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Weeratunga S, Gormal RS, Liu M, Eldershaw D, Livingstone EK, Malapaka A, Wallis TP, Bademosi AT, Jiang A, Healy MD, Meunier FA, Collins BM. Interrogation and validation of the interactome of neuronal Munc18-interacting Mint proteins with AlphaFold2. J Biol Chem 2024; 300:105541. [PMID: 38072052 PMCID: PMC10820826 DOI: 10.1016/j.jbc.2023.105541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/27/2023] [Accepted: 11/29/2023] [Indexed: 01/13/2024] Open
Abstract
Munc18-interacting proteins (Mints) are multidomain adaptors that regulate neuronal membrane trafficking, signaling, and neurotransmission. Mint1 and Mint2 are highly expressed in the brain with overlapping roles in the regulation of synaptic vesicle fusion required for neurotransmitter release by interacting with the essential synaptic protein Munc18-1. Here, we have used AlphaFold2 to identify and then validate the mechanisms that underpin both the specific interactions of neuronal Mint proteins with Munc18-1 as well as their wider interactome. We found that a short acidic α-helical motif within Mint1 and Mint2 is necessary and sufficient for specific binding to Munc18-1 and binds a conserved surface on Munc18-1 domain3b. In Munc18-1/2 double knockout neurosecretory cells, mutation of the Mint-binding site reduces the ability of Munc18-1 to rescue exocytosis, and although Munc18-1 can interact with Mint and Sx1a (Syntaxin1a) proteins simultaneously in vitro, we find that they have mutually reduced affinities, suggesting an allosteric coupling between the proteins. Using AlphaFold2 to then examine the entire cellular network of putative Mint interactors provides a structural model for their assembly with a variety of known and novel regulatory and cargo proteins including ADP-ribosylation factor (ARF3/ARF4) small GTPases and the AP3 clathrin adaptor complex. Validation of Mint1 interaction with a new predicted binder TJAP1 (tight junction-associated protein 1) provides experimental support that AlphaFold2 can correctly predict interactions across such large-scale datasets. Overall, our data provide insights into the diversity of interactions mediated by the Mint family and show that Mints may help facilitate a key trigger point in SNARE (soluble N-ethylmaleimide-sensitive factor attachment receptor) complex assembly and vesicle fusion.
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Affiliation(s)
- Saroja Weeratunga
- Institute for Molecular Bioscience, The University of Queensland, Queensland, Australia
| | - Rachel S Gormal
- Clem Jones Centre for Ageing and Dementia Research, Queensland Brain Institute, The University of Queensland, Queensland, Australia
| | - Meihan Liu
- Institute for Molecular Bioscience, The University of Queensland, Queensland, Australia
| | - Denaye Eldershaw
- Institute for Molecular Bioscience, The University of Queensland, Queensland, Australia
| | - Emma K Livingstone
- Institute for Molecular Bioscience, The University of Queensland, Queensland, Australia
| | - Anusha Malapaka
- Clem Jones Centre for Ageing and Dementia Research, Queensland Brain Institute, The University of Queensland, Queensland, Australia
| | - Tristan P Wallis
- Clem Jones Centre for Ageing and Dementia Research, Queensland Brain Institute, The University of Queensland, Queensland, Australia
| | - Adekunle T Bademosi
- Clem Jones Centre for Ageing and Dementia Research, Queensland Brain Institute, The University of Queensland, Queensland, Australia
| | - Anmin Jiang
- Clem Jones Centre for Ageing and Dementia Research, Queensland Brain Institute, The University of Queensland, Queensland, Australia
| | - Michael D Healy
- Institute for Molecular Bioscience, The University of Queensland, Queensland, Australia
| | - Frederic A Meunier
- Clem Jones Centre for Ageing and Dementia Research, Queensland Brain Institute, The University of Queensland, Queensland, Australia; School of Biomedical Sciences, The University of Queensland, Queensland, Australia
| | - Brett M Collins
- Institute for Molecular Bioscience, The University of Queensland, Queensland, Australia.
