<i>PRIMUS</i>: a Windows PC-based system for small-angle scattering data analysis

Edited by Michael IbbaATP-phosphoribosyltransferase (ATP-PRT) catalyses the first step of histidine biosynthesis. Two different forms of ATP-PRT have been described; the homo-hexameric long form, and the hetero-octameric short form. Lactococcus lactis possesses the short form ATP-PRT comprising four subunits of HisG S , the catalytic subunit, and four subunits of HisZ, a histidyl-tRNA synthetase paralogue. Previous studies have suggested that HisG S requires HisZ for catalysis. Here, we reveal that the dimeric HisG S does display ATP-PRT activity in the absence of HisZ. This result reflects the evolutionary relationship between the long and short form ATP-PRT, which acquired allosteric inhibition and enhanced catalysis via two divergent strategies.

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“…Guinear fits were made using PRIMUS [24]. All plots were checked for increasing intensity at low s, which is indicative of an aggregated sample.…”

Section: Saxs Data Processingmentioning

confidence: 99%

Independent catalysis of the short form HisG from Lactococcus lactis

et al. 2016

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“…Data processing and reduction were performed using an automated standard European Synchrotron Radiation Facility beamline software (BSxCuBE) (56) and PRIMUS (57). To eliminate interparticle effects, data from different concentrations were merged (see example in Fig.…”

Section: Saxs/sans Experiments and Data Reductionmentioning

confidence: 99%

“…SANS experiments were carried out on the small-angle diffractometer D22 at the ILL (Grenoble, France) at 1.4 m/1.4 m and 4 m/4 m setups (collimation length/sample-detector distances) with a fixed neutron wavelength (l) of 6 Å . SANS data reduction was performed in analogy to SAXS data, using the ILL software GRASP, version 3.4 (http://www.ill.eu/instruments-support/instruments-groups/ groups/lss/grasp/home/) and PRIMUS (57). Full details are provided in the Supporting Material.…”

Section: Saxs/sans Experiments and Data Reductionmentioning

confidence: 99%

SAXS/SANS on Supercharged Proteins Reveals Residue-Specific Modifications of the Hydration Shell

Kim

Martel

Girard

et al. 2016

Biophysical Journal

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Water molecules in the immediate vicinity of biomacromolecules, including proteins, constitute a hydration layer characterized by physicochemical properties different from those of bulk water and play a vital role in the activity and stability of these structures, as well as in intermolecular interactions. Previous studies using solution scattering, crystallography, and molecular dynamics simulations have provided valuable information about the properties of these hydration shells, including modifications in density and ionic concentration. Small-angle scattering of x-rays (SAXS) and neutrons (SANS) are particularly useful and complementary techniques to study biomacromolecular hydration shells due to their sensitivity to electronic and nuclear scattering-length density fluctuations, respectively. Although several sophisticated SAXS/SANS programs have been developed recently, the impact of physicochemical surface properties on the hydration layer remains controversial, and systematic experimental data from individual biomacromolecular systems are scarce. Here, we address the impact of physicochemical surface properties on the hydration shell by a systematic SAXS/SANS study using three mutants of a single protein, green fluorescent protein (GFP), with highly variable net charge (þ36, À6, and À29). The combined analysis of our data shows that the hydration shell is locally denser in the vicinity of acidic surface residues, whereas basic and hydrophilic/hydrophobic residues only mildly modify its density. Moreover, the data demonstrate that the density modifications result from the combined effect of residue-specific recruitment of ions from the bulk in combination with water structural rearrangements in their vicinity. Finally, we find that the specific surface-charge distributions of the different GFP mutants modulate the conformational space of flexible parts of the protein.

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“…The data were averaged after normalization to the intensity of the incident beam, corrected for the detector response, and the scattering of the buffer was subtracted. All data manipulations were performed by using the program package PRIMUS (Konarev et al, 2003). The program DAMMIF (Franke and Svergun, 2009), a fast version of DAMMIN (Svergun, 1999), was used to reconstruct the low resolution shape of AT3Q24, tubulin and AT3Q24-tubulin complexes.…”

Section: Small-angle X-ray Scattering (Saxs)mentioning

confidence: 99%

Interactions of ataxin-3 with its molecular partners in the protein machinery that sorts protein aggregates to the aggresome

Bonanomi

Mazzucchelli

D’Urzo

et al. 2014

The International Journal of Biochemistry & Cell Biology

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a b s t r a c tAtaxin-3 (AT3) is the protein that triggers the inherited neurodegenerative disorder spinocerebellar ataxia type 3 when its polyglutamine (polyQ) stretch close to the C-terminus exceeds a critical length. AT3 consists of the N-terminal globular Josephin domain (JD) and the C-terminal disordered one. It cleaves isopeptide bonds between ubiquitin monomers, an event involved in protein quality control mechanisms. AT3 has been implicated in the pathway that sorts aggregated protein to aggresomes via microtubules, in which dynein and histone deacetylase 6 (HDAC6) also seem to be involved. By taking advantage of small angle X-ray scattering (SAXS) and surface plasmon resonance (SPR), we have investigated the interaction of AT3 with tubulin and HDAC6. Based on SAXS results, the AT3 oligomer, consisting of 6-7 subunits, tightly binds to the tubulin hexameric oligomer in a "parallel" fashion. By SPR analysis we have demonstrated that AT3 binds to tubulin dimer with a 50 nM affinity. Binding fits with a Langmuir 1:1 model and involves a single binding interface. Nevertheless, the interaction surface consists of three distinct, discontinuous tubulin-binding regions (TBR), one located in the JD, and the two others in the disordered domain, upstream and downstream of the polyQ stretch. In the absence of any of the three TBRs, the affinity is drastically reduced. By SPR we have also provided the first evidence of direct binding of AT3 to HDAC6, with affinity in the range 0.1-1 M. These results shed light on the interactions among the components of the transport machinery that sorts aggregate protein to the aggresome, and pave the way to in vivo studies aimed at further clarifying their roles.

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PRIMUS: a Windows PC-based system for small-angle scattering data analysis

Cited by 2,785 publications

References 17 publications

Independent catalysis of the short form HisG from Lactococcus lactis

Independent catalysis of the short form HisG from Lactococcus lactis

SAXS/SANS on Supercharged Proteins Reveals Residue-Specific Modifications of the Hydration Shell

Interactions of ataxin-3 with its molecular partners in the protein machinery that sorts protein aggregates to the aggresome

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