Fibrinogen species as resolved by HPLC-SAXS data processing within the<i>UltraScan Solution Modeler</i>(<i>US-SOMO</i>) enhanced SAS module

Brookes, Emre; Pérez, Javier; Cardinali, Bárbara; Profumo, Aldo; Vachette, Patrice; Rocco, Mattia

doi:10.1107/s0021889813027751

Cited by 61 publications

(65 citation statements)

References 56 publications

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“…To partially obviate this coding necessity, approximations can be used in the bead generation step with minimal influence on the final hydrodynamic computations if the non-coded parts are limited to a small percentage of the total biomacromolecule (Brookes et al 2010a). Over the years, US-SOMO (Brookes et al 2010a, b) has grown to include a number of other tools, utilities and non-hydrodynamic data analysis and simulation methods, such as a discrete molecular dynamics [DMD (Ding and Dokholyan 2006;Dokholyan et al 1998)], a general small-angle scattering (SAS) and a dedicated high-performance liquid chromatography/small-angle X-ray scattering (HPLC-SAXS) module (Brookes et al 2013). A very detailed description of the hydrodynamic computation and analysis tools currently available in US-SOMO and of their operation can be found in Brookes and Rocco (2015).…”

Section: Introductionmentioning

confidence: 99%

Computing translational diffusion and sedimentation coefficients: an evaluation of experimental data and programs

Rocco

Byron

2015

Eur Biophys J

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Hydrodynamic characterisation of (bio)macromolecules is a well-established field. Observables linked to translational friction, such as the translational diffusion (Dt(0)(20,w)) and sedimentation (s(0)(20,w)) coefficients, are the most commonly used parameters. Both can be computed starting from high-resolution structures, with several methods available. We present here a comprehensive study of the performance of public-domain software, comparing the calculated Dt(0)(20,w) and s(0)(20,w) for a set of high-resolution structures (ranging in mass from 12,358 to 465,557 Da) with their critically appraised literature experimental counterparts. The methods/programs examined are AtoB, SoMo, BEST, Zeno (all implemented within the US-SOMO software suite) and HYDROPRO. Clear trends emerge: while all programs can reproduce Dt(0)(20,w) on average to within ±5% (range -8 to +7%), SoMo and AtoB slightly overestimate it (average +2 and +1%, range -2 to +7 and -4 to +5%, respectively), and BEST and HYDROPRO underestimate it slightly more (average -3 and -4%, range -7 to +2 and -8 to +2%, respectively). Similar trends are observed with s(0)(20,w), but the comparison is likely affected by the necessary inclusion of the partial specific volume in the computations. The somewhat less than ideal performances could result from the hydration treatment in BEST and HYDROPRO, and the bead overlap removal in SoMo and AtoB. Interestingly, a combination of SoMo overlapping bead models followed by Zeno computation produced better results, with a 0% average error (range -4 to +4%). Indeed, this might become the method of choice, once computational speed considerations now favouring the 5 Å-grid US-SOMO AtoB approach are overcome.

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Section: Introductionmentioning

confidence: 99%

Computing translational diffusion and sedimentation coefficients: an evaluation of experimental data and programs

Rocco

Byron

2015

Eur Biophys J

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“…Its implementation and detailed description are reported in the 32 likely reflect a slight but negligible tendency toward self-aggregation. We concluded these characterization and calibration measurements with a simple but crucial control in which the FG solution was mixed with buffer in the absence of enzyme and data were recorded exactly as in a polymerization run.…”

Section: ■ Resultsmentioning

confidence: 99%

A Comprehensive Mechanism of Fibrin Network Formation Involving Early Branching and Delayed Single- to Double-Strand Transition from Coupled Time-Resolved X-ray/Light-Scattering Detection

et al. 2014

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The formation of a fibrin network following fibrinogen enzymatic activation is the central event in blood coagulation and has important biomedical and biotechnological implications. A non-covalent polymerization reaction between macromolecular monomers, it consists basically of two complementary processes: elongation/branching generates an interconnected 3D scaffold of relatively thin fibrils, and cooperative lateral aggregation thickens them more than 10-fold. We have studied the early stages up to the gel point by fast fibrinogen:enzyme mixing experiments using simultaneous small-angle X-ray scattering and wide-angle, multi-angle light scattering detection. The coupled evolutions of the average molecular weight, size, and cross section of the solutes during the fibrils growth phase were thus recovered. They reveal that extended structures, thinner than those predicted by the classic halfstaggered, double-stranded mechanism, must quickly form. Following extensive modeling, an initial phase is proposed in which single-bonded "Y-ladder" polymers rapidly elongate before undergoing a delayed transition to the double-stranded fibrils. Consistent with the data, this alternative mechanism can intrinsically generate frequent, random branching points in each growing fibril. The model predicts that, as a consequence, some branches in these expanding "lumps" eventually interconnect, forming the pervasive 3D network. While still growing, other branches will then undergo a Ca 2+ /length-dependent cooperative collapse on the resulting network scaffolding filaments, explaining their sudden thickening, low final density, and basic mechanical properties.

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“…We also believe that the changes in the size exclusion chromatography elution profile observed for several mutants within the d1 interface were associated not with a dimer to monomer transition but with a tetramer to (compact) dimer transition. Actually, using the US-SOMO program (36) we calculated the Stokes radius for all four species (monomer, compact, and extended dimer and tetramer) and obtained comparable differences for both transitions.…”

Section: Discussionmentioning

confidence: 97%

The Activator of Apoptosis Smac-DIABLO Acts as a Tetramer in Solution

Mastrangelo

Vachette

Cossu

et al. 2015

Biophysical Journal

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Smac-DIABLO in its mature form (20.8 kDa) binds to baculoviral IAP repeat (BIR) domains of inhibitor of apoptosis proteins (IAPs) releasing their inhibitory effects on caspases, thus promoting cell death. Despite its apparent molecular mass (∼100 kDa), Smac-DIABLO was held to be a dimer in solution, simultaneously targeting two distinct BIR domains. We report an extensive biophysical characterization of the protein alone and in complex with the X-linked IAP (XIAP)-BIR2-BIR3 domains. Our data show that Smac-DIABLO adopts a tetrameric assembly in solution and that the tetramer is able to bind two BIR2-BIR3 pairs of domains. Our small-angle x-ray scattering-based tetrameric model of Smac-DIABLO/BIR2-BIR3 highlights some conformational freedom of the complex that may be related to optimization of IAPs binding.

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Fibrinogen species as resolved by HPLC-SAXS data processing within theUltraScan Solution Modeler(US-SOMO) enhanced SAS module

Cited by 61 publications

References 56 publications

Computing translational diffusion and sedimentation coefficients: an evaluation of experimental data and programs

Computing translational diffusion and sedimentation coefficients: an evaluation of experimental data and programs

A Comprehensive Mechanism of Fibrin Network Formation Involving Early Branching and Delayed Single- to Double-Strand Transition from Coupled Time-Resolved X-ray/Light-Scattering Detection

The Activator of Apoptosis Smac-DIABLO Acts as a Tetramer in Solution

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