Biology subjects

Murshudov, G. N.

Publications and source records attributed to Murshudov, G. N..

5 recordsLinked to original sources

bioRxiv2021

3D-Strudel - a novel model-dependent map-feature validation method for high-resolution cryo-EM structures

Recent technological advances in electron cryo-microscopy (cryo-EM) have led to significant improvements in the resolution of many single-particle reconstructions and a sharp increase in the number of entries released in the Electron Microscopy Data Bank (EMDB) every year, which in turn has opened new possibilities for data mining. Here we present a resolution-dependent library of rotamer-specific amino-acid map motifs mined from entries in the EMDB archive with reported resolution between 2.0 and 4.0[A]. We further describe 3D-Strudel, a method for map/model validation based on these libraries. 3D-Strudel calculates linear correlation coefficients between the map values of a map-motif from the library and the experimental map values around a target residue. We also present "Strudel Score", a plug-in for ChimeraX, as a user-friendly tool for visualisation of 3D-Strudel validation results.

bioinformatics↗

bioRxiv2021

EMDA: A Python package for Electron Microscopy Data Analysis

An open-source Python library EMDA for cryo-EM map and model manipulation is presented with a specific focus on validation. The use of several functionalities in the library is presented through several examples. The utility of local correlation as a metric for identifying map-model differences and unmodeled regions in maps, and how it is used as a metric of map-model validation is demonstrated. The mapping of local correlation to individual atoms, and its use to draw insights on local signal variations are discussed. EMDAs likelihood-based map overlay is demonstrated by carrying out a superposition of two domains in two related structures. The overlay is carried out first to bring both maps into the same coordinate frame and then to estimate the relative movement of domains. Finally, the map magnification refinement in EMDA is presented with an example to highlight the importance of adjusting the map magnification in structural comparison studies.

biophysics↗

bioRxiv2021

Cryo-EM single particle structure refinement and map calculation using Servalcat

In 2020, cryo-EM single particle analysis achieved true atomic resolution, thanks to technological developments in hardware and software. The number of high resolution reconstructions continues to grow, increasing the importance of accurate determination of atomic coordinates. Here, a new Python package and program called Servalcat is presented that is designed to facilitate atomic model refinement. Servalcat implements a refinement pipeline, using the program REFMAC5 from the CCP4 package. After the refinement, Servalcat calculates a weighted Fo - Fc difference map, which was derived from Bayesian statistics. This map helps manual and automatic model building in real space, as is common practice in crystallography. The Fo - Fc map helps visualisation of weak features including hydrogen densities. Although hydrogen densities are weak, they are stronger than in electron density maps produced by X-ray crystallography, and some hydrogen atoms are even visible at [~] 1.8 [A] resolution. Servalcat also facilitates atomic model refinement under symmetry constraints. If a point group symmetry has been applied to the map during reconstruction, the asymmetric unit model is refined with appropriate symmetry constraints.

biophysics↗

bioRxiv2021

Bipartite binding and partial inhibition links DEPTOR and mTOR in a mutually antagonistic embrace

mTORC1 is a kinase complex regulating cell growth, proliferation and survival. Because mis-regulation of DEPTOR, an endogenous mTORC1 inhibitor, is associated with some cancers, we reconstituted mTORC1 with DEPTOR to understand its function. We find that DEPTOR is a unique partial mTORC1 inhibitor that may have evolved to preserve feedback inhibition of PI3K. Counterintuitively, mTORC1 activated by RHEB or oncogenic mutation is much more potently inhibited by DEPTOR. Although DEPTOR partially inhibits mTORC1, mTORC1 prevents this inhibition by phosphorylating DEPTOR, a mutual antagonism that requires no exogenous factors. Structural analyses of the mTORC1/DEPTOR complex showed DEPTORs PDZ domain interacting with the mTOR FAT region, and the unstructured linker preceding the PDZ binding to the mTOR FRB domain. Here we show, in contrast to previous cellular studies, that both the PDZ and linker regions are essential for inhibition, and it is likely that interaction with the FRB is crucial to the unique partial inhibition.

biochemistry↗

bioRxiv2020

Local and global analysis of macromolecular Atomic Displacement Parameters

This paper describes the global and local analyses of Atomic Displacement Parameters (ADP) of macromolecules solved and refined using X-ray crystallography method. It is shown that the distribution of ADPs follows the (mixture of) Shifted Inverse Gamma distribution(s). The parameters of the mixture of SIGDs are estimated using Expectation/Maximisation methods. In addition, a method for resolution and individual ADP dependent local analysis of neighbouring atoms has been designed. This method facilitates the detection of the mismodelled atoms and indicates potential identity of heavy metal atoms. It also helps in detecting of disordered and/or wrongly modelled ligands. Both global and local analyses can be used to detect errors in atomic structures thus helping in (re)building, refinement and validation of macromolecular structures. It can also serve as an additional validation tool during data deposition to the PDB. SynopsisMacromolecular atomic B value distributions have been modelled using a mixture of Shifted Inverse Gamma Distribution. Also, B value and resolution dependent local ADP differences have been applied for validation of heavy atoms and ligands.

molecular biology↗