1
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McKerchar H, Dyer JM, Gerrard JA, Maes E, Clerens S, Dobson RC. Characterizing lysinoalanine crosslinks in food systems: Discovery of a diagnostic ion in model peptides using MALDI mass spectrometry. Food Chem X 2023; 19:100800. [PMID: 37780262 PMCID: PMC10534164 DOI: 10.1016/j.fochx.2023.100800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 07/03/2023] [Accepted: 07/14/2023] [Indexed: 10/03/2023] Open
Abstract
Formation of lysinoalanine protein-protein crosslinks during food processing adversely impacts nutritional value. However, mapping lysinoalanine directly in food is challenging. We characterized the fragmentation pattern of lysinoalanine crosslinks in synthetic peptide models over a range of pH and time treatments using mass spectrometry. A putative diagnostic ion resulting from the cleavage of the α-carbon and β-carbon of lysinoalanine is identified in MALDI MS/MS spectra. This represents the first step in mapping lysinoalanine in real food samples with higher precision than currently identifiable through standard or customized software. We then determined a correlated trend in the reduction of disulfide bonds and formation of lysinoalanine with increasing pH and time. Mapping lysinoalanine formation is critical to enhance our understanding of molecular processes impacting the nutritional value of foods, including notably in the development of protein alternatives that use alkaline treatment to extract protein isolates.
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Affiliation(s)
- Hannah McKerchar
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
- Riddet Institute, Based Massey University, Palmerston North 4442, New Zealand
- Proteins and Metabolites Team, AgResearch Lincoln Research Centre, Lincoln 7608, New Zealand
| | - Jolon M. Dyer
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
- The New Zealand Institute for Plant and Food Research, Lincoln Research Centre, Lincoln 7608, New Zealand
- Department of Wine, Food and Molecular Biosciences, Lincoln University, Lincoln 7647, New Zealand
| | - Juliet A. Gerrard
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
- Riddet Institute, Based Massey University, Palmerston North 4442, New Zealand
- School of Biological Sciences and School of Chemical Sciences, University of Auckland, Auckland, New Zealand
| | - Evelyne Maes
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
- Riddet Institute, Based Massey University, Palmerston North 4442, New Zealand
- Proteins and Metabolites Team, AgResearch Lincoln Research Centre, Lincoln 7608, New Zealand
| | - Stefan Clerens
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
- Riddet Institute, Based Massey University, Palmerston North 4442, New Zealand
- Proteins and Metabolites Team, AgResearch Lincoln Research Centre, Lincoln 7608, New Zealand
| | - Renwick C.J. Dobson
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
- Riddet Institute, Based Massey University, Palmerston North 4442, New Zealand
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia
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2
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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: 4] [Impact Index Per Article: 2.0] [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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3
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Qiang J, Xu Z, Li Y, Wang H, Zhang Y. Carboxypeptidase Y Assisted Disulfide-Bond Identification with Linearized Database Search. Anal Chem 2021; 93:14940-14945. [PMID: 34735112 DOI: 10.1021/acs.analchem.1c03932] [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
A disulfide bond is an important protein post-translational modification and plays a key role in regulating protein oxidation status, protein structure, and stability. Analysis of a disulfide bond using mass spectrometry is challenging because there lacks an efficient method to separate the disulfide-linked peptides from a complex protein digest, and the MS data requires sophisticated interpretation. Here, we developed a novel disulfide bond identification strategy, termed as "carboxypeptidase Y assisted disulfide-bond identification (CADI)". CADI is able to significantly reduce sample complexity by depleting ∼90% of the linear peptides while keeping the disulfide-bonded peptides. Furthermore, all CADI data can be directly analyzed by widely used protein database search engines, such as Mascot and MaxQuant. Our data show that CADI is able to sensitively identify disulfide bonds in peptides and proteins. However, CADI has not yet achieved a satisfied in-depth coverage on complex mammalian cell lysates due to the limited enzymatic activity of carboxypeptidase Y and low occurrences of disulfide bonds in a proteome. Altogether, CADI is a useful method that can get disulfide-linked peptides enriched and analyzed with regular search engines. CADI holds great potentials to deepen the analysis of disulfide bond and other types of cross-linked peptides on the proteome scale.
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Affiliation(s)
- Jiali Qiang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Road, Pudong, Shanghai 201210, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhimin Xu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Road, Pudong, Shanghai 201210, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yunxia Li
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Road, Pudong, Shanghai 201210, China
| | - Hongbin Wang
- The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Yaoyang Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Road, Pudong, Shanghai 201210, China
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4
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Chakrabarty JK, Sadananda SC, Bhat A, Naik AJ, Ostwal DV, Chowdhury SM. High Confidence Identification of Cross-Linked Peptides by an Enrichment-Based Dual Cleavable Cross-Linking Technology and Data Analysis tool Cleave-XL. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:173-182. [PMID: 32031390 DOI: 10.1021/jasms.9b00111] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Cleavable cross-linking technology requires further MS/MS of the cleavable fragments for unambiguous identification of cross-linked peptides. These spectra are sometimes very ambiguous due to the sensitivity and complex fragmentation pattern of the peptides with the cross-linked residues. We recently reported a dual cleavable cross-linking technology (DUCCT), which can enhance the confidence in the identification of cross-linked peptides. The heart of this strategy is a novel dual mass spectrometry cleavable cross linker that can be cleaved preferentially by two differential tandem mass spectrometry methods, collision induced dissociation and electron transfer dissociation (CID and ETD). Different signature ions from two different mass spectra for the same cross-linked peptide helped identify the cross-linked peptides with high confidence. In this study, we developed an enrichment-based photocleavable DUCCT (PC-DUCCT-biotin), where cross-linked products were enriched from biological samples using affinity purification, and subsequently, two sequential tandem (CID and ETD) mass spectrometry processes were utilized. Furthermore, we developed a prototype software called Cleave-XL to analyze cross-linked products generated by DUCCT. Photocleavable DUCCT was demonstrated in standard peptides and proteins. Efficiency of the software tools to search and compare CID and ETD data of photocleavable DUCCT biotin in standard peptides and proteins as well as regular DUCCT in protein complexes from immune cells were tested. The software is efficient in pinpointing cross-linked sites using CID and ETD cross-linking data. We believe this new DUCCT and associated software tool Cleave-XL will advance high confidence identification of protein cross-linking sites and automated identification of low-resolution protein structures.
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Affiliation(s)
- Jayanta K Chakrabarty
- Department of Chemistry and Biochemistry , University of Texas at Arlington , Arlington , Texas 76019 , United States
| | - Sandhya C Sadananda
- Department of Computer Science , University of Texas at Arlington , Arlington , Texas 76019 , United States
| | - Apeksha Bhat
- Department of Computer Science , University of Texas at Arlington , Arlington , Texas 76019 , United States
| | - Aishwarya J Naik
- Department of Computer Science , University of Texas at Arlington , Arlington , Texas 76019 , United States
| | - Dhanashri V Ostwal
- Department of Computer Science , University of Texas at Arlington , Arlington , Texas 76019 , United States
| | - Saiful M Chowdhury
- Department of Chemistry and Biochemistry , University of Texas at Arlington , Arlington , Texas 76019 , United States
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5
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Piotrowski C, Sinz A. Structural Investigation of Proteins and Protein Complexes by Chemical Cross-Linking/Mass Spectrometry. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1105:101-121. [PMID: 30617826 DOI: 10.1007/978-981-13-2200-6_8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
During the last two decades, cross-linking combined with mass spectrometry (MS) has evolved as a valuable tool to gain structural insights into proteins and protein assemblies. Structural information is obtained by introducing covalent connections between amino acids that are in spatial proximity in proteins and protein complexes. The distance constraints imposed by the cross-linking reagent provide information on the three-dimensional arrangement of the covalently connected amino acid residues and serve as basis for de-novo or homology modeling approaches. As cross-linking/MS allows investigating protein 3D-structures and protein-protein interactions not only in-vitro, but also in-vivo, it is especially appealing for studying protein systems in their native environment. In this chapter, we describe the principles of cross-linking/MS and illustrate its value for investigating protein 3D-structures and for unraveling protein interaction networks.
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Affiliation(s)
- Christine Piotrowski
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany.
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6
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Lampe JN. Advances in the Understanding of Protein-Protein Interactions in Drug Metabolizing Enzymes through the Use of Biophysical Techniques. Front Pharmacol 2017; 8:521. [PMID: 28848438 PMCID: PMC5550701 DOI: 10.3389/fphar.2017.00521] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Accepted: 07/24/2017] [Indexed: 02/01/2023] Open
Abstract
In recent years, a growing appreciation has developed for the importance of protein-protein interactions to modulate the function of drug metabolizing enzymes. Accompanied with this appreciation, new methods and technologies have been designed for analyzing protein-protein interactions both in vitro and in vivo. These technologies have been applied to several classes of drug metabolizing enzymes, including: cytochrome P450's (CYPs), monoamine oxidases (MAOs), UDP-glucuronosyltransferases (UGTs), glutathione S-transferases (GSTs), and sulfotransferases (SULTs). In this review, we offer a brief description and assessment of the impact of many of these technologies to the study of protein-protein interactions in drug disposition. The still expanding list of these techniques and assays has the potential to revolutionize our understanding of how these enzymes carry out their important functions in vivo.
