<i>ELLSTAT</i>: shape modeling for solution small-angle scattering of proteins and protein complexes with automated statistical characterization

Heller, William T.

doi:10.1107/s0021889806029591

Cited by 22 publications

(25 citation statements)

References 20 publications

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“…Additionally, each model is tested relative to models generated with the same number of free parameters, so the relative comparisons are not affected. In order to judge the range of structures that fit the experimental data collected for (UreABC-UreD) 3 and (UreABC-UreDF) 3 , the best 25 models found were maintained in an ordered list that was updated as better models were found, in a manner similar to previous work [43], making it possible to judge the reproducibility of the modeling. The uncertainties in measured SAXS intensities derive from specific assumptions about the counting statistics.…”

Section: Methodsmentioning

confidence: 99%

The structure of urease activation complexes examined by flexibility analysis, mutagenesis, and small-angle X-ray scattering

Quiroz-Valenzuela

Sukuru

Hausinger

et al. 2008

Archives of Biochemistry and Biophysics

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Conformational changes of Klebsiella aerogenes urease apoprotein (UreABC) 3 induced upon binding of the UreD and UreF accessory proteins were examined by a combination of flexibility analysis, mutagenesis, and small-angle x-ray scattering (SAXS). ProFlex analysis of urease provided evidence that the major domain of UreB can move in a hinge-like motion to account for prior chemical cross-linking results. Rigidification of the UreB hinge region, accomplished through a G11P mutation, reduced the extent of urease activation, in part by decreasing the nickel content of the mutant enzyme, and by sequestering a portion of the urease apoprotein in a novel activation complex that includes all of the accessory proteins. SAXS analyses of urease, (UreABC-UreD) 3 , and (UreABC-UreDF) 3 confirm that UreD and UreF bind near UreB at the periphery of the (UreAC) 3 structure. This study supports an activation model in which a domain-shifted UreB conformation in (UreABC-UreDF) 3 allows CO 2 and nickel ions to gain access to the nascent active site. KeywordsUrease; Activation; Flexibility; Small-angle X-ray scattering Urease is a nickel-containing enzyme that hydrolyzes urea [1,2]. Crystallographic analyses of ureases from bacterial and plant sources [3][4][5][6][7] reveal a basic trimeric structure with three active sites, each composed of two nickel ions coordinated by a carboxylated Lys, four His and an Asp. Genetic and biochemical studies carried out with plants, fungi, and bacteria [reviewed in [8][9][10]] have shown that additional genes encoding accessory proteins are required for proper assembly of the urease metallocenter, with the possible exception of that from Bacillus *Corresponding author. Address: Department of Microbiology & Molecular Genetics, 2215 Biomedical Physical Sciences, Michigan State University, East Lansing, Michigan 48824-4320, . E-mail: hausinge@msu.edu. Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. [17,18]. Urease activity is generated by incubating these complexes with high concentrations of bicarbonate (to supply the CO 2 needed for Lys carboxylation) and nickel ions, but the required levels of these additives (100 mM and 100 µM, respectively) are not physiologically relevant and only a portion of the proteins are activated [19,20]. In contrast, fully active urease is generated with only 100 µM bicarbonate and 20 µM nickel ions using (UreABC-UreDFG) 3 plus UreE (M r 17,558) and GTP [21]. UreE functions as a nickel-binding protein [22,23] that delivers the metal ion to (UreABC-UreDFG) 3 as GTP is hydrolyzed [24]. Although UreE is often referred to as...

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Section: Methodsmentioning

confidence: 99%

The structure of urease activation complexes examined by flexibility analysis, mutagenesis, and small-angle X-ray scattering

Quiroz-Valenzuela

Sukuru

Hausinger

et al. 2008

Archives of Biochemistry and Biophysics

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“…Models were checked for structural overlap of the various substructures, and those having too many unfavorable collisions were not tested against the SANS data using ORNL_SAS. A continuously updated set of the 25 best models found was output by the program to provide a measure of the variability of the range of models found that fit the data, as employed previously (39). Three independent runs of the modeling were performed, providing a set of 75 models for judging the variability and convergence of the modeling results.…”

Section: Methodsmentioning

confidence: 99%

The Roles of the RIIβ Linker and N-terminal Cyclic Nucleotide-binding Domain in Determining the Unique Structures of the Type IIβ Protein Kinase A

Blumenthal¹,

Copps²,

Smith-Nguyen³

et al. 2014

Journal of Biological Chemistry

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Background:The RII␤ subunit of PKA exhibits unique isoform-specific structural features. Results: The unique structural properties of RII␤ do not require the C-terminal cAMP-binding domain. Conclusion:The RII␤ linker and N-terminal cAMP-binding domain confer unique subunit structure and organization of the type II␤ holoenzyme. Significance: The subunit structure and organization of the type II␤ holoenzyme contribute to its unique isoform-specific biochemical properties and functions.

