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Membrane-binding mechanism of the EEA1 FYVE domain revealed by multi-scale molecular dynamics simulations [article]

Andreas Haahr Larsen, Lilya Tata, Laura John, Mark S.P. Sansom
2021 bioRxiv   pre-print
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

Andreas Haahr Larsen, Lilya Tata, Laura H. John, Mark S. P. Sansom, Erik Lindahl
2021 PLoS Computational Biology  
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]

Andreas Haahr Larsen, Laura H. John, Mark S.P. Sansom, Robin A. Corey
2022 arXiv   pre-print
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

Amit Kahana, Svetlana Maslov, Doron Lancet
2021 Chemical Society Reviews  
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

Chunmei Chang, Lindsey N. Young, Kyle L. Morris, Sören von Bülow, Johannes Schöneberg, Hitomi Yamamoto-Imoto, Yukako Oe, Kentaro Yamamoto, Shuhei Nakamura, Goran Stjepanovic, Gerhard Hummer, Tamotsu Yoshimori (+1 others)
2019 Molecular Cell  
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

André Schönichen, Bradley A. Webb, Matthew P. Jacobson, Diane L. Barber
2013 Annual Review of Biophysics  
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

Mélanie Carquin, Ludovic D'Auria, Hélène Pollet, Ernesto R. Bongarzone, Donatienne Tyteca
2016 Progress in lipid research  
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

Alison K Gillingham, Jessie Bertram, Farida Begum, Sean Munro
2019 eLife  
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

Alex E. Pozhitkov, Rafik Neme, Tomislav Domazet-Lošo, Brian G. Leroux, Shivani Soni, Diethard Tautz, Peter A. Noble
2017 Open Biology  
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

Chad P. Satori, Michelle M. Henderson, Elyse A. Krautkramer, Vratislav Kostal, Mark M. Distefano, Edgar A. Arriaga
2013 Chemical Reviews  
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?

Andreas H Larsen, Laura H John, Mark S P Sansom, Robin A Corey
2022
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

Adeline Colussi, Apollo-University Of Cambridge Repository, Apollo-University Of Cambridge Repository, Harvey T McMahon
2018
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]

York Posor, Universitätsbibliothek Der FU Berlin, Universitätsbibliothek Der FU Berlin
2013
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

Yuchao Li, Humboldt-Universität Zu Berlin, Humboldt-Universität Zu Berlin
2019
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

Abidemi Kappo, David Pugh, Abidemi Kappo, Abidemi Mautin, Kappo Phd
2009 unpublished
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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