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Townsend JA, Marty MT. What's the defect? Using mass defects to study oligomerization of membrane proteins and peptides in nanodiscs with native mass spectrometry. Methods 2023; 218:1-13. [PMID: 37482149 PMCID: PMC10529358 DOI: 10.1016/j.ymeth.2023.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/20/2023] [Accepted: 07/03/2023] [Indexed: 07/25/2023] Open
Abstract
Many membrane proteins form functional complexes that are either homo- or hetero-oligomeric. However, it is challenging to characterize membrane protein oligomerization in intact lipid bilayers, especially for polydisperse mixtures. Native mass spectrometry of membrane proteins and peptides inserted in lipid nanodiscs provides a unique method to study the oligomeric state distribution and lipid preferences of oligomeric assemblies. To interpret these complex spectra, we developed novel data analysis methods using macromolecular mass defect analysis. Here, we provide an overview of how mass defect analysis can be used to study oligomerization in nanodiscs, discuss potential limitations in interpretation, and explore strategies to resolve these ambiguities. Finally, we review recent work applying this technique to studying formation of antimicrobial peptide, amyloid protein, and viroporin complexes with lipid membranes.
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Affiliation(s)
- Julia A Townsend
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, AZ 85721, USA
| | - Michael T Marty
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, AZ 85721, USA.
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2
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Sun B, Kekenes-Huskey PM. Myofilament-associated proteins with intrinsic disorder (MAPIDs) and their resolution by computational modeling. Q Rev Biophys 2023; 56:e2. [PMID: 36628457 PMCID: PMC11070111 DOI: 10.1017/s003358352300001x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The cardiac sarcomere is a cellular structure in the heart that enables muscle cells to contract. Dozens of proteins belong to the cardiac sarcomere, which work in tandem to generate force and adapt to demands on cardiac output. Intriguingly, the majority of these proteins have significant intrinsic disorder that contributes to their functions, yet the biophysics of these intrinsically disordered regions (IDRs) have been characterized in limited detail. In this review, we first enumerate these myofilament-associated proteins with intrinsic disorder (MAPIDs) and recent biophysical studies to characterize their IDRs. We secondly summarize the biophysics governing IDR properties and the state-of-the-art in computational tools toward MAPID identification and characterization of their conformation ensembles. We conclude with an overview of future computational approaches toward broadening the understanding of intrinsic disorder in the cardiac sarcomere.
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Affiliation(s)
- Bin Sun
- Research Center for Pharmacoinformatics (The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, Harbin 150081, China
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3
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de Lima JY, Santos MDM, Murakami MT, Carvalho PC, de Souza TDACB. Cross-linking mass spectrometry reveals structural insights of the glutamine synthetase from Leishmania braziliensis. Mem Inst Oswaldo Cruz 2022; 116:e210209. [PMID: 35019070 PMCID: PMC8752055 DOI: 10.1590/0074-02760210209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 10/26/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Leishmaniasis is a neglected tropical disease caused by the parasite Leishmania braziliensis, commonly found in Brazil and associated with cutaneous and visceral forms of this disease. Like other organisms, L. braziliensis has an enzyme called glutamine synthetase (LbGS) that acts on the synthesis of glutamine from glutamate. This enzyme plays an essential role in the metabolism of these parasites and can be a potential therapeutic target for treating this disease. OBJECTIVES Investigate LbGS structure and generate structural models of the protein. METHODS We use the method of crosslinking mass spectrometry (XLMS) and generate structural models in silico using I-TASSER. FINDINGS 42 XLs peptides were identified, of which 37 are explained in a monomeric model with the other five indicating LbGS dimerization and pentamers interaction region. The comparison of 3D models generated in the presence and absence of XLMS restrictions probed the benefits of modeling with XLMS highlighting the inappropriate folding due to the absence of spatial restrictions. MAIN CONCLUSIONS In conclusion, we disclose the conservation of the active site and interface regions, but also unique features of LbGS showing the potential of XLMS to probe structural information and explore new drugs.
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Affiliation(s)
- Jhenifer Yonara de Lima
- Fundação Oswaldo Cruz-Fiocruz, Instituto Carlos Chagas, Laboratório de Proteômica Estrutural e Computacional, Curitiba, PR, Brasil
| | - Marlon Dias Mariano Santos
- Fundação Oswaldo Cruz-Fiocruz, Instituto Carlos Chagas, Laboratório de Proteômica Estrutural e Computacional, Curitiba, PR, Brasil
| | - Mario Tyago Murakami
- Centro Nacional de Pesquisa em Energia e Materiais, Laboratório Nacional de Biorrenováveis, Campinas, SP, Brasil
| | - Paulo Costa Carvalho
- Fundação Oswaldo Cruz-Fiocruz, Instituto Carlos Chagas, Laboratório de Proteômica Estrutural e Computacional, Curitiba, PR, Brasil
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4
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Zhao B, Reilly CP, Davis C, Matouschek A, Reilly JP. Use of Multiple Ion Fragmentation Methods to Identify Protein Cross-Links and Facilitate Comparison of Data Interpretation Algorithms. J Proteome Res 2020; 19:2758-2771. [PMID: 32496805 DOI: 10.1021/acs.jproteome.0c00111] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Multiple ion fragmentation methods involving collision-induced dissociation (CID), higher-energy collisional dissociation (HCD) with regular and very high energy settings, and electron-transfer dissociation with supplementary HCD (EThcD) are implemented to improve the confidence of cross-link identifications. Three different S. cerevisiae proteasome samples cross-linked by diethyl suberthioimidate (DEST) or bis(sulfosuccinimidyl)suberate (BS3) are analyzed. Two approaches are introduced to combine interpretations from the above four methods. Working with cleavable cross-linkers such as DEST, the first approach searches for cross-link diagnostic ions and consistency among the best interpretations derived from all four MS2 spectra associated with each precursor ion. Better agreement leads to a more definitive identification. Compatible with both cleavable and noncleavable cross-linkers such as BS3, the second approach multiplies scoring metrics from a number of fragmentation experiments to derive an overall best match. This significantly increases the scoring gap between the target and decoy matches. The validity of cross-links fragmented by HCD alone and identified by Kojak, MeroX, pLink, and Xi was evaluated using multiple fragmentation data. Possible ways to improve the identification credibility are discussed. Data are available via ProteomeXchange with identifier PXD018310.