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2
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Healy MD, Collins BM. The PDLIM family of actin-associated proteins and their emerging role in membrane trafficking. Biochem Soc Trans 2023; 51:2005-2016. [PMID: 38095060 PMCID: PMC10754285 DOI: 10.1042/bst20220804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/29/2023] [Accepted: 12/04/2023] [Indexed: 12/21/2023]
Abstract
The PDZ and LIM domain (PDLIM) proteins are associated with the actin cytoskeleton and have conserved in roles in metazoan actin organisation and function. They primarily function as scaffolds linking various proteins to actin and its binding partner α-actinin via two conserved domains; an N-terminal postsynaptic density 95, discs large and zonula occludens-1 (PDZ) domain, and either single or multiple C-terminal LIN-11, Isl-1 and MEC-3 (LIM) domains in the actinin-associated LIM protein (ALP)- and Enigma-related proteins, respectively. While their role in actin organisation, such as in stress fibres or in the Z-disc of muscle fibres is well known, emerging evidence also suggests a role in actin-dependent membrane trafficking in the endosomal system. This is mediated by a recently identified interaction with the sorting nexin 17 (SNX17) protein, an adaptor for the trafficking complex Commander which is itself intimately linked to actin-directed formation of endosomal recycling domains. In this review we focus on the currently understood structural basis for PDLIM function. The PDZ domains mediate direct binding to distinct classes of PDZ-binding motifs (PDZbms), including α-actinin and other actin-associated proteins, and a highly specific interaction with the type III PDZbm such as the one found in the C-terminus of SNX17. The structures of the LIM domains are less well characterised and how they engage with their ligands is completely unknown. Despite the lack of experimental structural data, we find that recently developed machine learning-based structure prediction methods provide insights into their potential interactions and provide a template for further studies of their molecular functions.
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Affiliation(s)
- Michael D. Healy
- The University of Queensland, Institute for Molecular Bioscience, St Lucia, Queensland 4072, Australia
| | - Brett M. Collins
- The University of Queensland, Institute for Molecular Bioscience, St Lucia, Queensland 4072, Australia
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3
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Healy MD, McNally KE, Butkovič R, Chilton M, Kato K, Sacharz J, McConville C, Moody ERR, Shaw S, Planelles-Herrero VJ, Yadav SKN, Ross J, Borucu U, Palmer CS, Chen KE, Croll TI, Hall RJ, Caruana NJ, Ghai R, Nguyen THD, Heesom KJ, Saitoh S, Berger I, Schaffitzel C, Williams TA, Stroud DA, Derivery E, Collins BM, Cullen PJ. Structure of the endosomal Commander complex linked to Ritscher-Schinzel syndrome. Cell 2023; 186:2219-2237.e29. [PMID: 37172566 PMCID: PMC10187114 DOI: 10.1016/j.cell.2023.04.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/23/2023] [Accepted: 04/04/2023] [Indexed: 05/15/2023]
Abstract
The Commander complex is required for endosomal recycling of diverse transmembrane cargos and is mutated in Ritscher-Schinzel syndrome. It comprises two sub-assemblies: Retriever composed of VPS35L, VPS26C, and VPS29; and the CCC complex which contains twelve subunits: COMMD1-COMMD10 and the coiled-coil domain-containing (CCDC) proteins CCDC22 and CCDC93. Combining X-ray crystallography, electron cryomicroscopy, and in silico predictions, we have assembled a complete structural model of Commander. Retriever is distantly related to the endosomal Retromer complex but has unique features preventing the shared VPS29 subunit from interacting with Retromer-associated factors. The COMMD proteins form a distinctive hetero-decameric ring stabilized by extensive interactions with CCDC22 and CCDC93. These adopt a coiled-coil structure that connects the CCC and Retriever assemblies and recruits a 16th subunit, DENND10, to form the complete Commander complex. The structure allows mapping of disease-causing mutations and reveals the molecular features required for the function of this evolutionarily conserved trafficking machinery.
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Affiliation(s)
- Michael D Healy
- Centre for Cell Biology of Chronic Disease, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Kerrie E McNally
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, BS8 1TD Bristol, UK; MRC Laboratory of Molecular Biology, CB2 0QH Cambridge, UK.
| | - Rebeka Butkovič
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, BS8 1TD Bristol, UK
| | - Molly Chilton
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, BS8 1TD Bristol, UK
| | - Kohji Kato
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, BS8 1TD Bristol, UK
| | - Joanna Sacharz
- Department of Biochemistry and Pharmacology, The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia
| | - Calum McConville
- Department of Biochemistry and Pharmacology, The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia
| | - Edmund R R Moody
- School of Biological Sciences, University of Bristol, BS8 1TD Bristol, UK
| | - Shrestha Shaw
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, BS8 1TD Bristol, UK
| | | | - Sathish K N Yadav
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, BS8 1TD Bristol, UK
| | - Jennifer Ross
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, BS8 1TD Bristol, UK
| | - Ufuk Borucu
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, BS8 1TD Bristol, UK
| | - Catherine S Palmer
- Department of Biochemistry and Pharmacology, The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia
| | - Kai-En Chen
- Centre for Cell Biology of Chronic Disease, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Tristan I Croll
- Cambridge Institute for Medical Research, University of Cambridge, CB2 0XY Cambridge, UK
| | - Ryan J Hall
- Centre for Cell Biology of Chronic Disease, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Nikeisha J Caruana
- Department of Biochemistry and Pharmacology, The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia; Institute of Health and Sport (iHeS), Victoria University, Melbourne, VIC Australia
| | - Rajesh Ghai
- Centre for Cell Biology of Chronic Disease, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Thi H D Nguyen
- MRC Laboratory of Molecular Biology, CB2 0QH Cambridge, UK
| | - Kate J Heesom
- Proteomics Facility, School of Biochemistry, Biomedical Sciences Building, University of Bristol, BS8 1TD Bristol, UK
| | - Shinji Saitoh
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences and Medical School, Nagoya, Japan
| | - Imre Berger
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, BS8 1TD Bristol, UK; Max Planck Bristol Centre for Minimal Biology, Department of Chemistry, University of Bristol, BS8 1TS Bristol, UK
| | - Christiane Schaffitzel
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, BS8 1TD Bristol, UK
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, BS8 1TD Bristol, UK
| | - David A Stroud
- Department of Biochemistry and Pharmacology, The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia; Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC Australia
| | | | - Brett M Collins
- Centre for Cell Biology of Chronic Disease, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia.
