News and Publications

Synthesis and 3-Dimensional Visualization of Multiresolution Structural Data

W. Wriggers, P. Chacón, J. Kovacs, S. Birmanns*

* John von Neumann Institut für Computing, Jülich, Germany

New insights into cellular processes require the synthesis of information obtained with low- to medium-resolution biophysical techniques, such as electron microscopy, with atomic-resolution structures. We are developing novel approaches for the registration of atomic-resolution subunits with low-resolution densities of large macromolecular aggregates.

FOURIER TEMPLATE CONVOLUTION

Template convolution takes advantage of Fourier correlation theory to rapidly scan the 6 translational and rotational degrees of freedom of a probe molecule relative to a (fixed) target density map (Fig. 1). X-ray crystallographic fitting methods, based on volumetric cross correlation, or the R value, are limited to resolutions less than 10 Å, the level at which densities show internal structure.

The major advantage of our quantitative docking method is that it extends the practical resolution range to approximately 30 Å by means of a laplacian operator that emphasizes contour (shape) information in addition to the traditional volumetric correlation. Laplacian-filtered density maps maximize the fitting contrast. Tests with synthetic low-resolution density models of oligomeric assemblies indicate that the difference in score between the correct fit and spurious fits increases by 35%-50% relative to the traditional volumetric correlation-based docking.

FLEXIBLE DOCKING

In the presence of induced-fit conformational changes, rigid-body docking alone gives poor alignment of the crystal and low resolution. Therefore, we devised alternative modeling techniques based on molecular dynamics simulation and point "landmarks" that bring deviating global features of biopolymers into register while preserving the crystal structure locally. We added a flexible alignment tool to our Situs docking package that is based on 3-dimensional "motion capture" technology used in the entertainment industry and in biomechanics. By freezing inessential degrees of freedom, skeletons of connected landmarks significantly reduce the effect of noise and thereby improve the stereochemical quality of the fitted structures relative to the unconstrained alignments. In collaboration with E.H. Egelman, University of Virginia, Charlottesville, we used skeleton-based flexible fitting to uniquely define a molecular model of cofilin bound to F-actin that was based solely on the monomeric crystal structures and on an electron microscopic reconstruction of actin filaments decorated with human cofilin.

VIRTUAL REALITY

In collaboration with S. Birmanns, John von Neumann Institut für Computing, Jülich, Germany, we are developing a 3-dimensional graphics extension for Situs, termed SenSitus, that can support virtual-reality devices such as stereo glasses, 3-dimensional trackers, and force-feedback (haptic) devices (Fig. 2). In addition to using automated fitting, microscopists must evaluate and manipulate docking models interactively "by eye." Three-dimensional capabilities and the "physics of touch" offer tangible benefits for modelers who wish to explore a variety of docking situations in a virtual-reality environment.

PUBLICATIONS
Galkin, V.E., Orlova, A., Lukoyanova, N., Wriggers, W., Egelman, E.H. Actin depolymerizing factor stabilizes an existing state of F-actin and can change the tilt of F-actin subunits. J. Cell Biol. 153:75, 2001.

Wriggers, W., Birmanns, S. Using Situs for flexible and rigid-body fitting of multi-resolution single molecule data. J. Struct. Biol., in press.

Wriggers, W., Chacón, P. Using Situs for the registration of protein structures with low-resolution bead models from x-ray solution scattering. J. Appl. Crystallogr., in press.

Xing, J., Wriggers, W., Jefferson, G.M., Stein, R., Cheung, H.C., Rosenfeld, S.S. Kinesin has three nucleotide-dependent conformations: Implications for strain-dependent release. J. Biol. Chem. 275:35413, 2000.

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