scholarly journals Computational simulations reveal that Abl activity controls cohesiveness of actin networks in growth cones

2021 ◽  
Author(s):  
Aravind Chandrasekaran ◽  
Akanni Clarke ◽  
Philip G. McQueen ◽  
Hsiao-Yu Fang ◽  
Garegin A Papoian ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Cell Biology ◽  
Large Scale ◽  
Axon Growth ◽  
Simulation Software ◽  
Striking Similarity ◽  
Neuronal Morphogenesis ◽  
Actin Networks ◽  
Downstream Effects

Extensive studies of growing axons have revealed many individual components and protein interactions that guide neuronal morphogenesis. Despite this, however, we lack any clear picture of the emergent mechanism by which this nanometer-scale biochemistry generates the multi-micron scale morphology and cell biology of axon growth and guidance in vivo. To address this, we studied the downstream effects of the Abl signaling pathway using a computer simulation software (MEDYAN) that accounts for mechanochemical dynamics of active polymers. Previous studies implicate two Abl effectors, Arp2/3 and Enabled, in Abl-dependent axon guidance decisions. We now find that Abl alters actin architecture primarily by activating Arp2/3, while Enabled plays a more limited role. Our simulations show that simulations mimicking modest levels of Abl activity bear striking similarity to actin profiles obtained experimentally from live-imaging of actin in wild type axons in vivo. Using a graph-theoretical filament-filament contact analysis, moreover, we find that networks mimicking hyperactivity of Abl (enhanced Arp2/3) are fragmented into smaller domains of actin that interact weakly with each other, consistent with the pattern of actin fragmentation observed upon Abl overexpression in vivo. Two perturbative simulations further confirm that high Arp2/3 actin networks are mechanically disconnected and fail to mount a cohesive response to perturbation. Taken together, these data provide a molecular-level picture of how the large-scale organization of the axonal cytoskeleton arises from the biophysics of actin networks.

scholarly journals Modulation of A2aR Oligomerisation by Conformational State and PIP2 Interactions Revealed by MD Simulations and Markov Models

2020 ◽  
Author(s):  
Wanling Song ◽  
Anna L. Duncan ◽  
Mark S.P. Sansom
Keyword(s):  
Protein Interactions ◽  
Large Scale ◽  
Markov Models ◽  
Transmembrane Helix ◽  
Receptor Activation ◽  
Membrane Lipid ◽  
Intracellular Loop ◽  
Gpcr Activation ◽  
State Models

AbstractG protein-coupled receptors (GPCRs) play key roles in cellular signalling. GPCRs are suggested to form dimers and higher order oligomers in response to activation. However, we do not fully understand GPCR activation at larger scales and in an in vivo context. We have characterised oligomeric configurations of the adenosine 2a receptor (A2aR) by combining large-scale molecular dynamics simulations with Markov state models. Receptor activation results in enhanced oligomerisation, more diverse oligomer populations, and a more connected oligomerisation network. The active state conformation of the A2aR shifts protein-protein association interfaces to those involving intracellular loop ICL3 and transmembrane helix TM6. Binding of PIP2 to A2aR stabilises protein-protein interactions via PIP2-mediated association interfaces. These results indicate that A2aR oligomerisation is responsive to the local membrane lipid environment. This in turn suggests a modulatory effect on A2aR whereby a given oligomerisation profile favours the dynamic formation of specific supra-molecular signalling complexes.

scholarly journals In Vivo Dynamics of Swi6 in Yeast: Evidence for a Stochastic Model of Heterochromatin

2004 ◽  
Vol 24 (8) ◽  
pp. 3157-3167 ◽  
Author(s):  
Thierry Cheutin ◽  
Stanislaw A. Gorski ◽  
Karen M. May ◽  
Prim B. Singh ◽  
Tom Misteli
Keyword(s):  
Stochastic Model ◽  
Fission Yeast ◽  
Protein Interactions ◽  
Mammalian Cells ◽  
Large Scale ◽  
Quantitative Estimation ◽  
Pericentric Heterochromatin ◽  
Heterochromatin Protein ◽  
Structural Heterochromatin

ABSTRACT The mechanism for transcriptional silencing of pericentric heterochromatin is conserved from fission yeast to mammals. Silenced genome regions are marked by epigenetic methylation of histone H3, which serves as a binding site for structural heterochromatin proteins. In the fission yeast Schizosaccharomyces pombe, the major structural heterochromatin protein is Swi6. To gain insight into Swi6 function in vivo, we have studied its dynamics in the nucleus of living yeast. We demonstrate that, in contrast to mammalian cells, yeast heterochromatin domains undergo rapid, large-scale motions within the nucleus. Similar to the situation in mammalian cells, Swi6 does not permanently associate with these chromatin domains but binds only transiently to euchromatin and heterochromatin. Swi6 binding dynamics are dependent on growth status and on the silencing factors Clr4 and Rik1, but not Clr1, Clr2, or Clr3. By comparing the kinetics of mutant Swi6 proteins in swi6− and swi6+ strains, we demonstrate that homotypic protein-protein interactions via the chromoshadow domain stabilize Swi6 binding to chromatin in vivo. Kinetic modeling allowed quantitative estimation of residence times and indicated the existence of at least two kinetically distinct populations of Swi6 in heterochromatin. The observed dynamics of Swi6 binding are consistent with a stochastic model of heterochromatin and indicate evolutionary conservation of heterochromatin protein binding properties from mammals to yeast.

