scholarly journals Cross-Linking Mass Spectrometry: An Emerging Technology for Interactomics and Structural Biology

2017 ◽  
Vol 90 (1) ◽  
pp. 144-165 ◽  
Author(s):  
Clinton Yu ◽  
Lan Huang
Keyword(s):  
Mass Spectrometry ◽  
Structural Biology ◽  
Emerging Technology ◽  
Cross Linking

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 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.

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.

scholarly journals Chemical cross-linking and native mass spectrometry: A fruitful combination for structural biology

2015 ◽  
Vol 24 (8) ◽  
pp. 1193-1209 ◽  
Author(s):  
Andrea Sinz ◽  
Christian Arlt ◽  
Dror Chorev ◽  
Michal Sharon
Keyword(s):  
Mass Spectrometry ◽  
Structural Biology ◽  
Native Mass Spectrometry ◽  
Cross Linking ◽  
Chemical Cross Linking

Statistical Force-Field for Structural Modeling Using Chemical Cross-Linking/mass Spectrometry Distance Constraints

2018 ◽  
Author(s):  
Allan J. R. Ferrari ◽  
Fabio C. Gozzo ◽  
Leandro Martinez
Keyword(s):  
Mass Spectrometry ◽  
Amino Acid ◽  
Force Field ◽  
Protein Structures ◽  
Protein Structure Determination ◽  
Structural Modeling ◽  
Cross Linking ◽  
Amino Acid Residues ◽  
Distance Constraints ◽  
Chemical Cross Linking

<div><p>Chemical cross-linking/Mass Spectrometry (XLMS) is an experimental method to obtain distance constraints between amino acid residues, which can be applied to structural modeling of tertiary and quaternary biomolecular structures. These constraints provide, in principle, only upper limits to the distance between amino acid residues along the surface of the biomolecule. In practice, attempts to use of XLMS constraints for tertiary protein structure determination have not been widely successful. This indicates the need of specifically designed strategies for the representation of these constraints within modeling algorithms. Here, a force-field designed to represent XLMS-derived constraints is proposed. The potential energy functions are obtained by computing, in the database of known protein structures, the probability of satisfaction of a topological cross-linking distance as a function of the Euclidean distance between amino acid residues. The force-field can be easily incorporated into current modeling methods and software. In this work, the force-field was implemented within the Rosetta ab initio relax protocol. We show a significant improvement in the quality of the models obtained relative to current strategies for constraint representation. This force-field contributes to the long-desired goal of obtaining the tertiary structures of proteins using XLMS data. Force-field parameters and usage instructions are freely available at http://m3g.iqm.unicamp.br/topolink/xlff <br></p></div><p></p><p></p>

Sign in / Sign up

Export Citation Format

Share Document