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Affiliation(s)
- Bingqing Zhao
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Colin P Reilly
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Caroline Davis
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Andreas Matouschek
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - James P Reilly
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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5
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Steigenberger B, Pieters RJ, Heck AJR, Scheltema RA. PhoX: An IMAC-Enrichable Cross-Linking Reagent. ACS CENTRAL SCIENCE 2019; 5:1514-1522. [PMID: 31572778 PMCID: PMC6764163 DOI: 10.1021/acscentsci.9b00416] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Indexed: 05/02/2023]
Abstract
Chemical cross-linking mass spectrometry is rapidly emerging as a prominent technique to study protein structures. Structural information is obtained by covalently connecting peptides in close proximity by small reagents and identifying the resulting peptide pairs by mass spectrometry. However, substoichiometric reaction efficiencies render routine detection of cross-linked peptides problematic. Here, we present a new trifunctional cross-linking reagent, termed PhoX, which is decorated with a stable phosphonic acid handle. This makes the cross-linked peptides amenable to the well-established immobilized metal affinity chromatography (IMAC) enrichment. The handle allows for 300× enrichment efficiency and 97% specificity. We exemplify the approach on various model proteins and protein complexes, e.g., resulting in a structural model of the LRP1/RAP complex. Almost completely removing linear peptides allows PhoX, although noncleavable, to be applied to complex lysates. Focusing the database search to the 1400 most abundant proteins, we were able to identify 1156 cross-links in a single 3 h measurement.
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Affiliation(s)
- Barbara Steigenberger
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet
Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences,
Utrecht University, Padualaan 8, 3584 CH Utrecht,
The Netherlands
- Netherlands Proteomics
Centre, Padualaan 8, 3584 CH Utrecht, The
Netherlands
- Department of Chemical Biology & Drug Discovery,
Utrecht Institute for Pharmaceutical Sciences, Utrecht
University, P.O. Box 80082, 3508 TB Utrecht, The
Netherlands
| | - Roland J. Pieters
- Department of Chemical Biology & Drug Discovery,
Utrecht Institute for Pharmaceutical Sciences, Utrecht
University, P.O. Box 80082, 3508 TB Utrecht, The
Netherlands
| | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet
Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences,
Utrecht University, Padualaan 8, 3584 CH Utrecht,
The Netherlands
- Netherlands Proteomics
Centre, Padualaan 8, 3584 CH Utrecht, The
Netherlands
- Phone: +31 30 253 6797. Fax: +31 30
253 69 18. E-mail:
| | - Richard A. Scheltema
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet
Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences,
Utrecht University, Padualaan 8, 3584 CH Utrecht,
The Netherlands
- Netherlands Proteomics
Centre, Padualaan 8, 3584 CH Utrecht, The
Netherlands
- Phone: +31 30 253 45 64. Fax: +31 30
253 69 18. E-mail:
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6
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Zhao B, Reilly CP, Reilly JP. ETD-Cleavable Linker for Confident Cross-linked Peptide Identifications. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:1631-1642. [PMID: 31098958 DOI: 10.1007/s13361-019-02227-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 04/12/2019] [Accepted: 04/13/2019] [Indexed: 06/09/2023]
Abstract
Peptide cross-links formed using the homobifunctional-linker diethyl suberthioimidate (DEST) are shown to be ETD-cleavable. DEST has a spacer arm consisting of a 6-carbon alkyl chain and it cleaves at the amidino groups created upon reaction with primary amines. In ETD MS2 spectra, DEST cross-links can be recognized based on mass pairs consisting of peptide-NH2• and peptide+linker+NH3 ions, and backbone cleavages are more equally distributed over the two constituent peptides compared with collisional activation. Dead ends that are often challenging to distinguish from cross-links are diagnosed by intense reporter ions. ETD mass pairs can be used in MS3 experiments to confirm cross-link identifications. These features provide a simple but reliable approach to identify cross-links that should facilitate studies of protein complexes.
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Affiliation(s)
- Bingqing Zhao
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, IN, 47405, USA
| | - Colin P Reilly
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, IN, 47405, USA
| | - James P Reilly
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, IN, 47405, USA.
