ATP/ADP modulates gp16–pRNA conformational change in the Phi29 DNA packaging motor

Abstract Packaging of phage phi29 genome requires the ATPase gp16 and prohead RNA (pRNA). The highly conserved pRNA forms the interface between the connector complex and gp16. Understanding how pRNA interacts with gp16 under packaging conditions can shed light on the molecular mechanism of the packaging motor. Here, we present 3D models of the pRNA–gp16 complex and its conformation change in response to ATP or ADP binding. Using a combination of crystallography, small angle X-ray scattering and chemical probing, we find that the pRNA and gp16 forms a ‘Z’-shaped complex, with gp16 specifically binds to pRNA domain II. The whole complex closes in the presence of ATP, and pRNA domain II rotates open as ATP hydrolyzes, before resetting after ADP is released. Our results suggest that pRNA domain II actively participates in the packaging process.

Download Full-text

Model reconstruction from Small angle X-ray Scattering data using deep learning methods

10.1101/691832 ◽

2019 ◽

Author(s):

Hao He ◽

Can Liu ◽

Haiguang Liu

Keyword(s):

Deep Learning ◽

Small Angle ◽

3D Models ◽

Scattering Data ◽

Learning Method ◽

Model Reconstruction ◽

Shape Information ◽

X Ray ◽

X Ray Scattering ◽

Ray Scattering

AbstractWe present an algorithm based on a deep learning method for model reconstruction from small angle X-ray scattering (SAXS) data. An auto-encoder for protein 3D models was trained to compress 3D shape information into vectors of a 200-dimensional latent space, and the vectors are optimized using genetic algorithms to build 3D models that are consistent with the scattering data. The algorithm was implemented using Python with the TensorFlow framework and tested with experimental data, demonstrating capacity and robustness of accurate model reconstruction even without using prior model size information.SynopsisA deep learning method based on the auto-encoder framework for model reconstruction from small angle scattering data

Download Full-text

Validation of electron microscopy initial models via small angle X-ray scattering curves

Bioinformatics ◽

10.1093/bioinformatics/bty985 ◽

2018 ◽

Vol 35 (14) ◽

pp. 2427-2433

Author(s):

Amaya Jiménez ◽

Slavica Jonic ◽

Tomas Majtner ◽

Joaquín Otón ◽

Jose Luis Vilas ◽

...

Keyword(s):

Electron Microscopy ◽

Small Angle ◽

Structural Information ◽

3D Models ◽

Particle Analysis ◽

Biological Macromolecules ◽

Low Resolution ◽

X Ray ◽

X Ray Scattering ◽

Ray Scattering

Abstract Motivation Cryo electron microscopy (EM) is currently one of the main tools to reveal the structural information of biological macromolecules. The re-construction of three-dimensional (3D) maps is typically carried out following an iterative process that requires an initial estimation of the 3D map to be refined in subsequent steps. Therefore, its determination is key in the quality of the final results, and there are cases in which it is still an open issue in single particle analysis (SPA). Small angle X-ray scattering (SAXS) is a well-known technique applied to structural biology. It is useful from small nanostructures up to macromolecular ensembles for its ability to obtain low resolution information of the biological sample measuring its X-ray scattering curve. These curves, together with further analysis, are able to yield information on the sizes, shapes and structures of the analyzed particles. Results In this paper, we show how the low resolution structural information revealed by SAXS is very useful for the validation of EM initial 3D models in SPA, helping the following refinement process to obtain more accurate 3D structures. For this purpose, we approximate the initial map by pseudo-atoms and predict the SAXS curve expected for this pseudo-atomic structure. The match between the predicted and experimental SAXS curves is considered as a good sign of the correctness of the EM initial map. Availability and implementation The algorithm is freely available as part of the Scipion 1.2 software at http://scipion.i2pc.es/.

Download Full-text

A Revised O2 Reduction Model in Li-O2 Batteries as Revealed by in Situ Small Angle X-Ray Scattering

10.26434/chemrxiv.11447775.v1 ◽

2019 ◽

Author(s):

Christian Prehal ◽

Aleksej Samojlov ◽

Manfred Nachtnebel ◽

Manfred Kriechbaum ◽

Heinz Amenitsch ◽

...

