scholarly journals Characterization of a A3G-VifHIV-1-CRL5-CBFβ structure using a cross-linking mass spectrometry pipeline for integrative modeling of host-pathogen complexes

2021 ◽  
pp. 100132
Author(s):  
Robyn M. Kaake ◽  
Ignacia Echeverria ◽  
Seung Joong Kim ◽  
John Von Dollen ◽  
Nicholas M. Chesarino ◽  
...  
Author(s):  
Lucía Quintana-Gallardo ◽  
Moisés Maestro-López ◽  
Jaime Martín-Benito ◽  
Miguel Marcilla ◽  
Daniel Rutz ◽  
...  

2002 ◽  
Vol 277 (48) ◽  
pp. 46487-46492 ◽  
Author(s):  
Thomas Taverner ◽  
Nathan E. Hall ◽  
Richard A. J. O'Hair ◽  
Richard J. Simpson

2021 ◽  
Author(s):  
Molly S. Blevins ◽  
Jada N. Walker ◽  
Jeffrey M. Schaub ◽  
Ilya J. Finkelstein ◽  
Jennifer S. Brodbelt

Ultraviolet photodissociation and native mass spectrometry allow characterization of the formation and binding interactions of protein-ssDNA complexes.


2021 ◽  
Author(s):  
Moriya Slavin ◽  
Joanna Zamel ◽  
Keren Zohar ◽  
Siona Eliyahu ◽  
Merav Braitbard ◽  
...  

AbstractAtomic structures of several proteins from the coronavirus family are still partial or unavailable. A possible reason for this gap is the instability of these proteins outside of the cellular context, thereby prompting the use of in-cell approaches. In situ cross-linking and mass spectrometry (in situ CLMS) can provide information on the structures of such proteins as they occur in the intact cell. Here, we applied targeted in situ CLMS to structurally probe Nsp1, Nsp2, and Nucleocapsid (N) proteins from SARS-CoV-2, and obtained cross-link sets with an average density of one cross-link per twenty residues. We then employed integrative modeling that computationally combined the cross-linking data with domain structures to determine full-length atomic models. For the Nsp2, the cross-links report on a complex topology with long-range interactions. Integrative modeling with structural prediction of individual domains by the AlphaFold2 system allowed us to generate a single consistent all-atom model of the full-length Nsp2. The model reveals three putative metal binding sites, and suggests a role for Nsp2 in zinc regulation within the replication-transcription complex. For the N protein, we identified multiple intra- and inter-domain cross-links. Our integrative model of the N dimer demonstrates that it can accommodate three single RNA strands simultaneously, both stereochemically and electrostatically. For the Nsp1, cross-links with the 40S ribosome were highly consistent with recent cryo-EM structures. These results highlight the importance of cellular context for the structural probing of recalcitrant proteins and demonstrate the effectiveness of targeted in situ CLMS and integrative modeling.


2018 ◽  
Vol 13 (3) ◽  
pp. 431-458 ◽  
Author(s):  
Diogo B Lima ◽  
John T Melchior ◽  
Jamie Morris ◽  
Valmir C Barbosa ◽  
Julia Chamot-Rooke ◽  
...  

2014 ◽  
Vol 289 (8) ◽  
pp. 4723-4734 ◽  
Author(s):  
Kimberly Coffman ◽  
Bing Yang ◽  
Jie Lu ◽  
Ashley L. Tetlow ◽  
Emelia Pelliccio ◽  
...  

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