News and Publications

Computational Structural Biology

W. Wriggers, P. Chacón, Y. Cong, J. Kovacs, E. Metwally, S. Birmanns*

* John von Neumann Institut für Computing, Jülich, Germany

COMBINING DATA FROM A VARIETY OF BIOPHYSICAL SOURCES

Three-dimensional shapes of proteins in solution are routinely determined by using 1-dimensional small-angle x-ray scattering data. We developed a set of visualization and registration procedures that combine atomic structures with low-resolution small-angle x-ray scattering models. The docking algorithm takes advantage of a reduced representation of the input data sets by using topology-representing neural networks to expedite the search. For >100 beads typically arising in small-angle x-ray scattering models, a docking precision <1 Å an be achieved.

A contour-based matching criterion was developed for the quantitative docking of high-resolution structures of components into low-resolution maps of macromolecular complexes. The proposed laplacian filter is combined with a 6-dimensional search by using fast Fourier transforms to rapidly scan the rigid-body degrees of freedom of a probe molecule relative to a fixed target density map. The new algorithm allows, for the first time, the reliable docking of smaller molecular components into electron microscopy densities of large biomolecular assemblies at resolutions as low as 30 Å. As an example of the contour-based fitting, a new pseudoatomic model of a microtubule was constructed from an electron microscopy map and from atomic structures of a - and b -tubulin subunits (Fig. 1).

FLEXIBLE DOCKING

A flexible alignment tool was recently added to our Situs docking package that is based on 3-dimensional "motion capture" technology used in the entertainment industry and in biomechanics. We used this tool in collaboration with S. Darst, Rockefeller University, New York City, in whose laboratory the structure of Escherichia coli core RNA polymerase was determined by electron cryomicroscopy and image processing of helical crystals to a resolution of 15 Å. Because of the high sequence conservation between the core RNA polymerase subunits, we were able to interpret the E coli structure in relation to the high-resolution x-ray structure of Thermus aquaticus core RNA polymerase. A very large conformational change of the electron cryomicroscopy RNA polymerase x-ray structure, corresponding to opening of the main DNA-RNA channel by nearly 25 Å, was required to fit the E coli map (Fig. 2). This finding revealed, at least partially, the range of conformational flexibility of the RNA polymerase, which most likely has functional implications for the initiation of transcription, in which the DNA template must be loaded into the channel.

VIRTUAL REALITY

One of the challenges in computational structural biology is the efficient use and interoperation of a diverse set of techniques to simulate, analyze, model, and visualize the complex architecture and interactions of macromolecular systems. Our latest development will enable scientists to build models, combine atomic and volumetric data, and perform morphing and warping (flexible docking) interactively within a single computational environment. 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.

A force-feedback device measures a user's hand position and exerts a precisely controlled force on the hand. Our software supports this functionality by calculating forces according to the correlation coefficient of density maps and crystallographic data. The high sampling frequency required for force feedback (refresh rate >1 kHz) is achieved by means of the topology-representing neural network algorithm developed in our group that reduces the complexity of the data representation to manageable levels.

PUBLICATIONS

Chacón, P., Wriggers, W. Multi-resolution contour-based fitting of macromolecular structures. J. Mol. Biol. 317:375, 2002.

Darst, S.A., Opalka, N., Chacón, P., Polyakov, A., Richter, C., Zhang, G., Wriggers, W. Conformational flexibility of bacterial RNA polymerase. Proc. Natl. Acad. Sci. U. S. A. 99:4296, 2002.

Wriggers, W., Birmanns, S. Using Situs for flexible and rigid-body fitting of multiresolution single-molecule data. J. Struct. Biol. 133:193, 2001.

Wriggers, W., Chacón, P. Modeling tricks and fitting techniques for multiresolution structures. Structure (Camb.) 9:779, 2001.

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. 34:773, 2001.

Yao, X., Nguyen, V., Wriggers, W., Rubenstein, P.A. Regulation of yeast actin behavior by interaction of charged residues across the interdomain cleft. J. Biol. Chem. 277:22875, 2002.