that the TSTO-based XL-MS platform is effective for mapping PPIs of protein complexes and cellular networks. The trimeric interactions captured by TSTO have uncovered new structural details that cannot be easily revealed by existing reagents, allowing in-depth description of PPIs to facilitate structural modeling. This development not only advances XL-MS technologies for global PPI profiling from living cells, but also offers a new direction for creating multifunctional MS-cleavable cross-linkers to further push structural systems biology forward in the future.
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Park J, Son A, Kim H. A protein-protein interaction analysis tool for targeted cross-linking mass spectrometry. Sci Rep 2023; 13:22103. [PMID: 38092875 PMCID: PMC10719354 DOI: 10.1038/s41598-023-49663-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 12/11/2023] [Indexed: 12/17/2023] Open
Abstract
Protein networking is critical to understanding the biological functions of proteins and the underlying mechanisms of disease. However, identifying physical protein-protein interactions (PPIs) can be challenging. To gain insights into target proteins that interact with a particular disease, we need to profile all the proteins involved in the disease beforehand. Although the cross-linking mass spectrometry (XL-MS) method is a representative approach to identify physical interactions between proteins, calculating theoretical mass values for application to targeted mass spectrometry can be difficult. To address this challenge, our research team developed PPIAT, a web application that integrates information on reviewed human proteins, protein-protein interactions, cross-linkers, enzymes, and modifications. PPIAT leverages publicly accessible databases such as STRING to identify interactomes associated with target proteins. Moreover, it autonomously computes the theoretical mass value, accounting for all potential cross-linking scenarios pertinent to the application of XL-MS in SRM analysis. The outputs generated by PPIAT can be concisely represented in terms of protein interaction probabilities, complemented by findings from alternative analytical tools like Prego. These comprehensive summaries enable researchers to customize the results according to specific experimental conditions. All functions of PPIAT are available for free on the web application, making it a valuable tool for researchers studying protein-protein interactions.
Collapse
Affiliation(s)
- Jongham Park
- Department of Bio-AI Convergence, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon, 34134, Republic of Korea
| | - Ahrum Son
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, 92037, USA
| | - Hyunsoo Kim
- Department of Bio-AI Convergence, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon, 34134, Republic of Korea.
- Department of Convergent Bioscience and Informatics, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon, 34134, Republic of Korea.
- SCICS, 99 Daehak-ro, Yuseong-gu, Daejeon, 34134, Republic of Korea.
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Bartolec TK, Vázquez-Campos X, Norman A, Luong C, Johnson M, Payne RJ, Wilkins MR, Mackay JP, Low JKK. Cross-linking mass spectrometry discovers, evaluates, and corroborates structures and protein-protein interactions in the human cell. Proc Natl Acad Sci U S A 2023; 120:e2219418120. [PMID: 37071682 PMCID: PMC10151615 DOI: 10.1073/pnas.2219418120] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 03/16/2023] [Indexed: 04/19/2023] Open
Abstract
Significant recent advances in structural biology, particularly in the field of cryoelectron microscopy, have dramatically expanded our ability to create structural models of proteins and protein complexes. However, many proteins remain refractory to these approaches because of their low abundance, low stability, or-in the case of complexes-simply not having yet been analyzed. Here, we demonstrate the power of using cross-linking mass spectrometry (XL-MS) for the high-throughput experimental assessment of the structures of proteins and protein complexes. This included those produced by high-resolution but in vitro experimental data, as well as in silico predictions based on amino acid sequence alone. We present the largest XL-MS dataset to date, describing 28,910 unique residue pairs captured across 4,084 unique human proteins and 2,110 unique protein-protein interactions. We show that models of proteins and their complexes predicted by AlphaFold2, and inspired and corroborated by the XL-MS data, offer opportunities to deeply mine the structural proteome and interactome and reveal mechanisms underlying protein structure and function.
Collapse
Affiliation(s)
- Tara K. Bartolec
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Randwick, NSW2052, Australia
| | - Xabier Vázquez-Campos
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Randwick, NSW2052, Australia
| | - Alexander Norman
- School of Chemistry, University of Sydney, Sydney, NSW2006, Australia
| | - Clement Luong
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW2006, Australia
| | - Marcus Johnson
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW2006, Australia
| | - Richard J. Payne
- School of Chemistry, University of Sydney, Sydney, NSW2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW2006, Australia
| | - Marc R. Wilkins
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Randwick, NSW2052, Australia
| | - Joel P. Mackay
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW2006, Australia
| | - Jason K. K. Low
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW2006, Australia
| |
Collapse
|
8
|
Yan Q, Li M, Zhang Y, Liu H, Liu F, Liao W, Wang Y, Duan H, Wei Z. A tyrosine, histidine-selective bifunctional cross-linker for protein structure analysis. Talanta 2023; 258:124421. [PMID: 36913793 DOI: 10.1016/j.talanta.2023.124421] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 03/01/2023] [Accepted: 03/04/2023] [Indexed: 03/11/2023]
Abstract
Chemical cross-linking mass spectrometry (XL-MS) significantly contributes to the analysis of protein structures and the elucidation of protein-protein interactions. Currently available cross-linkers mainly target N-terminus, lysine, glutamate, aspartate, and cysteine residues in protein. Herein, a bifunctional cross-linker, named [4,4'-(disulfanediylbis(ethane-2,1-diyl)) bis(1-methyl-1,2,4-triazolidine-3,5-dione)] (DBMT) has been designed and characterized aiming to extremely expand the application of XL-MS approach. DBMT is capable of selectively targeting tyrosine residue in protein via an electrochemical click reaction, and/or targeting histidine residue in protein in the presence of 1O2 generated under photocatalytic reaction. A novel cross-linking strategy based on this cross-linker has been developed and demonstrated using model proteins, which provides a complementary XL-MS tool analyzing protein structure, protein complexes, protein-protein interactions, and even protein dynamics.
