scholarly journals Cross-Linking Mass Spectrometry and Mutagenesis Confirm the Functional Importance of Surface Interactions between CYP3A4 and Holo/Apo Cytochrome b5

Biochemistry ◽  
2012 ◽  
Vol 51 (47) ◽  
pp. 9488-9500 ◽  
Author(s):  
Chunsheng Zhao ◽  
Qiuxia Gao ◽  
Arthur G. Roberts ◽  
Scott A. Shaffer ◽  
Catalin E. Doneanu ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Cytochrome B5 ◽  
Surface Interactions ◽  
Cross Linking ◽  
Functional Importance

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 Glycan-protein cross-linking mass spectrometry reveals sialic acid-mediated protein networks on cell surfaces

2021 ◽  
Author(s):  
Yixuan Xie ◽  
Siyu Chen ◽  
Qiongyu Li ◽  
Ying Sheng ◽  
Michael R Alvarez ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Sialic Acid ◽  
Membrane Proteins ◽  
Cell Membranes ◽  
Sialic Acids ◽  
Cross Linking ◽  
Protein Networks ◽  
Cell Surfaces ◽  
Protein Cross Linking

A cross-linking method is developed to elucidate the glycan-mediated interactions between membrane proteins through sialic acids. The method provides previously unknown extensive glycomic interactions on cell membranes. The vast majority...

scholarly journals The membrane-embedded segment of cytochrome b5 as studied by cross-linking with photoactivatable phospholipids.

1983 ◽  
Vol 258 (15) ◽  
pp. 9128-9135 ◽  
Author(s):  
Y Takagaki ◽  
R Radhakrishnan ◽  
C M Gupta ◽  
H G Khorana
Keyword(s):  
Cytochrome B5 ◽  
Cross Linking

scholarly journals The interactome of intact mitochondria by cross-linking mass spectrometry provides evidence for coexisting respiratory supercomplexes

2017 ◽  
Vol 17 (2) ◽  
pp. 216-232 ◽  
Author(s):  
Fan Liu ◽  
Philip Lössl ◽  
Beverley M. Rabbitts ◽  
Robert S. Balaban ◽  
Albert J. R. Heck
Keyword(s):  
Mass Spectrometry ◽  
Cross Linking ◽  
Respiratory Supercomplexes

scholarly journals CLMSVault: A Software Suite for Protein Cross-Linking Mass-Spectrometry Data Analysis and Visualization

2017 ◽  
Vol 16 (7) ◽  
pp. 2645-2652 ◽  
Author(s):  
Mathieu Courcelles ◽  
Jasmin Coulombe-Huntington ◽  
Émilie Cossette ◽  
Anne-Claude Gingras ◽  
Pierre Thibault ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Data Analysis ◽  
Mass Spectrometry Data ◽  
Cross Linking ◽  
Software Suite ◽  
Protein Cross Linking
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