The database BIOSCAT: a tool for structure research by scattering and hydrodynamic methods

The crystal structures of a large number of proteins and nucleic acids are known and the corresponding sets of coordinates are stored in the Brookhaven Protein Data Bank. For structure investigations of biological macromolecules in solution, scattering and hydrodynamical methods are powerful biophysical tools when starting the data interpretation on the basis of the crystal structure of the molecules. The database BIOSCAT covers the main structural parameters estimable by X-ray scattering, translation and rotation diffusion methods and the X-ray scattering intensities and low- and high-resolution real-space electron distance distribution functions of 70 biological macromolecules and of oligonucleotides in standard conformation. The parameters and the scattered intensities are calculated from the atomic coordinates using the improved cube method and the real-space functions are estimated via a termination-error-reduced Fourier sine transformation. The database access is organized by the program PASSDB, which can generally be used for 'readable' databases. A simple query language allows enquiries into the database without knowledge of a programming language. The program CONVSQL converts the database into normalized relations that can be handled by structured query languages (SQLs)

Single Honeybee Silk Protein Mimics Properties of Multi-Protein Silk

Honeybee silk is composed of four fibrous proteins that, unlike other silks, are readily synthesized at full-length and high yield. The four silk genes have been conserved for over 150 million years in all investigated bee, ant and hornet species, implying a distinct functional role for each protein. However, the amino acid composition and molecular architecture of the proteins are similar, suggesting functional redundancy. In this study we compare materials generated from a single honeybee silk protein to materials containing all four recombinant proteins or to natural honeybee silk. We analyse solution conformation by dynamic light scattering and circular dichroism, solid state structure by Fourier Transform Infrared spectroscopy and Raman spectroscopy, and fiber tensile properties by stress-strain analysis. The results demonstrate that fibers artificially generated from a single recombinant silk protein can reproduce the structural and mechanical properties of the natural silk. The importance of the four protein complex found in natural silk may lie in biological silk storage or hierarchical self-assembly. The finding that the functional properties of the mature material can be achieved with a single protein greatly simplifies the route to production for artificial honeybee silk

Spermine-DNA complexes build up metastable structures. Small-angle X-ray scattering and circular dichroism studies.

Spermine-DNA complexes have been examined by small-angle and wide-angle X-ray scattering as well as by circular dichroism studies. Condensed complexes are building up below a critical ionic strength. We have found that at one and the same ionic strength condensed complexes having two different supramolecular structures (Type I and Type II) can coexist. The structure of the condensates depends on the method of condensate formation. Phase transitions between these structures can be induced by thermal treatment. We conclude from these facts that with polyamine-DNA condensates metastable structures are of importance