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Affiliation(s)
- Jed N Lampe
- Department of Pharmacology, Toxicology, and Therapeutics, University of Kansas Medical CenterKansas City, MO, United States
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7
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Maes E, Dyer JM, McKerchar HJ, Deb-Choudhury S, Clerens S. Protein-protein cross-linking and human health: the challenge of elucidating with mass spectrometry. Expert Rev Proteomics 2017; 14:917-929. [PMID: 28759730 DOI: 10.1080/14789450.2017.1362336] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
INTRODUCTION In several biomedical research fields, the cross-linking of peptides and proteins has an important impact on health and wellbeing. It is therefore of crucial importance to study this class of post-translational modifications in detail. The huge potential of mass spectrometric technologies in the mapping of these protein-protein cross-links is however overshadowed by the challenges that the field has to overcome. Areas covered: In this review, we summarize the different pitfalls and challenges that the protein-protein cross-linking field is confronted with when using mass spectrometry approaches. We additionally focus on native disulfide bridges as an example and provide some examples of cross-links that are important in the biomedical field. Expert commentary: The current flow of methodological improvements, mainly from the chemical cross-linking field, has delivered a significant contribution to deciphering native and insult-induced cross-links. Although an automated data analysis of proteome-wide peptide cross-linking is currently only possible in chemical cross-linking experiments, the field is well on the way towards a more automated analysis of native and insult-induced cross-links in raw mass spectrometry data that will boost its potential in biomedical applications.
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Affiliation(s)
- Evelyne Maes
- a Food & Bio-Based Products, AgResearch Ltd ., Lincoln , New Zealand
| | - Jolon M Dyer
- a Food & Bio-Based Products, AgResearch Ltd ., Lincoln , New Zealand.,b Biomolecular Interaction Centre , University of Canterbury , Christchurch , New Zealand.,c Riddet Institute, Massey University , Palmerston North , New Zealand.,d Wine, Food & Molecular Biosciences , Lincoln University , Lincoln , New Zealand
| | - Hannah J McKerchar
- a Food & Bio-Based Products, AgResearch Ltd ., Lincoln , New Zealand.,b Biomolecular Interaction Centre , University of Canterbury , Christchurch , New Zealand
| | | | - Stefan Clerens
- a Food & Bio-Based Products, AgResearch Ltd ., Lincoln , New Zealand.,b Biomolecular Interaction Centre , University of Canterbury , Christchurch , New Zealand
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8
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Yılmaz Ş, Drepper F, Hulstaert N, Černič M, Gevaert K, Economou A, Warscheid B, Martens L, Vandermarliere E. Xilmass: A New Approach toward the Identification of Cross-Linked Peptides. Anal Chem 2016; 88:9949-9957. [PMID: 27642655 DOI: 10.1021/acs.analchem.6b01585] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Chemical cross-linking coupled with mass spectrometry plays an important role in unravelling protein interactions, especially weak and transient ones. Moreover, cross-linking complements several structural determination approaches such as cryo-EM. Although several computational approaches are available for the annotation of spectra obtained from cross-linked peptides, there remains room for improvement. Here, we present Xilmass, a novel algorithm to identify cross-linked peptides that introduces two new concepts: (i) the cross-linked peptides are represented in the search database such that the cross-linking sites are explicitly encoded, and (ii) the scoring function derived from the Andromeda algorithm was adapted to score against a theoretical tandem mass spectrometry (MS/MS) spectrum that contains the peaks from all possible fragment ions of a cross-linked peptide pair. The performance of Xilmass was evaluated against the recently published Kojak and the popular pLink algorithms on a calmodulin-plectin complex data set, as well as three additional, published data sets. The results show that Xilmass typically had the highest number of identified distinct cross-linked sites and also the highest number of predicted cross-linked sites.
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Affiliation(s)
- Şule Yılmaz
- Medical Biotechnology Center, VIB , 9000 Ghent, Belgium.,Department of Biochemistry, Ghent University , 9000 Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent University , 9000 Ghent, Belgium
| | - Friedel Drepper
- Department of Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg , 79104 Freiburg, Germany.,BIOSS Centre for Biological Signaling Studies, University of Freiburg , 79104 Freiburg, Germany
| | - Niels Hulstaert
- Medical Biotechnology Center, VIB , 9000 Ghent, Belgium.,Department of Biochemistry, Ghent University , 9000 Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent University , 9000 Ghent, Belgium
| | - Maša Černič
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins , Jamova Cesta 39, 1000 Ljubljana, Slovenia.,Faculty of Medicine, University of Ljubljana , 1000 Ljubljana, Slovenia
| | - Kris Gevaert
- Medical Biotechnology Center, VIB , 9000 Ghent, Belgium.,Department of Biochemistry, Ghent University , 9000 Ghent, Belgium
| | - Anastassios Economou
- KU Leuven-University of Leuven , Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, 3000 Leuven, Belgium.,Institute of Molecular Biology and Biotechnology-FoRTH and Department of Biology, University of Crete , Iraklio, 71100 Crete, Greece
| | - Bettina Warscheid
- Department of Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg , 79104 Freiburg, Germany.,BIOSS Centre for Biological Signaling Studies, University of Freiburg , 79104 Freiburg, Germany
| | - Lennart Martens
- Medical Biotechnology Center, VIB , 9000 Ghent, Belgium.,Department of Biochemistry, Ghent University , 9000 Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent University , 9000 Ghent, Belgium
| | - Elien Vandermarliere
- Medical Biotechnology Center, VIB , 9000 Ghent, Belgium.,Department of Biochemistry, Ghent University , 9000 Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent University , 9000 Ghent, Belgium
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9
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Sarpe V, Rafiei A, Hepburn M, Ostan N, Schryvers AB, Schriemer DC. High Sensitivity Crosslink Detection Coupled With Integrative Structure Modeling in the Mass Spec Studio. Mol Cell Proteomics 2016; 15:3071-80. [PMID: 27412762 DOI: 10.1074/mcp.o116.058685] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Indexed: 01/21/2023] Open
Abstract
The Mass Spec Studio package was designed to support the extraction of hydrogen-deuterium exchange and covalent labeling data for a range of mass spectrometry (MS)-based workflows, to integrate with restraint-driven protein modeling activities. In this report, we present an extension of the underlying Studio framework and provide a plug-in for crosslink (XL) detection. To accommodate flexibility in XL methods and applications, while maintaining efficient data processing, the plug-in employs a peptide library reduction strategy via a presearch of the tandem-MS data. We demonstrate that prescoring linear unmodified peptide tags using a probabilistic approach substantially reduces search space by requiring both crosslinked peptides to generate sparse data attributable to their linear forms. The method demonstrates highly sensitive crosslink peptide identification with a low false positive rate. Integration with a Haddock plug-in provides a resource that can combine multiple sources of data for protein modeling activities. We generated a structural model of porcine transferrin bound to TbpB, a membrane-bound receptor essential for iron acquisition in Actinobacillus pleuropneumoniae Using mutational data and crosslinking restraints, we confirm the mechanism by which TbpB recognizes the iron-loaded form of transferrin, and note the requirement for disparate sources of restraint data for accurate model construction. The software plugin is freely available at www.msstudio.ca.
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Affiliation(s)
- Vladimir Sarpe
- From the ‡Department of Biochemistry and Molecular Biology
| | | | - Morgan Hepburn
- From the ‡Department of Biochemistry and Molecular Biology
| | - Nicholas Ostan
- ¶Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Alberta, T2N 1N4, Canada
| | - Anthony B Schryvers
- From the ‡Department of Biochemistry and Molecular Biology, ¶Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Alberta, T2N 1N4, Canada
| | - David C Schriemer
- From the ‡Department of Biochemistry and Molecular Biology, §Department of Chemistry,
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10
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Protein Structural Analysis via Mass Spectrometry-Based Proteomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 919:397-431. [PMID: 27975228 DOI: 10.1007/978-3-319-41448-5_19] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Modern mass spectrometry (MS) technologies have provided a versatile platform that can be combined with a large number of techniques to analyze protein structure and dynamics. These techniques include the three detailed in this chapter: (1) hydrogen/deuterium exchange (HDX), (2) limited proteolysis, and (3) chemical crosslinking (CX). HDX relies on the change in mass of a protein upon its dilution into deuterated buffer, which results in varied deuterium content within its backbone amides. Structural information on surface exposed, flexible or disordered linker regions of proteins can be achieved through limited proteolysis, using a variety of proteases and only small extents of digestion. CX refers to the covalent coupling of distinct chemical species and has been used to analyze the structure, function and interactions of proteins by identifying crosslinking sites that are formed by small multi-functional reagents, termed crosslinkers. Each of these MS applications is capable of revealing structural information for proteins when used either with or without other typical high resolution techniques, including NMR and X-ray crystallography.
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11
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Sinz A, Arlt C, Chorev D, Sharon M. Chemical cross-linking and native mass spectrometry: A fruitful combination for structural biology. Protein Sci 2015; 24:1193-209. [PMID: 25970732 PMCID: PMC4534171 DOI: 10.1002/pro.2696] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 04/14/2015] [Accepted: 04/29/2015] [Indexed: 12/31/2022]
Abstract
Mass spectrometry (MS) is becoming increasingly popular in the field of structural biology for analyzing protein three-dimensional-structures and for mapping protein-protein interactions. In this review, the specific contributions of chemical crosslinking and native MS are outlined to reveal the structural features of proteins and protein assemblies. Both strategies are illustrated based on the examples of the tetrameric tumor suppressor protein p53 and multisubunit vinculin-Arp2/3 hybrid complexes. We describe the distinct advantages and limitations of each technique and highlight synergistic effects when both techniques are combined. Integrating both methods is especially useful for characterizing large protein assemblies and for capturing transient interactions. We also point out the future directions we foresee for a combination of in vivo crosslinking and native MS for structural investigation of intact protein assemblies.
