Quaternary Structure of the ATPase Complex of Human 26S Proteasomes Determined by Chemical Cross-Linking

2001 ◽  
Vol 386 (1) ◽  
pp. 89-94 ◽  
Author(s):  
Rasmus Hartmann-Petersen ◽  
Keiji Tanaka ◽  
Klavs B. Hendil
Keyword(s):  
Quaternary Structure ◽  
Cross Linking ◽  
Chemical Cross Linking

scholarly journals Proper evaluation of chemical cross-linking-based spatial restraints improves the precision of modeling homo-oligomeric protein complexes

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Aljaž Gaber ◽  
Gregor Gunčar ◽  
Miha Pavšič
Keyword(s):  
Quaternary Structure ◽  
Comprehensive Evaluation ◽  
Protein Complexes ◽  
Scoring Function ◽  
Cross Linking ◽  
High Resolution Data ◽  
Oligomeric Proteins ◽  
Oligomeric Protein ◽  
Accessible Surface ◽  
Chemical Cross Linking

Abstract Background The function of oligomeric proteins is inherently linked to their quaternary structure. In the absence of high-resolution data, low-resolution information in the form of spatial restraints can significantly contribute to the precision and accuracy of structural models obtained using computational approaches. To obtain such restraints, chemical cross-linking coupled with mass spectrometry (XL-MS) is commonly used. However, the use of XL-MS in the modeling of protein complexes comprised of identical subunits (homo-oligomers) is often hindered by the inherent ambiguity of intra- and inter-subunit connection assignment. Results We present a comprehensive evaluation of (1) different methods for inter-residue distance calculations, and (2) different approaches for the scoring of spatial restraints. Our results show that using Solvent Accessible Surface distances (SASDs) instead of Euclidean distances (EUCs) greatly reduces the assignation ambiguity and delivers better modeling precision. Furthermore, ambiguous connections should be considered as inter-subunit only when the intra-subunit alternative exceeds the distance threshold. Modeling performance can also be improved if symmetry, characteristic for most homo-oligomers, is explicitly defined in the scoring function. Conclusions Our findings provide guidelines for proper evaluation of chemical cross-linking-based spatial restraints in modeling homo-oligomeric protein complexes, which could facilitate structural characterization of this important group of proteins.

scholarly journals Quaternary Structure of the Tryptophan Synthase α-Subunit Homolog BX1 from Zea mays

2019 ◽  
Author(s):  
Andrew Norris ◽  
Florian Busch ◽  
Michael Schupfner ◽  
Reinhard Sterner ◽  
Vicki Wysocki
Keyword(s):  
Mass Spectrometry ◽  
Protein Interactions ◽  
Quaternary Structure ◽  
Early Time ◽  
Cross Linking ◽  
Tryptophan Synthase ◽  
Protein Protein Interactions ◽  
Α Subunit ◽  
Primary And Secondary Metabolism ◽  
Chemical Cross Linking

The manuscript describes the use of chemical cross-linking/mass spectrometry and mutagenesis to investigate the dimeric interface of the tryptophan synthase α-subunit homolog, BX1. This work indicates that BX1 homodimerization might have served as a mechanism to exclude an interaction with the tryptophan synthase β-subunit, TrpB, at an early time in evolution, thereby eliminating cross-talk between primary and secondary metabolism. This work would be of interest to mass spectrometrists and structural biologist as it presents a workflow to determine the physiological protein-protein interactions within crystal structures using chemical cross-linking/mass spectrometry and mutagenesis as complementary structural biology techniques, thereby eliminating ambiguity and potential mis-assignments due to the presence of additional (artificial) protein contacts formed during the crystallization process.

scholarly journals Quaternary Structure of the Tryptophan Synthase α-Subunit Homolog BX1 from Zea mays

2019 ◽  
Author(s):  
Andrew Norris ◽  
Florian Busch ◽  
Michael Schupfner ◽  
Reinhard Sterner ◽  
Vicki Wysocki
Keyword(s):  
Mass Spectrometry ◽  
Protein Interactions ◽  
Quaternary Structure ◽  
Early Time ◽  
Cross Linking ◽  
Tryptophan Synthase ◽  
Protein Protein Interactions ◽  
Α Subunit ◽  
Primary And Secondary Metabolism ◽  
Chemical Cross Linking

The manuscript describes the use of chemical cross-linking/mass spectrometry and mutagenesis to investigate the dimeric interface of the tryptophan synthase α-subunit homolog, BX1. This work indicates that BX1 homodimerization might have served as a mechanism to exclude an interaction with the tryptophan synthase β-subunit, TrpB, at an early time in evolution, thereby eliminating cross-talk between primary and secondary metabolism. This work would be of interest to mass spectrometrists and structural biologist as it presents a workflow to determine the physiological protein-protein interactions within crystal structures using chemical cross-linking/mass spectrometry and mutagenesis as complementary structural biology techniques, thereby eliminating ambiguity and potential mis-assignments due to the presence of additional (artificial) protein contacts formed during the crystallization process.

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