| | - Peter J Cullen
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, BS8 1TD Bristol, UK.
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Chen KE, Guo Q, Hill TA, Cui Y, Kendall AK, Yang Z, Hall RJ, Healy MD, Sacharz J, Norwood SJ, Fonseka S, Xie B, Reid RC, Leneva N, Parton RG, Ghai R, Stroud DA, Fairlie DP, Suga H, Jackson LP, Teasdale RD, Passioura T, Collins BM. De novo macrocyclic peptides for inhibiting, stabilizing, and probing the function of the retromer endosomal trafficking complex. Sci Adv 2021; 7:eabg4007. [PMID: 34851660 PMCID: PMC8635440 DOI: 10.1126/sciadv.abg4007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 10/14/2021] [Indexed: 05/27/2023]
Abstract
The retromer complex (Vps35-Vps26-Vps29) is essential for endosomal membrane trafficking and signaling. Mutation of the retromer subunit Vps35 causes late-onset Parkinson’s disease, while viral and bacterial pathogens can hijack the complex during cellular infection. To modulate and probe its function, we have created a novel series of macrocyclic peptides that bind retromer with high affinity and specificity. Crystal structures show that most of the cyclic peptides bind to Vps29 via a Pro-Leu–containing sequence, structurally mimicking known interactors such as TBC1D5 and blocking their interaction with retromer in vitro and in cells. By contrast, macrocyclic peptide RT-L4 binds retromer at the Vps35-Vps26 interface and is a more effective molecular chaperone than reported small molecules, suggesting a new therapeutic avenue for targeting retromer. Last, tagged peptides can be used to probe the cellular localization of retromer and its functional interactions in cells, providing novel tools for studying retromer function.
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Affiliation(s)
- Kai-En Chen
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Qian Guo
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Timothy A. Hill
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Yi Cui
- School of Biomedical Sciences, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Amy K. Kendall
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Zhe Yang
- School of Biomedical Sciences, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Ryan J. Hall
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Michael D. Healy
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Joanna Sacharz
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Suzanne J. Norwood
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Sachini Fonseka
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Boyang Xie
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Robert C. Reid
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Natalya Leneva
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Robert G. Parton
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
- Centre for Microscopy and Microanalysis, The University of Queensland, Queensland, Australia
| | - Rajesh Ghai
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - David A. Stroud
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3052, Australia
- Murdoch Children’s Research Institute, The Royal Children’s Hospital, Parkville, Victoria 3052, Australia
| | - David P. Fairlie
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo 113-0033, Japan
| | - Lauren P. Jackson
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Rohan D. Teasdale
- School of Biomedical Sciences, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Toby Passioura
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo 113-0033, Japan
- Sydney Analytical, School of Life and Environmental Sciences and School of Chemistry, The University of Sydney, Camperdown, New South Wales 2050, Australia
| | - Brett M. Collins
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
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5
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Chen K, Healy MD, Collins BM. Towards a molecular understanding of endosomal trafficking by Retromer and Retriever. Traffic 2019; 20:465-478. [DOI: 10.1111/tra.12649] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 04/15/2019] [Accepted: 04/15/2019] [Indexed: 12/16/2022]
Affiliation(s)
- Kai‐En Chen
- Institute for Molecular Bioscience University of Queensland St. Lucia Queensland Australia
| | - Michael D. Healy
- Institute for Molecular Bioscience University of Queensland St. Lucia Queensland Australia
| | - Brett M. Collins
- Institute for Molecular Bioscience University of Queensland St. Lucia Queensland Australia
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6
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Zhang AH, Edwards IA, Mishra BP, Sharma G, Healy MD, Elliott AG, Blaskovich MAT, Cooper MA, Collins BM, Jia X, Mobli M. Elucidating the Lipid Binding Properties of Membrane-Active Peptides Using Cyclised Nanodiscs. Front Chem 2019; 7:238. [PMID: 31058133 PMCID: PMC6477933 DOI: 10.3389/fchem.2019.00238] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 03/26/2019] [Indexed: 01/02/2023] Open
Abstract