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7
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Schmelter C, Fomo KN, Perumal N, Manicam C, Bell K, Pfeiffer N, Grus FH. Synthetic Polyclonal-Derived CDR Peptides as an Innovative Strategy in Glaucoma Therapy. J Clin Med 2019; 8:jcm8081222. [PMID: 31443184 PMCID: PMC6723090 DOI: 10.3390/jcm8081222] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 07/30/2019] [Accepted: 08/12/2019] [Indexed: 12/16/2022] Open
Abstract
The pathogenesis of glaucoma is strongly associated with the occurrence of autoimmune-mediated loss of retinal ganglion cells (RGCs) and additionally, recent evidence shows that specific antibody-derived signature peptides are significantly differentially expressed in sera of primary-open angle glaucoma patients (POAG) compared to healthy controls. Synthetically antibody-derived peptides can modulate various effector functions of the immune system and act as antimicrobial or antiviral molecules. In an ex vivo adolescent glaucoma model, this study, for the first time, demonstrates that polyclonal-derived complementarity-determining regions (CDRs) can significantly increase the survival rate of RGCs (p = 0.013). We subsequently performed affinity capture experiments that verified the mitochondrial serine protease HTRA2 (gene name: HTRA2) as a high-affinity retinal epitope target of CDR1 sequence motif ASGYTFTNYGLSWVR. Quantitative proteomic analysis of the CDR-treated retinal explants revealed increased expression of various anti-apoptotic and anti-oxidative proteins (e.g., VDAC2 and TXN) compared to untreated controls (p < 0.05) as well as decreased expression levels of cellular stress response markers (e.g., HSPE1 and HSP90AA1). Mitochondrial dysfunction, the protein ubiquitination pathway and oxidative phosphorylation were annotated as the most significantly affected signaling pathways and possibly can be traced back to the CDR-induced inhibition or modulation of the master regulator HTRA2. These findings emphasize the great potential of synthetic polyclonal-derived CDR peptides as therapeutic agents in future glaucoma therapy and provide an excellent basis for affinity-based biomarker discovery purposes.
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Affiliation(s)
- Carsten Schmelter
- Department of Experimental and Translational Ophthalmology, University Medical Center, Johannes Gutenberg University, 55131 Mainz, Germany
| | - Kristian Nzogang Fomo
- Department of Experimental and Translational Ophthalmology, University Medical Center, Johannes Gutenberg University, 55131 Mainz, Germany
| | - Natarajan Perumal
- Department of Experimental and Translational Ophthalmology, University Medical Center, Johannes Gutenberg University, 55131 Mainz, Germany
| | - Caroline Manicam
- Department of Experimental and Translational Ophthalmology, University Medical Center, Johannes Gutenberg University, 55131 Mainz, Germany
| | - Katharina Bell
- Department of Experimental and Translational Ophthalmology, University Medical Center, Johannes Gutenberg University, 55131 Mainz, Germany
| | - Norbert Pfeiffer
- Department of Experimental and Translational Ophthalmology, University Medical Center, Johannes Gutenberg University, 55131 Mainz, Germany
| | - Franz H Grus
- Department of Experimental and Translational Ophthalmology, University Medical Center, Johannes Gutenberg University, 55131 Mainz, Germany.
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8
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Iacobucci C, Schäfer M, Sinz A. Free radical-initiated peptide sequencing (FRIPS)-based cross-linkers for improved peptide and protein structure analysis. MASS SPECTROMETRY REVIEWS 2019; 38:187-201. [PMID: 29660147 DOI: 10.1002/mas.21568] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Accepted: 03/09/2018] [Indexed: 06/08/2023]
Abstract
Free radical-initiated peptide sequencing (FRIPS) has recently been introduced as an analytical strategy to create peptide radical ions in a predictable and effective way by collisional activation of specifically modified peptides ions. FRIPS is based on the unimolecular dissociation of open-shell ions and yields fragments that resemble those obtained by electron capture dissociation (ECD) or electron transfer dissociation (ETD). In this review article, we describe the fundamentals of FRIPS and highlight its fruitful combination with chemical cross-linking/mass spectrometry (MS) as a highly promising option to derive complementary structural information of peptides and proteins. FRIPS does not only yield exhaustive sequence information of cross-linked peptides, but also defines the exact cross-linking sites of the connected peptides. The development of more advanced FRIPS cross-linkers that extend the FRIPS-based cross-linking/MS approach to the study of large protein assemblies and protein interaction networks can be eagerly anticipated.
