Search bioRxiv⌕ Search

Biology subjects

Strelkov, S. V.

Publications and source records attributed to Strelkov, S. V..

3 recordsLinked to original sources

Crystallography of lamin A facilitated by chimeric fusions

All proteins of the intermediate filament (IF) family contain the signature central -helical domain which forms a coiled-coil dimer. Because of its length, past structural studies relied on a divide-and-conquer strategy whereby fragments of this domain were recombinantly produced, crystallized and analysed using X-rays. Here we describe a further development of this approach towards structural studies of nuclear IF protein lamin. To this end, we have fused lamin A fragments to short N- and C-terminal capping motifs which provide for the correct formation of parallel, in-register coiled-coil dimers. As the result, a chimeric construct containing lamin A residues 17-70 C-terminally capped by the Eb1 domain was solved to 1.83 [A] resolution. Another chimera containing lamin A residues 327-403 N-terminally capped by the Gp7 domain was solved to 2.9 [A]. In the latter case the capping motif was additionally modified to include a disulphide bridge at the dimer interface. We discuss multiple benefits of fusing coiled-coil dimers with such capping motifs, including a convenient crystallographic phasing by either molecular replacement or sulphur single-wavelength anomalous dispersion (S-SAD) measurements.

molecular biology↗

Optimal data-driven parameterization of coiled coils

-helical coiled coils (CCs) represent an important, highly regular protein folding motif. To date, many thousands of CC structures have been determined experimentally. Their geometry is usually modelled by theoretical equations introduced by F. Crick that involve a predefined set of parameters. Here we have addressed the problem of efficient CC parameterization from scratch by performing a statistical evaluation of all available CC structures. The procedure is based on the principal component analysis and yields a minimal set of independent parameters that provide for the reconstruction of the complete CC structure at a required precision. The approach is successfully validated on a set of canonical parallel CC dimers. Its applications include all cases where an efficient sampling of the CC geometry is important, such as for solving the phase problem in crystallography.

bioinformatics↗

Z-score to evaluate the absolute quality of macromolecular models based on SAXS data

Small-angle X-ray scattering (SAXS) is a highly popular technique to assess the native three-dimensional structure of biological macromolecules in solution. Here we introduce a statistical criterion, Z-score, as a novel quality measure of SAXS-based structural models which positively correlates with data quality. We propose that, besides a goodness-of-fit (GOF) measure such as reduced {chi}2, the Z-score reflecting the ability of a given SAXS curve to differentiate between possible models should always be reported.

bioinformatics↗