1
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Lu H, Zhu Z, Fields L, Zhang H, Li L. Mass Spectrometry Structural Proteomics Enabled by Limited Proteolysis and Cross-Linking. MASS SPECTROMETRY REVIEWS 2024. [PMID: 39300771 DOI: 10.1002/mas.21908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 08/31/2024] [Accepted: 09/02/2024] [Indexed: 09/22/2024]
Abstract
The exploration of protein structure and function stands at the forefront of life science and represents an ever-expanding focus in the development of proteomics. As mass spectrometry (MS) offers readout of protein conformational changes at both the protein and peptide levels, MS-based structural proteomics is making significant strides in the realms of structural and molecular biology, complementing traditional structural biology techniques. This review focuses on two powerful MS-based techniques for peptide-level readout, namely limited proteolysis-mass spectrometry (LiP-MS) and cross-linking mass spectrometry (XL-MS). First, we discuss the principles, features, and different workflows of these two methods. Subsequently, we delve into the bioinformatics strategies and software tools used for interpreting data associated with these protein conformation readouts and how the data can be integrated with other computational tools. Furthermore, we provide a comprehensive summary of the noteworthy applications of LiP-MS and XL-MS in diverse areas including neurodegenerative diseases, interactome studies, membrane proteins, and artificial intelligence-based structural analysis. Finally, we discuss the factors that modulate protein conformational changes. We also highlight the remaining challenges in understanding the intricacies of protein conformational changes by LiP-MS and XL-MS technologies.
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Affiliation(s)
- Haiyan Lu
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Zexin Zhu
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Lauren Fields
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Hua Zhang
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
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2
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Ryan KA, Bruening ML. Online protein digestion in membranes between capillary electrophoresis and mass spectrometry. Analyst 2023; 148:1611-1619. [PMID: 36912593 DOI: 10.1039/d3an00106g] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
This research employs pepsin-containing membranes to digest proteins online after a capillary electrophoresis (CE) separation and prior to tandem mass spectrometry. Proteolysis after the separation allows the peptides from a given protein to enter the mass spectrometer in a single plug. Thus, migration time can serve as an additional criterion for confirming the identification of a peptide. The membrane resides in a sheath-flow electrospray ionization (ESI) source to enable digestion immediately before spray into the mass spectrometer, thus limiting separation of the digested peptides. Using the same membrane, digestion occurred reproducibly during 20 consecutive CE analyses performed over a 10 h period. Additionally, after separating a mixture of six unreduced proteins with CE, online digestion facilitated protein identification with at least 2 identifiable peptides for all the proteins. Sequence coverages were >75% for myoglobin and carbonic anhydrase II but much lower for proteins containing disulfide bonds. Development of methods for efficient separation of reduced proteins or identification of cross-linked peptides should enhance sequence coverages for proteins with disulfide bonds. Migration times for the peptides identified from a specific protein differed by <∼30 s, which allows for rejection of some spurious peptide identifications.
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Affiliation(s)
- Kendall A Ryan
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Merlin L Bruening
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA. .,Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
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3
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Na S, Paek E. Computational methods in mass spectrometry-based structural proteomics for studying protein structure, dynamics, and interactions. Comput Struct Biotechnol J 2020; 18:1391-1402. [PMID: 32637038 PMCID: PMC7322682 DOI: 10.1016/j.csbj.2020.06.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 06/01/2020] [Accepted: 06/01/2020] [Indexed: 12/28/2022] Open
Abstract
Mass spectrometry (MS) has made enormous contributions to comprehensive protein identification and quantification in proteomics. MS is also gaining momentum for structural biology in a variety of ways, complementing conventional structural biology techniques. Here, we will review how MS-based techniques, such as hydrogen/deuterium exchange, covalent labeling, and chemical cross-linking, enable the characterization of protein structure, dynamics, and interactions, especially from a perspective of their data analyses. Structural information encoded by chemical probes in intact proteins is decoded by interpreting MS data at a peptide level, i.e., revealing conformational and dynamic changes in local regions of proteins. The structural MS data are not amenable to data analyses in traditional proteomics workflow, requiring dedicated software for each type of data. We first provide basic principles of data interpretation, including isotopic distribution and peptide sequencing. We then focus particularly on computational methods for structural MS data analyses and discuss outstanding challenges in a proteome-wide large scale analysis.