The lipid composition of the cellular membrane plays an important role in a number of biological processes including the binding of membrane-active peptides. Characterization of membrane binding remains challenging, due to the technical limitations associated with the use of standard biophysical techniques and available membrane models. Here, we investigate the lipid binding properties of two membrane-active peptides, VSTx1, a well characterized ion-channel inhibitor, identified from spider venom, that preferentially binds to anionic lipid mixtures, and AA139 an antimicrobial β-hairpin peptide with uncharacterised lipid binding properties, currently in pre-clinical development. The lipid binding properties of these peptides are elucidated using nanodiscs formed by both linear and circularized (sortase-mediated) forms of a membrane scaffold protein (MSP1D1ΔH5). We find that nanodiscs formed by circularized MSPs—in contrast to those formed by linear MSPs—are sufficiently stable under sample conditions typically used for biophysical measurements (including lipid composition, a range of buffers, temperatures and concentrations). Using these circularized nanodiscs, we are able to extract detailed thermodynamic data using isothermal titration calorimetry (ITC) as well as atomic resolution mapping of the lipid binding interfaces of our isotope labeled peptides using solution-state, heteronuclear, nuclear magnetic resonance (NMR) spectroscopy. This represents a novel and general approach for elucidating the thermodynamics and molecular interface of membrane-active peptides toward flat lipid bilayers of variable composition. Our approach is validated by first determining the thermodynamic parameters and binding interface of VSTx1 toward the lipid bilayer, which shows good agreement with previous studies using lipid micelles and liposomes. The method is then applied to AA139, where the membrane binding properties are unknown. This characterization, involved solving the high-resolution structure of AA139 in solution using NMR spectroscopy and the development of a suitable expression system for isotope labeling. AA139 was found to bind exclusively to anionic membranes with moderate affinity (Kd~low μM), and was found to have a lipid binding interface involving the termini of the β-hairpin structure. The preference of AA139 for anionic lipids supports a role for membrane binding in the mode-of-action of this peptide, which is also consistent with its higher inhibitory activity against bacterial cells compared to mammalian cells. The described approach is a powerful method for investigation of the membrane binding properties of this important class of molecules.
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Affiliation(s)
- Alan H Zhang
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD, Australia
| | - Ingrid A Edwards
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Biswa P Mishra
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD, Australia
| | - Gagan Sharma
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD, Australia
| | - Michael D Healy
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Alysha G Elliott
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Mark A T Blaskovich
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Matthew A Cooper
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Brett M Collins
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Xinying Jia
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD, Australia
| | - Mehdi Mobli
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD, Australia
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7
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Healy MD, Hospenthal MK, Hall RJ, Chandra M, Chilton M, Tillu V, Chen KE, Celligoi DJ, McDonald FJ, Cullen PJ, Lott JS, Collins BM, Ghai R. Structural insights into the architecture and membrane interactions of the conserved COMMD proteins. eLife 2018; 7:e35898. [PMID: 30067224 PMCID: PMC6089597 DOI: 10.7554/elife.35898] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 07/31/2018] [Indexed: 12/31/2022] Open
Abstract
The COMMD proteins are a conserved family of proteins with central roles in intracellular membrane trafficking and transcription. They form oligomeric complexes with each other and act as components of a larger assembly called the CCC complex, which is localized to endosomal compartments and mediates the transport of several transmembrane cargos. How these complexes are formed however is completely unknown. Here, we have systematically characterised the interactions between human COMMD proteins, and determined structures of COMMD proteins using X-ray crystallography and X-ray scattering to provide insights into the underlying mechanisms of homo- and heteromeric assembly. All COMMD proteins possess an α-helical N-terminal domain, and a highly conserved C-terminal domain that forms a tightly interlocked dimeric structure responsible for COMMD-COMMD interactions. The COMM domains also bind directly to components of CCC and mediate non-specific membrane association. Overall these studies show that COMMD proteins function as obligatory dimers with conserved domain architectures.