Collapse
Affiliation(s)
- Qibo Yan
- College of Chemistry, Jilin University, Changchun, 130012, Jilin, China
| | - Ming Li
- Division of Chemical Metrology & Analytical Science, National Institute of Metrology, Beijing, 100029, China.
| | - Yanxin Zhang
- College of Chemistry, Jilin University, Changchun, 130012, Jilin, China
| | - Hailong Liu
- GeneScience Pharmaceuticals Co., Ltd., Changchun, 130012, China
| | - Feng Liu
- GeneScience Pharmaceuticals Co., Ltd., Changchun, 130012, China
| | - Weiwei Liao
- College of Chemistry, Jilin University, Changchun, 130012, Jilin, China
| | - Yingwu Wang
- Key Laboratory for Molecular Enzymology and Engineering, The Ministry of Education, School of Life Science, Jilin University, Changchun, 130012, China
| | - Haifeng Duan
- College of Chemistry, Jilin University, Changchun, 130012, Jilin, China
| | - Zhonglin Wei
- College of Chemistry, Jilin University, Changchun, 130012, Jilin, China.
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Gao H, Zhao Q, Gong Z, Zhong B, Chen J, Sui Z, Li X, Liang Z, Zhang Y, Zhang L. Alkynyl-Enrichable Carboxyl-Selective Crosslinkers to Increase the Crosslinking Coverage for Deciphering Protein Structures. Anal Chem 2022; 94:12398-12406. [PMID: 36031802 DOI: 10.1021/acs.analchem.2c02205] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The coverage of chemical crosslinking coupled with mass spectrometry (CXMS) is of great importance to determine its ability for deciphering protein structures. At present, N-hydroxysuccinimidyl (NHS) ester-based crosslinkers targeting lysines have been predominantly used in CXMS. However, they are not always effective for some proteins with few lysines. Other amino acid residues such as carboxyl could be crosslinked to complement lysines and improve the crosslinking coverage of CXMS, but the low intrinsic chemical reactivity of carboxyl compromises the application of carboxyl-selective crosslinkers for complex samples. To enhance the crosslinking efficiency targeting acidic residues and realize in-depth crosslinking analysis of complex samples, we developed three new alkynyl-enrichable carboxyl-selective crosslinkers with different reactive groups such as hydrazide, amino, and aminooxy. The crosslinking efficiencies of the three crosslinkers were systematically evaluated, giving the best reactivity of the amino-functionalized crosslinker BAP. Furthermore, BAP was extended to the crosslinking analysis of Escherichia coli lysate in combination with efficient crosslink enrichment. A total of 1291 D/E-D/E crosslinks involved in 392 proteins were identified under a false discovery rate (FDR) of ≤1%. Obvious structural complementarity of BAP was exhibited to the lysine-targeting crosslinker, facilitating the capability of CXMS for protein structure elucidation. To the best of our knowledge, this was the first time for the carboxyl-selective crosslinker to achieve proteome-wide crosslinking analysis of the whole cell lysate. Collectively, we believe that this work not only expands on a promising toolkit of CXMS targeting acidic residues but also provides a valuable guideline to advance the performance of carboxyl-selective crosslinkers.
Collapse
Affiliation(s)
- Hang Gao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian116023, Liaoning, China.,University of Chinese Academy of Sciences, Beijing100039, China
| | - Qun Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian116023, Liaoning, China
| | - Zhou Gong
- CAS Innovation Academy for Precision Measurement Science and Technology, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Chinese Academy of Sciences, Wuhan430071, Hubei, China
| | - Bowen Zhong
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian116023, Liaoning, China
| | - Jing Chen
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian116023, Liaoning, China.,School of Chemistry and Material Science, University of Science and Technology of China, Hefei230026, Anhui, China
| | - Zhigang Sui
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian116023, Liaoning, China
| | - Xiao Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian116023, Liaoning, China
| | - Zhen Liang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian116023, Liaoning, China
| | - Yukui Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian116023, Liaoning, China
| | - Lihua Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian116023, Liaoning, China
| |
Collapse
|
11
|
Dawson JE, Smith IN, Martin W, Khan K, Cheng F, Eng C. Shape shifting: The multiple conformational substates of the PTEN N-terminal PIP 2 -binding domain. Protein Sci 2022; 31:e4308. [PMID: 35481646 PMCID: PMC9004235 DOI: 10.1002/pro.4308] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 03/12/2022] [Accepted: 03/20/2022] [Indexed: 12/14/2022]
Abstract
The Phosphatase and TENsin homolog deleted on chromosome 10 (PTEN) is a chief regulator of a variety of cellular processes including cell proliferation, migration, growth, and death. It is also a major tumor suppressor gene that is frequently mutated or lost under cancerous conditions. PTEN encodes a dual-specificity (lipid and protein) phosphatase that negatively regulates the PI3K/AKT/mTOR signaling pathway where the PIP2 -binding domain (PBD) regulates the lipid phosphatase function. Unfortunately, despite two decades of research, a full-length structure of PTEN remains elusive, leaving open questions regarding PTEN's disordered regions that mediate protein stability, post-translational modifications, protein-protein interactions, while also hindering the design of small molecules that can regulate PTEN's function. Here, we utilized a combination of crosslinking mass spectrometry, in silico predicted structural modeling (including AlphaFold2), molecular docking, molecular dynamics simulations, and residue interaction network modeling to obtain structural details and molecular insight into the behavior of the PBD of PTEN. Our study shows that the PBD exists in multiple conformations which suggests its ability to regulate PTEN's variety of functions. Studying how these specific conformational substates contribute to PTEN function is imperative to defining its function in disease pathogenesis, and to delineate ways to modulate its tumor suppressor activity.