Keyword(s):

Small Angle ◽

Wide Angle ◽

Reduction Mechanism ◽

Reduction Model ◽

X Ray ◽

X Ray Scattering ◽

O2 Reduction ◽

Ray Scattering

Here we use in situ small and wide angle X-ray scattering to elucidate unexpected mechanistic insights of the O2 reduction mechanism in Li-O2 batteries.

Download Full-text

In situ Time-Resolved Small-Angle X-ray Scattering Reveals the Formation Kinetics of Polyelectrolyte Complex Micelles

10.26434/chemrxiv.9876395.v1 ◽

2019 ◽

Author(s):

Hao Wu ◽

Jeffrey Ting ◽

Siqi Meng ◽

Matthew Tirrell

Keyword(s):

Small Angle ◽

Self Assembly ◽

Electrostatic Interactions ◽

Polyelectrolyte Complex ◽

Time Resolved ◽

X Ray ◽

X Ray Scattering ◽

Kinetics Of ◽

Ray Scattering

We have directly observed the in situ self-assembly kinetics of polyelectrolyte complex (PEC) micelles by synchrotron time-resolved small-angle X-ray scattering, equipped with a stopped-flow device that provides millisecond temporal resolution. This work has elucidated one general kinetic pathway for the process of PEC micelle formation, which provides useful physical insights for increasing our fundamental understanding of complexation and self-assembly dynamics driven by electrostatic interactions that occur on ultrafast timescales.

Download Full-text

Faculty Opinions recommendation of Time-resolved small-angle X-ray scattering investigation of the folding dynamics of heme oxygenase: implication of the scaling relationship for the submillisecond intermediates of protein folding.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1007608.373952 ◽

2006 ◽

Author(s):

Kunihiro Kuwajima

Keyword(s):

Protein Folding ◽

Heme Oxygenase ◽

Small Angle ◽

Time Resolved ◽

X Ray ◽

X Ray Scattering ◽

Scaling Relationship ◽

Folding Dynamics ◽

Ray Scattering

Download Full-text

Faculty Opinions recommendation of The statistical conformation of a highly flexible protein: small-angle X-ray scattering of S. aureus protein A.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.718519299.793501063 ◽

2014 ◽

Author(s):

Walter Chazin

Keyword(s):

Small Angle ◽

Protein A ◽

X Ray ◽

X Ray Scattering ◽

Flexible Protein ◽

Ray Scattering

Download Full-text

Faculty Opinions recommendation of Exploring the "minimal" structure of a functional ADAMTS13 by mutagenesis and small-angle X-ray scattering.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.734935818.793562162 ◽

2019 ◽

Author(s):

Toshiyuki Miyata

Keyword(s):

Small Angle ◽

X Ray ◽

X Ray Scattering ◽

Minimal Structure ◽

Ray Scattering

Download Full-text

Small angle X-ray scattering study of porosity variation in a styrene-divinylbenzene copolymer

Collection of Czechoslovak Chemical Communications ◽

10.1135/cccc19811675 ◽

1981 ◽

Vol 46 (7) ◽

pp. 1675-1681 ◽

Cited By ~ 13

Author(s):

Josef Baldrian ◽

Božena N. Kolarz ◽

Henrik Galina

Keyword(s):

Small Angle ◽

Structural Parameters ◽

Two Phase ◽

X Ray ◽

Porosity Variation ◽

Swelling Agent ◽

X Ray Scattering ◽

Styrene Divinylbenzene ◽

Ray Scattering

Porosity variations induced by swelling agent exchange were studied in a styrene-divinylbenzene copolymer. Standard methods were used in the characterization of copolymer porosity in the dry state and the results were compared with related structural parameters derived from small angle X-ray scattering (SAXS) measurements as developed for the characterization of two-phase systems. The SAXS method was also used for porosity determination in swollen samples. The differences in the porosity of dry samples were found to be an effect of the drying process, while in the swollen state the sample swells and deswells isotropically.

Download Full-text