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Affiliation(s)
- Michael D Healy
- Institute for Molecular BioscienceThe University of QueenslandSt. LuciaAustralia
| | | | - Ryan J Hall
- Institute for Molecular BioscienceThe University of QueenslandSt. LuciaAustralia
| | - Mintu Chandra
- Institute for Molecular BioscienceThe University of QueenslandSt. LuciaAustralia
| | - Molly Chilton
- School of Biochemistry, Biomedical Sciences BuildingUniversity of BristolBristolUnited Kingdom
| | - Vikas Tillu
- Institute for Molecular BioscienceThe University of QueenslandSt. LuciaAustralia
| | - Kai-En Chen
- Institute for Molecular BioscienceThe University of QueenslandSt. LuciaAustralia
| | - Dion J Celligoi
- School of Biological SciencesThe University of AucklandAucklandNew Zealand
| | | | - Peter J Cullen
- School of Biochemistry, Biomedical Sciences BuildingUniversity of BristolBristolUnited Kingdom
| | - J Shaun Lott
- School of Biological SciencesThe University of AucklandAucklandNew Zealand
| | - Brett M Collins
- Institute for Molecular BioscienceThe University of QueenslandSt. LuciaAustralia
| | - Rajesh Ghai
- Institute for Molecular BioscienceThe University of QueenslandSt. LuciaAustralia
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8
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Abraham J, Abreu P, Aglietta M, Aguirre C, Allard D, Allekotte I, Allen J, Allison P, Alvarez-Muñiz J, Ambrosio M, Anchordoqui L, Andringa S, Anzalone A, Aramo C, Argirò S, Arisaka K, Armengaud E, Arneodo F, Arqueros F, Asch T, Asorey H, Assis P, Atulugama BS, Aublin J, Ave M, Avila G, Bäcker T, Badagnani D, Barbosa AF, Barnhill D, Barroso SLC, Baughman B, Bauleo P, Beatty JJ, Beau T, Becker BR, Becker KH, Bellido JA, Benzvi S, Berat C, Bergmann T, Bernardini P, Bertou X, Biermann PL, Billoir P, Blanch-Bigas O, Blanco F, Blasi P, Bleve C, Blümer H, Bohácová M, Bonifazi C, Bonino R, Brack J, Brogueira P, Brown WC, Buchholz P, Bueno A, Burton RE, Busca NG, Caballero-Mora KS, Cai B, Camin DV, Caramete L, Caruso R, Carvalho W, Castellina A, Catalano O, Cataldi G, Cazon L, Cester R, Chauvin J, Chiavassa A, Chinellato JA, Chou A, Chudoba J, Chye J, Clark PDJ, Clay RW, Colombo E, Conceição R, Connolly B, Contreras F, Coppens J, Cordier A, Cotti U, Coutu S, Covault CE, Creusot A, Criss A, Cronin J, Curutiu A, Dagoret-Campagne S, Daumiller K, Dawson BR, de Almeida RM, De Donato C, de Jong SJ, De La Vega G, Junior WJMDM, Neto JRTDM, De Mitri I, de Souza V, Del Peral L, Deligny O, Della Selva A, Fratte CD, Dembinski H, Di Giulio C, Diaz JC, Diep PN, Dobrigkeit C, D'Olivo JC, Dong PN, Dornic D, Dorofeev A, Dos Anjos JC, Dova MT, D'Urso D, Dutan I, Duvernois MA, Engel R, Epele L, Erdmann M, Escobar CO, Etchegoyen A, Luis PFS, Falcke H, Farrar G, Fauth AC, Fazzini N, Ferrer F, Ferrero A, Fick B, Filevich A, Filipcic A, Fleck I, Fracchiolla CE, Fulgione W, García B, Gámez DG, Garcia-Pinto D, Garrido X, Geenen H, Gelmini G, Gemmeke H, Ghia PL, Giller M, Glass H, Gold MS, Golup G, Albarracin FG, Berisso MG, Gonçalves P, do Amaral MG, Gonzalez D, Gonzalez JG, González M, Góra D, Gorgi A, Gouffon P, Grassi V, Grillo AF, Grunfeld C, Guardincerri Y, Guarino F, Guedes GP, Gutiérrez J, Hague JD, Halenka V, Hamilton JC, Hansen P, Harari D, Harmsma S, Harton JL, Haungs A, Hauschildt T, Healy MD, Hebbeker T, Hebrero G, Heck D, Hojvat C, Holmes VC, Homola P, Hörandel JR, Horneffer A, Hrabovský M, Huege T, Hussain M, Iarlori M, Insolia A, Ionita F, Italiano A, Kaducak M, Kampert KH, Karova T, Kasper P, Kégl B, Keilhauer B, Kemp E, Kieckhafer RM, Klages HO, Kleifges M, Kleinfeller J, Knapik R, Knapp J, Koang DH, Krieger A, Krömer