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Affiliation(s)
- Seungjin Na
- Dept. of Computer Science, Hanyang University, Seoul 04763, Republic of Korea
| | - Eunok Paek
- Dept. of Computer Science, Hanyang University, Seoul 04763, Republic of Korea
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4
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Riffle M, Jaschob D, Zelter A, Davis TN. Proxl (Protein Cross-Linking Database): A Public Server, QC Tools, and Other Major Updates. J Proteome Res 2019; 18:759-764. [PMID: 30525651 DOI: 10.1021/acs.jproteome.8b00726] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Proxl is an open-source web application for sharing, visualizing, and analyzing bottom-up protein cross-linking mass spectrometry data and results. Proxl's core features include comparing data sets, structural analysis, customizable and interactive data visualizations, access to all underlying mass spectrometry data, and quality-control tools. All features of Proxl are designed to be independent of specific cross-linker chemistry or software analysis pipelines. Proxl's sharing tools allow users to share their data with the public or securely restrict access to trusted collaborators. Since being published in 2016, Proxl has continued to be expanded and improved through active development and collaboration with cross-linking researchers. Some of Proxl's new features include a centralized, public site for sharing data, greatly expanded quality-control tools and visualizations, support for stable isotope-labeled peptides, and general improvements that make Proxl easier to use, data easier to share and import, and data visualizations more customizable. Source code and more information are found at http://proxl-ms.org/ .
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Affiliation(s)
- Michael Riffle
- Department of Biochemistry , University of Washington , Seattle , Washington 98195 , United States.,Department of Genome Sciences , University of Washington , Seattle , Washington 98195 , United States
| | - Daniel Jaschob
- Department of Biochemistry , University of Washington , Seattle , Washington 98195 , United States
| | - Alex Zelter
- Department of Biochemistry , University of Washington , Seattle , Washington 98195 , United States
| | - Trisha N Davis
- Department of Biochemistry , University of Washington , Seattle , Washington 98195 , United States
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5
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Downard KM, Maleknia SD. Mass spectrometry in structural proteomics: The case for radical probe protein footprinting. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2018.11.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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6
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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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7
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Mohr JP, Perumalla P, Chavez JD, Eng JK, Bruce JE. Mango: A General Tool for Collision Induced Dissociation-Cleavable Cross-Linked Peptide Identification. Anal Chem 2018; 90:6028-6034. [PMID: 29676898 PMCID: PMC5959040 DOI: 10.1021/acs.analchem.7b04991] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Chemical cross-linking combined with mass spectrometry provides a method to study protein structures and interactions. The introduction of cleavable bonds in a cross-linker provides an avenue to decouple released peptide masses from their precursor species, greatly simplifying the downstream search, allowing for whole proteome investigations to be performed. Typically, these experiments have been challenging to carry out, often utilizing nonstandard methods to fully identify cross-linked peptides. Mango is an open source software tool that extracts precursor masses from chimeric spectra generated using cleavable cross-linkers, greatly simplifying the downstream search. As it is designed to work with chimeric spectra, Mango can be used on traditional high-resolution tandem mass spectrometry (MS/MS) capable mass spectrometers without the need for additional modifications. When paired with a traditional proteomics search engine, Mango can be used to identify several thousand cross-linked peptide pairs searching against the entire Escherichia coli proteome. Mango provides an avenue to perform whole proteome cross-linking experiments without specialized instrumentation or access to nonstandard methods.
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Affiliation(s)
- Jared P. Mohr
- Department of Genome Sciences, University of Washington, Seattle, Washington 98105, United States
| | - Poorna Perumalla
- Department of Genome Sciences, University of Washington, Seattle, Washington 98105, United States
| | - Juan D. Chavez
- Department of Genome Sciences, University of Washington, Seattle, Washington 98105, United States
| | - Jimmy K. Eng
- Department of Genome Sciences, University of Washington, Seattle, Washington 98105, United States
| | - James E. Bruce
- Department of Genome Sciences, University of Washington, Seattle, Washington 98105, United States
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8
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Hoopmann MR, Mendoza L, Deutsch EW, Shteynberg D, Moritz RL. An Open Data Format for Visualization and Analysis of Cross-Linked Mass Spectrometry Results. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1728-1734. [PMID: 27469004 PMCID: PMC5061604 DOI: 10.1007/s13361-016-1435-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 05/23/2016] [Accepted: 05/23/2016] [Indexed: 06/06/2023]
Abstract
Protein-protein interactions are an important element in the understanding of protein function, and chemical cross-linking shotgun mass spectrometry is rapidly becoming a routine approach to identify these specific interfaces and topographical interactions. Protein cross-link data analysis is aided by dozens of algorithm choices, but hindered by a lack of a common format for representing results. Consequently, interoperability between algorithms and pipelines utilizing chemical cross-linking remains a challenge. pepXML is an open, widely-used format for representing spectral search algorithm results that has facilitated information exchange and pipeline development for typical shotgun mass spectrometry analyses. We describe an extension of this format to incorporate cross-linking spectral search results. We demonstrate application of the extension by representing results of multiple cross-linking search algorithms. In addition, we demonstrate adapting existing pepXML-supporting software pipelines to analyze protein cross-linking results formatted in pepXML. Graphical Abstract ᅟ.