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Affiliation(s)
- Claudio Iacobucci
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle (Saale), D-06120, Germany
| | - Mathias Schäfer
- Department of Chemistry, Institute of Organic Chemistry, University of Cologne, Cologne, D-50939, Germany
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle (Saale), D-06120, Germany
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9
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Rey M, Dupré M, Lopez-Neira I, Duchateau M, Chamot-Rooke J. eXL-MS: An Enhanced Cross-Linking Mass Spectrometry Workflow To Study Protein Complexes. Anal Chem 2018; 90:10707-10714. [PMID: 30125099 DOI: 10.1021/acs.analchem.8b00737] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The analysis of proteins and protein complexes by cross-linking mass spectrometry (XL-MS) has expanded in the past decade. However, mostly used approaches suffer important limitations in term of efficiency and sensitivity. We describe here a new workflow based on the advanced use of the trifunctional cross-linker NNP9. NNP9 carries an azido group allowing the quantitative and selective introduction of a biotin molecule into cross-linked proteins. The incorporation is performed by click-chemistry using an adapted version of the enhanced filter-aided sample preparation (eFASP) protocol. This protocol, based on the use of a molecular filter, allows a very high recovery of peptides after enzymatic digestion and complete removal of contaminants. This in turn offers the possibility for one to analyze very large membrane proteins solubilized in detergent. After trypsin digestion, biotinylated peptides can be easily enriched on monoavidin beads and analyzed by LC-MS/MS. The whole workflow was developed on creatine kinase in the presence of detergent. It led to a drastic improvement in the number of identified cross-linked peptides (407 vs 81), compared to the conventional approach using a gel-based separation. One great advantage of our enhanced cross-linking mass spectrometry (eXL-MS) workflow is its high efficiency, allowing the analysis of a very low amount of material (15 μg). We also demonstrate that higher-energy collision dissociation (HCD) outperforms electron-transfer/higher-energy collision dissociation (EThcD) in terms of number of cross-linked peptides identified, but EThcD leads to better sequence coverage than HCD and thus easier localization of cross-linking sites.
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Affiliation(s)
- Martial Rey
- Mass Spectrometry for Biology Unit, CNRS USR 2000 , Institut Pasteur , Paris , 75015 , France
| | - Mathieu Dupré
- Mass Spectrometry for Biology Unit, CNRS USR 2000 , Institut Pasteur , Paris , 75015 , France
| | - Isabel Lopez-Neira
- Mass Spectrometry for Biology Unit, CNRS USR 2000 , Institut Pasteur , Paris , 75015 , France
| | - Magalie Duchateau
- Mass Spectrometry for Biology Unit, CNRS USR 2000 , Institut Pasteur , Paris , 75015 , France
| | - Julia Chamot-Rooke
- Mass Spectrometry for Biology Unit, CNRS USR 2000 , Institut Pasteur , Paris , 75015 , France
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10
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Chu F, Thornton DT, Nguyen HT. Chemical cross-linking in the structural analysis of protein assemblies. Methods 2018; 144:53-63. [PMID: 29857191 DOI: 10.1016/j.ymeth.2018.05.023] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 05/22/2018] [Accepted: 05/25/2018] [Indexed: 12/31/2022] Open
Abstract
For decades, chemical cross-linking of proteins has been an established method to study protein interaction partners. The chemical cross-linking approach has recently been revived by mass spectrometric analysis of the cross-linking reaction products. Chemical cross-linking and mass spectrometric analysis (CXMS) enables the identification of residues that are close in three-dimensional (3D) space but not necessarily close in primary sequence. Therefore, this approach provides medium resolution information to guide de novo structure prediction, protein interface mapping and protein complex model building. The robustness and compatibility of the CXMS approach with multiple biochemical methods have made it especially appealing for challenging systems with multiple biochemical compositions and conformation states. This review provides an overview of the CXMS approach, describing general procedures in sample processing, data acquisition and analysis. Selection of proper chemical cross-linking reagents, strategies for cross-linked peptide identification, and successful application of CXMS in structural characterization of proteins and protein complexes are discussed.
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Affiliation(s)
- Feixia Chu
- Department of Molecular, Cellular & Biomedical Sciences, University of New Hampshire, Durham, NH 03824, United States; Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH 03824, United States.
| | - Daniel T Thornton
- Department of Molecular, Cellular & Biomedical Sciences, University of New Hampshire, Durham, NH 03824, United States
| | - Hieu T Nguyen
- Department of Molecular, Cellular & Biomedical Sciences, University of New Hampshire, Durham, NH 03824, United States
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11
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Rozbeský D, Rosůlek M, Kukačka Z, Chmelík J, Man P, Novák P. Impact of Chemical Cross-Linking on Protein Structure and Function. Anal Chem 2018; 90:1104-1113. [DOI: 10.1021/acs.analchem.7b02863] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Daniel Rozbeský
- Institute of Microbiology, v.v.i., Czech Academy of Sciences, 14220 Prague, Czech Republic
- Department
of Biochemistry, Faculty of Science, Charles University in Prague, 12843 Prague, Czech Republic
| | - Michal Rosůlek
- Institute of Microbiology, v.v.i., Czech Academy of Sciences, 14220 Prague, Czech Republic
- Department
of Biochemistry, Faculty of Science, Charles University in Prague, 12843 Prague, Czech Republic
| | - Zdeněk Kukačka
- Institute of Microbiology, v.v.i., Czech Academy of Sciences, 14220 Prague, Czech Republic
- Department
of Biochemistry, Faculty of Science, Charles University in Prague, 12843 Prague, Czech Republic
| | - Josef Chmelík
- Institute of Microbiology, v.v.i., Czech Academy of Sciences, 14220 Prague, Czech Republic
- Department
of Biochemistry, Faculty of Science, Charles University in Prague, 12843 Prague, Czech Republic
| | - Petr Man
- Institute of Microbiology, v.v.i., Czech Academy of Sciences, 14220 Prague, Czech Republic
- Department
of Biochemistry, Faculty of Science, Charles University in Prague, 12843 Prague, Czech Republic
| | - Petr Novák
- Institute of Microbiology, v.v.i., Czech Academy of Sciences, 14220 Prague, Czech Republic
- Department
of Biochemistry, Faculty of Science, Charles University in Prague, 12843 Prague, Czech Republic
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12
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Bassard JE, Halkier BA. How to prove the existence of metabolons? PHYTOCHEMISTRY REVIEWS : PROCEEDINGS OF THE PHYTOCHEMICAL SOCIETY OF EUROPE 2018; 17:211-227. [PMID: 29755303 PMCID: PMC5932110 DOI: 10.1007/s11101-017-9509-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 04/19/2017] [Indexed: 05/21/2023]
Abstract
