scholarly journals Lysine and Arginine Side Chains in Glycosaminoglycan−Protein Complexes Investigated by NMR, Cross-Linking, and Mass Spectrometry: A Case Study of the Factor H−Heparin Interaction

2010 ◽  
Vol 132 (18) ◽  
pp. 6374-6381 ◽  
Author(s):  
Bärbel S. Blaum ◽  
Jon A. Deakin ◽  
Conny M. Johansson ◽  
Andrew P. Herbert ◽  
Paul N. Barlow ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Protein Complexes ◽  
Factor H ◽  
Cross Linking ◽  
Side Chains ◽  
Heparin Interaction

scholarly journals Mass spectrometry-based cross-linking study shows that the Psb28 protein binds to cytochrome b559 in Photosystem II

2017 ◽  
Vol 114 (9) ◽  
pp. 2224-2229 ◽  
Author(s):  
Daniel A. Weisz ◽  
Haijun Liu ◽  
Hao Zhang ◽  
Sundarapandian Thangapandian ◽  
Emad Tajkhorshid ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Photosystem Ii ◽  
Protein Interactions ◽  
Protein Complexes ◽  
Protein Docking ◽  
Cross Linking ◽  
Protein Protein Interactions ◽  
Cytochrome B559 ◽  
Reaction Center Complex ◽  
Assembly Intermediate

Photosystem II (PSII), a large pigment protein complex, undergoes rapid turnover under natural conditions. During assembly of PSII, oxidative damage to vulnerable assembly intermediate complexes must be prevented. Psb28, the only cytoplasmic extrinsic protein in PSII, protects the RC47 assembly intermediate of PSII and assists its efficient conversion into functional PSII. Its role is particularly important under stress conditions when PSII damage occurs frequently. Psb28 is not found, however, in any PSII crystal structure, and its structural location has remained unknown. In this study, we used chemical cross-linking combined with mass spectrometry to capture the transient interaction of Psb28 with PSII. We detected three cross-links between Psb28 and the α- and β-subunits of cytochrome b559, an essential component of the PSII reaction-center complex. These distance restraints enable us to position Psb28 on the cytosolic surface of PSII directly above cytochrome b559, in close proximity to the QB site. Protein–protein docking results also support Psb28 binding in this region. Determination of the Psb28 binding site and other biochemical evidence allow us to propose a mechanism by which Psb28 exerts its protective effect on the RC47 intermediate. This study also shows that isotope-encoded cross-linking with the “mass tags” selection criteria allows confident identification of more cross-linked peptides in PSII than has been previously reported. This approach thus holds promise to identify other transient protein–protein interactions in membrane protein complexes.

eXL-MS: An Enhanced Cross-Linking Mass Spectrometry Workflow To Study Protein Complexes

2018 ◽  
Vol 90 (18) ◽  
pp. 10707-10714 ◽  
Author(s):  
Martial Rey ◽  
Mathieu Dupré ◽  
Isabel Lopez-Neira ◽  
Magalie Duchateau ◽  
Julia Chamot-Rooke
Keyword(s):  
Mass Spectrometry ◽  
Protein Complexes ◽  
Cross Linking

Combining Electron Microscopy (EM) and Cross-Linking Mass Spectrometry (XL-MS) for Structural Characterization of Protein Complexes

2021 ◽  
pp. 217-232
Author(s):  
Lucía Quintana-Gallardo ◽  
Moisés Maestro-López ◽  
Jaime Martín-Benito ◽  
Miguel Marcilla ◽  
Daniel Rutz ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Mass Spectrometry ◽  
Structural Characterization ◽  
Protein Complexes ◽  
Cross Linking

scholarly journals Driving integrative structural modeling with serial capture affinity purification

2020 ◽  
Vol 117 (50) ◽  
pp. 31861-31870
Author(s):  
Xingyu Liu ◽  
Ying Zhang ◽  
Zhihui Wen ◽  
Yan Hao ◽  
Charles A. S. Banks ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Structural Model ◽  
Protein Complexes ◽  
Affinity Purification ◽  
Quantitative Imaging ◽  
Resonance Energy ◽  
Correlation Spectroscopy ◽  
Cross Linking ◽  
Affinity Enrichment

Streamlined characterization of protein complexes remains a challenge for the study of protein interaction networks. Here we describe serial capture affinity purification (SCAP), in which two separate proteins are tagged with either the HaloTag or the SNAP-tag, permitting a multistep affinity enrichment of specific protein complexes. The multifunctional capabilities of this protein-tagging system also permit in vivo validation of interactions using acceptor photobleaching Förster resonance energy transfer and fluorescence cross-correlation spectroscopy quantitative imaging. By coupling SCAP to cross-linking mass spectrometry, an integrative structural model of the complex of interest can be generated. We demonstrate this approach using the Spindlin1 and SPINDOC protein complex, culminating in a structural model with two SPINDOC molecules docked on one SPIN1 molecule. In this model, SPINDOC interacts with the SPIN1 interface previously shown to bind a lysine and arginine methylated sequence of histone H3. Our approach combines serial affinity purification, live cell imaging, and cross-linking mass spectrometry to build integrative structural models of protein complexes.

A Generic Strategy To Analyze the Spatial Organization of Multi-Protein Complexes by Cross-Linking and Mass Spectrometry

2000 ◽  
Vol 72 (2) ◽  
pp. 267-275 ◽  
Author(s):  
Juri Rappsilber ◽  
Symeon Siniossoglou ◽  
Eduard C. Hurt ◽  
Matthias Mann
Keyword(s):  
Mass Spectrometry ◽  
Spatial Organization ◽  
Protein Complexes ◽  
Cross Linking ◽  
Generic Strategy

scholarly journals Chemical cross-linking/mass spectrometry targeting acidic residues in proteins and protein complexes

2014 ◽  
Vol 111 (26) ◽  
pp. 9455-9460 ◽  
Author(s):  
Alexander Leitner ◽  
Lukasz A. Joachimiak ◽  
Pia Unverdorben ◽  
Thomas Walzthoeni ◽  
Judith Frydman ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Protein Complexes ◽  
Cross Linking ◽  
Acidic Residues ◽  
Chemical Cross Linking
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