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Affiliation(s)
- Andrea Sinz
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-WittenbergD-06120, Halle, Germany
| | - Christian Arlt
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-WittenbergD-06120, Halle, Germany
| | - Dror Chorev
- Department of Biological Chemistry, Weizmann Institute of ScienceRehovot, 76100, Israel
| | - Michal Sharon
- Department of Biological Chemistry, Weizmann Institute of ScienceRehovot, 76100, Israel
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12
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Tran BQ, Goodlett DR, Goo YA. Advances in protein complex analysis by chemical cross-linking coupled with mass spectrometry (CXMS) and bioinformatics. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1864:123-9. [PMID: 26025770 DOI: 10.1016/j.bbapap.2015.05.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 05/07/2015] [Accepted: 05/18/2015] [Indexed: 01/12/2023]
Abstract
For the analysis of protein-protein interactions and protein conformations, cross-linking coupled with mass spectrometry (CXMS) has become an essential tool in recent years. A variety of cross-linking reagents are used to covalently link interacting amino acids to identify protein-binding partners. The spatial proximity of cross-linked amino acid residues is used to elucidate structural models of protein complexes. The main challenges for mapping protein-protein interaction are low stoichiometry and low frequency of cross-linked peptides relative to unmodified linear peptides as well as accurate and efficient matches to corresponding peptide sequences with low false discovery rates for identifying the site of cross-link. We evaluate the current state of chemical cross-linking and mass spectrometry applications with the special emphasis on the recent development of informatics data processing and analysis tools that help complexity of interpreting CXMS data. This article is part of a Special Issue entitled:Physiological Enzymology and Protein Functions.
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Affiliation(s)
- Bao Quoc Tran
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, USA.
| | - David R Goodlett
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, USA.
| | - Young Ah Goo
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, USA.
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13
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Hoopmann MR, Zelter A, Johnson RS, Riffle M, MacCoss MJ, Davis TN, Moritz RL. Kojak: efficient analysis of chemically cross-linked protein complexes. J Proteome Res 2015; 14:2190-8. [PMID: 25812159 DOI: 10.1021/pr501321h] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Protein chemical cross-linking and mass spectrometry enable the analysis of protein-protein interactions and protein topologies; however, complicated cross-linked peptide spectra require specialized algorithms to identify interacting sites. The Kojak cross-linking software application is a new, efficient approach to identify cross-linked peptides, enabling large-scale analysis of protein-protein interactions by chemical cross-linking techniques. The algorithm integrates spectral processing and scoring schemes adopted from traditional database search algorithms and can identify cross-linked peptides using many different chemical cross-linkers with or without heavy isotope labels. Kojak was used to analyze both novel and existing data sets and was compared to existing cross-linking algorithms. The algorithm provided increased cross-link identifications over existing algorithms and, equally importantly, the results in a fraction of computational time. The Kojak algorithm is open-source, cross-platform, and freely available. This software provides both existing and new cross-linking researchers alike an effective way to derive additional cross-link identifications from new or existing data sets. For new users, it provides a simple analytical resource resulting in more cross-link identifications than other methods.
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Affiliation(s)
- Michael R Hoopmann
- †Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109, United States
| | - Alex Zelter
- ‡Department of Biochemistry, University of Washington, 1705 North East Pacific Street, Seattle, Washington 98195, United States
| | - Richard S Johnson
- §Department of Genome Sciences, University of Washington, 3720 15th Avenue North East, Seattle, Washington 98195, United States
| | - Michael Riffle
- ‡Department of Biochemistry, University of Washington, 1705 North East Pacific Street, Seattle, Washington 98195, United States
| | - Michael J MacCoss
- §Department of Genome Sciences, University of Washington, 3720 15th Avenue North East, Seattle, Washington 98195, United States
| | - Trisha N Davis
- ‡Department of Biochemistry, University of Washington, 1705 North East Pacific Street, Seattle, Washington 98195, United States
| | - Robert L Moritz
- †Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109, United States
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14
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Fan SB, Meng JM, Lu S, Zhang K, Yang H, Chi H, Sun RX, Dong MQ, He SM. Using pLink to Analyze Cross-Linked Peptides. ACTA ACUST UNITED AC 2015; 49:8.21.1-8.21.19. [PMID: 25754995 DOI: 10.1002/0471250953.bi0821s49] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
pLink is a search engine for high-throughput identification of cross-linked peptides from their tandem mass spectra, which is the data-analysis step in chemical cross-linking of proteins coupled with mass spectrometry analysis. pLink has accumulated more than 200 registered users from all over the world since its first release in 2012. After 2 years of continual development, a new version of pLink has been released, which is at least 40 times faster, more versatile, and more user-friendly. Also, the function of the new pLink has been expanded to identifying endogenous protein cross-linking sites such as disulfide bonds and SUMO (Small Ubiquitin-like MOdifier) modification sites. Integrated into the new version are two accessory tools: pLabel, to annotate spectra of cross-linked peptides for visual inspection and publication, and pConfig, to assist users in setting up search parameters. Here, we provide detailed guidance on running a database search for identification of protein cross-links using the 2014 version of pLink.
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Affiliation(s)
- Sheng-Bo Fan
- Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Jia-Ming Meng
- Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Shan Lu
- National Institute of Biological Sciences, Beijing, China
| | - Kun Zhang
- Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Hao Yang
- Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Hao Chi
- Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, China
| | - Rui-Xiang Sun
- Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, China
| | - Si-Min He
- Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, China
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15
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Kosinski J, von Appen A, Ori A, Karius K, Müller CW, Beck M. Xlink Analyzer: software for analysis and visualization of cross-linking data in the context of three-dimensional structures. J Struct Biol 2015; 189:177-83. [PMID: 25661704 PMCID: PMC4359615 DOI: 10.1016/j.jsb.2015.01.014] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 01/26/2015] [Accepted: 01/28/2015] [Indexed: 12/25/2022]
Abstract
Structural characterization of large multi-subunit protein complexes often requires integrating various experimental techniques. Cross-linking mass spectrometry (XL-MS) identifies proximal protein residues and thus is increasingly used to map protein interactions and determine the relative orientation of subunits within the structure of protein complexes. To fully adapt XL-MS as a structure characterization technique, we developed Xlink Analyzer, a software tool for visualization and analysis of XL-MS data in the context of the three-dimensional structures. Xlink Analyzer enables automatic visualization of cross-links, identifies cross-links violating spatial restraints, calculates violation statistics, maps chemically modified surfaces, and allows interactive manipulations that facilitate analysis of XL-MS data and aid designing new experiments. We demonstrate these features by mapping interaction sites within RNA polymerase I and the Rvb1/2 complex. Xlink Analyzer is implemented as a plugin to UCSF Chimera, a standard structural biology software tool, and thus enables seamless integration of XL-MS data with, e.g. fitting of X-ray structures to EM maps. Xlink Analyzer is available for download at http://www.beck.embl.de/XlinkAnalyzer.html.
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Affiliation(s)
- Jan Kosinski
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Alexander von Appen
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Alessandro Ori
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Kai Karius
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Christoph W Müller
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Martin Beck
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany.
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16
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Liu M, Zhang Z, Cheetham J, Ren D, Zhou ZS. Discovery and characterization of a photo-oxidative histidine-histidine cross-link in IgG1 antibody utilizing ¹⁸O-labeling and mass spectrometry. Anal Chem 2014; 86:4940-8. [PMID: 24738698 PMCID: PMC4030806 DOI: 10.1021/ac500334k] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A novel photo-oxidative cross-linking
between two histidines (His-His)
has been discovered and characterized in an IgG1 antibody via the
workflow of XChem-Finder, 18O labeling and mass spectrometry
(2013, 85, 5900−590823634697). Its structure was elucidated by peptide
mapping with multiple proteases with various specificities (e.g.,
trypsin, Asp-N, and GluC combined with trypsin or Asp-N) and mass
spectrometry with complementary fragmentation modes (e.g., collision-induced
dissociation (CID) and electron-transfer dissociation (ETD)). Our
data indicated that cross-linking occurred across two identical conserved
histidine residues on two separate heavy chains in the hinge region,
which is highly flexible and solvent accessible. On the basis of model
studies with short peptides, it has been proposed that singlet oxygen
reacts with the histidyl imidazole ring to form an endoperoxide and
then converted to the 2-oxo-histidine (2-oxo-His) and His+32 intermediates, the latter is
subject to a
nucleophilic attack by the unmodified histidine; and finally, elimination
of a water molecule leads to the final adduct with a net mass increase
of 14 Da. Our findings are consistent with this mechanism. Successful
discovery of cross-linked His-His again demonstrates the broad applicability
and utility of our XChem-Finder approach in the discovery and elucidation
of protein cross-linking, particularly without a priori knowledge of the chemical nature and site of cross-linking.
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Affiliation(s)
- Min Liu
- Analytical Research and Development, Amgen , One Amgen Center Drive, Thousand Oaks, California 91320, United States
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17
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Tinnefeld V, Sickmann A, Ahrends R. Catch me if you can: challenges and applications of cross-linking approaches. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2014; 20:99-116. [PMID: 24881459 DOI: 10.1255/ejms.1259] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Biomolecular complexes are the groundwork of life and the basis for cell signaling, energy transfer, motion, stability and cellular metabolism. Understanding the underlying complex interactions on the molecular level is an essential step to obtain a comprehensive insight into cellular and systems biology. For the investigation of molecular interactions, various methods, including Förster resonance energy transfer, nuclear magnetic resonance spectroscopy, X-ray crystallography and yeast two-hybrid screening, can be utilized. Nevertheless, the most reliable approach for structural proteomics and the identification of novel protein-binding partners is chemical cross-linking. The rationale is that upon forming a covalent bond between a protein and its interaction partner (protein, lipid, RNA/DNA, carbohydrate) the native complex state is "frozen" and accessible for detailed mass spectrometric analysis. In this review we provide a synopsis on crosslinker design, chemistry, pitfalls, limitations and novel applications in the field, and feature an overview of current software applications.