Sequential enzymes in biosynthetic pathways are organized in metabolons. It is challenging to provide experimental evidence for the existence of metabolons as biosynthetic pathways are composed of highly dynamic protein-protein interactions. Many different methods are being applied, each with strengths and weaknesses. We will present and evaluate several techniques that have been applied in providing evidence for the orchestration of the biosynthetic pathways of cyanogenic glucosides and glucosinolates in metabolons. These evolutionarily related pathways have ER-localized cytochromes P450 that are proposed to function as anchoring site for assembly of the enzymes into metabolons. Additionally, we have included commonly used techniques, even though they have not been used (yet) on these two pathways. In the review, special attention will be given to less-exploited fluorescence-based methods such as FCS and FLIM. Ultimately, understanding the orchestration of biosynthetic pathways may contribute to successful engineering in heterologous hosts.
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Affiliation(s)
- Jean-Etienne Bassard
- Plant Biochemistry Laboratory, Center for Synthetic Biology, VILLUM Research Center “Plant Plasticity”, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Barbara Ann Halkier
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
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13
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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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14
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Ulrich V, Cryle MJ. SNaPe: a versatile method to generate multiplexed protein fusions using synthetic linker peptides for in vitro applications. J Pept Sci 2016; 23:16-27. [PMID: 27910178 DOI: 10.1002/psc.2943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 10/26/2016] [Accepted: 11/06/2016] [Indexed: 11/10/2022]
Abstract
Understanding the structure and function of protein complexes and multi-domain proteins is highly important in biology, although the in vitro characterization of these systems is often complicated by their size or the transient nature of protein/protein interactions. To assist in the characterization of such protein complexes, we have developed a modular approach to fusion protein generation that relies upon Sortase-mediated and Native chemical ligation using synthetic Peptide linkers (SNaPe) to link two separately expressed proteins. In this approach, we utilize two separate linking steps - sortase-mediated and native chemical ligation - together with a library of peptide linkers to generate libraries of fusion proteins. We have demonstrated the viability of SNaPe to generate libraries from fusion protein constructs taken from the biosynthetic enzymes responsible for late stage aglycone assembly during glycopeptide antibiotic biosynthesis. Crucially, SNaPe was able to generate fusion proteins that are inaccessible via direct expression of the fusion construct itself. This highlights the advantages of SNaPe to not only access fusion proteins that have been previously unavailable for biochemical and structural characterization but also to do so in a manner that enables the linker itself to be controlled as an experimental parameter of fusion protein generation. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.
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Affiliation(s)
- Veronika Ulrich
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Max J Cryle
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120, Heidelberg, Germany.,EMBL Australia, Monash University, Clayton, Victoria, 3800, Australia.,The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology and ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, 3800, Australia
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15
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Abstract
Laminin, an ∼800-kDa heterotrimeric protein, is a major functional component of the extracellular matrix, contributing to tissue development and maintenance. The unique architecture of laminin is not currently amenable to determination at high resolution, as its flexible and narrow segments complicate both crystallization and single-particle reconstruction by electron microscopy. Therefore, we used cross-linking and MS, evaluated using computational methods, to address key questions regarding laminin quaternary structure. This approach was particularly well suited to the ∼750-Å coiled coil that mediates trimer assembly, and our results support revision of the subunit order typically presented in laminin schematics. Furthermore, information on the subunit register in the coiled coil and cross-links to downstream domains provide insights into the self-assembly required for interaction with other extracellular matrix and cell surface proteins.
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16
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The novel isotopically coded short-range photo-reactive crosslinker 2,4,6-triazido-1,3,5-triazine (TATA) for studying protein structures. J Proteomics 2016; 149:69-76. [DOI: 10.1016/j.jprot.2016.02.024] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Revised: 02/18/2016] [Accepted: 02/21/2016] [Indexed: 11/17/2022]
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17
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Ji C, Li S, Reilly JP, Radivojac P, Tang H. XLSearch: a Probabilistic Database Search Algorithm for Identifying Cross-Linked Peptides. J Proteome Res 2016; 15:1830-41. [PMID: 27068484 PMCID: PMC5770149 DOI: 10.1021/acs.jproteome.6b00004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chemical cross-linking combined with mass spectrometric analysis has become an important technique for probing protein three-dimensional structure and protein-protein interactions. A key step in this process is the accurate identification and validation of cross-linked peptides from tandem mass spectra. The identification of cross-linked peptides, however, presents challenges related to the expanded nature of the search space (all pairs of peptides in a sequence database) and the fact that some peptide-spectrum matches (PSMs) contain one correct and one incorrect peptide but often receive scores that are comparable to those in which both peptides are correctly identified. To address these problems and improve detection of cross-linked peptides, we propose a new database search algorithm, XLSearch, for identifying cross-linked peptides. Our approach is based on a data-driven scoring scheme that independently estimates the probability of correctly identifying each individual peptide in the cross-link given knowledge of the correct or incorrect identification of the other peptide. These conditional probabilities are subsequently used to estimate the joint posterior probability that both peptides are correctly identified. Using the data from two previous cross-link studies, we show the effectiveness of this scoring scheme, particularly in distinguishing between true identifications and those containing one incorrect peptide. We also provide evidence that XLSearch achieves more identifications than two alternative methods at the same false discovery rate (availability: https://github.com/COL-IU/XLSearch ).