Collapse
Affiliation(s)
- Jennifer E. Dawson
- Genomic Medicine Institute, Lerner Research InstituteCleveland ClinicClevelandOhioUSA
- Cleveland Clinic Lerner College of MedicineCase Western Reserve UniversityClevelandOhioUSA
| | - Iris Nira Smith
- Genomic Medicine Institute, Lerner Research InstituteCleveland ClinicClevelandOhioUSA
- Cleveland Clinic Lerner College of MedicineCase Western Reserve UniversityClevelandOhioUSA
| | - William Martin
- Genomic Medicine Institute, Lerner Research InstituteCleveland ClinicClevelandOhioUSA
| | - Krishnendu Khan
- Department of Cardiovascular and Metabolic Sciences, Lerner Research InstituteCleveland ClinicClevelandOhioUSA
| | - Feixiong Cheng
- Genomic Medicine Institute, Lerner Research InstituteCleveland ClinicClevelandOhioUSA
- Cleveland Clinic Lerner College of MedicineCase Western Reserve UniversityClevelandOhioUSA
- Case Comprehensive Cancer CenterCase Western Reserve University School of MedicineClevelandOhioUSA
| | - Charis Eng
- Genomic Medicine Institute, Lerner Research InstituteCleveland ClinicClevelandOhioUSA
- Cleveland Clinic Lerner College of MedicineCase Western Reserve UniversityClevelandOhioUSA
- Department of Cardiovascular and Metabolic Sciences, Lerner Research InstituteCleveland ClinicClevelandOhioUSA
- Taussig Cancer InstituteCleveland ClinicClevelandOhioUSA
- Department of Genetics and Genome SciencesCase Western Reserve University School of MedicineClevelandOhioUSA
- Department of Computational and Systems Biology, School of MedicineUniversity of PittsburghPittsburghPennsylvaniaUSA
| |
Collapse
|
12
|
Characterization of protein unfolding by fast cross-linking mass spectrometry using di-ortho-phthalaldehyde cross-linkers. Nat Commun 2022; 13:1468. [PMID: 35304446 PMCID: PMC8933431 DOI: 10.1038/s41467-022-28879-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 02/10/2022] [Indexed: 01/16/2023] Open
Abstract
Chemical cross-linking of proteins coupled with mass spectrometry is widely used in protein structural analysis. In this study we develop a class of non-hydrolyzable amine-selective di-ortho-phthalaldehyde (DOPA) cross-linkers, one of which is called DOPA2. Cross-linking of proteins with DOPA2 is 60-120 times faster than that with the N-hydroxysuccinimide ester cross-linker DSS. Compared with DSS cross-links, DOPA2 cross-links show better agreement with the crystal structures of tested proteins. More importantly, DOPA2 has unique advantages when working at low pH, low temperature, or in the presence of denaturants. Using staphylococcal nuclease, bovine serum albumin, and bovine pancreatic ribonuclease A, we demonstrate that DOPA2 cross-linking provides abundant spatial information about the conformations of progressively denatured forms of these proteins. Furthermore, DOPA2 cross-linking allows time-course analysis of protein conformational changes during denaturant-induced unfolding.
Collapse
|
13
|
An optimized protocol for in vitro and in cellulo structural determination of the multi-tRNA synthetase complex by cross-linking mass spectrometry. STAR Protoc 2022; 3:101201. [PMID: 35284842 PMCID: PMC8914369 DOI: 10.1016/j.xpro.2022.101201] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Despite recent advances in structural determination of individual proteins, elucidating the 3-dimensional architecture of large, multiprotein complexes remains challenging, partly because of issues related to structural integrity during purification. Here, we describe a protocol to determine the 3-dimensional architecture of the 11-constituent, multi-tRNA synthetase complex (MSC) using chemical cross-linking coupled with mass-spectrometry (XL-MS). The protocol does not require purification and is broadly applicable, facilitating determination of native structures in cell lysates and in non-disrupted cells as well as in purified complexes. For complete details on the use and execution of this protocol, please refer to Khan et al. (2020). Determines in vitro and in cellulo structures of multi-protein complexes Facilitates analysis of multi-protein-complex architecture without purification Reveals spatial relationships of disordered domains Refines structures derived from X-ray crystallography which may be distorted by packing
Collapse
|
14
|
Yu C, Wang X, Huang L. Developing a Targeted Quantitative Strategy for Sulfoxide-Containing MS-Cleavable Cross-Linked Peptides to Probe Conformational Dynamics of Protein Complexes. Anal Chem 2022; 94:4390-4398. [PMID: 35193351 DOI: 10.1021/acs.analchem.1c05298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In recent years, cross-linking mass spectrometry (XL-MS) has made enormous strides as a technology for probing protein-protein interactions (PPIs) and elucidating architectures of multisubunit assemblies. To define conformational and interaction dynamics of protein complexes under different physiological conditions, various quantitative cross-linking mass spectrometry (QXL-MS) strategies based on stable isotope labeling have been developed. These QXL-MS approaches have effectively allowed comparative analysis of cross-links to determine their relative abundance changes at global scales. Although successful, it remains challenging to consistently obtain quantitative measurements on low-abundant cross-links. Therefore, targeted QXL-MS is needed to enable MS "Western" analysis of cross-links to enhance sensitivity and reliability in quantitation. To this end, we have established a robust parallel reaction monitoring (PRM)-based targeted QXL-MS platform using sulfoxide-containing MS-cleavable cross-linker disuccinimidyl sulfoxide (DSSO), permitting label-free comparative analysis of selected cross-links across multiple samples. In addition, we have applied this methodology to study phosphorylation-dependent conformational dynamics of the human 26S proteasome. The PRM-based targeted QXL-MS analytical platform described here is applicable for all sulfoxide-containing MS-cleavable cross-linkers and can be directly adopted for comparative studies of protein-protein interactions in various cellular contexts.
