A Set Of Computer Programs For Tee Construction, The Evaluation And The Representation Of Hydrodynamic Models Of Proteins

Ruggiero, Carmelina; Piccinini, L.; Spotorno, Bruno; Tassara, Giovanni; Molinao, F.; Rocco, Mattia

doi:10.1109/iembs.1990.691928

Cited by 2 publications

(1 citation statement)

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“…Bead models were constructed, visualized, and analyzed using the BEAMS (beads modeling system) ensemble of computer programs developed in Genova on the basis of the hydrodynamic theory for multisubunit particles (Garcia de la Torre & Bloomfield, 1981). BEAMS was written in C language and runs on an HP9000-300 series computer system consisting of HP345 unit and HP375 graphic accelerator unit (both equipped with MC68030 microprocessor and MC68882 math coprocessor), HP98789A and HP98754A graphic terminals, and an HP7550A eightcolor graphic plotter (Ruggiero et al, 1990). In short, BEAMS allows the computation, from the coordinates of the center, the radius, and the mass of each bead, of the following basic hydrodynamic parameters for arrays of nonoverlapping beads up to 500 beads: translational and rotational frictional coefficients and intrinsic viscosity.…”

Section: Bead Modelingmentioning

confidence: 99%

Modeling the α_IIbβ₃ integrin solution conformation

1993

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The (~l I b P 3 platelet integrin is the prototypical member of a widely distributed class of transmembrane receptors formed by the noncovalent association of a and fi subunits. Electron microscopic (EM) images of the a[& complex show an asymmetric particle with a globular domain from which two extended regions protrude to contact the lipid bilayer. Distance constraints provided by disulfide bond patterns, epitope mapping, and ligand mimetic cross-linking studies rather suggest a somewhat more compact conformation for the a r [ b & complex.We have studied the shape of detergent-solubilized a l I b & by employing a low-resolution modeling procedure in which each polypeptide has been represented as an array of interconnected, nonoverlapping spheres (beads) of various sizes. The number, size, and three-dimensional relationships among the beads were defined either solely by dimensions obtained from published EM images of integrin receptors (EM models, 21 beads), or solely by interdomain constraints derived from published biochemical data (biochemical model, 37 beads). Interestingly, although no EM data were employed in its construction, the resulting overall shape of the biochemical model was still compatible with the EM data. Both kinds of models were then evaluated for their calculated solution properties. The more elongated EM models have diffusion and sedimentation coefficients that differ, at best, by +2% and -18% from the experimental values, determined, respectively, in octyl glucoside and Triton X-100. On the other hand, the parameters calculated for the more compact biochemical model showed a more consistent agreement with experimental values, differing by -7% (octyl glucoside) to -6% (Triton X-100).Thus, it appears that using the biochemical constraints as a starting point has resulted in not only a more detailed model of the detergent-solubilized ~111bP3 complex, where the relative spatial location of specific domains the size of 5-10 kDa can be tentatively mapped, but in a model that can also reconcile the electron microscopy with the biochemical and the solution data.

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Section: Bead Modelingmentioning

confidence: 99%