The purpose of this investigation was to determine what structural changes convert "inert" alphaIIbbeta3 integrins into "activated" high-affinity receptors for adhesive proteins. Light scattering, analytical ultracentrifugation, electron microscopy, and molecular modeling were used to probe the conformational states of the alphaIIbbeta3 integrin. Isolated from human blood platelets in octyl glucoside, the alphaIIbbeta3 complex behaved as an asymmetric 230 kDa macromolecule with a z-average translational diffusion coefficient of 2.9 F and a weight-average sedimentation coefficient of 7.7 S. Dynamic light scattering showed that ligand-mimetic peptides (RGDX, X = F, W, S) caused prompt, concentration-dependent increases in the Stokes radius (R(s)) of the alphaIIbbeta3 complex, whereas control peptides of reversed sequence (XDGR, X = F, W, S) had no significant effect. Sedimentation velocity data coupled with time-derivative analyses showed that RGDX peptides shifted the distribution of alphaIIbbeta3 sedimenting species toward smaller s values. Sedimentation equilibrium measurements indicated that a slower increase in the alphaIIbbeta3 molecular weight distribution took place in the presence of RGDX ligand-mimetics. Electron microscopy showed a split of alphaIIbbeta3's globular domain into two distinct nodules in the presence of RGDX peptides; oligomers joined through their stalk regions were seen frequently. These observations suggest that receptor occupancy by ligand-mimetic RGDX peptides is tightly coupled to relatively large changes in the structure of the alphaIIbbeta3 complex. alphaIIbbeta3 bead models were developed to describe quantitatively the ligand-induced transition from a "closed" to an "open" integrin conformation and the limited oligomerization that follows. This provides a new mechanistic framework for understanding integrin activation and the formation of signaling clusters on the surface of stimulated platelets.
The structure and kinetics of fibrin gels grown from fibrinogen solutions under quasiphysiological conditions, but in absence of Ca++, were investigated by means of elastic light scattering. By combining classical light scattering and low-angle elastic light scattering, an overall wave-vector range of about three decades was spanned, from q approximately 3 x 10(2) to q approximately 3 x 10(5) cm(-1). The scattered intensity distribution of the gels was measured in absolute units and fitted to a single function, which was able to reproduce accurately the data over the entire wave-vector range. From the fitting, it was possible to estimate the average diameter d of the fibrin fibers, the average crossover length xi of the gel, and establish the fractal nature of the gel structure, with a measure of its fractal dimension D(m). The measure of the intensity in absolute units also allowed the estimate of the density rho of the fibrin fibers and provided an independent measure of their size. The kinetics of formation of the gel was described in terms of a simple growth model: the scaffold of the network is formed very early in the course of the gelation process, at a "networking time," t(n), which is much smaller than the time required to form the final gel. At times t>t(n), the gel structure remains substantially unchanged and the successive growth consists only in a thickening of the gel fibers. Gels prepared under the same physical-chemical conditions, but at different fibrinogen concentrations, exhibited rather similar structures and kinetics, showing that the modalities of the gelation process are mainly governed by the solution conditions, and only secondarily by the fibrinogen concentration. For gels at fibrinogen concentration of approximately 0.24 mg/ml, the gel parameters were d approximately 130 nm, xi approximately 27 microm, D(m) approximately 1.3, and rho approximately 0.4 g/cm(3). Our d and rho values are in very good agreement with electron microscopy- and turbidity-derived literature data, respectively, while xi seems to be related to the mesh size of the initial scaffold formed at t(n), rather than to the mesh size of the final aged gel.
The interpretation of solution hydrodynamic data in terms of macromolecular structural parameters is not a straightforward task. Over the years, several approaches have been developed to cope with this problem, the most widely used being bead modeling in various flavors. We report here the implementation of the SOMO (SOlution MOdeller; Rai et al. in Structure 13:723-734, 2005) bead modeling suite within one of the most widely used analytical ultracentrifugation data analysis software packages, UltraScan (Demeler in Modern analytical ultracentrifugation: techniques and methods, Royal Society of Chemistry, UK, 2005). The US-SOMO version is now under complete graphical interface control, and has been freed from several constraints present in the original implementation. In the direct beads-per-atoms method, virtually any kind of residue as defined in the Protein Data Bank (e.g., proteins, nucleic acids, carbohydrates, prosthetic groups, detergents, etc.) can be now represented with beads whose number, size and position are all defined in usereditable tables. For large structures, a cubic grid method based on the original AtoB program (Byron in Biophys J 72:408-415, 1997) can be applied either directly on the atomic structure, or on a previously generated bead model. The hydrodynamic parameters are then computed in the rigid-body approximation. An extensive set of tests was conducted to further validate the method, and the results are presented here. Owing to its accuracy, speed, and versatility, US-SOMO should allow to fully take advantage of the potential of solution hydrodynamics as a complement to higher resolution techniques in biomacromolecular modeling.Correspondence to: Mattia Rocco, mattia.rocco@istge.it.
The platelet integrin ␣IIb3 is representative of a class of heterodimeric receptors that upon activation bind extracellular macromolecular ligands and form signaling clusters. This study examined how occupancy of ␣IIb3's fibrinogen binding site affected the receptor's solution structure and stability. Eptifibatide, an integrin antagonist developed to treat cardiovascular disease, served as a high-affinity, monovalent model ligand with fibrinogen-like selectivity for ␣IIb3. Eptifibatide binding promptly and reversibly perturbed the conformation of the ␣IIb3 complex. Ligand-specific decreases in its diffusion and sedimentation coefficient were observed at near-stoichiometric eptifibatide concentrations, in contrast to the receptorperturbing effects of RGD ligands that we previously observed only at a 70-fold molar excess. Eptifibatide promoted ␣IIb3 dimerization 10-fold more effectively than less selective RGD ligands, as determined by sedimentation equilibrium. Eptifibatide-bound integrin receptors displayed an ectodomain separation and enhanced assembly of dimers and larger oligomers linked through their stalk regions, as seen by transmission electron microscopy. Ligation with eptifibatide protected ␣IIb3 from SDS-induced subunit dissociation, an effect on electrophoretic mobility not seen with RGD ligands. Despite its distinct cleft, the open conformer resisted guanidine unfolding as effectively as the ligand-free integrin. Thus, we provide the first demonstration that binding a monovalent ligand to ␣IIb3's extracellular fibrinogen-recognition site stabilizes the receptor's open conformation and enhances self-association through its distant transmembrane and/or cytoplasmic domains. By showing how eptifibatide and RGD peptides, ligands with distinct binding sites, each affects ␣IIb3's conformation, our findings provide new mechanistic insights into ligand-linked integrin activation, clustering and signaling.
The US-SOMO HPLC-SAXS (high-performance liquid chromatography coupled with small-angle X-ray scattering) module is an advanced tool for the comprehensive analysis of SEC-SAXS (size-exclusion chromatography coupled with SAXS) data. It includes baseline and band-broadening correction routines, and Gaussian decomposition of overlapping skewed peaks into pure components.
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