O, Kuempel D, Kunka N, Kusenko A, La Rosa G, Lachaud C, Lago BL, Lebrun D, Lebrun P, Lee J, de Oliveira MAL, Letessier-Selvon A, Leuthold M, Lhenry-Yvon I, López R, Agüera AL, Bahilo JL, Lucero A, García RL, Maccarone MC, Macolino C, Maldera S, Mancarella G, Manceñido ME, Mandat D, Mantsch P, Mariazzi AG, Maris IC, Falcon HRM, Martello D, Martínez J, Bravo OM, Mathes HJ, Matthews J, Matthews JAJ, Matthiae G, Maurizio D, Mazur PO, McCauley T, McEwen M, McNeil RR, Medina MC, Medina-Tanco G, Melo D, Menichetti E, Menschikov A, Meurer C, Meyhandan R, Micheletti MI, Miele G, Miller W, Mollerach S, Monasor M, Ragaigne DM, Montanet F, Morales B, Morello C, Moreno JC, Morris C, Mostafá M, Muller MA, Mussa R, Navarra G, Navarro JL, Navas S, Necesal P, Nellen L, Newman-Holmes C, Newton D, Nhung PT, Nierstenhoefer N, Nitz D, Nosek D, Nozka L, Oehlschläger J, Ohnuki T, Olinto A, Olmos-Gilbaja VM, Ortiz M, Ortolani F, Ostapchenko S, Otero L, Pacheco N, Selmi-Dei DP, Palatka M, Pallotta J, Parente G, Parizot E, Parlati S, Pastor S, Patel M, Paul T, Pavlidou V, Payet K, Pech M, Pekala J, Pelayo R, Pepe IM, Perrone L, Pesce R, Petrera S, Petrinca P, Petrov Y, Pichel A, Piegaia R, Pierog T, Pimenta M, Pinto T, Pirronello V, Pisanti O, Platino M, Pochon J, Privitera P, Prouza M, Quel EJ, Rautenberg J, Redondo A, Reucroft S, Revenu B, Rezende FAS, Ridky J, Riggi S, Risse M, Rivière C, Rizi V, Roberts M, Robledo C, Rodriguez G, Martino JR, Rojo JR, Rodriguez-Cabo I, Rodríguez-Frías MD, Ros G, Rosado J, Roth M, Rouillé-d'Orfeuil B, Roulet E, Rovero AC, Salamida F, Salazar H, Salina G, Sánchez F, Santander M, Santo CE, Santos EM, Sarazin F, Sarkar S, Sato R, Scherini V, Schieler H, Schmidt A, Schmidt F, Schmidt T, Scholten O, Schovánek P, Schroeder F, Schulte S, Schüssler F, Sciutto SJ, Scuderi M, Segreto A, Semikoz D, Settimo M, Shellard RC, Sidelnik I, Siffert BB, Sigl G, Grande NSD, Smiałkowski A, Smída R, Smith AGK, Smith BE, Snow GR, Sokolsky P, Sommers P, Sorokin J, Spinka H, Squartini R, Strazzeri E, Stutz A, Suarez F, Suomijärvi T, Supanitsky AD, Sutherland MS, Swain J, Szadkowski Z, Takahashi J, Tamashiro A, Tamburro A, Tarutina T, Taşcău O, Tcaciuc R, Thao NT, Thomas D, Ticona R, Tiffenberg J, Timmermans C, Tkaczyk W, Peixoto CJT, Tomé B, Tonachini A, Torres I, Travnicek P, Tripathi A, Tristram G, Tscherniakhovski D, Tuci V, Tueros M, Tunnicliffe V, Ulrich R, Unger M, Urban M, Galicia JFV, Valiño I, Valore L, van den Berg AM, van Elewyck V, Vázquez RA, Veberic D, Veiga A, Velarde A, Venters T, Verzi V, Videla M, Villaseñor L, Vorobiov S, Voyvodic L, Wahlberg H, Wahrlich P, Wainberg O, Walker P, Warner D, Watson AA, Westerhoff S, Wieczorek G, Wiencke L, Wilczyńska B, Wilczyński H, Wileman C, Winnick MG, Wu H, Wundheiler B, Yamamoto T, Younk P, Zas E, Zavrtanik D, Zavrtanik M, Zaw I, Zepeda A, Ziolkowski M. Observation of the suppression of the flux of cosmic rays above 4 x 10 (19) eV. Phys Rev Lett 2008; 101:061101. [PMID: 18764444 DOI: 10.1103/physrevlett.101.061101] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2008] [Indexed: 05/26/2023]
Abstract
The energy spectrum of cosmic rays above 2.5 x 10;{18} eV, derived from 20,000 events recorded at the Pierre Auger Observatory, is described. The spectral index gamma of the particle flux, J proportional, variantE;{-gamma}, at energies between 4 x 10;{18} eV and 4 x 10;{19} eV is 2.69+/-0.02(stat)+/-0.06(syst), steepening to 4.2+/-0.4(stat)+/-0.06(syst) at higher energies. The hypothesis of a single power law is rejected with a significance greater than 6 standard deviations. The data are consistent with the prediction by Greisen and by Zatsepin and Kuz'min.