Collapse
Affiliation(s)
- Clinton Yu
- Department of Physiology & Biophysics, University of California, Irvine, Medical Science I, D233, Irvine, California 92697-4560, United States
| | - Xiaorong Wang
- Department of Physiology & Biophysics, University of California, Irvine, Medical Science I, D233, Irvine, California 92697-4560, United States
| | - Lan Huang
- Department of Physiology & Biophysics, University of California, Irvine, Medical Science I, D233, Irvine, California 92697-4560, United States
| |
Collapse
|
15
|
Yugandhar K, Zhao Q, Gupta S, Xiong D, Yu H. Progress in methodologies and quality-control strategies in protein cross-linking mass spectrometry. Proteomics 2021; 21:e2100145. [PMID: 34647422 DOI: 10.1002/pmic.202100145] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 10/04/2021] [Indexed: 11/10/2022]
Abstract
Deciphering the interaction networks and structural dynamics of proteins is pivotal to better understanding their biological functions. Cross-linking mass spectrometry (XL-MS) is a powerful and increasingly popular technology that provides information about protein-protein interactions and their structural constraints for individual proteins and multiprotein complexes on a proteome-scale. In this review, we first assess the coverage and depth of the XL-MS technique by utilizing publicly available datasets. We then delve into the progress in XL-MS experimental and computational methodologies and examine different quality-control strategies reported in the literature. Finally, we discuss the progress in XL-MS applications along with the scope for future improvements.
Collapse
Affiliation(s)
- Kumar Yugandhar
- Department of Computational Biology, Cornell University, New York, USA.,Weill Institute for Cell and Molecular Biology, Cornell University, New York, USA
| | - Qiuye Zhao
- Department of Computational Biology, Cornell University, New York, USA.,Weill Institute for Cell and Molecular Biology, Cornell University, New York, USA
| | - Shobhita Gupta
- Department of Computational Biology, Cornell University, New York, USA.,Weill Institute for Cell and Molecular Biology, Cornell University, New York, USA
| | - Dapeng Xiong
- Department of Computational Biology, Cornell University, New York, USA.,Weill Institute for Cell and Molecular Biology, Cornell University, New York, USA
| | - Haiyuan Yu
- Department of Computational Biology, Cornell University, New York, USA.,Weill Institute for Cell and Molecular Biology, Cornell University, New York, USA
| |
Collapse
|
16
|
Protein interaction landscapes revealed by advanced in vivo cross-linking-mass spectrometry. Proc Natl Acad Sci U S A 2021; 118:2023360118. [PMID: 34349018 DOI: 10.1073/pnas.2023360118] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Defining protein-protein interactions (PPIs) in their native environment is crucial to understanding protein structure and function. Cross-linking-mass spectrometry (XL-MS) has proven effective in capturing PPIs in living cells; however, the proteome coverage remains limited. Here, we have developed a robust in vivo XL-MS platform to facilitate in-depth PPI mapping by integrating a multifunctional MS-cleavable cross-linker with sample preparation strategies and high-resolution MS. The advancement of click chemistry-based enrichment significantly enhanced the detection of cross-linked peptides for proteome-wide analyses. This platform enabled the identification of 13,904 unique lysine-lysine linkages from in vivo cross-linked HEK 293 cells, permitting construction of the largest in vivo PPI network to date, comprising 6,439 interactions among 2,484 proteins. These results allowed us to generate a highly detailed yet panoramic portrait of human interactomes associated with diverse cellular pathways. The strategy presented here signifies a technological advancement for in vivo PPI mapping at the systems level and can be generalized for charting protein interaction landscapes in any organisms.
Collapse
|
17
|
Gutierrez C, Salituro LJ, Yu C, Wang X, DePeter SF, Rychnovsky SD, Huang L. Enabling Photoactivated Cross-Linking Mass Spectrometric Analysis of Protein Complexes by Novel MS-Cleavable Cross-Linkers. Mol Cell Proteomics 2021; 20:100084. [PMID: 33915260 PMCID: PMC8214149 DOI: 10.1016/j.mcpro.2021.100084] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/02/2021] [Accepted: 04/21/2021] [Indexed: 12/15/2022] Open
Abstract
Cross-linking mass spectrometry (XL-MS) is a powerful tool for studying protein-protein interactions and elucidating architectures of protein complexes. While residue-specific XL-MS studies have been very successful, accessibility of interaction regions nontargetable by specific chemistries remain difficult. Photochemistry has shown great potential in capturing those regions because of nonspecific reactivity, but low yields and high complexities of photocross-linked products have hindered their identification, limiting current studies predominantly to single proteins. Here, we describe the development of three novel MS-cleavable heterobifunctional cross-linkers, namely SDASO (Succinimidyl diazirine sulfoxide), to enable fast and accurate identification of photocross-linked peptides by MSn. The MSn-based workflow allowed SDASO XL-MS analysis of the yeast 26S proteasome, demonstrating the feasibility of photocross-linking of large protein complexes for the first time. Comparative analyses have revealed that SDASO cross-linking is robust and captures interactions complementary to residue-specific reagents, providing the foundation for future applications of photocross-linking in complex XL-MS studies.
