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Membrane-binding mechanism of the EEA1 FYVE domain revealed by multi-scale molecular dynamics simulations
[article]
2021
bioRxiv
pre-print
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The C-terminal FYVE domain of EEA1 binds endosomal membranes, which contain phosphatidylinositol-3-phosphate (PI(3)P). ...
FYVE, which is a homodimer, binds the membrane via a hinge mechanism, where the C-terminus of one monomer first attaches to the membrane, followed by the C-terminus of the other monomer. ...
Acknowledgements The authors would like to thank Robin Corey for input on running free energy calculations, Owen ...
doi:10.1101/2021.02.18.431783
fatcat:2mqsedatdrbglaz3occtil2xr4
Membrane-binding mechanism of the EEA1 FYVE domain revealed by multi-scale molecular dynamics simulations
2021
PLoS Computational Biology
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FYVE, which is a homodimer, binds the membrane via a hinge mechanism, where the C-terminus of one monomer first attaches to the membrane, followed by the C-terminus of the other monomer. ...
The C-terminal FYVE domain of EEA1 binds endosomal membranes, which contain phosphatidylinositol-3-phosphate (PI(3)P). ...
for the analysis. ...
doi:10.1371/journal.pcbi.1008807
pmid:34555023
pmcid:PMC8491906
fatcat:3bprv742pve5tg42ju7dfxunzi
Specific interactions of peripheral membrane proteins with lipids: what can molecular simulations show us?
[article]
2022
arXiv
pre-print
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To provide a detailed molecular view of peripheral membrane protein interactions with the membrane, computational methods such as molecular dynamics (MD) simulations can be applied. ...
Structures of these proteins and of their lipid-binding domains are typically solved in a soluble form, sometimes with a lipid or lipid headgroup at the binding site. ...
Free energy calculations were run using the ARCHER/ARCHER2 UK National Supercomputing Service (http://www.archer.ac.uk), provided by HECBioSim, the UK High End Computing Consortium for Biomolecular Simulation ...
arXiv:2202.00492v1
fatcat:nojmfkwlovctrdua2isu6lkhsy
Dynamic lipid aptamers: non-polymeric chemical path to early life
2021
Chemical Society Reviews
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Mixed lipid assemblies form dynamic aptamers that possess protein-like stereospecific recognition. ...
Acknowledgements Supported by a Minerva foundation grant number 711473, ''The emergence and evolution of early life under extreme planetary conditions'' and by DC-ren grant from Horizon 2020 EU number ...
848011 ''Drug combinations for rewriting trajectories of renal pathologies in type II diabetes''. ...
doi:10.1039/d1cs00633a
pmid:34541591
fatcat:ozuvernoxfbfhh2kljioswx7ma
Bidirectional Control of Autophagy by BECN1 BARA Domain Dynamics
2019
Molecular Cell
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These data reveal how BECN1 switches on and off PI3KC3 binding to membranes. ...
This mechanism was confirmed using protein engineering, giant unilamellar vesicle assays, and molecular simulations. ...
Grob for cryo-EM support and members of the UC Berkeley cryo-EM supergroup for helpful discussions. ...
doi:10.1016/j.molcel.2018.10.035
pmid:30581147
pmcid:PMC6450660
fatcat:we3c575qkres3d65ngzf4vf7di
Considering Protonation as a Posttranslational Modification Regulating Protein Structure and Function
2013
Annual Review of Biophysics
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Work on the structure and function of actin-binding pH sensors was supported by a Research Fellowship of the Deutsche Forschungsgemeinschaft (SCHO 1410/1-1) to A.S., a Canadian Institutes of Health Research ...
ACKNOWLEDGMENTS We thank members of the Diane Barber and the Torsten Wittmann groups for helpful suggestions; Bree Grillo-Hill for help creating Figure 2 ; Jamil S. ...
The FYVE (Fab1p, YOTB, Vac1p, and EEA1) domain (72) , the ENTH and ANTH (Epsin and AP180 N-terminal) domains (54) , and the PH domain of FAPP1 (four-phosphate-adaptor protein 1) (51) have increased phosphoinositide ...
doi:10.1146/annurev-biophys-050511-102349
pmid:23451893
pmcid:PMC4041481
fatcat:yno3ue2fbbe33gjow4nqxvs2ye
Recent progress on lipid lateral heterogeneity in plasma membranes: From rafts to submicrometric domains
2016
Progress in lipid research
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We will integrate documented mechanisms involved in the formation and maintenance of these domains, and provide a perspective on their relevance on membrane deformability and regulation of membrane protein ...
The concept of transient nanometric domains known as lipid rafts has brought interest to reassess the validity of the Singer-Nicholson model of a fluid bilayer for cell membranes. ...
(LDA), The Legacy of Angels Foundation (ERB) and the National Institutes of Health (R01 NS065808, ERB). ...
doi:10.1016/j.plipres.2015.12.004
pmid:26738447
pmcid:PMC4851880
fatcat:6ag7352hzna7bgj462kp7agr6u
In vivo identification of GTPase interactors by mitochondrial relocalization and proximity biotinylation
2019
eLife
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The GTPases of the Ras superfamily regulate cell growth, membrane traffic and the cytoskeleton, and a wide range of diseases are caused by mutations in particular members. ...
They function as switchable landmarks with the active GTP-bound form recruiting to the membrane a specific set of effector proteins. ...