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Affiliation(s)
| | - Luis Mendoza
- Institute for Systems Biology, Seattle, Washington, 98109, USA
| | - Eric W Deutsch
- Institute for Systems Biology, Seattle, Washington, 98109, USA
| | | | - Robert L Moritz
- Institute for Systems Biology, Seattle, Washington, 98109, USA
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9
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Riffle M, Jaschob D, Zelter A, Davis TN. ProXL (Protein Cross-Linking Database): A Platform for Analysis, Visualization, and Sharing of Protein Cross-Linking Mass Spectrometry Data. J Proteome Res 2016; 15:2863-70. [PMID: 27302480 PMCID: PMC4977572 DOI: 10.1021/acs.jproteome.6b00274] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
![]()
ProXL
is a Web application and accompanying database designed for
sharing, visualizing, and analyzing bottom-up protein cross-linking
mass spectrometry data with an emphasis on structural analysis and
quality control. ProXL is designed to be independent of any particular
software pipeline. The import process is simplified by the use of
the ProXL XML data format, which shields developers of data importers
from the relative complexity of the relational database schema. The
database and Web interfaces function equally well for any software
pipeline and allow data from disparate pipelines to be merged and
contrasted. ProXL includes robust public and private data sharing
capabilities, including a project-based interface designed to ensure
security and facilitate collaboration among multiple researchers.
ProXL provides multiple interactive and highly dynamic data visualizations
that facilitate structural-based analysis of the observed cross-links
as well as quality control. ProXL is open-source, well-documented,
and freely available at https://github.com/yeastrc/proxl-web-app.
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Affiliation(s)
- Michael Riffle
- Department of Biochemistry, University of Washington , Seattle, Washington 98195, United States.,Department of Genome Sciences, University of Washington , Seattle, Washington 98195, United States
| | - Daniel Jaschob
- Department of Biochemistry, University of Washington , Seattle, Washington 98195, United States
| | - Alex Zelter
- Department of Biochemistry, University of Washington , Seattle, Washington 98195, United States
| | - Trisha N Davis
- Department of Biochemistry, University of Washington , Seattle, Washington 98195, United States
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10
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Yu F, Li N, Yu W. ECL: an exhaustive search tool for the identification of cross-linked peptides using whole database. BMC Bioinformatics 2016; 17:217. [PMID: 27206479 PMCID: PMC4874008 DOI: 10.1186/s12859-016-1073-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 05/07/2016] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Chemical cross-linking combined with mass spectrometry (CX-MS) is a high-throughput approach to studying protein-protein interactions. The number of peptide-peptide combinations grows quadratically with respect to the number of proteins, resulting in a high computational complexity. Widely used methods including xQuest (Rinner et al., Nat Methods 5(4):315-8, 2008; Walzthoeni et al., Nat Methods 9(9):901-3, 2012), pLink (Yang et al., Nat Methods 9(9):904-6, 2012), ProteinProspector (Chu et al., Mol Cell Proteomics 9:25-31, 2010; Trnka et al., 13(2):420-34, 2014) and Kojak (Hoopmann et al., J Proteome Res 14(5):2190-198, 2015) avoid searching all peptide-peptide combinations by pre-selecting peptides with heuristic approaches. However, pre-selection procedures may cause missing findings. The most intuitive approach is searching all possible candidates. A tool that can exhaustively search a whole database without any heuristic pre-selection procedure is therefore desirable. RESULTS We have developed a cross-linked peptides identification tool named ECL. It can exhaustively search a whole database in a reasonable period of time without any heuristic pre-selection procedure. Tests showed that searching a database containing 5200 proteins took 7 h. ECL identified more non-redundant cross-linked peptides than xQuest, pLink, and ProteinProspector. Experiments showed that about 30 % of these additional identified peptides were not pre-selected by Kojak. We used protein crystal structures from the protein data bank to check the intra-protein cross-linked peptides. Most of the distances between cross-linking sites were smaller than 30 Å. CONCLUSIONS To the best of our knowledge, ECL is the first tool that can exhaustively search all candidates in cross-linked peptides identification. The experiments showed that ECL could identify more peptides than xQuest, pLink, and ProteinProspector. A further analysis indicated that some of the additional identified results were thanks to the exhaustive search.
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Affiliation(s)
- Fengchao Yu
- Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Ning Li
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China.
| | - Weichuan Yu
- Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Hong Kong, China.
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong, China.
