ChemInform Abstract: Cross-Linking and Other Structural Proteomics Techniques: How Chemistry Is Enabling Mass Spectrometry Applications in Structural Biology

ChemInform ◽  
2016 ◽  
Vol 47 (38) ◽  
Author(s):  
Alexander Leitner
Keyword(s):  
Mass Spectrometry ◽  
Structural Biology ◽  
Structural Proteomics ◽  
Cross Linking

scholarly journals Cross-linking and other structural proteomics techniques: how chemistry is enabling mass spectrometry applications in structural biology

2016 ◽  
Vol 7 (8) ◽  
pp. 4792-4803 ◽  
Author(s):  
Alexander Leitner
Keyword(s):  
Mass Spectrometry ◽  
Structural Biology ◽  
Higher Order ◽  
Structural Proteomics ◽  
Cross Linking ◽  
Protein Assemblies ◽  
Chemical Methods

In this perspective, I highlight the contribution of chemical methods to the field of structural proteomics, where mass spectrometry is used to probe the structures of proteins and higher-order protein assemblies.

scholarly journals Insights in luteovirid structural biology guided by chemical cross-linking and high resolution mass spectrometry

2017 ◽  
Vol 241 ◽  
pp. 42-52 ◽  
Author(s):  
Mariko M. Alexander ◽  
Jared P. Mohr ◽  
Stacy L. DeBlasio ◽  
Juan D. Chavez ◽  
Veronique Ziegler-Graff ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
High Resolution ◽  
Structural Biology ◽  
High Resolution Mass Spectrometry ◽  
Cross Linking ◽  
High Resolution Mass ◽  
Chemical Cross Linking ◽  
Resolution Mass

scholarly journals Interfaces with Structure Dynamics of the Workhorses from Cells Revealed through Cross-Linking Mass Spectrometry (CLMS)

Biomolecules ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 382 ◽  
Author(s):  
Umesh Kalathiya ◽  
Monikaben Padariya ◽  
Jakub Faktor ◽  
Etienne Coyaud ◽  
Javier A. Alfaro ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Structural Proteomics ◽  
Cross Linking ◽  
Diverse Range ◽  
Interaction Sites ◽  
Structural Systems Biology ◽  
Rna Complexes

The fundamentals of how protein–protein/RNA/DNA interactions influence the structures and functions of the workhorses from the cells have been well documented in the 20th century. A diverse set of methods exist to determine such interactions between different components, particularly, the mass spectrometry (MS) methods, with its advanced instrumentation, has become a significant approach to analyze a diverse range of biomolecules, as well as bring insights to their biomolecular processes. This review highlights the principal role of chemistry in MS-based structural proteomics approaches, with a particular focus on the chemical cross-linking of protein–protein/DNA/RNA complexes. In addition, we discuss different methods to prepare the cross-linked samples for MS analysis and tools to identify cross-linked peptides. Cross-linking mass spectrometry (CLMS) holds promise to identify interaction sites in larger and more complex biological systems. The typical CLMS workflow allows for the measurement of the proximity in three-dimensional space of amino acids, identifying proteins in direct contact with DNA or RNA, and it provides information on the folds of proteins as well as their topology in the complexes. Principal CLMS applications, its notable successes, as well as common pipelines that bridge proteomics, molecular biology, structural systems biology, and interactomics are outlined.

scholarly journals Cross-linking/Mass Spectrometry Combined with Ion Mobility on a timsTOF Pro Instrument for Structural Proteomics

2021 ◽  
Author(s):  
Christian H Ihling ◽  
Lolita Piersimoni ◽  
Marc Kipping ◽  
Andrea Sinz
Keyword(s):  
Mass Spectrometry ◽  
Cross Sections ◽  
Protein Interaction ◽  
Protein Interactions ◽  
Ion Mobility ◽  
Hek293t Cell ◽  
Structural Proteomics ◽  
Cross Linking ◽  
E Coli ◽  
Interaction Studies