Collapse
Affiliation(s)
- Craig Gutierrez
- Department of Physiology and Biophysics, University of California, Irvine, California, USA
| | - Leah J Salituro
- Department of Chemistry, University of California, Irvine, California, USA
| | - Clinton Yu
- Department of Physiology and Biophysics, University of California, Irvine, California, USA
| | - Xiaorong Wang
- Department of Physiology and Biophysics, University of California, Irvine, California, USA
| | - Sadie F DePeter
- Department of Chemistry, University of California, Irvine, California, USA
| | - Scott D Rychnovsky
- Department of Chemistry, University of California, Irvine, California, USA
| | - Lan Huang
- Department of Physiology and Biophysics, University of California, Irvine, California, USA.
| |
Collapse
|
18
|
Cui L, Ma Y, Li M, Wei Z, Huan Y, Li H, Fei Q, Zheng L. Tyrosine-Reactive Cross-Linker for Probing Protein Three-Dimensional Structures. Anal Chem 2021; 93:4434-4440. [PMID: 33660978 DOI: 10.1021/acs.analchem.0c04337] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Cross-linking mass spectrometry (XL-MS) has made significant progress in understanding the structure of protein and elucidating architectures of larger protein complexes. Current XL-MS applications are limited to targeting lysine, glutamic acid, aspartic acid, and cysteine residues. There remains a need for the development of novel cross-linkers enabling selective targeting of other amino acid residues in proteins. Here, a novel simple cross-linker, namely, [4,4'-(disulfanediylbis(ethane-2,1-diyl)) bis(1,2,4-triazolidine-3,5-dione)] (DBB), has been designed, synthesized, and characterized. This cross-linker can react selectively with tyrosine residues in protein through the electrochemical click reaction. The DBB cross-links produced the characteristic peptides before and after electrochemical reduction, thus permitting the simplified data analysis and accurate identification for the cross-linked products. This is the first time a cross-linker is developed for targeting tyrosine residues on protein without using photoirradiation or a metal catalyst. This strategy might potentially be used as a complementary tool for XL-MS to probe protein 3D structures, protein complexes, and protein-protein interaction.
Collapse
Affiliation(s)
- Lili Cui
- College of Chemistry, Jilin University, Changchun 130012, China
| | - Yongge Ma
- School of Pharmaceutical Sciences, Jilin University, Changchun 130021, China
| | - Ming Li
- Division of Chemical Metrology & Analytical Science, National Institute of Metrology, Beijing 100029, China
| | - Zhonglin Wei
- College of Chemistry, Jilin University, Changchun 130012, China
| | - Yanfu Huan
- College of Chemistry, Jilin University, Changchun 130012, China
| | - Hongmei Li
- Division of Chemical Metrology & Analytical Science, National Institute of Metrology, Beijing 100029, China
| | - Qiang Fei
- College of Chemistry, Jilin University, Changchun 130012, China
| | - Lianyou Zheng
- School of Pharmaceutical Sciences, Jilin University, Changchun 130021, China
| |
Collapse
|
19
|
Matzinger M, Mechtler K. Cleavable Cross-Linkers and Mass Spectrometry for the Ultimate Task of Profiling Protein-Protein Interaction Networks in Vivo. J Proteome Res 2021; 20:78-93. [PMID: 33151691 PMCID: PMC7786381 DOI: 10.1021/acs.jproteome.0c00583] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Indexed: 12/11/2022]
Abstract
Cross-linking mass spectrometry (XL-MS) has matured into a potent tool to identify protein-protein interactions or to uncover protein structures in living cells, tissues, or organelles. The unique ability to investigate the interplay of proteins within their native environment delivers valuable complementary information to other advanced structural biology techniques. This Review gives a comprehensive overview of the current possible applications as well as the remaining limitations of the technique, focusing on cross-linking in highly complex biological systems like cells, organelles, or tissues. Thanks to the commercial availability of most reagents and advances in user-friendly data analysis, validation, and visualization tools, studies using XL-MS can, in theory, now also be utilized by nonexpert laboratories.
Collapse
Affiliation(s)
- Manuel Matzinger
- Research
Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, Vienna 1030, Austria
| | - Karl Mechtler
- Research
Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, Vienna 1030, Austria
| |
Collapse
|
20
|
Huang R, Gao X, Xu Z, Zhu W, Wei D, Jiang B, Chen H, Chen W. Decision Tree Searching Strategy to Boost the Identification of Cross-Linked Peptides. Anal Chem 2020; 92:13702-13710. [DOI: 10.1021/acs.analchem.0c00452] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Rong Huang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Pudong, Shanghai 201210, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Xiuxia Gao
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Pudong, Shanghai 201210, China
| | - Zili Xu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Pudong, Shanghai 201210, China
| | - Wei Zhu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Pudong, Shanghai 201210, China
| | - Ding Wei
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Pudong, Shanghai 201210, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Biao Jiang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Pudong, Shanghai 201210, China
| | - Hongli Chen
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Pudong, Shanghai 201210, China
| | - Wenzhang Chen
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Pudong, Shanghai 201210, China
| |
Collapse
|
21
|
Cui L, Ma Y, Li M, Wei Z, Huan Y, Fei Q, Li H, Zheng L. An acidic residue reactive and disulfide bond-containing cleavable cross-linker for probing protein 3D structures based on electrochemical mass spectrometry. Talanta 2020; 216:120964. [PMID: 32456912 DOI: 10.1016/j.talanta.2020.120964] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Revised: 03/21/2020] [Accepted: 03/23/2020] [Indexed: 12/27/2022]
Abstract
Cross-linking mass spectrometry (XL-MS) has attracted broad attention because of the capability to probe three-dimensional structure of proteins. Up to now, several amine-reactive cross-linkers have been developed for characterization of proteins and protein complexes. However, spatial information retrieved by XL-MS is still limited, partly because the strategies using an acidic residue reactive cross-linker have been rarely reported. In this paper, an acidic residue (e.g. aspartic acid, glutamic acid)-specific, disulfide bond-containing, cleavable cross-linker with a length of 13.1 Å, named 3,3'-dithiobis(propanoic dihydrazide), was presented for the first time. In addition, a novel approach using the cross-linker was proposed for unambiguous characterization of peptides and proteins with disulfide bonds. After cross-linked, the peptides could be electrochemically reduced, then characterized by high performance liquid chromatography mass spectrometry. For demonstration, the approach has been adopted to characterize the emideltide, insulin, and myoglobin, of which four pairs of intrachain cross-links have been successfully identified in myoglobin. The results showed that the cross-links displayed predictable fragmentation pattern upon collision induced dissociation (CID), thus admitting simplifying data analysis. In summary, this work introduces a novel type of cross-linker utilized for cross-linking and a new strategy to XL-MS technology for comprehensively understanding the three-dimensional structure of proteins.