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11
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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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12
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Argo AS, Shi C, Liu F, Goshe MB. Performing protein crosslinking using gas-phase cleavable chemical crosslinkers and liquid chromatography-tandem mass spectrometry. Methods 2015; 89:64-73. [DOI: 10.1016/j.ymeth.2015.06.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 05/12/2015] [Accepted: 06/09/2015] [Indexed: 12/13/2022] Open
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13
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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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14
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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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15
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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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16
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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: 25] [Impact Index Per Article: 2.8] [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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17
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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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18
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Pereira MBM, Santos AM, Gonçalves DC, Cardoso AC, Consonni SR, Gozzo FC, Oliveira PS, Pereira AHM, Figueiredo AR, Tiroli-Cepeda AO, Ramos CHI, de Thomaz AA, Cesar CL, Franchini KG. αB-crystallin interacts with and prevents stress-activated proteolysis of focal adhesion kinase by calpain in cardiomyocytes. Nat Commun 2014; 5:5159. [PMID: 25319025 DOI: 10.1038/ncomms6159] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 09/05/2014] [Indexed: 12/14/2022] Open
Abstract
Focal adhesion kinase (FAK) contributes to cellular homeostasis under stress conditions. Here we show that αB-crystallin interacts with and confers protection to FAK against calpain-mediated proteolysis in cardiomyocytes. A hydrophobic patch mapped between helices 1 and 4 of the FAK FAT domain was found to bind to the β4-β8 groove of αB-crystallin. Such an interaction requires FAK tyrosine 925 and is enhanced following its phosphorylation by Src, which occurs upon FAK stimulation. αB-crystallin silencing results in calpain-dependent FAK depletion and in the increased apoptosis of cardiomyocytes in response to mechanical stress. FAK overexpression protects cardiomyocytes depleted of αB-crystallin against the stretch-induced apoptosis. Consistently, load-induced apoptosis is blunted in the hearts from cardiac-specific FAK transgenic mice transiently depleted of αB-crystallin by RNA interference. These studies define a role for αB-crystallin in controlling FAK function and cardiomyocyte survival through the prevention of calpain-mediated degradation of FAK.
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Affiliation(s)
- Michelle B M Pereira
- Brazilian National Laboratory for Biosciences, Center for Research in Energy and Materials, Campinas, São Paulo 13084-971, Brazil
| | - Aline M Santos
- Brazilian National Laboratory for Biosciences, Center for Research in Energy and Materials, Campinas, São Paulo 13084-971, Brazil
| | - Danieli C Gonçalves
- Brazilian National Laboratory for Biosciences, Center for Research in Energy and Materials, Campinas, São Paulo 13084-971, Brazil
| | - Alisson C Cardoso
- Brazilian National Laboratory for Biosciences, Center for Research in Energy and Materials, Campinas, São Paulo 13084-971, Brazil
| | - Sílvio R Consonni
- Brazilian National Laboratory for Biosciences, Center for Research in Energy and Materials, Campinas, São Paulo 13084-971, Brazil
| | - Fabio C Gozzo
- Chemistry Institute, University of Campinas, Campinas, São Paulo 13083-970, Brazil
| | - Paulo S Oliveira
- Brazilian National Laboratory for Biosciences, Center for Research in Energy and Materials, Campinas, São Paulo 13084-971, Brazil
| | - Ana Helena M Pereira
- Brazilian National Laboratory for Biosciences, Center for Research in Energy and Materials, Campinas, São Paulo 13084-971, Brazil
| | - Alana R Figueiredo
- Chemistry Institute, University of Campinas, Campinas, São Paulo 13083-970, Brazil
| | - Ana O Tiroli-Cepeda
- Chemistry Institute, University of Campinas, Campinas, São Paulo 13083-970, Brazil
| | - Carlos H I Ramos
- Chemistry Institute, University of Campinas, Campinas, São Paulo 13083-970, Brazil
| | - André A de Thomaz
- Gleb Wataghin Physics Institute, University of Campinas, Campinas, São Paulo 13083-859, Brazil
| | - Carlos L Cesar
- Gleb Wataghin Physics Institute, University of Campinas, Campinas, São Paulo 13083-859, Brazil
| | - Kleber G Franchini
- 1] Brazilian National Laboratory for Biosciences, Center for Research in Energy and Materials, Campinas, São Paulo 13084-971, Brazil [2] Department of Internal Medicine, School of Medicine, University of Campinas, Campinas, São Paulo 13081-970, Brazil
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19
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A mass spectrometry view of stable and transient protein interactions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 806:263-82. [PMID: 24952186 DOI: 10.1007/978-3-319-06068-2_11] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Through an impressive range of dynamic interactions, proteins succeed to carry out the majority of functions in a cell. These temporally and spatially regulated interactions provide the means through which one single protein can perform diverse functions and modulate different cellular pathways. Understanding the identity and nature of these interactions is therefore critical for defining protein functions and their contribution to health and disease processes. Here, we provide an overview of workflows that incorporate immunoaffinity purifications and quantitative mass spectrometry (frequently abbreviated as IP-MS or AP-MS) for characterizing protein-protein interactions. We discuss experimental aspects that should be considered when optimizing the isolation of a protein complex. As the presence of nonspecific associations is a concern in these experiments, we discuss the common sources of nonspecific interactions and present label-free and metabolic labeling mass spectrometry-based methods that can help determine the specificity of interactions. The effective regulation of cellular pathways and the rapid reaction to various environmental stresses rely on the formation of stable, transient, and fast-exchanging protein-protein interactions. While determining the exact nature of an interaction remains challenging, we review cross-linking and metabolic labeling approaches that can help address this important aspect of characterizing protein interactions and macromolecular assemblies.