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18
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Holding AN, Lamers MH, Stephens E, Skehel JM. Hekate: software suite for the mass spectrometric analysis and three-dimensional visualization of cross-linked protein samples. J Proteome Res 2013; 12:5923-33. [PMID: 24010795 PMCID: PMC3859183 DOI: 10.1021/pr4003867] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
Chemical cross-linking
of proteins combined with mass spectrometry
provides an attractive and novel method for the analysis of native
protein structures and protein complexes. Analysis of the data however
is complex. Only a small number of cross-linked peptides are produced
during sample preparation and must be identified against a background
of more abundant native peptides. To facilitate the search and identification
of cross-linked peptides, we have developed a novel software suite,
named Hekate. Hekate is a suite of tools that address the challenges
involved in analyzing protein cross-linking experiments when combined
with mass spectrometry. The software is an integrated pipeline for
the automation of the data analysis workflow and provides a novel
scoring system based on principles of linear peptide analysis. In
addition, it provides a tool for the visualization of identified cross-links
using three-dimensional models, which is particularly useful when
combining chemical cross-linking with other structural techniques.
Hekate was validated by the comparative analysis of cytochrome c (bovine heart) against previously reported data.1 Further validation was carried out on known structural
elements of DNA polymerase III, the catalytic α-subunit of the Escherichia coli DNA replisome along with new insight
into the previously uncharacterized C-terminal domain of the protein.
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Affiliation(s)
- Andrew N Holding
- MRC Laboratory of Molecular Biology , Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
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19
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Goyder MS, Rebeaud F, Pfeifer ME, Kálmán F. Strategies in mass spectrometry for the assignment of Cys-Cys disulfide connectivities in proteins. Expert Rev Proteomics 2013; 10:489-501. [PMID: 24087910 DOI: 10.1586/14789450.2013.837663] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Elucidating disulfide linkage patterns is a crucial part of protein characterization, for which mass spectrometry (MS) is now an indispensable analytical tool. In many cases, MS-based disulfide connectivity assignment is straightforwardly achieved using one-step protein fragmentation in the unreduced form followed by mass measurement of bridged fragments. By contrast, venom proteins, which are receiving increasing interest as potential therapeutics, are a challenge for MS-based disulfide assignment due to their numerous closely spaced cysteines and knotted disulfide structure, requiring creative strategies to determine their connectivity. Today, these include the use of an array of reagents for enzymatic and/or chemical cleavage, partial reduction, differential cysteine labeling and tandem MS. This review aims to describe the toolkit of techniques available to MS users approaching both straightforward and complex disulfide bridge assignments, with a particular focus on strategies utilizing standard instrumentation found in a well-equipped analytical or proteomics laboratory.
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Affiliation(s)
- Miriam S Goyder
- Institute of Life Technologies, University of Applied Sciences Western Switzerland (HES-SO Valais/Wallis), 1950 Sion, Switzerland
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20
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Liu M, Zhang Z, Zang T, Spahr C, Cheetham J, Ren D, Sunny Zhou Z. Discovery of undefined protein cross-linking chemistry: a comprehensive methodology utilizing 18O-labeling and mass spectrometry. Anal Chem 2013; 85:5900-8. [PMID: 23634697 PMCID: PMC3691076 DOI: 10.1021/ac400666p] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Characterization of protein cross-linking, particularly without prior knowledge of the chemical nature and site of cross-linking, poses a significant challenge, because of their intrinsic structural complexity and the lack of a comprehensive analytical approach. Toward this end, we have developed a generally applicable workflow-XChem-Finder-that involves four stages: (1) detection of cross-linked peptides via (18)O-labeling at C-termini; (2) determination of the putative partial sequences of each cross-linked peptide pair using a fragment ion mass database search against known protein sequences coupled with a de novo sequence tag search; (3) extension to full sequences based on protease specificity, the unique combination of mass, and other constraints; and (4) deduction of cross-linking chemistry and site. The mass difference between the sum of two putative full-length peptides and the cross-linked peptide provides the formulas (elemental composition analysis) for the functional groups involved in each cross-linking. Combined with sequence restraint from MS/MS data, plausible cross-linking chemistry and site were inferred, and ultimately confirmed, by matching with all data. Applying our approach to a stressed IgG2 antibody, 10 cross-linked peptides were discovered and found to be connected via thioethers originating from disulfides at locations that had not been previously recognized. Furthermore, once the cross-link chemistry was revealed, a targeted cross-link search yielded 4 additional cross-linked peptides that all contain the C-terminus of the light chain.
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Affiliation(s)
- Min Liu
- Analytical Research and Development, Amgen, One Amgen Center Drive, Thousand Oaks, CA 91320, USA
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA
| | - Zhongqi Zhang
- Process and Product Development, Amgen, One Amgen Center Drive, Thousand Oaks, CA 91320, USA
| | - Tianzhu Zang
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA
| | - Chris Spahr
- Biologic Optimization, Amgen, One Amgen Center Drive, Thousand Oaks, CA 91320, USA
| | - Janet Cheetham
- Analytical Research and Development, Amgen, One Amgen Center Drive, Thousand Oaks, CA 91320, USA
| | - Da Ren
- Process and Product Development, Amgen, One Amgen Center Drive, Thousand Oaks, CA 91320, USA
| | - Zhaohui Sunny Zhou
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA
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21
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Zybailov BL, Glazko GV, Jaiswal M, Raney KD. Large Scale Chemical Cross-linking Mass Spectrometry Perspectives. ACTA ACUST UNITED AC 2013; 6:001. [PMID: 25045217 PMCID: PMC4101816 DOI: 10.4172/jpb.s2-001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The spectacular heterogeneity of a complex protein mixture from biological samples becomes even more difficult to tackle when one’s attention is shifted towards different protein complex topologies, transient interactions, or localization of PPIs. Meticulous protein-by-protein affinity pull-downs and yeast-two-hybrid screens are the two approaches currently used to decipher proteome-wide interaction networks. Another method is to employ chemical cross-linking, which gives not only identities of interactors, but could also provide information on the sites of interactions and interaction interfaces. Despite significant advances in mass spectrometry instrumentation over the last decade, mapping Protein-Protein Interactions (PPIs) using chemical cross-linking remains time consuming and requires substantial expertise, even in the simplest of systems. While robust methodologies and software exist for the analysis of binary PPIs and also for the single protein structure refinement using cross-linking-derived constraints, undertaking a proteome-wide cross-linking study is highly complex. Difficulties include i) identifying cross-linkers of the right length and selectivity that could capture interactions of interest; ii) enrichment of the cross-linked species; iii) identification and validation of the cross-linked peptides and cross-linked sites. In this review we examine existing literature aimed at the large-scale protein cross-linking and discuss possible paths for improvement. We also discuss short-length cross-linkers of broad specificity such as formaldehyde and diazirine-based photo-cross-linkers. These cross-linkers could potentially capture many types of interactions, without strict requirement for a particular amino-acid to be present at a given protein-protein interface. How these shortlength, broad specificity cross-linkers be applied to proteome-wide studies? We will suggest specific advances in methodology, instrumentation and software that are needed to make such a leap.
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Affiliation(s)
- Boris L Zybailov
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Galina V Glazko
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Mihir Jaiswal
- UALR/UAMS Joint Bioinformatics Program, University of Arkansas Little Rock, Little Rock, AR, USA
| | - Kevin D Raney
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
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22
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Abstract
Proteins are a remarkable class of molecules that exhibit wide diversity of shapes or topological features that underpin protein interactions and give rise to biological function. In addition to quantitation of abundance levels of proteins in biological systems under a variety of conditions, the field of proteome research has as a primary mission the assignment of function for proteins and if possible, illumination of factors that enable function. For many years, chemical cross-linking methods have been used to provide structural data on single purified proteins and purified protein complexes. However, these methods also offer the alluring possibility to extend capabilities to complex biological samples such as cell lysates or intact living cells where proteins may exhibit native topological features that do not exist in purified form. Recent efforts are beginning to provide glimpses of protein complexes and topologies in cells that suggest continued development will yield novel capabilities to view functional topological features of many proteins and complexes as they exist in cells, tissues, or other complex samples. This review will describe rationale, challenges, and a few success stories along the path of development of cross-linking technologies for measurement of in vivo protein interaction topologies.
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Affiliation(s)
- James E Bruce
- Department of Genome Sciences, University of Washington, Seattle, WA 98109, USA.
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23
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Hyung SJ, Ruotolo BT. Integrating mass spectrometry of intact protein complexes into structural proteomics. Proteomics 2012; 12:1547-64. [PMID: 22611037 DOI: 10.1002/pmic.201100520] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
MS analysis of intact protein complexes has emerged as an established technology for assessing the composition and connectivity within dynamic, heterogeneous multiprotein complexes at low concentrations and in the context of mixtures. As this technology continues to move forward, one of the main challenges is to integrate the information content of such intact protein complex measurements with other MS approaches in structural biology. Methods such as H/D exchange, oxidative foot-printing, chemical cross-linking, affinity purification, and ion mobility separation add complementary information that allows access to every level of protein structure and organization. Here, we survey the structural information that can be retrieved by such experiments, demonstrate the applicability of integrative MS approaches in structural proteomics, and look to the future to explore upcoming innovations in this rapidly advancing area.