Collapse
Affiliation(s)
- Lili Cui
- College of Chemistry, Jilin University, Changchun, 130012, China
| | - Yongge Ma
- School of Pharmaceutical Sciences, Jilin University, Changchun, 130021, China
| | - Ming Li
- Department of Chemistry, National Institute of Metrology, Beijing, 100029, China.
| | - Zhonglin Wei
- College of Chemistry, Jilin University, Changchun, 130012, China
| | - Yanfu Huan
- College of Chemistry, Jilin University, Changchun, 130012, China.
| | - Qiang Fei
- College of Chemistry, Jilin University, Changchun, 130012, China
| | - Hongmei Li
- Department of Chemistry, National Institute of Metrology, Beijing, 100029, China.
| | - Lianyou Zheng
- School of Pharmaceutical Sciences, Jilin University, Changchun, 130021, China
| |
Collapse
|
22
|
Cross-linking/mass spectrometry to get a closer view on protein interaction networks. Curr Opin Biotechnol 2020; 63:48-53. [DOI: 10.1016/j.copbio.2019.12.009] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 12/02/2019] [Accepted: 12/09/2019] [Indexed: 12/21/2022]
|
23
|
Chakrabarty JK, Bugarin A, Chowdhury SM. Evaluating the performance of an ETD-cleavable cross-linking strategy for elucidating protein structures. J Proteomics 2020; 225:103846. [PMID: 32480079 DOI: 10.1016/j.jprot.2020.103846] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 05/20/2020] [Accepted: 05/24/2020] [Indexed: 01/08/2023]
Abstract
Chemical cross-linking is a powerful strategy for elucidating the structures of protein or protein complexes. The distance constraints obtained from cross-linked peptides represent the three-dimensional structures of the protein complexes. Unfortunately, structural analysis using cross-linking approach demands a significant amount of data to elucidate protein structures. This requires the development of several cleavable cross-linkers with different range of spacer chains. An Electron Transfer Dissociation (ETD) tandem mass spectrometry cleavable bond hydrazone was reported. Its fragmentation with conjugated peptides showed promise for the development of a new ETD cleavable cross-linker. However, no cross-linker was developed utilizing this ETD cleavable bond. For the first time, we attempted to develop an ETD cleavable cross-linker utilizing a hydrazone bond. We overcome the pitfall for the synthesis of this cross-linker and an easy synthesis scheme is reported. In this report, we evaluated the performance of this cross-linker called Hydrazone Incorporated ETD cleavable cross-linker (HI-ETD-XL) in model peptides and proteins. The characteristic fragmentation behavior of HI-ETD-XL during electron transfer dissociation and subsequent sequence identification of the peptide fragment ions by tandem mass spectrometry allowed the identification of cross-linked peptides unambiguously. We believe the availability of this ETD cleavable cross-linker will advance structural proteomics research significantly. SIGNIFICANCE: Many cellular processes rely on the structural dynamics of protein complexes. The detailed knowledge of the structure and dynamics of protein complexes is crucial for understanding their biological functions and regulations. However, most of the structure of these multiprotein entities remain uncharacterized and sometimes is very challenging to reveal with biophysical techniques alone. Chemical cross-linking combined with mass spectrometry (MS) has proven to be a dependable strategy in structural proteomics field. However, data complexity and false identifications are significant hindrances for unambiguous identification of cross-linked peptides. Confident identifications demand structural studies with cross-linkers with different properties and variable spacer chain lengths. This new ETD cleavable cross-linking workflow will provide additional confidence to overcome these drawbacks and allow us to pinpoint cross-linked peptides confidently.