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20
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McIlwain S, Tamura K, Kertesz-Farkas A, Grant CE, Diament B, Frewen B, Howbert JJ, Hoopmann MR, Käll L, Eng JK, MacCoss MJ, Noble WS. Crux: rapid open source protein tandem mass spectrometry analysis. J Proteome Res 2014; 13:4488-91. [PMID: 25182276 PMCID: PMC4184452 DOI: 10.1021/pr500741y] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Efficiently and accurately analyzing big protein tandem mass spectrometry data sets requires robust software that incorporates state-of-the-art computational, machine learning, and statistical methods. The Crux mass spectrometry analysis software toolkit ( http://cruxtoolkit.sourceforge.net ) is an open source project that aims to provide users with a cross-platform suite of analysis tools for interpreting protein mass spectrometry data.
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Affiliation(s)
- Sean McIlwain
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison , 1552 University Avenue, Madison, Wisconsin 53726, United States
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21
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Koolen HHF, Gomes AF, Schwab NV, Eberlin MN, Gozzo FC. Imidate-based cross-linkers for structural proteomics: increased charge of protein and peptide ions and CID and ECD fragmentation studies. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:1181-1191. [PMID: 24781457 DOI: 10.1007/s13361-014-0900-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 03/21/2014] [Accepted: 03/21/2014] [Indexed: 06/03/2023]
Abstract
Chemical cross-linking is an attractive low-resolution technique for structural studies of protein complexes. Distance constraints obtained from cross-linked peptides identified by mass spectrometry (MS) are used to construct and validate protein models. Amidinating cross-linkers such as diethyl suberthioimidate (DEST) have been used successfully in chemical cross-linking experiments. In this work, the application of a commercial diimidate cross-linking reagent, dimethyl suberimidate (DMS), was evaluated with model peptides and proteins. The peptides were designed with acetylated N-termini followed by random sequences containing two Lys residues separated by an Arg residue. After cross-linking reactions, intra- and intermolecular cross-linked species were submitted to CID and ECD dissociations to study their fragmentation features in the gas phase. Fragmentation of intramolecular peptides by collision induced dissociation (CID) demonstrates a unique two-step fragmentation pathway involving formation of a ketimine as intermediate. Electron capture and electron transfer dissociation (ECD and ETD) experiments demonstrated that the cyclic moiety is not dissociated. Intermolecular species demonstrated previously described fragmentation behavior in both CID and ECD experiments. The charge state distributions (CSD) obtained after reaction with DMS were compared with those obtained with disuccinimidyl suberate (DSS). CSDs for peptides and proteins were increased after their reaction with DMS, owing to the higher basicity of DMS modified species. These features were also observed in LC-MS experiments with bovine carbonic anhydrase II (BCA) after cross-linking with DMS and tryptic proteolysis. Cross-linked peptides derived from this protein were identified at high confidence and those species were in agreement with the crystal structure of BCA.
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Affiliation(s)
- Hector H F Koolen
- Institute of Chemistry, University of Campinas and Instituto Nacional de Ciência e Tecnologia de Bioanalítica, Sao Paulo, 13083-970, Brazil
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22
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Maes E, Valkenborg D, Mertens I, Broeckx V, Baggerman G, Sagaert X, Landuyt B, Prenen H, Schoofs L. Proteomic analysis of formalin-fixed paraffin-embedded colorectal cancer tissue using tandem mass tag protein labeling. MOLECULAR BIOSYSTEMS 2014; 9:2686-95. [PMID: 23986405 DOI: 10.1039/c3mb70177h] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In clinical research, repositories of biological samples form a rich source of clinical material for biomarker studies. Banked material, however, is often not stored in optimal conditions regarding the technology used for biomarker research. A case in point is formalin-fixed paraffin-embedded (FFPE) tissue that could be used to obtain large cohorts of samples over a short period of time, as these tissues are routinely prepared for pathological analysis. However, in the context of mass spectrometry based peptide-centric proteomics, protein extraction and identification can be hampered by formalin-induced crosslinking. Furthermore, the molecular formalin crosslinks might be entangled differently across various samples, making it more difficult to reproducibly extract the same proteins from different samples. In this study, we establish the crosslink variability using Tandem Mass Tag (TMT) protein labeling followed by digestion, separation, identification and quantification of proteins extracted from FFPE colorectal cancer and paired healthy tissues. Moreover, by applying de novo interpretation of tandem mass spectra and subsequent analysis by Peaks PTM, unspecified modifications could be elucidated, leading to increased protein and proteome coverage. This approach might be useful for future FFPE proteomics studies.
