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

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 Oligomerisation of Synaptobrevin-2 Studied by Native Mass Spectrometry and Chemical Cross-Linking

2018 ◽  
Vol 30 (1) ◽  
pp. 149-160 ◽  
Author(s):  
Sabine Wittig ◽  
Caroline Haupt ◽  
Waldemar Hoffmann ◽  
Susann Kostmann ◽  
Kevin Pagel ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Native Mass Spectrometry ◽  
Cross Linking ◽  
Chemical Cross Linking

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.

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>

scholarly journals Structural insights into Escherichia coli phosphopantothenoylcysteine synthetase by native ion mobility–mass spectrometry

2019 ◽  
Vol 476 (21) ◽  
pp. 3125-3139 ◽  
Author(s):  
Daniel Shiu-Hin Chan ◽  
Jeannine Hess ◽  
Elen Shaw ◽  
Christina Spry ◽  
Robert Starley ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Escherichia Coli ◽  
Structural Biology ◽  
Ion Mobility ◽  
Biosynthetic Pathway ◽  
Screening Tool ◽  
Native Mass Spectrometry ◽  
Ion Mobility Mass Spectrometry ◽  
E Coli ◽  
Structural Insights

Abstract CoaBC, part of the vital coenzyme A biosynthetic pathway in bacteria, has recently been validated as a promising antimicrobial target. In this work, we employed native ion mobility–mass spectrometry to gain structural insights into the phosphopantothenoylcysteine synthetase domain of E. coli CoaBC. Moreover, native mass spectrometry was validated as a screening tool to identify novel inhibitors of this enzyme, highlighting the utility and versatility of this technique both for structural biology and for drug discovery.

Sign in / Sign up

Export Citation Format

Share Document