A Structural Model of the Urease Activation Complex Derived from Ion Mobility-Mass Spectrometry and Integrative Modeling

Eschweiler, Joseph D.; Farrugia, Mark A.; Dixit, Sugyan M.; Hausinger, Robert P.; Ruotolo, Brandon T.

doi:10.1016/j.str.2018.03.001

Cited by 30 publications

(25 citation statements)

References 38 publications

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“…In coarse-grained modeling, one globular protein chain is usually represented as one sphere whereas a protein complex would consist of several overlapping spheres [32,33,49]. Our Initial attempts to model the apoE tetramer using one sphere per monomer, however, resulted in no models in agreement with both basic connectivity [50,51] requirements and the experimentally derived CCS restraints.…”

Section: Coarse-grained Model Of Apoe Tetramermentioning

confidence: 94%

Native Mass Spectrometry, Ion Mobility, Electron-Capture Dissociation, and Modeling Provide Structural Information for Gas-Phase Apolipoprotein E Oligomers

Wang

Eschweiler

Cui

et al. 2019

J. Am. Soc. Mass Spectrom.

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Apolipoprotein E (apoE) is an essential protein in lipid and cholesterol metabolism. Although the three common isoforms in humans differ only at two sites, their consequences in Alzheimer's disease (AD) are dramatically different: only the ε4 allele is a major genetic risk factor for lateonset Alzheimer's disease. The isoforms exist as a mixture of oligomers, primarily tetramer, at low μM concentrations in a lipid-free environment. This self-association is involved in equilibrium with the lipid-free state, and the oligomerization interface overlaps with lipid-binding region. Elucidation of apoE wild-type (WT) structures at an oligomeric state, however, has not yet been achieved. To address this need, we used native electrospray ionization and mass spectrometry (native MS) coupled with ion mobility (IM) to exam the monomer and tetramer of the three WT isoforms. Although collision-induced unfolding (CIU) cannot distinguish the isoforms, the monomeric mutant (MM) of apoE3 shows higher stability when submitted to CIU than the WT monomer. From ion-mobility measurements, we obtained the collision cross section and built a coarse-grained model for the tetramer. Application of electron-capture dissociation (ECD) to the tetramer causes unfolding starting from the C-terminal domain, in good agreement with solution denaturation data and provides additional support for the C4 symmetry structure of the tetramer.

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Section: Coarse-grained Model Of Apoe Tetramermentioning

confidence: 94%

Native Mass Spectrometry, Ion Mobility, Electron-Capture Dissociation, and Modeling Provide Structural Information for Gas-Phase Apolipoprotein E Oligomers

Wang

Eschweiler

Cui

et al. 2019

J. Am. Soc. Mass Spectrom.

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“…While major progress has been made on how urease accessory proteins interplay to deliver Ni 2+ to ureases, some interesting questions remain unanswered. (1) The structure of the activation complex is not known despite several structural models that have been proposed previously [126,127]. A high-resolution structure of the activation complex should provide novel structural insights into how GTPase activity of UreG is stimulated and the mechanism of nickel transfer within the complex.…”

Section: Future Perspectivesmentioning

confidence: 99%

The Maturation Pathway of Nickel Urease

Nim

Wong

2019

Inorganics

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Maturation of urease involves post-translational insertion of nickel ions to form an active site with a carbamylated lysine ligand and is assisted by urease accessory proteins UreD, UreE, UreF and UreG. Here, we review our current understandings on how these urease accessory proteins facilitate the urease maturation. The urease maturation pathway involves the transfer of Ni2+ from UreE → UreG → UreF/UreD → urease. To avoid the release of the toxic metal to the cytoplasm, Ni2+ is transferred from one urease accessory protein to another through specific protein–protein interactions. One central theme depicts the role of guanosine triphosphate (GTP) binding/hydrolysis in regulating the binding/release of nickel ions and the formation of the protein complexes. The urease and [NiFe]-hydrogenase maturation pathways cross-talk with each other as UreE receives Ni2+ from hydrogenase maturation factor HypA. Finally, the druggability of the urease maturation pathway is reviewed.

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“…While these methods can be successfully utilized in the absence of experimental data, sparse experimental data are often used to guide and improve modeling 19,21,22 . Experimental data from various MS techniques have recently proved pivotal within integrative structural biology frameworks 14,17,[23][24][25][26][27][28][29][30][31][32][33][34][35][36][37][38][39][40] .…”

Section: Introductionmentioning

confidence: 99%

Protein shape sampled by ion mobility mass spectrometry consistently improves protein structure prediction

Sba

et al. 2021

Preprint

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Among a wide variety of mass spectrometry (MS) methodologies available for structural characterizations of proteins, ion mobility (IM) provides structural information about protein shape and size in the form of an orientationally averaged collision cross-section (CCS). While IM data have been predominantly employed for the structural assessment of protein complexes, CCS data from IM experiments have not yet been used to predict tertiary structure from sequence. Here, we are showing that IM data can significantly improve protein structure determination using the modeling suite Rosetta. The Rosetta Projection Approximation using Rough Circular Shapes (PARCS) algorithm was developed that allows for fast and accurate prediction of CCS from structure. Following successful rigorous testing for accuracy, speed, and convergence of PARCS, an integrative modelling approach was developed in Rosetta to use CCS data from IM experiments. Using this method, we predicted protein structures from sequence for a benchmark set of 23 proteins. When using IM data, the predicted structure improved or remained unchanged for all 23 proteins, compared to the predicted models in the absence of CCS data. For 15/23 proteins, the RMSD (root-mean-square deviation) of the predicted model was less than 5.50 Å, compared to only 10/23 without IM data. We also developed a confidence metric that successfully identified near-native models in the absence of a native structure. These results demonstrate the ability of IM data in de novo structure determination.

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A Structural Model of the Urease Activation Complex Derived from Ion Mobility-Mass Spectrometry and Integrative Modeling

Cited by 30 publications

References 38 publications

Native Mass Spectrometry, Ion Mobility, Electron-Capture Dissociation, and Modeling Provide Structural Information for Gas-Phase Apolipoprotein E Oligomers

Native Mass Spectrometry, Ion Mobility, Electron-Capture Dissociation, and Modeling Provide Structural Information for Gas-Phase Apolipoprotein E Oligomers

The Maturation Pathway of Nickel Urease

Protein shape sampled by ion mobility mass spectrometry consistently improves protein structure prediction

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