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Affiliation(s)
- Evelyne Maes
- Flemish Institute for Technological Research (VITO), Mol, Belgium
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23
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Tiroli-Cepeda AO, Lima TB, Balbuena TS, Gozzo FC, Ramos CHI. Structural and functional characterization of the chaperone Hsp70 from sugarcane. Insights into conformational changes during cycling from cross-linking/mass spectrometry assays. J Proteomics 2014; 104:48-56. [PMID: 24530624 DOI: 10.1016/j.jprot.2014.02.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2013] [Revised: 01/28/2014] [Accepted: 02/02/2014] [Indexed: 01/20/2023]
Abstract
UNLABELLED Hsp70 cycles from an ATP-bound state, in which the affinity for unfolded polypeptides is low, to an ADP-bound state, in which the affinity for unfolded polypeptides is high, to assist with cell proteostasis. Such cycling also depends on co-chaperones because these proteins control both the Hsp70 ATPase activity and the delivery of unfolded polypeptide chains. Although it is very important, structural information on the entire protein is still scarce. This work describes the first cloning of a cDNA predicted to code for a cytosolic Saccharum spp. (sugarcane) Hsp70, named SsHsp70 here, the purification of the recombinant protein and the characterization of its structural conformation in solution by chemical cross-linking coupled to mass spectrometry. The in vivo expression of SsHsp70 in sugarcane extracts was confirmed by Western blot. Recombinant SsHsp70 was monomeric, both ADP and ATP binding increased its stability and it was efficient in cooperating with co-chaperones: ATPase activity was stimulated by Hsp40s, and it aided the refolding of an unfolded polypeptide delivered by a member of the small Hsp family. The structural conformation results favor a model in which nucleotide-free SsHsp70 is highly dynamic and may fluctuate among different conformations that may resemble those in which nucleotide is bound. BIOLOGICAL SIGNIFICANCE Validation of a sugarcane EST as a true mRNA that encodes a cytosolic Hsp70 (SsHsp70) as confirmed by in vivo expression and characterization of the structure and function of the recombinant protein. SsHsp70 was monomeric, both ADP and ATP binding increased its stability and was efficient in interacting and cooperating with co-chaperones to enhance ATPase activity and refold unfolded proteins. The conformation of nucleotide-free SsHsp70 in solution was much more dynamic than suggested by crystal structures of other Hsp70s. This article is part of a Special Issue entitled: Environmental and structural proteomics.
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Affiliation(s)
- Ana O Tiroli-Cepeda
- Institute of Chemistry, University of Campinas-UNICAMP, P.O. Box 6154, 13083-970 Campinas, SP, Brazil; Instituto Nacional de Ciência e Tecnologia em Biologia Estrutural e Bioimagem, Brazil
| | - Tatiani B Lima
- Institute of Chemistry, University of Campinas-UNICAMP, P.O. Box 6154, 13083-970 Campinas, SP, Brazil
| | - Tiago S Balbuena
- Faculdade de Ciências Agrárias e Veterinárias, UNESP Universidade Estadual Paulista, Campus de Jaboticabal, Jaboticabal, SP 14884-900, Brazil
| | - Fábio C Gozzo
- Institute of Chemistry, University of Campinas-UNICAMP, P.O. Box 6154, 13083-970 Campinas, SP, Brazil
| | - Carlos H I Ramos
- Institute of Chemistry, University of Campinas-UNICAMP, P.O. Box 6154, 13083-970 Campinas, SP, Brazil; Instituto Nacional de Ciência e Tecnologia em Biologia Estrutural e Bioimagem, Brazil.
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24
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Wang J, Anania VG, Knott J, Rush J, Lill JR, Bourne PE, Bandeira N. Combinatorial approach for large-scale identification of linked peptides from tandem mass spectrometry spectra. Mol Cell Proteomics 2014; 13:1128-36. [PMID: 24493012 DOI: 10.1074/mcp.m113.035758] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The combination of chemical cross-linking and mass spectrometry has recently been shown to constitute a powerful tool for studying protein-protein interactions and elucidating the structure of large protein complexes. However, computational methods for interpreting the complex MS/MS spectra from linked peptides are still in their infancy, making the high-throughput application of this approach largely impractical. Because of the lack of large annotated datasets, most current approaches do not capture the specific fragmentation patterns of linked peptides and therefore are not optimal for the identification of cross-linked peptides. Here we propose a generic approach to address this problem and demonstrate it using disulfide-bridged peptide libraries to (i) efficiently generate large mass spectral reference data for linked peptides at a low cost and (ii) automatically train an algorithm that can efficiently and accurately identify linked peptides from MS/MS spectra. We show that using this approach we were able to identify thousands of MS/MS spectra from disulfide-bridged peptides through comparison with proteome-scale sequence databases and significantly improve the sensitivity of cross-linked peptide identification. This allowed us to identify 60% more direct pairwise interactions between the protein subunits in the 20S proteasome complex than existing tools on cross-linking studies of the proteasome complexes. The basic framework of this approach and the MS/MS reference dataset generated should be valuable resources for the future development of new tools for the identification of linked peptides.