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Affiliation(s)
- J Abraham
- Universidad Tecnológica Nacional, FR-Mendoza, Argentina
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Abraham J, Abreu P, Aglietta M, Aguirre C, Allard D, Allekotte I, Allen J, Allison P, Alvarez-Muñiz J, Ambrosio M, Anchordoqui L, Andringa S, Anzalone A, Aramo C, Argirò S, Arisaka K, Armengaud E, Arneodo F, Arqueros F, Asch T, Asorey H, Assis P, Atulugama BS, Aublin J, Ave M, Avila G, Bäcker T, Badagnani D, Barbosa AF, Barnhill D, Barroso SLC, Bauleo P, Beatty JJ, Beau T, Becker BR, Becker KH, Bellido JA, BenZvi S, Berat C, Bergmann T, Bernardini P, Bertou X, Biermann PL, Billoir P, Blanch-Bigas O, Blanco F, Blasi P, Bleve C, Blümer H, Bohácová M, Bonifazi C, Bonino R, Boratav M, Brack J, Brogueira P, Brown WC, Buchholz P, Bueno A, Burton RE, Busca NG, Caballero-Mora KS, Cai B, Camin DV, Caramete L, Caruso R, Carvalho W, Castellina A, Catalano O, Cataldi G, Cazon L, Cester R, Chauvin J, Chiavassa A, Chinellato JA, Chou A, Chye J, Clark PDJ, Clay RW, Colombo E, Conceição R, Connolly B, Contreras F, Coppens J, Cordier A, Cotti U, Coutu S, Covault CE, Creusot A, Criss A, Cronin J, Curutiu A, Dagoret-Campagne S, Daumiller K, Dawson BR, de Almeida RM, De Donato C, de Jong SJ, De La Vega G, de Mello Junior WJM, de Mello Neto JRT, DeMitri I, de Souza V, del Peral L, Deligny O, Della Selva A, Delle Fratte C, Dembinski H, Di Giulio C, Diaz JC, Dobrigkeit C, D'Olivo JC, Dornic D, Dorofeev A, dos Anjos JC, Dova MT, D'Urso D, Dutan I, DuVernois MA, Engel R, Epele L, Erdmann M, Escobar CO, Etchegoyen A, Facal San Luis P, Falcke H, Farrar G, Fauth AC, Fazzini N, Ferrer F, Ferry S, Fick B, Filevich A, Filipcic A, Fleck I, Fonte R, Fracchiolla CE, Fulgione W, García B, García Gámez D, Garcia-Pinto D, Garrido X, Geenen H, Gelmini G, Gemmeke H, Ghia PL, Giller M, Glass H, Gold MS, Golup G, Gomez Albarracin F, Gómez Berisso M, Gómez Herrero R, Gonçalves P, Gonçalves do Amaral M, Gonzalez D, Gonzalez JG, González M, Góra D, Gorgi A, Gouffon P, Grassi V, Grillo AF, Grunfeld C, Guardincerri Y, Guarino F, Guedes GP, Gutiérrez J, Hague JD, Hamilton JC, Hansen P, Harari D, Harmsma S, Harton JL, Haungs A, Hauschildt T, Healy MD, Hebbeker T, Hebrero G, Heck D, Hojvat C, Holmes VC, Homola P, Hörandel J, Horneffer A, Horvat M, Hrabovský M, Huege T, Hussain M, Iarlori M, Insolia A, Ionita F, Italiano A, Kaducak M, Kampert KH, Karova T, Kégl B, Keilhauer B, Kemp E, Kieckhafer RM, Klages HO, Kleifges M, Kleinfeller J, Knapik R, Knapp J, Koang DH, Krieger A, Krömer O, Kuempel D, Kunka N, Kusenko A, La Rosa G, Lachaud C, Lago BL, Lebrun D, Lebrun P, Lee J, Leigui de Oliveira MA, Letessier-Selvon A, Leuthold M, Lhenry-Yvon I, López R, Lopez Agüera A, Lozano Bahilo J, Luna García R, Maccarone MC, Macolino C, Maldera S, Mancarella G, Manceñido ME, Mandat D, Mantsch P, Mariazzi AG, Maris IC, Marquez Falcon HR, Martello D, Martínez J, Martínez Bravo O, Mathes HJ, Matthews J, Matthews JAJ, Matthiae G, Maurizio D, Mazur PO, McCauley T, McEwen M, McNeil RR, Medina MC, Medina-Tanco G, Meli A, Melo D, Menichetti E, Menschikov A, Meurer C, Meyhandan R, Micheletti MI, Miele G, Miller W, Mollerach S, Monasor M, Monnier Ragaigne D, Montanet F, Morales B, Morello C, Moreno JC, Morris C, Mostafá M, Muller MA, Mussa R, Navarra G, Navarro JL, Navas S, Necesal P, Nellen L, Newman-Holmes C, Newton D, Nguyen Thi T, Nierstenhoefer N, Nitz D, Nosek D, Nozka L, Oehlschläger J, Ohnuki T, Olinto A, Olmos-Gilbaja VM, Ortiz