Biology subjects

Sachse, C.

Publications and source records attributed to Sachse, C..

3 recordsLinked to original sources

bioRxiv2018

Thresholding of cryo-EM density maps by false discovery rate control

Cryo-EM now commonly generates close-to-atomic resolution as well as intermediate resolution maps from macromolecules observed in isolation and in situ. Interpreting these maps remains a challenging task due to poor signal in the highest resolution shells and the necessity to select a threshold for density analysis. In order to facilitate this process, we developed a statistical framework for the generation of confidence maps by multiple hypothesis testing and false discovery rate (FDR) control. In this way, 3D confidence maps contain separated signal from background noise in the form of local detection rates of EM density values. We demonstrate that confidence maps and FDR-based thresholding can be used for the interpretation of near-atomic resolution single-particle structures as well as lower resolution maps determined by subtomogram averaging. Confidence maps represent a conservative way of interpreting molecular structures due to minimized noise. At the same time they provide a detection error with respect to background noise, which is associated with the density and particularly beneficial for the interpretation of weaker cryo-EM densities in cases of conformational flexibility and lower occupancy of bound molecules and ions to the structure.

biophysics↗

bioRxiv2017

The small non-coding vault RNA1-1 acts as a riboregulator of autophagy

Vault RNAs (vtRNA) are small, 88-100nt non-coding RNAs found in many eukaryotes. Although they have been linked to drug resistance, apoptosis and nuclear transport, their function remains unclear. Here we show that a human vtRNA, RNA1-1, specifically binds to the autophagy receptor sequestosome-1/p62. Antisense-mediated depletion of vault RNA1-1 augments, whereas increased vault RNA1-1 expression restricts, autophagic flux in a p62-dependent manner. Bulk autophagy induced by starvation reduces the levels of vault RNA1-1 and the fraction of RNA-bound p62. These findings show that RNAs can act as riboregulators of biological processes by interacting with proteins, and assign a function to a vault RNA.

molecular biology↗

bioRxiv2017

Iterative model-based density improvement yields better atomic structures from cryo-EM maps

Atomic models based on high-resolution density maps are the ultimate result of the cryo-EM structure determination process. Current cryo-EM model refinement procedures work with the experimental density map that remains constant throughout the process. Here, we introduce a general procedure that iteratively improves cryo-EM density maps based on prior knowledge of an atomic reference structure. The procedure optimizes contrast of cryo-EM densities by local amplitude scaling (LocScale) based on an atomic model without introducing model bias. We alternate the procedure with consecutive rounds of model refinement and tested it on four cryo-EM structures of TRPV1, {beta}-galactosidase, {gamma}-secretase and RNA polymerase III. We demonstrate that LocScale density improvement reveals previously undiscovered map features and improves the quality of atomic models. The presented approach enhances the interpretability of cryo-EM density maps and provides an implementation reminiscent of iterative density improvement as it is routinely employed in the refinement of X-ray crystallographic models.

biophysics↗