The combination of cross-linking/mass spectrometry (XL-MS) and ion mobility is still underexplored for conducting protein conformational and protein-protein interaction studies. We present a method for analyzing cross-linking mixtures on a timsTOF Pro mass spectrometer that allows separating ions based on their gas phase mobilities. Cross-linking was performed with three urea-based MS-cleavable cross-linkers that deliver distinct fragmentation patterns for cross-linked species upon collisional activation. The discrimination of cross-linked species from non-cross-linked peptides was readily performed based on their collisional cross sections. We demonstrate the general feasibility of our combined XL-MS/ion mobility approach for three protein systems of increasing complexity: (i) Bovine serum albumin, (ii) E. coli ribosome, and (iii) HEK293T cell nuclear lysates. We identified a total of 508 unique cross-linking sites for BSA, 868 for the E. coli ribosome, and 1,623 unique cross-links for nuclear lysates, corresponding to 1,088 intra- and 535 interprotein interactions and yielding 564 distinct protein-protein interactions. Our results underline the strength of combining XL-MS with ion mobility not only for deriving 3D-structures of single proteins, but also for performing system-wide protein interaction studies.

Chemical Cross-linking and Mass Spectrometry for the Structural Analysis of Protein Assemblies

2013 ◽  
Vol 66 (7) ◽  
pp. 749 ◽  
Author(s):  
Antonio N. Calabrese ◽  
Tara L. Pukala
Keyword(s):  
Mass Spectrometry ◽  
Structural Biology ◽  
Structural Information ◽  
Cross Linking ◽  
Spectrometric Analysis ◽  
Protein Assemblies ◽  
Cellular Functions ◽  
The Past ◽  
And Function ◽  
Chemical Cross Linking

Cellular functions are performed and regulated at a molecular level by the coordinated action of intricate protein assemblies, and hence the study of protein folding, structure, and interactions is vital to the appreciation and understanding of complex biological problems. In the past decade, continued development of chemical cross-linking methodologies combined with mass spectrometry has seen this approach develop to enable detailed structural information to be elucidated for protein assemblies often intractable by traditional structural biology methods. In this review article, we describe recent advances in reagent design, cross-linking protocols, mass spectrometric analysis, and incorporation of cross-linking constraints into structural models, which are contributing to overcoming the intrinsic challenges of the cross-linking method. We also highlight pioneering applications of chemical cross-linking mass spectrometry approaches to the study of structure and function of protein assemblies.

scholarly journals Systems structural biology measurements by in vivo cross-linking with mass spectrometry

2019 ◽  
Vol 14 (8) ◽  
pp. 2318-2343 ◽  
Author(s):  
Juan D. Chavez ◽  
Jared P. Mohr ◽  
Martin Mathay ◽  
Xuefei Zhong ◽  
Andrew Keller ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Structural Biology ◽  
Cross Linking

scholarly journals Analysis of the Dynamic Proteasome Structure by Cross-Linking Mass Spectrometry

Biomolecules ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 505
Author(s):  
Marta L. Mendes ◽  
Gunnar Dittmar
Keyword(s):  
Electron Microscopy ◽  
Mass Spectrometry ◽  
Structural Biology ◽  
26S Proteasome ◽  
Cross Linking ◽  
Macromolecular Complex ◽  
Dynamic Nature ◽  
Cryo Electron Microscopy ◽  
Integrative Structural Biology ◽  
Regulatory Particle

The 26S proteasome is a macromolecular complex that degrades proteins maintaining cell homeostasis; thus, determining its structure is a priority to understand its function. Although the 20S proteasome’s structure has been known for some years, the highly dynamic nature of the 19S regulatory particle has presented a challenge to structural biologists. Advances in cryo-electron microscopy (cryo-EM) made it possible to determine the structure of the 19S regulatory particle and showed at least seven different conformational states of the proteasome. However, there are still many questions to be answered. Cross-linking mass spectrometry (CLMS) is now routinely used in integrative structural biology studies, and it promises to take integrative structural biology to the next level, answering some of these questions.

Integrated Workflow for Structural Proteomics Studies Based on Cross-Linking/Mass Spectrometry with an MS/MS Cleavable Cross-Linker

2016 ◽  
Vol 88 (16) ◽  
pp. 7930-7937 ◽  
Author(s):  
Christian Arlt ◽  
Michael Götze ◽  
Christian H. Ihling ◽  
Christoph Hage ◽  
Mathias Schäfer ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Structural Proteomics ◽  
Cross Linking ◽  
Cross Linker
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