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Affiliation(s)
- Suk-Joon Hyung
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
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24
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Luo J, Fishburn J, Hahn S, Ranish J. An integrated chemical cross-linking and mass spectrometry approach to study protein complex architecture and function. Mol Cell Proteomics 2011; 11:M111.008318. [PMID: 22067100 DOI: 10.1074/mcp.m111.008318] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Knowledge of protein structures and protein-protein interactions is essential for understanding biological processes. Chemical cross-linking combined with mass spectrometry is an attractive approach for studying protein-protein interactions and protein structure, but to date its use has been limited largely by low yields of informative cross-links (because of inefficient cross-linking reactions) and by the difficulty of confidently identifying the sequences of cross-linked peptide pairs from their fragmentation spectra. Here we present an approach based on a new MS labile cross-linking reagent, BDRG (biotin-aspartate-Rink-glycine), which addresses these issues. BDRG incorporates a biotin handle (for enrichment of cross-linked peptides prior to MS analysis), two pentafluorophenyl ester groups that react with peptide amines, and a labile Rink-based bond between the pentafluorophenyl groups that allows cross-linked peptides to be separated during MS and confidently identified by database searching of their fragmentation spectra. We developed a protocol for the identification of BDRG cross-linked peptides derived from purified or partially purified protein complexes, including software to aid in the identification of different classes of cross-linker-modified peptides. Importantly, our approach permits the use of high accuracy precursor mass measurements to verify the database search results. We demonstrate the utility of the approach by applying it to purified yeast TFIIE, a heterodimeric transcription factor complex, and to a single-step affinity-purified preparation of the 12-subunit RNA polymerase II complex. The results show that the method is effective at identifying cross-linked peptides derived from purified and partially purified protein complexes and provides complementary information to that from other structural approaches. As such, it is an attractive approach to study the topology of protein complexes.
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Affiliation(s)
- Jie Luo
- Institute for Systems Biology, Seattle, Washington 98109, USA
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25
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Clark DF, Go EP, Toumi ML, Desaire H. Collision induced dissociation products of disulfide-bonded peptides: ions result from the cleavage of more than one bond. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:492-8. [PMID: 21472567 PMCID: PMC3543116 DOI: 10.1007/s13361-010-0064-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2010] [Revised: 11/19/2010] [Accepted: 12/16/2010] [Indexed: 05/04/2023]
Abstract
Disulfide bonds are a post-translational modification (PTM) that can be scrambled or shuffled to non-native bonds during recombinant expression, sample handling, or sample purification. Currently, mapping of disulfide bonds is not easy because of various sample requirements and data analysis difficulties. One step towards facilitating this difficult work is developing a better understanding of how disulfide-bonded peptides fragment during collision induced dissociation (CID). Most automated analysis algorithms function based on the assumption that the preponderance of product ions observed during the dissociation of disulfide-bonded peptides result from the cleavage of just one peptide bond, and in this report we tested that assumption by extensively analyzing the product ions generated when several disulfide-bonded peptides are subjected to CID on a quadrupole time of flight (QTOF) instrument. We found that one of the most common types of product ions generated resulted from two peptide bond cleavages, or a double cleavage. We found that for several of the disulfide-bonded peptides analyzed, the number of double cleavage product ions outnumbered those of single cleavages. The influence of charge state and precursor ion size was investigated, to determine if those parameters dictated the amount of double cleavage product ions formed. It was found in this sample set that no strong correlation existed between the charge state or peptide size and the portion of product ions assigned as double cleavages. These data show that these ions could account for many of the product ions detected in CID data of disulfide bonded peptides. We also showed the utility of double cleavage product ions on a peptide with multiple cysteines present. Double cleavage products were able to fully characterize the bonding pattern of each cysteine where typical single b/y cleavage products could not.
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Affiliation(s)
| | | | | | - Heather Desaire
- To whom correspondence should be addressed. Phone: (785) 864-3015, Fax: 785-864-5396,
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26
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Du X, Chowdhury SM, Manes NP, Wu S, Mayer MU, Adkins JN, Anderson GA, Smith RD. Xlink-identifier: an automated data analysis platform for confident identifications of chemically cross-linked peptides using tandem mass spectrometry. J Proteome Res 2011; 10:923-31. [PMID: 21175198 DOI: 10.1021/pr100848a] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Chemical cross-linking combined with mass spectrometry provides a powerful method for identifying protein-protein interactions and probing the structure of protein complexes. A number of strategies have been reported that take advantage of the high sensitivity and high resolution of modern mass spectrometers. Approaches typically include synthesis of novel cross-linking compounds, and/or isotopic labeling of the cross-linking reagent and/or protein, and label-free methods. We report Xlink-Identifier, a comprehensive data analysis platform that has been developed to support label-free analyses. It can identify interpeptide, intrapeptide, and deadend cross-links as well as underivatized peptides. The software streamlines data preprocessing, peptide scoring, and visualization and provides an overall data analysis strategy for studying protein-protein interactions and protein structure using mass spectrometry. The software has been evaluated using a custom synthesized cross-linking reagent that features an enrichment tag. Xlink-Identifier offers the potential to perform large-scale identifications of protein-protein interactions using tandem mass spectrometry.
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Affiliation(s)
- Xiuxia Du
- Department of Bioinformatics & Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina 28023, USA.
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27
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Mayne SLN, Patterton HG. Bioinformatics tools for the structural elucidation of multi-subunit protein complexes by mass spectrometric analysis of protein-protein cross-links. Brief Bioinform 2011; 12:660-71. [PMID: 22101029 DOI: 10.1093/bib/bbq087] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Multi-subunit protein complexes are involved in many essential biochemical processes including signal transduction, protein synthesis, RNA synthesis, DNA replication and protein degradation. An accurate description of the relative structural arrangement of the constituent subunits in such complexes is crucial for an understanding of the molecular mechanism of the complex as a whole. Many complexes, however, lie in the mega-Dalton range, and are not amenable to X-ray crystallographic or nuclear magnetic resonance analysis. Techniques that are suited to structural studies of such large complexes, such as cryo-electron microscopy, do not provide the resolution required for a mechanistic insight. Mass spectrometry (MS) has increasingly been applied to identify the residues that are involved in chemical cross-links in compound protein assemblies, and have provided valuable insight into the molecular arrangement, orientation and contact surfaces of subunits within such large complexes. This approach is known as MS3D, and involves the MS analysis of cross-linked di-peptides following the enzymatic cleavage of a chemically cross-linked complex. A major challenge of this approach is the identification of the cross-linked di-peptides in a composite mixture of peptides, as well as the identification of the residues involved in the cross-link. These analyses require bioinformatics tools with capabilities beyond that of general, MS-based proteomic analysis software. Many MS3D software tools have appeared, often designed for very specific experimental methods. Here, we provide a review of all major MS3D bioinformatics programmes, reviewing their applicability to different workflows, specific experimental requirements and the computational approach taken by each.
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Affiliation(s)
- Shannon L N Mayne
- Department of Biotechnology, University of the Free State, Bloemfontein 9300, South Africa
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28
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Rappsilber J. The beginning of a beautiful friendship: cross-linking/mass spectrometry and modelling of proteins and multi-protein complexes. J Struct Biol 2010; 173:530-40. [PMID: 21029779 PMCID: PMC3043253 DOI: 10.1016/j.jsb.2010.10.014] [Citation(s) in RCA: 319] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Revised: 10/21/2010] [Accepted: 10/21/2010] [Indexed: 11/17/2022]
Abstract
After more than a decade of method development, cross-linking in combination with mass spectrometry and bioinformatics is finally coming of age. This technology now provides improved opportunities for modelling by mapping structural details of functional complexes in solution. The structure of proteins or protein complexes is ascertained by identifying amino acid pairs that are positioned in close proximity to each other. The validity of this technique has recently been benchmarked for large multi-protein complexes, by comparing cross-link data with that from a crystal structure of RNA polymerase II. Here, the specific nature of this cross-linking data will be discussed to assess the technical challenges and opportunities for model building. We believe that once remaining technological challenges of cross-linking/mass spectrometry have been addressed and cross-linking/mass spectrometry data has been incorporated into modelling algorithms it will quickly become an indispensable companion of protein and protein complex modelling and a corner-stone of integrated structural biology.
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Affiliation(s)
- Juri Rappsilber
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Michael Swann Building, King's Buildings, Mayfield Road, Edinburgh, EH9 3JR Scotland, UK.
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29
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McIlwain S, Draghicescu P, Singh P, Goodlett DR, Noble WS. Detecting cross-linked peptides by searching against a database of cross-linked peptide pairs. J Proteome Res 2010; 9:2488-95. [PMID: 20349954 DOI: 10.1021/pr901163d] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Mass spectrometric identification of cross-linked peptides can provide valuable information about the structure of protein complexes. We describe a straightforward database search scheme that identifies and assigns statistical confidence estimates to spectra from cross-linked peptides. The method is well suited to targeted analysis of a single protein complex, without requiring an isotope labeling strategy. Our approach uses a SEQUEST-style search procedure in which the database is comprised of a mixture of single peptides with and without linkers attached and cross-linked products. In contrast to several previous approaches, we generate theoretical spectra that account for all of the expected peaks from a cross-linked product, and we employ an empirical curve-fitting procedure to estimate statistical confidence measures. We show that our fully automated procedure successfully reidentifies spectra from a previous study, and we provide evidence that our statistical confidence estimates are accurate.