scholarly journals Extensive In vivo Metabolite‐Protein Interactions Revealed by Large‐Scale Systematic Analyses

2012 ◽  
Vol 26 (S1) ◽  
Author(s):  
Michael Snyder ◽  
Xiyan Li ◽  
Tara Gianoulis ◽  
Kevin Yip ◽  
Mark Gerstein
Keyword(s):  
Protein Interactions ◽  
Large Scale

scholarly journals Generation of a versatile BiFC ORFeome library for analyzing protein-protein interactions in live Drosophila

2018 ◽  
Author(s):  
J. Bischof ◽  
M. Duffraisse ◽  
E. Furger ◽  
L. Ajuria ◽  
G. Giraud ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Protein Interactions ◽  
Large Scale ◽  
Bimolecular Fluorescence Complementation ◽  
Protein Protein Interactions ◽  
Expression Domain ◽  
Hox Proteins ◽  
Non Invasive ◽  
Tripartite Interactions

AbstractTranscription factors achieve specificity by establishing intricate interaction networks that will change depending on the cell context. Capturing these interactions in live condition is however a challenging issue that requires sensitive and non-invasive methods. We present a set of fly lines, called “multicolor BiFC library”, which covers most of the Drosophila transcription factors for performing Bimolecular Fluorescence Complementation (BiFC). The multicolor BiFC library can be used to probe binary or tripartite interactions and is compatible for large-scale interaction screens. The library can also be coupled with established Drosophila genetic resources to analyze interactions in the developmentally relevant expression domain of each protein partner. We provide proof of principle experiments of these various applications, using Hox proteins in the live Drosophila embryo as a case study. Overall this novel collection of ready-to-use fly lines constitutes an unprecedented genetic toolbox for the identification and analysis of protein-protein interactions in vivo.

scholarly journals Generation of a versatile BiFC ORFeome library for analyzing protein–protein interactions in live Drosophila

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Johannes Bischof ◽  
Marilyne Duffraisse ◽  
Edy Furger ◽  
Leiore Ajuria ◽  
Guillaume Giraud ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Protein Interactions ◽  
Large Scale ◽  
Drosophila Embryo ◽  
Bimolecular Fluorescence Complementation ◽  
Protein Protein Interactions ◽  
Expression Domain ◽  
Hox Proteins ◽  
Non Invasive

Transcription factors achieve specificity by establishing intricate interaction networks that will change depending on the cell context. Capturing these interactions in live condition is however a challenging issue that requires sensitive and non-invasive methods.We present a set of fly lines, called ‘multicolor BiFC library’, which covers most of the Drosophila transcription factors for performing Bimolecular Fluorescence Complementation (BiFC). The multicolor BiFC library can be used to probe two different binary interactions simultaneously and is compatible for large-scale interaction screens. The library can also be coupled with established Drosophila genetic resources to analyze interactions in the developmentally relevant expression domain of each protein partner. We provide proof of principle experiments of these various applications, using Hox proteins in the live Drosophila embryo as a case study. Overall this novel collection of ready-to-use fly lines constitutes an unprecedented genetic toolbox for the identification and analysis of protein-protein interactions in vivo.

scholarly journals Extensive In Vivo Metabolite-Protein Interactions Revealed by Large-Scale Systematic Analyses

Cell ◽  
2010 ◽  
Vol 143 (4) ◽  
pp. 639-650 ◽  
Author(s):  
Xiyan Li ◽  
Tara A. Gianoulis ◽  
Kevin Y. Yip ◽  
Mark Gerstein ◽  
Michael Snyder
Keyword(s):  
Protein Interactions ◽  
Large Scale

scholarly journals Development of a compact alkynyl-enrichable crosslinker for in-depth in-vivo crosslinking analysis

2021 ◽  
Author(s):  
Hang Gao ◽  
Li Li Zhao ◽  
Qun Zhao ◽  
Hua Li Zhang ◽  
Feng Bao Zhao ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Large Scale ◽  
High Efficiency ◽  
Protein Complexes ◽  
Protein Structures ◽  
High Sensitivity ◽  
Protein Protein Interactions ◽  
Cross Links ◽  
First Time

Chemical crosslinking coupled with mass spectrometry (CXMS) has emerged as a powerful technique to capture the dynamic information of protein complexes with high sensitivity, throughput and sample universality. To advance the study of in-vivo protein structures and protein-protein interactions on the large scale, a new alkynyl-enrichable crosslinker was developed with high efficiency of membrane penetration, reactivity and enrichment. The crosslinker was successfully used for in-vivo crosslinking of intact human cells, resulting in 6820 non-redundant crosslinks identified at a false discovery rate (FDR) of 1% using pLink 2.0, which 4898 (71.8%) of the cross-links were assigned as intraprotein and 1922 (28.2%) were interprotein links. To our knowledge, this is also the first time to realize the in-vivo crosslinking with a non-cleavable cross-linker for homo species cells.

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