Collapse
Affiliation(s)
| | - Alejandro Bugarin
- Department of Chemistry and Biochemistry, University of Texas at Arlington, TX, USA; Department of Chemistry & Physics, Florida Gulf Coast University, FL, USA
| | - Saiful M Chowdhury
- Department of Chemistry and Biochemistry, University of Texas at Arlington, TX, USA.
| |
Collapse
|
24
|
Yu C, Novitsky EJ, Cheng NW, Rychnovsky SD, Huang L. Exploring Spacer Arm Structures for Designs of Asymmetric Sulfoxide-Containing MS-Cleavable Cross-Linkers. Anal Chem 2020; 92:6026-6033. [PMID: 32202417 PMCID: PMC7363200 DOI: 10.1021/acs.analchem.0c00298] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cross-linking mass spectrometry (XL-MS) has become a powerful structural tool for defining protein-protein interactions (PPIs) and elucidating architectures of large protein assemblies. To advance XL-MS studies, we have previously developed a series of sulfoxide-containing MS-cleavable cross-linkers to facilitate the detection and identification of cross-linked peptides using multistage mass spectrometry (MSn). While current sulfoxide-based cross-linkers are effective for in vivo and in vitro XL-MS studies at the systems-level, new reagents are still needed to help expand PPI coverage. To this end, we have designed and synthesized six variable-length derivatives of disuccinimidyl sulfoxide (DSSO) to better understand the effects of spacer arm modulation on MS-cleavability, fragmentation characteristics, and MS identification of cross-linked peptides. In addition, the impact on cross-linking reactivity was evaluated. Moreover, alternative MS2-based workflows were explored to determine their feasibility for analyzing new sulfoxide-containing cross-linked products. Based on the results of synthetic peptides and a model protein, we have further demonstrated the robustness and predictability of sulfoxide chemistry in designing MS-cleavable cross-linkers. Importantly, we have identified a unique asymmetric design that exhibits preferential fragmentation of cross-links over peptide backbones, a desired feature for MSn analysis. This work has established a solid foundation for further development of sulfoxide-containing MS-cleavable cross-linkers with new functionalities.
Collapse
Affiliation(s)
- Clinton Yu
- Department of Physiology and Biophysics, University of California, Irvine, CA 92697
| | - Eric J. Novitsky
- Department of Chemistry, University of California, Irvine, CA 92697
| | - Nicholas W. Cheng
- Department of Physiology and Biophysics, University of California, Irvine, CA 92697
| | | | - Lan Huang
- Department of Physiology and Biophysics, University of California, Irvine, CA 92697
| |
Collapse
|
25
|
Structural dynamics of the human COP9 signalosome revealed by cross-linking mass spectrometry and integrative modeling. Proc Natl Acad Sci U S A 2020; 117:4088-4098. [PMID: 32034103 DOI: 10.1073/pnas.1915542117] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The COP9 signalosome (CSN) is an evolutionarily conserved eight-subunit (CSN1-8) protein complex that controls protein ubiquitination by deneddylating Cullin-RING E3 ligases (CRLs). The activation and function of CSN hinges on its structural dynamics, which has been challenging to decipher by conventional tools. Here, we have developed a multichemistry cross-linking mass spectrometry approach enabled by three mass spectometry-cleavable cross-linkers to generate highly reliable cross-link data. We applied this approach with integrative structure modeling to determine the interaction and structural dynamics of CSN with the recently discovered ninth subunit, CSN9, in solution. Our results determined the localization of CSN9 binding sites and revealed CSN9-dependent structural changes of CSN. Together with biochemical analysis, we propose a structural model in which CSN9 binding triggers CSN to adopt a configuration that facilitates CSN-CRL interactions, thereby augmenting CSN deneddylase activity. Our integrative structure analysis workflow can be generalized to define in-solution architectures of dynamic protein complexes that remain inaccessible to other approaches.
Collapse
|
26
|
Genereux JC. Mass spectrometric approaches for profiling protein folding and stability. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2019; 118:111-144. [PMID: 31928723 DOI: 10.1016/bs.apcsb.2019.09.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Protein stability reports on protein homeostasis, function, and binding interactions, such as to other proteins, metabolites and drugs. As such, there is a pressing need for technologies that can report on protein stability. The ideal technique could be applied in vitro or in vivo systems, proteome-wide, independently of matrix, under native conditions, with residue-level resolution, and on protein at endogenous levels. Mass spectrometry has rapidly become a preferred technology for identifying and quantifying proteins. As such, it has been increasingly incorporated into methodologies for interrogating protein stability and folding. Although no single technology can satisfy all desired applications, several emerging approaches have shown outstanding success at providing biological insight into the stability of the proteome. This chapter outlines some of these recent emerging technologies.
Collapse
Affiliation(s)
- Joseph C Genereux
- Department of Chemistry, University of California, Riverside, CA, United States
| |
Collapse
|
27
|
Huang R, Zhu W, Wu Y, Chen J, Yu J, Jiang B, Chen H, Chen W. A novel mass spectrometry-cleavable, phosphate-based enrichable and multi-targeting protein cross-linker. Chem Sci 2019; 10:6443-6447. [PMID: 31341596 PMCID: PMC6611067 DOI: 10.1039/c9sc00893d] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 05/23/2019] [Indexed: 12/13/2022] Open
Abstract
Chemical cross-linking mass spectrometry (XL-MS) is a powerful technology for obtaining protein structural information and studying protein-protein interactions. We report phospho-bisvinylsulfone (pBVS) as a novel water-soluble, MS-cleavable, phosphate-based enrichable and multi-targeting cross-linker. In this approach, the fragmentation of pBVS cross-linked peptides occurs in situ through retro-Michael addition. The phosphate group is successfully used as a small affinity tag to isolate cross-linked peptides from the highly abundant non-cross-linked peptides. In addition, the linker targets multiple types of amino acid residues, including cysteine, lysine and histidine. This method was applied to cross-link bovine serum albumin (BSA), myoglobin and Lbcpf1 demonstrating the ability to yield accurate and abundant information to facilitate protein structure elucidation.