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Affiliation(s)
- Chao Ji
- Department of Computer Science and Informatics, Indiana University, Bloomington, Indiana 47405, United States
| | - Sujun Li
- Department of Computer Science and Informatics, Indiana University, Bloomington, Indiana 47405, United States
| | - James P. Reilly
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Predrag Radivojac
- Department of Computer Science and Informatics, Indiana University, Bloomington, Indiana 47405, United States
| | - Haixu Tang
- Department of Computer Science and Informatics, Indiana University, Bloomington, Indiana 47405, United States
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18
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Automated structure modeling of large protein assemblies using crosslinks as distance restraints. Nat Methods 2016; 13:515-20. [PMID: 27111507 DOI: 10.1038/nmeth.3838] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 03/19/2016] [Indexed: 11/08/2022]
Abstract
Crosslinking mass spectrometry is increasingly used for structural characterization of multisubunit protein complexes. Chemical crosslinking captures conformational heterogeneity, which typically results in conflicting crosslinks that cannot be satisfied in a single model, making detailed modeling a challenging task. Here we introduce an automated modeling method dedicated to large protein assemblies ('XL-MOD' software is available at http://aria.pasteur.fr/supplementary-data/x-links) that (i) uses a form of spatial restraints that realistically reflects the distribution of experimentally observed crosslinked distances; (ii) automatically deals with ambiguous and/or conflicting crosslinks and identifies alternative conformations within a Bayesian framework; and (iii) allows subunit structures to be flexible during conformational sampling. We demonstrate our method by testing it on known structures and available crosslinking data. We also crosslinked and modeled the 17-subunit yeast RNA polymerase III at atomic resolution; the resulting model agrees remarkably well with recently published cryoelectron microscopy structures and provides additional insights into the polymerase structure.
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19
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Challenges and opportunities of using liquid chromatography and mass spectrometry methods to develop complex vaccine antigens as pharmaceutical dosage forms. J Chromatogr B Analyt Technol Biomed Life Sci 2016; 1032:23-38. [PMID: 27071526 DOI: 10.1016/j.jchromb.2016.04.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 03/31/2016] [Accepted: 04/01/2016] [Indexed: 12/22/2022]
Abstract
Liquid chromatographic methods, combined with mass spectrometry, offer exciting and important opportunities to better characterize complex vaccine antigens including recombinant proteins, virus-like particles, inactivated viruses, polysaccharides, and protein-polysaccharide conjugates. The current abilities and limitations of these physicochemical methods to complement traditional in vitro and in vivo vaccine potency assays are explored in this review through the use of illustrative case studies. Various applications of these state-of-the art techniques are illustrated that include the analysis of influenza vaccines (inactivated whole virus and recombinant hemagglutinin), virus-like particle vaccines (human papillomavirus and hepatitis B), and polysaccharide linked to protein carrier vaccines (pneumococcal). Examples of utilizing these analytical methods to characterize vaccine antigens in the presence of adjuvants, which are often included to boost immune responses as part of the final vaccine dosage form, are also presented. Some of the challenges of using chromatographic and LC-MS as physicochemical assays to routinely test complex vaccine antigens are also discussed.
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20
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Rivera-Santiago RF, Sriswasdi S, Harper SL, Speicher DW. Probing structures of large protein complexes using zero-length cross-linking. Methods 2015; 89:99-111. [PMID: 25937394 PMCID: PMC4628899 DOI: 10.1016/j.ymeth.2015.04.031] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 04/10/2015] [Accepted: 04/24/2015] [Indexed: 02/02/2023] Open
Abstract
Structural mass spectrometry (MS) is a field with growing applicability for addressing complex biophysical questions regarding proteins and protein complexes. One of the major structural MS approaches involves the use of chemical cross-linking coupled with MS analysis (CX-MS) to identify proximal sites within macromolecules. Identified cross-linked sites can be used to probe novel protein-protein interactions or the derived distance constraints can be used to verify and refine molecular models. This review focuses on recent advances of "zero-length" cross-linking. Zero-length cross-linking reagents do not add any atoms to the cross-linked species due to the lack of a spacer arm. This provides a major advantage in the form of providing more precise distance constraints as the cross-linkable groups must be within salt bridge distances in order to react. However, identification of cross-linked peptides using these reagents presents unique challenges. We discuss recent efforts by our group to minimize these challenges by using multiple cycles of LC-MS/MS analysis and software specifically developed and optimized for identification of zero-length cross-linked peptides. Representative data utilizing our current protocol are presented and discussed.
