<i>GENFIT</i>: software for the analysis of small-angle X-ray and neutron scattering data of macromolecules in solution

Spinozzi, Francesco; Ferrero, C.; Ortore, María Grazia; Antolinos, Alejandro De María; Mariani, Paolo

doi:10.1107/s1600576714005147

Cited by 98 publications

(122 citation statements)

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“…The thicknesses are designated R pol , R CH2 , and R CH3 for the polar head group, the paraffinic chains, and the CH 3 region, respectively. The theoretical scattering profiles were fitted against the experimental SAXS curves using the GENFIT software (51). This software also allows the combination (sum) of different theoretical models in order to better describe the studied system.…”

Section: Discussionmentioning

confidence: 99%

Nanoliposomal Buparvaquone Immunomodulates Leishmania infantum-Infected Macrophages and Is Highly Effective in a Murine Model

Costa-Silva

Galisteo

Lindoso

et al. 2017

Antimicrob Agents Chemother

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Visceral leishmaniasis is a fatal parasitic neglected disease affecting 1.5 million people worldwide. Based on a drug repositioning approach, the aim of this work was to investigate the in vitro immunomodulatory potential of buparvaquone (BPQ) and to establish a safe regimen to evaluate the in vivo efficacy of BPQ entrapped by negatively charged nanoliposomes (BPQ-LP) in Leishmania infantum-infected hamsters. Small-angle X-ray scattering, dynamic light scattering, and the -potential were applied in order to study the influence of BPQ on the liposome structure. Our data revealed that BPQ was located in the polar-apolar interface, snorkeling the polar region, and protected against aggregation inside the lipophilic region. The presence of BPQ also decreased the Z-average hydrodynamic diameter and increased the surface charge. Compared to intravenous and intramuscular administration, a subcutaneous route was a more effective route for BPQ-LP; at 0.4 mg/kg, BPQ-LP reduced infection in the spleen and liver by 98 and 96%, respectively. Treatment for 5 days resulted in limited efficacy, but 10 days of treatment resulted in an efficacy similar to that of a 15-day regimen. The nanoliposomal drug was highly effective, with a mean 50% effective dose of 0.25 mg/kg, reducing the parasite load in bone marrow by 80%, as detected using quantitative PCR analysis. In addition, flow cytometry studies showed that BPQ upregulated cytokines as tumor necrosis factor, monocyte chemoattractant protein 1, interleukin-10 (IL-10), and IL-6 in Leishmania-infected macrophages, eliminating the parasites via a nitric oxide-independent mechanism. This new formulation proved to be a safe and effective treatment for murine leishmaniasis that could be a useful candidate against visceral leishmaniasis.KEYWORDS Leishmania, drug delivery, liposomes, therapy T he worldwide prevalence and severity of leishmaniasis has led the World Health Organization to consider it a priority infectious disease (1). Due to the complexity of host-parasite interaction, as well as contradictory results from vaccination models, the control of infection is mainly dependent on chemotherapeutic intervention (2). There are now a number of therapies for various forms of leishmaniasis; the preferences for first-line and second-line treatment vary based on the type of disease and are often guided by regional practice. Pentavalent antimonials, such as Pentostam and Glucantime, have been used to treat leishmaniasis for the last 70 years (3). However, these drugs have multiple adverse effects and decreasing effectiveness due to the development of parasite resistance, limiting their application (4). In Brazil, pentavalent antimony is still effective for treating most infections, despite its high toxicity. Until now, Citation da Costa-Silva TA, Galisteo AJ, Jr, Lindoso JAL, Barbosa LRS, Tempone AG. 2017. Nanoliposomal buparvaquone immunomodulates Leishmania infantuminfected macrophages and is highly effective in a murine model. Antimicrob Agents

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Section: Discussionmentioning

confidence: 99%

Nanoliposomal Buparvaquone Immunomodulates Leishmania infantum-Infected Macrophages and Is Highly Effective in a Murine Model