Large scale screening for novel Rab effectors reveals unexpected broad Rab binding specificityhttps://doi.org/10.1074/mcp.M700569-MCP200 Molecular & Cellular Proteomics 7 :1031–1042. ...
doi:10.7554/elife.45916
pmid:31294692
pmcid:PMC6639074
fatcat:p64pfogpkza3jmqjnrhptba2ra
Tracing the dynamics of gene transcripts after organismal death
2017
Open Biology
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Ordination plots revealed non-random patterns in the profiles by time. While most of these transcript levels increased within 0.5 h postmortem, some increased only at 24 and 48 h postmortem. ...
Functional characterization of the most abundant transcripts revealed the following categories: stress, immunity, inflammation, apoptosis, transport, development, epigenetic regulation and cancer. ...
We thank Till Sckerl for help with sacrificing the mice, Nicole Thomsen for help with tissue and RNA processing, and Elke Blohm-Sievers for microarray work. ...
doi:10.1098/rsob.160267
pmid:28123054
pmcid:PMC5303275
fatcat:vwlmaul4pbhl3nfsz3lg7gnzny
Bioanalysis of Eukaryotic Organelles
2013
Chemical Reviews
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that in human embryonic kidney cell the autophagosomal membrane originated from the omegasome. 438 A GFP fusion protein of double FYVE domain-containing protein 1 (DFCP1), which binds to phosphatidylinositol ...
Inhibiting the function of early endosomal auto antigen 1 (EEA1), which is used in binding vesicles, by treatment with anti-EEA1 antibody inhibited the fission of early endosomes (i.e. the fluorescent ...
GSSG
Glutathione disulfide
HCD Higher energy collision dissociation Topic included in the manuscript are marked with an asterisk (*). ...
doi:10.1021/cr300354g
pmid:23570618
pmcid:PMC3676536
fatcat:3xuwqf2lpvcv3kuaoaas42oxje
Specific interactions of peripheral membrane proteins with lipids: what can molecular simulations show us?
2022
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2022; you can also visit the original URL.
The file type is application/pdf.
To provide a detailed molecular view of peripheral membrane protein interactions with the membrane, computational methods such as molecular dynamics (MD) simulations can be applied. ...
Structures of these proteins and of their lipid-binding domains are typically solved in a soluble form, sometimes with a lipid or lipid headgroup at the binding site. ...
Free energy calculations were run using the ARCHER/ARCHER2 UK National Supercomputing Service (http://www.archer.ac.uk), provided by HECBioSim, the UK High End Computing Consortium for Biomolecular Simulation ...
doi:10.1042/bsr20211406
pmid:35297484
pmcid:PMC9008707
fatcat:pni4fwswtjcbxfdlojauvoqzbu
Understanding Membrane Curvature Sensing
2018
Preserved Fulltext
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Eukaryotic cells are characterised by membranes with varied and dynamic compositions and shapes. ...
I then expanded the range of targets and showed that this assay is also capable of detecting curvature preferences for a variety of other lipid-binding domain families. ...
Acknowledgements First, I would like to thank my supervisor, Harvey McMahon, for giving me the opportunity of working in his lab and introducing me to the wonderful world of membrane curvature. ...
doi:10.17863/cam.17212
fatcat:wh4oya4jwnhstoecxydjodt3zq
Spatiotemporal control of clathrin-mediated endocytosis by PI3K C2α and phosphatidylinositol-3,4-bisphosphate
[article]
2013
Preserved Fulltext
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A comprehensive analysis of endocytic proteins revealed the PX-BAR domain protein sorting nexin 9 (SNX9) as an effector of PI(3,4)P2. The recruitment of SNX9 to CCPs arrested a [...] ...
However, the mechanism of PI conversion on the endocytic route from a PI(4,5)P2 to a PI(3)P enriched membrane is still enigmatic. ...
Strikingly, the PI(3)P-dependent early endosomal tethering factor EEA1 and the PI(3)P-binding FYVE-domain displayed only minor alterations in Vps34depleted cells. ...
doi:10.17169/refubium-16249
fatcat:p4wfmgzvpfhejkwhorpa5sqnoa
SPATIOTEMPORAL CONTROL OF TGFβ SIGNALING WITH LIGHT
2019
Preserved Fulltext
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Although the principal components of TGFβ signaling have been identified and explored in recent decades, understanding its dynamic behavior is limited by the lack of tools that allow the control of TGFβ ...
First, we validated the functionality of the optoTGFβ system by comparing it with the endogenous TGFβ signaling system. ...
(Fab1, YOTB/ZK632.12, Vac1 and EEA1) domain 92, 93 . ...
doi:10.18452/20264
fatcat:wl7g2skfcjbbzndl7h2opqe27u
Solution structure of the RING finger domain from the human splicing-associated protein RBBP6 using heteronuclear Nuclear Magnetic Resonance (NMR) Spectroscopy Solution structure of the RING finger domain from the human splicing-associated protein RBBP6 using heteronuclear Nuclear Magnetic Resonance (NMR) Spectroscopy
2009
unpublished
Preserved Fulltext
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Preliminary NMR analysis of the fragment revealed that the domain was folded, but that it was preceded by an unstructured region at the N-terminus. ...
RBBP6 using heteronuclear Nuclear Magnetic Resonance (NMR) Spectroscopy University of the Western Cape Retinoblastoma-binding protein 6 (RBBP6) is a multi-domain human protein known to play a role in ...
Fig. 1 . 8 : 18 Cartoon representation of the solution structure of the FYVE domain of early endosome antigen 1 (EEA1) protein determined by heteronuclear NMR spectroscopy (PDB: 1HYJ). ...
fatcat:6omdjp4gqncctmzxny2kwkgdyy
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