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Affiliation(s)
- Sean McIlwain
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
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30
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Leitner A, Walzthoeni T, Kahraman A, Herzog F, Rinner O, Beck M, Aebersold R. Probing native protein structures by chemical cross-linking, mass spectrometry, and bioinformatics. Mol Cell Proteomics 2010; 9:1634-49. [PMID: 20360032 PMCID: PMC2938055 DOI: 10.1074/mcp.r000001-mcp201] [Citation(s) in RCA: 368] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2010] [Revised: 03/30/2010] [Indexed: 12/16/2022] Open
Abstract
Chemical cross-linking of reactive groups in native proteins and protein complexes in combination with the identification of cross-linked sites by mass spectrometry has been in use for more than a decade. Recent advances in instrumentation, cross-linking protocols, and analysis software have led to a renewed interest in this technique, which promises to provide important information about native protein structure and the topology of protein complexes. In this article, we discuss the critical steps of chemical cross-linking and its implications for (structural) biology: reagent design and cross-linking protocols, separation and mass spectrometric analysis of cross-linked samples, dedicated software for data analysis, and the use of cross-linking data for computational modeling. Finally, the impact of protein cross-linking on various biological disciplines is highlighted.
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Affiliation(s)
- Alexander Leitner
- From the Institute of Molecular Systems Biology, Eidgenössiche Technische Hochschule (ETH) Zurich, Wolfgang-Pauli-Strasse 16, 8093 Zurich, Switzerland
- Department of Analytical Chemistry and Food Chemistry, University of Vienna, Waehringer Strasse 38, 1090 Vienna, Austria
| | - Thomas Walzthoeni
- From the Institute of Molecular Systems Biology, Eidgenössiche Technische Hochschule (ETH) Zurich, Wolfgang-Pauli-Strasse 16, 8093 Zurich, Switzerland
- Ph.D. Program in Molecular Life Sciences, University of Zurich/ETH Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Abdullah Kahraman
- From the Institute of Molecular Systems Biology, Eidgenössiche Technische Hochschule (ETH) Zurich, Wolfgang-Pauli-Strasse 16, 8093 Zurich, Switzerland
| | - Franz Herzog
- From the Institute of Molecular Systems Biology, Eidgenössiche Technische Hochschule (ETH) Zurich, Wolfgang-Pauli-Strasse 16, 8093 Zurich, Switzerland
| | - Oliver Rinner
- From the Institute of Molecular Systems Biology, Eidgenössiche Technische Hochschule (ETH) Zurich, Wolfgang-Pauli-Strasse 16, 8093 Zurich, Switzerland
- Biognosys AG, Wolfgang-Pauli-Strasse 16, 8093 Zurich, Switzerland
| | - Martin Beck
- From the Institute of Molecular Systems Biology, Eidgenössiche Technische Hochschule (ETH) Zurich, Wolfgang-Pauli-Strasse 16, 8093 Zurich, Switzerland
| | - Ruedi Aebersold
- From the Institute of Molecular Systems Biology, Eidgenössiche Technische Hochschule (ETH) Zurich, Wolfgang-Pauli-Strasse 16, 8093 Zurich, Switzerland
- Faculty of Science, University of Zurich, Zurich, Switzerland, and
- Competence Center for Systems Physiology and Metabolic Diseases, Zurich, Switzerland
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31
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Fabris D, Yu ET. Elucidating the higher-order structure of biopolymers by structural probing and mass spectrometry: MS3D. JOURNAL OF MASS SPECTROMETRY : JMS 2010; 45:841-60. [PMID: 20648672 PMCID: PMC3432860 DOI: 10.1002/jms.1762] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Chemical probing represents a very versatile alternative for studying the structure and dynamics of substrates that are intractable by established high-resolution techniques. The implementation of MS-based strategies for the characterization of probing products has not only extended the range of applicability to virtually all types of biopolymers but has also paved the way for the introduction of new reagents that would not have been viable with traditional analytical platforms. As the availability of probing data is steadily increasing on the wings of the development of dedicated interpretation aids, powerful computational approaches have been explored to enable the effective utilization of such information to generate valid molecular models. This combination of factors has contributed to making the possibility of obtaining actual 3D structures by MS-based technologies (MS3D) a reality. Although approaches for achieving structure determination of unknown targets or assessing the dynamics of known structures may share similar reagents and development trajectories, they clearly involve distinctive experimental strategies, analytical concerns and interpretation paradigms. This Perspective offers a commentary on methods aimed at obtaining distance constraints for the modeling of full-fledged structures while highlighting common elements, salient distinctions and complementary capabilities exhibited by methods used in dynamics studies. We discuss critical factors to be addressed for completing effective structural determinations and expose possible pitfalls of chemical methods. We survey programs developed for facilitating the interpretation of experimental data and discuss possible computational strategies for translating sparse spatial constraints into all-atom models. Examples are provided to illustrate how the concerted application of very diverse probing techniques can lead to the solution of actual biological systems.
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Affiliation(s)
- Daniele Fabris
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD, USA.
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32
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Singh P, Panchaud A, Goodlett DR. Chemical Cross-Linking and Mass Spectrometry As a Low-Resolution Protein Structure Determination Technique. Anal Chem 2010; 82:2636-42. [DOI: 10.1021/ac1000724] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Pragya Singh
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195-7610
| | - Alexandre Panchaud
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195-7610
| | - David R. Goodlett
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195-7610
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Petrotchenko EV, Borchers CH. ICC-CLASS: isotopically-coded cleavable crosslinking analysis software suite. BMC Bioinformatics 2010; 11:64. [PMID: 20109223 PMCID: PMC2827373 DOI: 10.1186/1471-2105-11-64] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2009] [Accepted: 01/28/2010] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Successful application of crosslinking combined with mass spectrometry for studying proteins and protein complexes requires specifically-designed crosslinking reagents, experimental techniques, and data analysis software. Using isotopically-coded ("heavy and light") versions of the crosslinker and cleavable crosslinking reagents is analytically advantageous for mass spectrometric applications and provides a "handle" that can be used to distinguish crosslinked peptides of different types, and to increase the confidence of the identification of the crosslinks. RESULTS Here, we describe a program suite designed for the analysis of mass spectrometric data obtained with isotopically-coded cleavable crosslinkers. The suite contains three programs called: DX, DXDX, and DXMSMS. DX searches the mass spectra for the presence of ion signal doublets resulting from the light and heavy isotopic forms of the isotopically-coded crosslinking reagent used. DXDX searches for possible mass matches between cleaved and uncleaved isotopically-coded crosslinks based on the established chemistry of the cleavage reaction for a given crosslinking reagent. DXMSMS assigns the crosslinks to the known protein sequences, based on the isotopically-coded and un-coded MS/MS fragmentation data of uncleaved and cleaved peptide crosslinks. CONCLUSION The combination of these three programs, which are tailored to the analytical features of the specific isotopically-coded cleavable crosslinking reagents used, represents a powerful software tool for automated high-accuracy peptide crosslink identification. See: http://www.creativemolecules.com/CM_Software.htm.
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Affiliation(s)
- Evgeniy V Petrotchenko
- University of Victoria Genome British Columbia Protein Centre, Department of Biochemistry & Microbiology, University of Victoria, #3101-4464 Markham Street, Vancouver Island Technology Park, Victoria, BC, Canada
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Chu F, Baker PR, Burlingame AL, Chalkley RJ. Finding chimeras: a bioinformatics strategy for identification of cross-linked peptides. Mol Cell Proteomics 2009; 9:25-31. [PMID: 19809093 DOI: 10.1074/mcp.m800555-mcp200] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Chemical cross-linking, followed by identification of the cross-linked residues, is a powerful approach to probe the topologies and interacting surfaces of protein assemblies. In this work, we demonstrate a new bioinformatics approach using multiple program modules within the software package "Protein Prospector" that greatly facilitates the discovery of cross-linked peptides in chemical cross-linking studies. Examples are given for how this approach has been used for defining interfaces in heterodimeric and homodimeric protein complexes, both of which provide results in close agreement with crystal structures, verifying the reliability of the approach.
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Affiliation(s)
- Feixia Chu
- Mass Spectrometry Facility, Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA
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35
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Sprung RW, Brock JWC, Tanksley JP, Li M, Washington MK, Slebos RJC, Liebler DC. Equivalence of protein inventories obtained from formalin-fixed paraffin-embedded and frozen tissue in multidimensional liquid chromatography-tandem mass spectrometry shotgun proteomic analysis. Mol Cell Proteomics 2009; 8:1988-98. [PMID: 19467989 PMCID: PMC2722776 DOI: 10.1074/mcp.m800518-mcp200] [Citation(s) in RCA: 153] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissue specimens comprise a potentially valuable resource for retrospective biomarker discovery studies, and recent work indicates the feasibility of using shotgun proteomics to characterize FFPE tissue proteins. A critical question in the field is whether proteomes characterized in FFPE specimens are equivalent to proteomes in corresponding fresh or frozen tissue specimens. Here we compared shotgun proteomic analyses of frozen and FFPE specimens prepared from the same colon adenoma tissues. Following deparaffinization, rehydration, and tryptic digestion under mild conditions, FFPE specimens corresponding to 200 microg of protein yielded approximately 400 confident protein identifications in a one-dimensional reverse phase liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. The major difference between frozen and FFPE proteomes was a decrease in the proportions of lysine C-terminal to arginine C-terminal peptides observed, but these differences had little effect on the proteins identified. No covalent peptide modifications attributable to formaldehyde chemistry were detected by analyses of the MS/MS datasets, which suggests that undetected, cross-linked peptides comprise the major class of modifications in FFPE tissues. Fixation of tissue for up to 2 days in neutral buffered formalin did not adversely impact protein identifications. Analysis of archival colon adenoma FFPE specimens indicated equivalent numbers of MS/MS spectral counts and protein group identifications from specimens stored for 1, 3, 5, and 10 years. Combination of peptide isoelectric focusing-based separation with reverse phase LC-MS/MS identified 2554 protein groups in 600 ng of protein from frozen tissue and 2302 protein groups from FFPE tissue with at least two distinct peptide identifications per protein. Analysis of the combined frozen and FFPE data showed a 92% overlap in the protein groups identified. Comparison of gene ontology categories of identified proteins revealed no bias in protein identification based on subcellular localization. Although the status of posttranslational modifications was not examined in this study, archival samples displayed a modest increase in methionine oxidation, from approximately 17% after one year of storage to approximately 25% after 10 years. These data demonstrate the equivalence of proteome inventories obtained from FFPE and frozen tissue specimens and provide support for retrospective proteomic analysis of FFPE tissues for biomarker discovery.