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Affiliation(s)
- Jian Wang
- Bioinformatics Program, University of California, San Diego, La Jolla, California
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25
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Sriswasdi S, Harper SL, Tang HY, Speicher DW. Enhanced identification of zero-length chemical cross-links using label-free quantitation and high-resolution fragment ion spectra. J Proteome Res 2014; 13:898-914. [PMID: 24369724 DOI: 10.1021/pr400953w] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Chemical cross-linking coupled to mass spectrometry provides structural information that is useful for probing protein conformations and providing experimental support for molecular models. "Zero-length" cross-links have greater value for these applications than longer cross-links because they provide more stringent distance constraints. However, this method is less commonly utilized because it cannot take advantage of isotopic labels, MS-labile bonds, or enrichment tags to facilitate identification. In this study, we combined label-free precursor ion quantitation and targeted tandem mass spectrometry with a new software tool, Zero-length Cross-link Miner (ZXMiner), to form a multitiered analysis strategy. A major, critical objective was to simultaneously achieve very high accuracy with essentially no false-positive cross-link identifications while maintaining a good depth of analysis. Our strategy was optimized on several proteins with known crystal structures. Comparison of ZXMiner to several existing cross-link analysis software showed that other algorithms detected less true positive cross-links and were far less accurate. Although prior use of zero-length cross-linking was typically restricted to small proteins, ZXMiner and the associated strategy enable facile analysis of very large protein complexes. This was demonstrated by identification of zero-length cross-links using purified 526 kDa spectrin heterodimers and intact red cell membranes and membrane skeletons.
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Affiliation(s)
- Sira Sriswasdi
- Center for Systems and Computational Biology and Molecular and Cellular Oncogenesis Program, The Wistar Institute , 3601 Spruce Street, Philadelphia, Pennsylvania 19104, United States
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26
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Mayne SLN, Patterton HG. AnchorMS: a bioinformatics tool to derive structural information from the mass spectra of cross-linked protein complexes. Bioinformatics 2013; 30:125-6. [DOI: 10.1093/bioinformatics/btt617] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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27
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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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28
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da Silva VCH, Cagliari TC, Lima TB, Gozzo FC, Ramos CHI. Conformational and functional studies of a cytosolic 90 kDa heat shock protein Hsp90 from sugarcane. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2013; 68:16-22. [PMID: 23619240 DOI: 10.1016/j.plaphy.2013.03.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 03/20/2013] [Indexed: 06/02/2023]
Abstract
Hsp90s are involved in several cellular processes, such as signaling, proteostasis, epigenetics, differentiation and stress defense. Although Hsp90s from different organisms are highly similar, they usually have small variations in conformation and function. Thus, the characterization of different Hsp90s is important to gain insight into the structure-function relationship that makes these chaperones key regulators in protein homeostasis. This work describes the characterization of a cytosolic Hsp90 from sugarcane and its comparison with Hsp90s from other plants. Previous expressed sequence tag (EST) studies in Saccharum spp. (sugarcane) predicted the presence of an mRNA coding for a cytosolic Hsp90. The corresponding cDNA was cloned, and the recombinant protein was purified and its conformation and function characterized. The structural conformation of Hsp90 was assessed by chemical cross-linking and hydrogen/deuterium exchange using mass spectrometry and hydrodynamic assays, which revealed regions accessible to solvent and that Hsp90 is an elongated dimer in solution. The in vivo expression of Hsp90 in sugarcane leaves was confirmed by western blot, and in vitro functional characterization indicated that sugarcane Hsp90 has strong chaperone activity.