Collapse
Affiliation(s)
- Rong Huang
- Shanghai Institute for Advanced Immunochemical Studies , ShanghaiTech University , 393 Middle Huaxia Road , Pudong , Shanghai 201210 , China . ; ;
- University of Chinese Academy of Sciences , 19A Yuquan Road, Shijingshan District , Beijing , 100049 , China
| | - Wei Zhu
- Shanghai Institute for Advanced Immunochemical Studies , ShanghaiTech University , 393 Middle Huaxia Road , Pudong , Shanghai 201210 , China . ; ;
| | - Yue Wu
- Shanghai Institute for Advanced Immunochemical Studies , ShanghaiTech University , 393 Middle Huaxia Road , Pudong , Shanghai 201210 , China . ; ;
| | - Jiakang Chen
- Shanghai Institute for Advanced Immunochemical Studies , ShanghaiTech University , 393 Middle Huaxia Road , Pudong , Shanghai 201210 , China . ; ;
| | - Jianghui Yu
- Shanghai Institute for Advanced Immunochemical Studies , ShanghaiTech University , 393 Middle Huaxia Road , Pudong , Shanghai 201210 , China . ; ;
- University of Chinese Academy of Sciences , 19A Yuquan Road, Shijingshan District , Beijing , 100049 , China
| | - Biao Jiang
- Shanghai Institute for Advanced Immunochemical Studies , ShanghaiTech University , 393 Middle Huaxia Road , Pudong , Shanghai 201210 , China . ; ;
| | - Hongli Chen
- Shanghai Institute for Advanced Immunochemical Studies , ShanghaiTech University , 393 Middle Huaxia Road , Pudong , Shanghai 201210 , China . ; ;
| | - Wenzhang Chen
- Shanghai Institute for Advanced Immunochemical Studies , ShanghaiTech University , 393 Middle Huaxia Road , Pudong , Shanghai 201210 , China . ; ;
| |
Collapse
|
28
|
Stieger CE, Doppler P, Mechtler K. Optimized Fragmentation Improves the Identification of Peptides Cross-Linked by MS-Cleavable Reagents. J Proteome Res 2019; 18:1363-1370. [DOI: 10.1021/acs.jproteome.8b00947] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Christian E. Stieger
- Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna 1030, Austria
| | - Philipp Doppler
- Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna 1030, Austria
| | - Karl Mechtler
- Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna 1030, Austria
- Institute of Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna 1030, Austria
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna 1030, Austria
| |
Collapse
|
29
|
de Graaf SC, Klykov O, van den Toorn H, Scheltema RA. Cross-ID: Analysis and Visualization of Complex XL-MS-Driven Protein Interaction Networks. J Proteome Res 2019; 18:642-651. [PMID: 30575379 PMCID: PMC6407916 DOI: 10.1021/acs.jproteome.8b00725] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Protein interactions enable much more complex behavior than the sum of the individual protein parts would suggest and represents a level of biological complexity requiring full understanding when unravelling cellular processes. Cross-linking mass spectrometry has emerged as an attractive approach to study these interactions, and recent advances in mass spectrometry and data analysis software have enabled the identification of thousands of cross-links from a single experiment. The resulting data complexity is, however, difficult to understand and requires interactive software tools. Even though solutions are available, these represent an agglomerate of possibilities, and each features its own input format, often forcing manual conversion. Here we present Cross-ID, a visualization platform that links directly into the output of XlinkX for Proteome Discoverer but also plays well with other platforms by supporting a user-controllable text-file importer. The platform includes features like grouping, spectral viewer, gene ontology (GO) enrichment, post-translational modification (PTM) visualization, domains and secondary structure mapping, data set comparison, previsualization overlap check, and more. Validation of detected cross-links is available for proteins and complexes with known structure or for protein complexes through the DisVis online platform ( http://milou.science.uu.nl/cgi/services/DISVIS/disvis/ ). Graphs are exportable in PDF format, and data sets can be exported in tab-separated text files for evaluation through other software.
Collapse
Affiliation(s)
- Sebastiaan C de Graaf
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, and Utrecht Institute for Pharmaceutical Sciences , Utrecht University , Padualaan 8 , 3584 CH Utrecht , The Netherlands.,Netherlands Proteomics Centre , Padualaan 8 , 3584 CH Utrecht , The Netherlands
| | - Oleg Klykov
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, and Utrecht Institute for Pharmaceutical Sciences , Utrecht University , Padualaan 8 , 3584 CH Utrecht , The Netherlands.,Netherlands Proteomics Centre , Padualaan 8 , 3584 CH Utrecht , The Netherlands
| | - Henk van den Toorn
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, and Utrecht Institute for Pharmaceutical Sciences , Utrecht University , Padualaan 8 , 3584 CH Utrecht , The Netherlands.,Netherlands Proteomics Centre , Padualaan 8 , 3584 CH Utrecht , The Netherlands
| | - Richard A Scheltema
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, and Utrecht Institute for Pharmaceutical Sciences , Utrecht University , Padualaan 8 , 3584 CH Utrecht , The Netherlands.,Netherlands Proteomics Centre , Padualaan 8 , 3584 CH Utrecht , The Netherlands
| |
Collapse
|
30
|
Huang T, Armbruster MR, Coulton JB, Edwards JL. Chemical Tagging in Mass Spectrometry for Systems Biology. Anal Chem 2018; 91:109-125. [DOI: 10.1021/acs.analchem.8b04951] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Tianjiao Huang
- Department of Chemistry, Saint Louis University, 3501 Laclede Avenue, St. Louis, Missouri 63103, United States
| | - Michael R. Armbruster
- Department of Chemistry, Saint Louis University, 3501 Laclede Avenue, St. Louis, Missouri 63103, United States
| | - John B. Coulton
- Department of Chemistry, Saint Louis University, 3501 Laclede Avenue, St. Louis, Missouri 63103, United States
| | - James L. Edwards
- Department of Chemistry, Saint Louis University, 3501 Laclede Avenue, St. Louis, Missouri 63103, United States
| |
Collapse
|