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Affiliation(s)
- Robert W Sprung
- Jim Ayers Institute for Precancer Detection and Diagnosis, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-8575, USA
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36
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Fenselau C, Yao X. 18O2-Labeling in Quantitative Proteomic Strategies: A Status Report. J Proteome Res 2009; 8:2140-3. [DOI: 10.1021/pr8009879] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Catherine Fenselau
- Department of Chemistry & Biochemistry, University of Maryland, College Park, Maryland 20742, and Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269
| | - Xudong Yao
- Department of Chemistry & Biochemistry, University of Maryland, College Park, Maryland 20742, and Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269
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37
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Singh P, Shaffer SA, Scherl A, Holman C, Pfuetzner RA, Larson Freeman TJ, Miller SI, Hernandez P, Appel RD, Goodlett DR. Characterization of protein cross-links via mass spectrometry and an open-modification search strategy. Anal Chem 2008; 80:8799-806. [PMID: 18947195 DOI: 10.1021/ac801646f] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Protein-protein interactions are key to function and regulation of many biological pathways. To facilitate characterization of protein-protein interactions using mass spectrometry, a new data acquisition/analysis pipeline was designed. The goal for this pipeline was to provide a generic strategy for identifying cross-linked peptides from single LC/MS/MS data sets, without using specialized cross-linkers or custom-written software. To achieve this, each peptide in the pair of cross-linked peptides was considered to be "post-translationally" modified with an unknown mass at an unknown amino acid. This allowed use of an open-modification search engine, Popitam, to interpret the tandem mass spectra of cross-linked peptides. False positives were reduced and database selectivity increased by acquiring precursors and fragments at high mass accuracy. Additionally, a high-charge-state-driven data acquisition scheme was utilized to enrich data sets for cross-linked peptides. This open-modification search based pipeline was shown to be useful for characterizing both chemical as well as native cross-links in proteins. The pipeline was validated by characterizing the known interactions in the chemically cross-linked CYP2E1-b5 complex. Utility of this method in identifying native cross-links was demonstrated by mapping disulfide bridges in RcsF, an outer membrane lipoprotein involved in Rcs phosphorelay.
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Affiliation(s)
- Pragya Singh
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, USA
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38
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Heymann M, Paramelle D, Subra G, Forest E, Martinez J, Geourjon C, Deléage G. MSX-3D: a tool to validate 3D protein models using mass spectrometry. Bioinformatics 2008; 24:2782-3. [PMID: 18826958 DOI: 10.1093/bioinformatics/btn510] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
MOTIVATION The technique of chemical cross-linking followed by mass spectrometry has proven to bring valuable information about the protein structure and interactions between proteic subunits. It is an effective and efficient way to experimentally investigate some aspects of a protein structure when NMR and X-ray crystallography data are lacking. RESULTS We introduce MSX-3D, a tool specifically geared to validate protein models using mass spectrometry. In addition to classical peptides identifications, it allows an interactive 3D visualization of the distance constraints derived from a cross-linking experiment. AVAILABILITY Freely available at http://proteomics-pbil.ibcp.fr
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Affiliation(s)
- Michaël Heymann
- Institut de Biologie et Chimie des Protéines (IBCP) UMR5086 CNRS, Université Lyon 1, France
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39
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Gardner MW, Vasicek LA, Shabbir S, Anslyn EV, Brodbelt JS. Chromogenic cross-linker for the characterization of protein structure by infrared multiphoton dissociation mass spectrometry. Anal Chem 2008; 80:4807-19. [PMID: 18517224 DOI: 10.1021/ac800625x] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We have developed a new IR chromogenic cross-linker (IRCX) to aid in rapidly distinguishing cross-linked peptides from unmodified species in complex mixtures. By incorporating a phosphate functional group into the cross-linker, one can take advantage of its unique IR absorption properties, affording selective infrared multiphoton dissociation (IRMPD) of the cross-linked peptides. In a mock mixture of unmodified peptides and IRCX-cross-linked peptides (intramolecularly and intermolecularly cross-linked), only the peptides containing the IRCX modification were shown to dissociate upon exposure to 50 ms of 10.6-microm radiation. LC-IRMPD-MS proved to be an effective method to distinguish the cross-linked peptides in a tryptic digest of IRCX-cross-linked ubiquitin. A total of four intermolecular cross-links and two dead-end modifications were identified using IRCX and LC-IRMPD-MS. IRMPD of these cross-linked peptides resulted in secondary dissociation of all primary fragment ions containing the chromophore, producing a series of unmodified b- or y-type ions that allowed the cross-linked peptides to be sequenced without the need for collision-induced dissociation.
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Affiliation(s)
- Myles W Gardner
- Department of Chemistry and Biochemistry, The University of Texas at Austin, 1 University Station A5300, Austin, Texas, USA 78712, USA
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40
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Yang W, Steen H, Freeman MR. Proteomic approaches to the analysis of multiprotein signaling complexes. Proteomics 2008; 8:832-51. [PMID: 18297654 DOI: 10.1002/pmic.200700650] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Signal transduction is one of the most active fields in modern biomedical research. Increasing evidence has shown that signaling proteins associate with each other in characteristic ways to form large signaling complexes. These diverse structures operate to boost signaling efficiency, ensure specificity and increase sensitivity of the biochemical circuitry. Traditional methods of protein analysis are inadequate to fully characterize and understand these structures, which are intricate, contain many components and are highly dynamic. Instead, proteomics technologies are currently being applied to investigate the nature and composition of multimeric signaling complexes. This review presents commonly used and potential proteomic methods of analyzing diverse protein complexes along with a discussion and a brief evaluation of alternative approaches. Challenges associated with proteomic analysis of signaling complexes are also discussed.
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Affiliation(s)
- Wei Yang
- The Urological Diseases Research Center, Department of Urology, Children's Hospital Boston, Boston, MA 02115, USA
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41
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Identification of cross-linked peptides from large sequence databases. Nat Methods 2008; 5:315-8. [PMID: 18327264 DOI: 10.1038/nmeth.1192] [Citation(s) in RCA: 303] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2007] [Accepted: 01/30/2008] [Indexed: 12/22/2022]
Abstract
We describe a method to identify cross-linked peptides from complex samples and large protein sequence databases by combining isotopically tagged cross-linkers, chromatographic enrichment, targeted proteomics and a new search engine called xQuest. This software reduces the search space by an upstream candidate-peptide search before the recombination step. We showed that xQuest can identify cross-linked peptides from a total Escherichia coli lysate with an unrestricted database search.
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42
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Gardner MW, Brodbelt JS. Impact of proline and aspartic acid residues on the dissociation of intermolecularly crosslinked peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2008; 19:344-357. [PMID: 18083526 DOI: 10.1016/j.jasms.2007.11.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2007] [Revised: 11/02/2007] [Accepted: 11/06/2007] [Indexed: 05/25/2023]
Abstract
The dissociation of intermolecularly crosslinked peptides was evaluated for a series of peptides with proline or aspartic acid residues positioned adjacent to the crosslinking sites (lysine residues). The peptides were crosslinked with either disuccinimidyl suberate (DSS) or disuccinimidyl L-tartrate (DST), and the influence of proline and aspartic acid residues on the fragmentation patterns were investigated for precursor ions with and without a mobile proton. Collisionally activated dissociation (CAD) spectra of aspartic acid-containing crosslinked peptide ions, doubly-charged with both protons sequestered, were dominated by cleavage C-terminal to the Asp residue, similar to that of unmodified peptides. The proline-containing crosslinked peptides exhibited a high degree of internal ion formation, with the resulting product ions having an N-terminal proline residue. Upon dissociation of the doubly-charged crosslinked peptides, twenty to fifty percent of the fragment ion abundance was accounted for by multiple cleavage products. Crosslinked peptides possessing a mobile proton yielded almost a full series of b- and y-type fragment ions, with only proline-directed fragments still observed at high abundances. Interestingly, the crosslinked peptides exhibited a tendency to dissociate at the amide bond C-terminal to the crosslinked lysine residue, relative to the N-terminal side. One could envision updating computer algorithms to include these crosslinker specific product ions--particularly for precursor ions with localized protons--that provide complementary and confirmatory information, to offer more confident identification of both the crosslinked peptides and the location of the crosslink, as well as affording predictive guidelines for interpretation of the product-ion spectra of crosslinked peptides.