Costa-Silva

Galisteo

Lindoso

et al. 2017

Antimicrob Agents Chemother

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“…Small-angle scattering of x-rays (SAXS) and neutrons (SANS) are particularly suited to probe the structural properties of hydration layers around biomacromolecules in solution (28)(29)(30)(31)(32)(33). SAXS and SANS are sensitive to the electronic and nuclear scattering-length density (SLD) fluctuations, Dr, respectively, between solutes (i.e., biomacromolecules) and the bulk solvent (29).…”

Section: Introductionmentioning

confidence: 99%

“…SAXS and SANS have the advantage that the respective contribution of the hydration layer (or shell) to the overall scattering from the macromolecules varies both in magnitude and sign (34). The HS contribution has been implemented in a number of programs to back-calculate SAXS (and, more rarely, SANS) curves from atomic structures, either as a homogeneous shell of a specific thickness (30)(31)(32)35), as grid elements (36,37), as dummy atoms (38,39), as explicit water molecules (40)(41)(42)(43)(44)(45), as a density map (46,47), or by voxelization (48). Accurate description of the HS is essential for the growing field of quasiatomic protein-structure modeling from solution data (34).…”

Section: Introductionmentioning

confidence: 99%

“…Care was taken to ensure sample quality in solution, especially with respect to monodispersity and ideality, which are paramount aspects of accurate SAXS/SANS data interpretation in terms of form factors of individual particles (50,51). Full-length GFP models including two flexible tails of a total of 14 residues (10 at the C-and 4 at the N-terminus (52)) were generated using the statistical coil algorithm flexible-meccano (53), and SAXS data were subsequently analyzed by several programs: CRYSOL (35), FOXS (39), and GENFIT (32). CRYSON (30) and GENFIT (32) were used to perform the SANS data analyses.…”

Section: Introductionmentioning

confidence: 99%

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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 aggregation number N agg is the number of aSN monomers that form each flexible chain and is determined by the ratio πR 2 aSN L aS N /V 1 , where V 1 is aSN monomer volume. Experimental SAXS curves fitted by means of GENFIT software [40] resulted to be coherent with the hypothesis of monomeric disordered peptides in solution (N agg ≃ 1.1 ± 0.2), and the resulting parameters are reported in the Supplementary Materials.…”

Section: Saxsmentioning

confidence: 99%

Pressure effects on α-synuclein amyloid fibrils: An experimental investigation on their dissociation and reversible nature

Piccirilli

Plotegher

Spinozzi

et al. 2017

Archives of Biochemistry and Biophysics

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Abstractα-synuclein amyloid fibrils are found in surviving neurons of Parkinson's disease affected patients, but the role they play in the disease development is still under debate. A growing number of evidences point to soluble oligomers as the major cytotoxic species, while insoluble fibrillar aggregates could even play a protection role. In this work, we investigate α-synuclein fibrils dissociation induced at high pressure by means of Small Angle X-ray Scattering and Fourier Transform Infrared Spectroscopy. Fibrils were produced from wild type α-synuclein and two mutants associated with Parkinson's disease, A30P and A53T. Our results enlighten the different reversible nature of α-synuclein fibrils fragmentation at high pressure and suggest water excluded volumes presence in the fibrils core. Wild type and A30P species stabilized at high pressure are highly amyloidogenic and quickly re-associate into fibrils upon decompression, while A53T species shows a partial reversibility of the process likely due to the presence of an intermediate oligomeric state stabilized at high pressure. The amyloid fibrils dissociation process is here suggested to be associated to a negative activation volume, supporting the notion that α-synuclein fibrils are in a high-volume and high-compressibility state and hinting at the presence of a hydration-mediated activated state from which dissociation occurs.

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GENFIT: software for the analysis of small-angle X-ray and neutron scattering data of macromolecules in solution

Cited by 98 publications

References 50 publications

Nanoliposomal Buparvaquone Immunomodulates Leishmania infantum-Infected Macrophages and Is Highly Effective in a Murine Model

Nanoliposomal Buparvaquone Immunomodulates Leishmania infantum-Infected Macrophages and Is Highly Effective in a Murine Model

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

Pressure effects on α-synuclein amyloid fibrils: An experimental investigation on their dissociation and reversible nature

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