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Affiliation(s)
- Roland F Rivera-Santiago
- The Center for Systems and Computational Biology and Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA 19104, United States; Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Sira Sriswasdi
- The Center for Systems and Computational Biology and Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA 19104, United States; Department of Biological Sciences, Graduate School of Sciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Sandra L Harper
- The Center for Systems and Computational Biology and Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA 19104, United States
| | - David W Speicher
- The Center for Systems and Computational Biology and Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA 19104, United States; Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, United States.
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21
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Zheng H, Handing KB, Zimmerman MD, Shabalin IG, Almo SC, Minor W. X-ray crystallography over the past decade for novel drug discovery - where are we heading next? Expert Opin Drug Discov 2015; 10:975-89. [PMID: 26177814 DOI: 10.1517/17460441.2015.1061991] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
INTRODUCTION Macromolecular X-ray crystallography has been the primary methodology for determining the three-dimensional structures of proteins, nucleic acids and viruses. Structural information has paved the way for structure-guided drug discovery and laid the foundations for structural bioinformatics. However, X-ray crystallography still has a few fundamental limitations, some of which may be overcome and complemented using emerging methods and technologies in other areas of structural biology. AREAS COVERED This review describes how structural knowledge gained from X-ray crystallography has been used to advance other biophysical methods for structure determination (and vice versa). This article also covers current practices for integrating data generated by other biochemical and biophysical methods with those obtained from X-ray crystallography. Finally, the authors articulate their vision about how a combination of structural and biochemical/biophysical methods may improve our understanding of biological processes and interactions. EXPERT OPINION X-ray crystallography has been, and will continue to serve as, the central source of experimental structural biology data used in the discovery of new drugs. However, other structural biology techniques are useful not only to overcome the major limitation of X-ray crystallography, but also to provide complementary structural data that is useful in drug discovery. The use of recent advancements in biochemical, spectroscopy and bioinformatics methods may revolutionize drug discovery, albeit only when these data are combined and analyzed with effective data management systems. Accurate and complete data management is crucial for developing experimental procedures that are robust and reproducible.
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Affiliation(s)
- Heping Zheng
- University of Virginia, Department of Molecular Physiology and Biological Physics , 1340 Jefferson Park Avenue, Charlottesville, VA 22908 , USA +1 434 243 6865 ; +1 434 243 2981 ;
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22
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Nguyen-Huynh NT, Sharov G, Potel C, Fichter P, Trowitzsch S, Berger I, Lamour V, Schultz P, Potier N, Leize-Wagner E. Chemical cross-linking and mass spectrometry to determine the subunit interaction network in a recombinant human SAGA HAT subcomplex. Protein Sci 2015; 24:1232-46. [PMID: 25753033 DOI: 10.1002/pro.2676] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 03/03/2015] [Accepted: 03/03/2015] [Indexed: 01/04/2023]
Abstract
Understanding the way how proteins interact with each other to form transient or stable protein complexes is a key aspect in structural biology. In this study, we combined chemical cross-linking with mass spectrometry to determine the binding stoichiometry and map the protein-protein interaction network of a human SAGA HAT subcomplex. MALDI-MS equipped with high mass detection was used to follow the cross-linking reaction using bis[sulfosuccinimidyl] suberate (BS3) and confirm the heterotetrameric stoichiometry of the specific stabilized subcomplex. Cross-linking with isotopically labeled BS3 d0-d4 followed by trypsin digestion allowed the identification of intra- and intercross-linked peptides using two dedicated search engines: pLink and xQuest. The identified interlinked peptides suggest a strong network of interaction between GCN5, ADA2B and ADA3 subunits; SGF29 is interacting with GCN5 and ADA3 but not with ADA2B. These restraint data were combined to molecular modeling and a low-resolution interacting model for the human SAGA HAT subcomplex could be proposed, illustrating the potential of an integrative strategy using cross-linking and mass spectrometry for addressing the structural architecture of multiprotein complexes.
