scholarly journals Cryo-EM analysis of PIP2 regulation in mammalian GIRK channels

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Yiming Niu ◽  
Xiao Tao ◽  
Kouki K Touhara ◽  
Roderick MacKinnon
Keyword(s):  
Conformational Changes ◽  
Cytoplasmic Membrane ◽  
Membrane Surface ◽  
Cytoplasmic Domain ◽  
Inward Rectifier ◽  
Particle Analysis ◽  
Single Particle Analysis ◽  
Girk Channels ◽  
Binding Surface ◽  
To Receive

G-protein-gated inward rectifier potassium (GIRK) channels are regulated by G proteins and PIP2. Here, using cryo-EM single particle analysis we describe the equilibrium ensemble of structures of neuronal GIRK2 as a function of the C8-PIP2 concentration. We find that PIP2 shifts the equilibrium between two distinguishable structures of neuronal GIRK (GIRK2), extended and docked, towards the docked form. In the docked form the cytoplasmic domain, to which Gβγ binds, becomes accessible to the cytoplasmic membrane surface where Gβγ resides. Furthermore, PIP2 binding reshapes the Gβγ binding surface on the cytoplasmic domain, preparing it to receive Gβγ. We find that cardiac GIRK (GIRK1/4) can also exist in both extended and docked conformations. These findings lead us to conclude that PIP2 influences GIRK channels in a structurally similar manner to Kir2.2 channels. In Kir2.2 channels, the PIP2-induced conformational changes open the pore. In GIRK channels, they prepare the channel for activation by Gβγ.

scholarly journals CryoDRGN: Reconstruction of heterogeneous structures from cryo-electron micrographs using neural networks

2020 ◽  
Author(s):  
Ellen D. Zhong ◽  
Tristan Bepler ◽  
Bonnie Berger ◽  
Joseph H. Davis
Keyword(s):  
Neural Networks ◽  
Conformational Changes ◽  
Deep Neural Networks ◽  
Protein Complexes ◽  
Structural Heterogeneity ◽  
Particle Analysis ◽  
Single Particle Analysis ◽  
Current Analysis ◽  
Heterogeneous Structures ◽  
First Time

AbstractCryo-EM single-particle analysis has proven powerful in determining the structures of rigid macromolecules. However, many protein complexes are flexible and can change conformation and composition as a result of functionally-associated dynamics. Such dynamics are poorly captured by current analysis methods. Here, we present cryoDRGN, an algorithm that for the first time leverages the representation power of deep neural networks to efficiently reconstruct highly heterogeneous complexes and continuous trajectories of protein motion. We apply this tool to two synthetic and three publicly available cryo-EM datasets, and we show that cryoDRGN provides an interpretable representation of structural heterogeneity that can be used to identify discrete states as well as continuous conformational changes. This ability enables cryoDRGN to discover previously overlooked structural states and to visualize molecules in motion.

scholarly journals Survey of the analysis of continuous conformational variability of biological macromolecules by electron microscopy

2019 ◽  
Vol 75 (1) ◽  
pp. 19-32 ◽  
Author(s):  
C. O. S. Sorzano ◽  
A. Jiménez ◽  
J. Mota ◽  
J. L. Vilas ◽  
D. Maluenda ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Image Processing ◽  
High Resolution ◽  
Conformational Changes ◽  
Three Dimensional ◽  
Particle Analysis ◽  
Biological Macromolecules ◽  
Single Particle Analysis ◽  
Conformational Variability ◽  
Established Technique

Single-particle analysis by electron microscopy is a well established technique for analyzing the three-dimensional structures of biological macromolecules. Besides its ability to produce high-resolution structures, it also provides insights into the dynamic behavior of the structures by elucidating their conformational variability. Here, the different image-processing methods currently available to study continuous conformational changes are reviewed.

scholarly journals Molecular Basis for RNA Polymerase-Dependent Transcription Complex Recycling By The Helicase-like Motor Protein HelD.

2020 ◽  
Author(s):  
Timothy Newing ◽  
Aaron Oakley ◽  
Michael Miller ◽  
Catherine Dawson ◽  
Simon Brown ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Conformational Changes ◽  
Molecular Basis ◽  
Particle Analysis ◽  
Single Particle Analysis ◽  
Replication Machinery ◽  
Gram Positive Bacteria ◽  
Cryo Electron Microscopy ◽  
Transcription Complexes ◽  
Primary Channel

Abstract In bacteria, transcription complexes stalled on DNA represent a major source of roadblocks for the DNA replication machinery that must be removed in order to prevent damaging collisions. Gram-positive bacteria contain a transcription factor HelD that is able to remove and recycle stalled complexes, but it was not known how it performed this function. Here, using cryo-electron microscopy and single-particle analysis, we have determined the structures of Bacillus subtilis RNA polymerase (RNAP) elongation and HelD complexes, enabling analysis of the extraordinary conformational changes that occur in RNAP driven by HelD interaction. HelD has a unique 2-armed structure which penetrates deep into the primary and secondary channels of RNA polymerase. One arm removes nucleic acids from the active site, and the other induces a dramatic conformational change in the primary channel leading to removal and recycling of the stalled polymerase.

Role of spectrin in membrane fusion and in shape change of human erythrocyte ghost

1978 ◽  
Vol 36 (2) ◽  
pp. 328-329
Author(s):  
Hideo Hayashi ◽  
Yoshikazu Hirai ◽  
John T. Penniston
Keyword(s):  
Conformational Changes ◽  
Human Erythrocyte ◽  
Shape Change ◽  
Membrane Surface ◽  
Slight Modification ◽  
Active Role ◽  
Main Role ◽  
Bank Blood ◽  
Human Erythrocyte Ghost

Spectrin is a membrane associated protein most of which properties have been tentatively elucidated. A main role of the protein has been assumed to give a supporting structure to inside of the membrane. As reported previously, however, the isolated spectrin molecule underwent self assemble to form such as fibrous, meshwork, dispersed or aggregated arrangements depending upon the buffer suspended and was suggested to play an active role in the membrane conformational changes. In this study, the role of spectrin and actin was examined in terms of the molecular arrangements on the erythrocyte membrane surface with correlation to the functional states of the ghosts.Human erythrocyte ghosts were prepared from either freshly drawn or stocked bank blood by the method of Dodge et al with a slight modification as described before. Anti-spectrin antibody was raised against rabbit by injection of purified spectrin and partially purified.

scholarly journals Thermo Scientific™ Tundra Cryo-TEM: 100kV Cryo-TEM dedicated for Single Particle Analysis

2021 ◽  
Vol 27 (S1) ◽  
pp. 1330-1332
Author(s):  
Zuzana Hlavenková ◽  
Dimple Karia ◽  
Miloš Malínský ◽  
Daniel Němeček ◽  
Fanis Grollios ◽  
...  
Keyword(s):  
Single Particle ◽  
Particle Analysis ◽  
Single Particle Analysis

SINGLE PARTICLE ANALYSIS OF FIXED FOG DROPLETS USING SR X-RAY MICROPROBE SYSTEM

2001 ◽  
Vol 32 ◽  
pp. 873-874
Author(s):  
S. TOHNO ◽  
S. HAYAKAWA ◽  
A. NAKAMURA ◽  
A. HAMAMOTO ◽  
M. SUZUKI ◽  
...  
Keyword(s):  
Single Particle ◽  
Particle Analysis ◽  
Single Particle Analysis ◽  
X Ray
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