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Affiliation(s)
- Viviane C H da Silva
- Institute of Chemistry, University of Campinas-UNICAMP, P.O. Box 6154, 13083-970 Campinas, SP, Brazil
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29
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Miteva YV, Budayeva HG, Cristea IM. Proteomics-based methods for discovery, quantification, and validation of protein-protein interactions. Anal Chem 2013; 85:749-68. [PMID: 23157382 PMCID: PMC3666915 DOI: 10.1021/ac3033257] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | - Ileana M. Cristea
- Corresponding author: Ileana M. Cristea 210 Lewis Thomas Laboratory Department of Molecular Biology Princeton University Princeton, NJ 08544 Tel: 6092589417 Fax: 6092584575
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30
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Fioramonte M, dos Santos AM, McIlwain S, Noble WS, Franchini KG, Gozzo FC. Analysis of secondary structure in proteins by chemical cross-linking coupled to MS. Proteomics 2013; 12:2746-52. [PMID: 22778071 DOI: 10.1002/pmic.201200040] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Chemical cross-linking is an attractive technique for the study of the structure of protein complexes due to its low sample consumption and short analysis time. Furthermore, distance constraints obtained from the identification of cross-linked peptides by MS can be used to construct and validate protein models. If a sufficient number of distance constraints are obtained, then determining the secondary structure of a protein can allow inference of the protein's fold. In this work, we show how the distance constraints obtained from cross-linking experiments can identify secondary structures within the protein sequence. Molecular modeling of alpha helices and beta sheets reveals that each secondary structure presents different cross-linking possibilities due to the topological distances between reactive residues. Cross-linking experiments performed with amine reactive cross-linkers with model alpha helix containing proteins corroborated the molecular modeling predictions. The cross-linking patterns established here can be extended to other cross-linkers with known lengths for the determination of secondary structures in proteins.
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31
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McIlwain S, Mathews M, Bereman MS, Rubel EW, MacCoss MJ, Noble WS. Estimating relative abundances of proteins from shotgun proteomics data. BMC Bioinformatics 2012; 13:308. [PMID: 23164367 PMCID: PMC3599300 DOI: 10.1186/1471-2105-13-308] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Accepted: 10/31/2012] [Indexed: 11/10/2022] Open
Abstract
Background Spectral counting methods provide an easy means of identifying proteins with differing abundances between complex mixtures using shotgun proteomics data. The crux spectral-counts command, implemented as part of the Crux software toolkit, implements four previously reported spectral counting methods, the spectral index (SIN), the exponentially modified protein abundance index (emPAI), the normalized spectral abundance factor (NSAF), and the distributed normalized spectral abundance factor (dNSAF). Results We compared the reproducibility and the linearity relative to each protein’s abundance of the four spectral counting metrics. Our analysis suggests that NSAF yields the most reproducible counts across technical and biological replicates, and both SIN and NSAF achieve the best linearity. Conclusions With the crux spectral-counts command, Crux provides open-source modular methods to analyze mass spectrometry data for identifying and now quantifying peptides and proteins. The C++ source code, compiled binaries, spectra and sequence databases are available at
http://noble.gs.washington.edu/proj/crux-spectral-counts.
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Affiliation(s)
- Sean McIlwain
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
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32
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Li W, O'Neill HA, Wysocki VH. SQID-XLink: implementation of an intensity-incorporated algorithm for cross-linked peptide identification. ACTA ACUST UNITED AC 2012; 28:2548-50. [PMID: 22796956 DOI: 10.1093/bioinformatics/bts442] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
SUMMARY Peptide identification algorithm is a major bottleneck for mass spectrometry based chemical cross-linking experiments. Our lab recently developed an intensity-incorporated peptide identification algorithm, and here we implemented this scheme for cross-linked peptide discovery. Our program, SQID-XLink, searches all regular, dead-end, intra and inter cross-linked peptides simultaneously, and its effectiveness is validated by testing a published dataset. This new algorithm provides an alternative approach for high confidence cross-linking identification. AVAILABILITY SQID-XLink program is freely available for download from http://quiz2.chem.arizona.edu/wysocki/bioinformatics.htm SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online. CONTACT vwysocki@email.arizona.edu.
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Affiliation(s)
- Wenzhou Li
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
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33
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Stengel F, Aebersold R, Robinson CV. Joining forces: integrating proteomics and cross-linking with the mass spectrometry of intact complexes. Mol Cell Proteomics 2011; 11:R111.014027. [PMID: 22180098 PMCID: PMC3316738 DOI: 10.1074/mcp.r111.014027] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Protein assemblies are critical for cellular function and understanding their physical organization is the key aim of structural biology. However, applying conventional structural biology approaches is challenging for transient, dynamic, or polydisperse assemblies. There is therefore a growing demand for hybrid technologies that are able to complement classical structural biology methods and thereby broaden our arsenal for the study of these important complexes. Exciting new developments in the field of mass spectrometry and proteomics have added a new dimension to the study of protein-protein interactions and protein complex architecture. In this review, we focus on how complementary mass spectrometry-based techniques can greatly facilitate structural understanding of protein assemblies.
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Affiliation(s)
- Florian Stengel
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford, OX1 3TA United Kingdom
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Ning Z, Zhou H, Wang F, Abu-Farha M, Figeys D. Analytical Aspects of Proteomics: 2009–2010. Anal Chem 2011; 83:4407-26. [DOI: 10.1021/ac200857t] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
| | - Hu Zhou
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China 201203
| | - Fangjun Wang
- Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China 116023
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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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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: 322] [Impact Index Per Article: 23.0] [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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