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Affiliation(s)
- Nha-Thi Nguyen-Huynh
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS) UMR 7140 CNRS/Université de Strasbourg - "Chimie de la Matière Complexe", 1 Rue Blaise Pascal, 67008, Strasbourg, France
| | - Grigory Sharov
- Integrated Structural Biology Department, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104, INSERM U964, 1 rue Laurent Fries, 67404, Illkirch, France
| | - Clément Potel
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS) UMR 7140 CNRS/Université de Strasbourg - "Chimie de la Matière Complexe", 1 Rue Blaise Pascal, 67008, Strasbourg, France
| | - Pélagie Fichter
- Integrated Structural Biology Department, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104, INSERM U964, 1 rue Laurent Fries, 67404, Illkirch, France
| | - Simon Trowitzsch
- European Molecular Biology Laboratory (EMBL), Grenoble Outstation, 6 rue Jules Horowitz, 38042 Grenoble, France
| | - Imre Berger
- European Molecular Biology Laboratory (EMBL), Grenoble Outstation, 6 rue Jules Horowitz, 38042 Grenoble, France
| | - Valérie Lamour
- Integrated Structural Biology Department, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104, INSERM U964, 1 rue Laurent Fries, 67404, Illkirch, France
| | - Patrick Schultz
- Integrated Structural Biology Department, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104, INSERM U964, 1 rue Laurent Fries, 67404, Illkirch, France
| | - Noëlle Potier
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS) UMR 7140 CNRS/Université de Strasbourg - "Chimie de la Matière Complexe", 1 Rue Blaise Pascal, 67008, Strasbourg, France
| | - Emmanuelle Leize-Wagner
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS) UMR 7140 CNRS/Université de Strasbourg - "Chimie de la Matière Complexe", 1 Rue Blaise Pascal, 67008, Strasbourg, France
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23
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Lima DB, de Lima TB, Balbuena TS, Neves-Ferreira AGC, Barbosa VC, Gozzo FC, Carvalho PC. SIM-XL: A powerful and user-friendly tool for peptide cross-linking analysis. J Proteomics 2015; 129:51-55. [PMID: 25638023 DOI: 10.1016/j.jprot.2015.01.013] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 01/15/2015] [Accepted: 01/21/2015] [Indexed: 12/21/2022]
Abstract
Chemical cross-linking has emerged as a powerful approach for the structural characterization of proteins and protein complexes. However, the correct identification of covalently linked (cross-linked or XL) peptides analyzed by tandem mass spectrometry is still an open challenge. Here we present SIM-XL, a software tool that can analyze data generated through commonly used cross-linkers (e.g., BS3/DSS). Our software introduces a new paradigm for search-space reduction, which ultimately accounts for its increase in speed and sensitivity. Moreover, our search engine is the first to capitalize on reporter ions for selecting tandem mass spectra derived from cross-linked peptides. It also makes available a 2D interaction map and a spectrum-annotation tool unmatched by any of its kind. We show SIM-XL to be more sensitive and faster than a competing tool when analyzing a data set obtained from the human HSP90. The software is freely available for academic use at http://patternlabforproteomics.org/sim-xl. A video demonstrating the tool is available at http://patternlabforproteomics.org/sim-xl/video. SIM-XL is the first tool to support XL data in the mzIdentML format; all data are thus available from the ProteomeXchange consortium (identifier PXD001677). This article is part of a Special Issue entitled: Computational Proteomics.
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Affiliation(s)
- Diogo B Lima
- Laboratory for Proteomics and Protein Engineering, Carlos Chagas Institute, Fiocruz, Paraná, Brazil.
| | - Tatiani B de Lima
- Dalton Mass Spectrometry Laboratory, University of Campinas, São Paulo, Brazil
| | - Tiago S Balbuena
- College of Agricultural and Veterinary Sciences, State University of São Paulo, Jaboticabal, São Paulo, Brazil
| | | | - Valmir C Barbosa
- Systems Engineering and Computer Science Program, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fábio C Gozzo
- Dalton Mass Spectrometry Laboratory, University of Campinas, São Paulo, Brazil.
| | - Paulo C Carvalho
- Laboratory for Proteomics and Protein Engineering, Carlos Chagas Institute, Fiocruz, Paraná, Brazil.
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24
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Merkley ED, Rysavy S, Kahraman A, Hafen RP, Daggett V, Adkins JN. Distance restraints from crosslinking mass spectrometry: mining a molecular dynamics simulation database to evaluate lysine-lysine distances. Protein Sci 2014; 23:747-59. [PMID: 24639379 DOI: 10.1002/pro.2458] [Citation(s) in RCA: 203] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 03/13/2014] [Accepted: 03/14/2014] [Indexed: 12/24/2022]
Abstract
Integrative structural biology attempts to model the structures of protein complexes that are challenging or intractable by classical structural methods (due to size, dynamics, or heterogeneity) by combining computational structural modeling with data from experimental methods. One such experimental method is chemical crosslinking mass spectrometry (XL-MS), in which protein complexes are crosslinked and characterized using liquid chromatography-mass spectrometry to pinpoint specific amino acid residues in close structural proximity. The commonly used lysine-reactive N-hydroxysuccinimide ester reagents disuccinimidylsuberate (DSS) and bis(sulfosuccinimidyl)suberate (BS(3) ) have a linker arm that is 11.4 Å long when fully extended, allowing Cα (alpha carbon of protein backbone) atoms of crosslinked lysine residues to be up to ∼24 Å apart. However, XL-MS studies on proteins of known structure frequently report crosslinks that exceed this distance. Typically, a tolerance of ∼3 Å is added to the theoretical maximum to account for this observation, with limited justification for the chosen value. We used the Dynameomics database, a repository of high-quality molecular dynamics simulations of 807 proteins representative of diverse protein folds, to investigate the relationship between lysine-lysine distances in experimental starting structures and in simulation ensembles. We conclude that for DSS/BS(3), a distance constraint of 26-30 Å between Cα atoms is appropriate. This analysis provides a theoretical basis for the widespread practice of adding a tolerance to the crosslinker length when comparing XL-MS results to structures or in modeling. We also discuss the comparison of XL-MS results to MD simulations and known structures as a means to test and validate experimental XL-MS methods.
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Affiliation(s)
- Eric D Merkley
- Biological Sciences Division, Pacific Northwest National Laboratories, Richland, Washington, 99352-1793
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