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“…(13,14). The scattering intensities in the contrast series were then calculated from the model using equation 4 and compared to the entire contrast variation series of data simultaneously using the reduced 2 , as described previously (11,37). To efficiently search the potential parameter space, a Monte Carlo search was employed.…”

Section: Methodsmentioning

confidence: 99%

“…Over 15 million models were tested during the fitting of each of the pH 7.2 and pH 6.4 contrast variation series data. The variability of the results of the modeling was characterized as described previously (11).…”

Section: Methodsmentioning

confidence: 99%

Conformational Changes in Sindbis Virus Induced by Decreased pH Are Revealed by Small-Angle Neutron Scattering

Piper

Meilleur

et al. 2012

J Virol

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Alphaviruses, such as Sindbis virus, undergo dramatic changes in three-dimensional structure upon exposure to low pH, and such exposure can establish conditions allowing fusion of the virus membrane with a cell plasma membrane upon return to neutral pH. While exposure to low pH is not required for entry of Sindbis virus into vertebrate or invertebrate cells, the conformational changes occurring at low pH may mimic those occurring upon virus-receptor interaction. Here, we employed small-angle neutron scattering with contrast variation to probe how the structure of a mammalian-grown Sindbis virus responds to moderately acidic pH. Several changes took place throughout the virion structure when the pH decreased from 7.2 to 6.4. Specifically, the RNA in the virion core underwent a conformational change. Additionally, the protein was redistributed. A significant amount of protein moved from the layer containing the lipid bilayer to the exterior of the virion. The results improve our understanding of the pH-driven alteration of Sindbis virus structure. Sindbis virus is the archetypal Alphavirus. It is composed of two concentric protein layers separated by a lipid bilayer. The inner core contains the nucleocapsid, which is comprised of the capsid protein condensed around the genomic plus-polarity single-stranded RNA. The glycoproteins E1 and E2, which are organized as heterotrimers, are embedded in the lipid bilayer, which is derived from the host cell. The outer and inner protein layers are anchored together through interactions of the glycoprotein E2 endodomain with the nucleocapsid core. As such, it is a relatively simple enveloped virus and an excellent model system for studies of structure and function.Sindbis virus is an infectious molecular motor designed to deliver the genomic RNA to a suitable host cell for the purpose of virus propagation. Developing an understanding of the mechanism by which this macromolecular assembly delivers its infectious RNA cargo into the host cell has proven to be challenging. Two models of alphavirus infectivity have been proposed. One model proposes infection by endocytosis followed by fusion of the virus membrane with the membrane of the acidified endosome (22). The second model presents arguments for the direct penetration of the virus particle at the cell surface in the absence of endocytosis or acidification (25,26,33). In this model, the target cell membrane is breached by the formation of a pore that allows entry.Both models postulate that conformational changes in the virus are important to the mechanism of infection. In the fusion model, the decrease in solution pH is the trigger that drives the particle to rearrange and expose the virus membrane for fusion and the release of the RNA into the cell cytoplasm. In the directpenetration model, interactions of the virus glycoproteins with host receptors are proposed to trigger conformational changes, which may be the same as those induced by acidic pH, that open proteinaceous pores in the virus and the cell membrane through which...

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ELLSTAT: shape modeling for solution small-angle scattering of proteins and protein complexes with automated statistical characterization

Cited by 22 publications

References 20 publications

The structure of urease activation complexes examined by flexibility analysis, mutagenesis, and small-angle X-ray scattering

The structure of urease activation complexes examined by flexibility analysis, mutagenesis, and small-angle X-ray scattering

The Roles of the RIIβ Linker and N-terminal Cyclic Nucleotide-binding Domain in Determining the Unique Structures of the Type IIβ Protein Kinase A

Conformational Changes in Sindbis Virus Induced by Decreased pH Are Revealed by Small-Angle Neutron Scattering

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