Biology subjects

Sjors Scheres

Publications and source records attributed to Sjors Scheres.

3 recordsLinked to original sources

bioRxiv2016

A pipeline approach to single-particle processing in RELION

We describe the formal concept of a workflow to single-particle analysis of cryo-electron microscopy (cryo-EM) images in the RELION program. In this approach, the structure determination process is considered as a graph, where intermediate results in the form of images or metadata are the vertices, and different functionalities of the program are the edges. The new implementation automatically logs all user actions, facilitates file management and disk cleaning, and allows convenient browsing of a projects history. Moreover, new functionality to iteratively execute consecutive jobs allows on-the-fly image processing, which will lead to more efficient data acquisition by providing faster feedback on data quality. The possibility to exchange data processing procedures among users will con-tribute to the development of standardised image processing procedures, and hence increase accessibility for new users in this rapidly expanding field.

Biophysics↗

bioRxiv2016

Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2

By reaching near-atomic resolution for a wide range of specimens, single-particle cryo-EM structure determination is transforming structural biology. However, the necessary calculations come at increased computational costs, introducing a bottleneck that is currently limiting throughput and the development of new methods. Here, we present an implementation of the O_SCPCAPRELIONC_SCPCAP image processing software that uses graphics processors (GPUs) to address the most computationally intensive steps of its cryo-EM structure determination workflow. Both image classification and high-resolution refinement have been accelerated up to 40-fold, and template-based particle selection has been accelerated almost 1000-fold on desktop hardware. Memory requirements on GPUs have been reduced to fit widely available hard-ware, and we show that the use of single precision arithmetic does not adversely affect results. This enables high-resolution cryo-EM structure determination in a matter of days on a single workstation.

Biophysics↗

bioRxiv2015

Sampling the conformational space of the catalytic subunit of human γ-secretase

Human {gamma}-secretase is an intra-membrane protease that cleaves many different substrates. Aberrant cleavage of Notch is implicated in cancer, while abnormalities in cutting amyloid precursor protein lead to Alzheimers disease. Our previous cryo-EM structure of {gamma}-secretase revealed considerable disorder in its catalytic subunit presenilin. Here, we introduce an image classification procedure that characterizes molecular plasticity at the secondary structure level, and apply this method to identify three distinct conformations in our previous sample. In one of these conformations, an additional transmembrane helix is visible that cannot be attributed to the known components of {gamma}-secretase. In addition, we present a {gamma}-secretase structure in complex with the dipeptidic inhibitor N-[N-(3,5-difluorophenacetyl)-L-alanyl]-S-phenylglycine t-butyl ester (DAPT). Our results reveal how conformational mobility in the second and sixth transmembrane helices of presenilin is greatly reduced upon binding of DAPT or the additional helix, and form the basis for a new model of how substrate enters the transmembrane domain.

Molecular Biology↗