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Affiliation(s)
- Myles W Gardner
- Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, Texas 78712, USA
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43
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Nadeau OW, Wyckoff GJ, Paschall JE, Artigues A, Sage J, Villar MT, Carlson GM. CrossSearch, a user-friendly search engine for detecting chemically cross-linked peptides in conjugated proteins. Mol Cell Proteomics 2008; 7:739-49. [PMID: 18281724 DOI: 10.1074/mcp.m800020-mcp200] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Chemical cross-linking and high resolution MS have been integrated successfully to capture protein interactions and provide low resolution structural data for proteins that are refractive to analyses by NMR or crystallography. Despite the versatility of these combined techniques, the array of products that is generated from the cross-linking and proteolytic digestion of proteins is immense and generally requires the use of labeling strategies and/or data base search algorithms to distinguish actual cross-linked peptides from the many side products of cross-linking. Most strategies reported to date have focused on the analysis of small cross-linked protein complexes (<60 kDa) because the number of potential forms of covalently modified peptides increases dramatically with the number of peptides generated from the digestion of such complexes. We report herein the development of a user-friendly search engine, CrossSearch, that provides the foundation for an overarching strategy to detect cross-linked peptides from the digests of large (>or=170-kDa) cross-linked proteins, i.e. conjugates. Our strategy combines the use of a low excess of cross-linker, data base searching, and Fourier transform ion cyclotron resonance MS to experimentally minimize and theoretically cull the side products of cross-linking. Using this strategy, the (alpha beta gamma delta)(4) phosphorylase kinase model complex was cross-linked to form with high specificity a 170-kDa betagamma conjugate in which we identified residues involved in the intramolecular cross-linking of the 125-kDa beta subunit between its regulatory N terminus and its C terminus. This finding provides an explanation for previously published homodimeric two-hybrid interactions of the beta subunit and suggests a dynamic structural role for the regulatory N terminus of that subunit. The results offer proof of concept for the CrossSearch strategy for analyzing conjugates and are the first to reveal a tertiary structural element of either homologous alpha or beta regulatory subunit of phosphorylase kinase.
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Affiliation(s)
- Owen W Nadeau
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas 66160, USA
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44
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Jin Lee Y. Mass spectrometric analysis of cross-linking sites for the structure of proteins and protein complexes. MOLECULAR BIOSYSTEMS 2008; 4:816-23. [DOI: 10.1039/b801810c] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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45
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Wilkins BJ, Daggett KA, Cropp TA. Peptide mass fingerprinting using isotopically encoded photo-crosslinking amino acids. MOLECULAR BIOSYSTEMS 2008; 4:934-6. [DOI: 10.1039/b801512k] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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46
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Gao Q, Xue S, Shaffer SA, Doneanu CE, Goodlett DR, Nelson SD. Minimize the detection of false positives by the software program DetectShift for 18O-labeled cross-linked peptide analysis. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2008; 14:275-280. [PMID: 19023145 PMCID: PMC2749487 DOI: 10.1255/ejms.939] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
In order to speed up the process of cross-linked peptide identification and characterization, we have previously reported the development of Pro-CrossLink, a suite of software tools consisting of three programs, DetectShift, IdentifyXLink and AssignXLink for mass spectrometric data analysis. Since its public disclosure, Pro-CrossLink has been downloaded by 101 research groups. Pro-CrossLink users have provided us with valuable feedback on the use of the DetectShift program. Here we assess some reasons for the generation of false positives by DetectShift. In addition, we provide users with suggestions on optimal parameter setting and efficient use of the software program.
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Affiliation(s)
- Qiuxia Gao
- Amgen Inc., 1201 Amgen Court West, Seattle, Washington 98119
| | - Song Xue
- Microsoft Corporation, One Microsoft Way, Redmond, Washington 98052
| | - Scott A. Shaffer
- Department of Medicinal Chemistry, University of Washington, Box 357610, Seattle, Washington 98195
| | - Catalin E. Doneanu
- Department of Medicinal Chemistry, University of Washington, Box 357610, Seattle, Washington 98195
| | - David R. Goodlett
- Department of Medicinal Chemistry, University of Washington, Box 357610, Seattle, Washington 98195
| | - Sidney D. Nelson
- Department of Medicinal Chemistry, University of Washington, Box 357610, Seattle, Washington 98195
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47
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Maiolica A, Cittaro D, Borsotti D, Sennels L, Ciferri C, Tarricone C, Musacchio A, Rappsilber J. Structural analysis of multiprotein complexes by cross-linking, mass spectrometry, and database searching. Mol Cell Proteomics 2007; 6:2200-11. [PMID: 17921176 DOI: 10.1074/mcp.m700274-mcp200] [Citation(s) in RCA: 179] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Most protein complexes are inaccessible to high resolution structural analysis. We report the results of a combined approach of cross-linking, mass spectrometry, and bioinformatics to two human complexes containing large coiled-coil segments, the NDEL1 homodimer and the NDC80 heterotetramer. An important limitation of the cross-linking approach, so far, was the identification of cross-linked peptides from fragmentation spectra. Our novel approach overcomes the data analysis bottleneck of cross-linking and mass spectrometry. We constructed a purpose-built database to match spectra with cross-linked peptides, define a score that expresses the quality of our identification, and estimate false positive rates. We show that our analysis sheds light on critical structural parameters such as the directionality of the homodimeric coiled coil of NDEL1, the register of the heterodimeric coiled coils of the NDC80 complex, and the organization of a tetramerization region in the NDC80 complex. Our approach is especially useful to address complexes that are difficult in addressing by standard structural methods.
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Affiliation(s)
- Alessio Maiolica
- FIRC Institute of Molecular Oncology Foundation, Via Adamello 16, 20139 Milan, Italy
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Anderson GA, Tolic N, Tang X, Zheng C, Bruce JE. Informatics strategies for large-scale novel cross-linking analysis. J Proteome Res 2007; 6:3412-21. [PMID: 17676784 PMCID: PMC2475505 DOI: 10.1021/pr070035z] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The detection of protein interactions in biological systems represents a significant challenge for today's technology. Chemical cross-linking provides the potential to impart new chemical bonds in a complex system that result in mass changes in a set of tryptic peptides detected by mass spectrometry. However, system complexity and cross-linking product heterogeneity have precluded widespread chemical cross-linking use for large-scale identification of protein-protein interactions. The development of mass spectrometry identifiable cross-linkers called protein interaction reporters (PIRs) has enabled on-cell chemical cross-linking experiments with product type differentiation. However, the complex datasets resultant from PIR experiments demand new informatics capabilities to allow interpretation. This manuscript details our efforts to develop such capabilities and describes the program X-links, which allows PIR product type differentiation. Furthermore, we also present the results from Monte Carlo simulation of PIR-type experiments to provide false discovery rate estimates for the PIR product type identification through observed precursor and released peptide masses. Our simulations also provide peptide identification calculations based on accurate masses and database complexity that can provide an estimation of false discovery rates for peptide identification. Overall, the calculations show a low rate of false discovery of PIR product types due to random mass matching of approximately 12% with 10 ppm mass measurement accuracy and spectral complexity resulting from 100 peptides. In addition, consideration of a reduced database resulting from stage 1 analysis of Shewanella oneidensis MR-1 containing 367 proteins resulted in a significant reduction of expected identification false discovery rate estimation compared to that from the entire Shewanella oneidensis MR-1 proteome.
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Affiliation(s)
| | | | | | | | - James E. Bruce
- * To whom correspondence should be addressed. James E. Bruce, Department of Chemistry, Washington State University, Pullman, Washington 99164-4630; Tel, 509-335-2116; Fax, 509-335-8867; E-mail,
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Kasper PT, Back JW, Vitale M, Hartog AF, Roseboom W, de Koning LJ, van Maarseveen JH, Muijsers AO, de Koster CG, de Jong L. An Aptly Positioned Azido Group in the Spacer of a Protein Cross-Linker for Facile Mapping of Lysines in Close Proximity. Chembiochem 2007; 8:1281-92. [PMID: 17600791 DOI: 10.1002/cbic.200700150] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Cross-links between amino acid residues in close proximity can provide distance constraints for the validation of models of the 3D structure proteins. The mapping of cross-links by the identification of linked peptides in proteolytic digests is facilitated by cleavable cross-linkers that enable isolation of the cleavage products while preserving information about the linkage. We present an amine-specific cross-linker, bis(succinimidyl)-3-azidomethyl glutarate (BAMG), that fulfils these requirements. Two parallel reaction pathways are induced by tris(carboxyethyl)phosphine (TCEP) in cross-linked peptides from BAMG-treated cytochrome c. One pathway leads to cleavage of the cross-linked species, while in the other the azido group of BAMG is reduced to an amino group without cleavage. Cross-linked peptides and peptides modified by partially hydrolysed BAMG yield distinct sets of TCEP-induced reaction products. These can be isolated by reversed-phase diagonal chromatography and identified by mass spectrometry to reveal the identity of the parent compounds. The ease with which cross-link-derived reaction products can be isolated and identified indicates that the mapping of cross-links in complex biological assemblies and mixtures of protein complexes might become feasible in the near future.
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Affiliation(s)
- Piotr T Kasper
- Swammerdam Institute for Life Sciences, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands
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Current literature in mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2007; 42:127-38. [PMID: 17199253 PMCID: PMC7166443 DOI: 10.1002/jms.1070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
In order to keep subscribers up‐to‐date with the latest developments in their field, John Wiley & Sons are providing a current awareness service in each issue of the journal. The bibliography contains newly published material in the field of mass spectrometry. Each bibliography is divided into 11 sections: 1 Books, Reviews & Symposia; 2 Instrumental Techniques & Methods; 3 Gas Phase Ion Chemistry; 4 Biology/Biochemistry: Amino Acids, Peptides & Proteins; Carbohydrates; Lipids; Nucleic Acids; 5 Pharmacology/Toxicology; 6 Natural Products; 7 Analysis of Organic Compounds; 8 Analysis of Inorganics/Organometallics; 9 Surface Analysis; 10 Environmental Analysis; 11 Elemental Analysis. Within each section, articles are listed in alphabetical order with respect to author (6 Weeks journals ‐ Search completed at 4th. Oct. 2006)
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