Molecular Model of an α-Helical Prion Protein Dimer and Its Monomeric Subunits as Derived from Chemical Cross-linking and Molecular Modeling Calculations

2008 ◽  
Vol 376 (2) ◽  
pp. 582-596 ◽  
Author(s):  
T. Kaimann ◽  
S. Metzger ◽  
K. Kuhlmann ◽  
B. Brandt ◽  
E. Birkmann ◽  
...  
Cells ◽  
2020 ◽  
Vol 9 (7) ◽  
pp. 1633 ◽  
Author(s):  
Giel Stalmans ◽  
Anastasia V. Lilina ◽  
Pieter-Jan Vermeire ◽  
Jan Fiala ◽  
Petr Novák ◽  
...  

The molecular architecture and assembly mechanism of intermediate filaments have been enigmatic for decades. Among those, lamin filaments are of particular interest due to their universal role in cell nucleus and numerous disease-related mutations. Filament assembly is driven by specific interactions of the elementary dimers, which consist of the central coiled-coil rod domain flanked by non-helical head and tail domains. We aimed to investigate the longitudinal ‘head-to-tail’ interaction of lamin dimers (the so-called ACN interaction), which is crucial for filament assembly. To this end, we prepared a series of recombinant fragments of human lamin A centred around the N- and C-termini of the rod. The fragments were stabilized by fusions to heterologous capping motifs which provide for a correct formation of parallel, in-register coiled-coil dimers. As a result, we established crystal structures of two N-terminal fragments one of which highlights the propensity of the coiled-coil to open up, and one C-terminal rod fragment. Additional studies highlighted the capacity of such N- and C-terminal fragments to form specific complexes in solution, which were further characterized using chemical cross-linking. These data yielded a molecular model of the ACN complex which features a 6.5 nm overlap of the rod ends.


2008 ◽  
Vol 43 (2) ◽  
pp. 185-195 ◽  
Author(s):  
Tatiana Pimenova ◽  
Alexis Nazabal ◽  
Bernd Roschitzki ◽  
Jan Seebacher ◽  
Oliver Rinner ◽  
...  

Biochemistry ◽  
2013 ◽  
Vol 52 (9) ◽  
pp. 1568-1582 ◽  
Author(s):  
Bradley G. Fritz ◽  
Sue A. Roberts ◽  
Aqeel Ahmed ◽  
Linda Breci ◽  
Wenzhou Li ◽  
...  

2018 ◽  
Author(s):  
Allan J. R. Ferrari ◽  
Fabio C. Gozzo ◽  
Leandro Martinez

<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>


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