M, Ortolani F, Ostapchenko S, Otero L, Pacheco N, Pakk Selmi-Dei D, Palatka M, Pallotta J, Parente G, Parizot E, Parlati S, Pastor S, Patel M, Paul T, Pavlidou V, Payet K, Pech M, Pekala J, Pelayo R, Pepe IM, Perrone L, Petrera S, Petrinca P, Petrov Y, Pham Ngoc D, Pham Ngoc D, Pham Thi TN, Pichel A, Piegaia R, Pierog T, Pimenta M, Pinto T, Pirronello V, Pisanti O, Platino M, Pochon J, Privitera P, Prouza M, Quel EJ, Rautenberg J, Redondo A, Reucroft S, Revenu B, Rezende FAS, Ridky J, Riggi S, Risse M, Rivière C, Rizi V, Roberts M, Robledo C, Rodriguez G, Rodríguez Frías D, Rodriguez Martino J, Rodriguez Rojo J, Rodriguez-Cabo I, Ros G, Rosado J, Roth M, Rouillé-d'Orfeuil B, Roulet E, Rovero AC, Salamida F, Salazar H, Salina G, Sánchez F, Santander M, Santo CE, Santos EM, Sarazin F, Sarkar S, Sato R, Scherini V, Schieler H, Schmidt A, Schmidt F, Schmidt T, Scholten O, Schovánek P, Schüssler F, Sciutto SJ, Scuderi M, Segreto A, Semikoz D, Settimo M, Shellard RC, Sidelnik I, Siffert BB, Sigl G, Smetniansky De Grande N, Smiałkowski A, Smída R, Smith AGK, Smith BE, Snow GR, Sokolsky P, Sommers P, Sorokin J, Spinka H, Squartini R, Strazzeri E, Stutz A, Suarez F, Suomijärvi T, Supanitsky AD, Sutherland MS, Swain J, Szadkowski Z, Takahashi J, Tamashiro A, Tamburro A, Taşcău O, Tcaciuc R, Thomas D, Ticona R, Tiffenberg J, Timmermans C, Tkaczyk W, Todero Peixoto CJ, Tomé B, Tonachini A, Torres I, Torresi D, Travnicek P, Tripathi A, Tristram G, Tscherniakhovski D, Tueros M, Tunnicliffe V, Ulrich R, Unger M, Urban M, Valdés Galicia JF, Valiño I, Valore L, van den Berg AM, van Elewyck V, Vázquez RA, Veberic D, Veiga A, Velarde A, Venters T, Verzi V, Videla M, Villaseñor L, Vorobiov S, Voyvodic L, Wahlberg H, Wainberg O, Walker P, Warner D, Watson AA, Westerhoff S, Wieczorek G, Wiencke L, Wilczyńska B, Wilczyński H, Wileman C, Winnick MG, Wu H, Wundheiler B, Yamamoto T, Younk P, Zas E, Zavrtanik D, Zavrtanik M, Zech A, Zepeda A, Ziolkowski M. Upper limit on the diffuse flux of ultrahigh energy tau neutrinos from the Pierre Auger Observatory. Phys Rev Lett 2008; 100:211101. [PMID: 18518595 DOI: 10.1103/physrevlett.100.211101] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2007] [Indexed: 05/26/2023]
Abstract
The surface detector array of the Pierre Auger Observatory is sensitive to Earth-skimming tau neutrinos that interact in Earth's crust. Tau leptons from nu(tau) charged-current interactions can emerge and decay in the atmosphere to produce a nearly horizontal shower with a significant electromagnetic component. The data collected between 1 January 2004 and 31 August 2007 are used to place an upper limit on the diffuse flux of nu(tau) at EeV energies. Assuming an E(nu)(-2) differential energy spectrum the limit set at 90% C.L. is E(nu)(2)dN(nu)(tau)/dE(nu)<1.3 x 10(-7) GeV cm(-2) s(-1) sr(-1) in the energy range 2 x 10(17) eV< E(nu)< 2 x 10(19) eV.
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Affiliation(s)
- J Abraham
- Centro de Investigaciones en Laseres y Aplicaciones, CITEFA and CONICET, Argentina
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Skoufos E, Healy MD, Singer MS, Nadkarni PM, Miller PL, Shepherd GM. Olfactory Receptor Database: a database of the largest eukaryotic gene family. Nucleic Acids Res 1999; 27:343-5. [PMID: 9847223 PMCID: PMC148178 DOI: 10.1093/nar/27.1.343] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Olfactory Receptor Database (ORDB) is a WWW-accessible database that stores data on Olfactory Receptor-like molecules (ORs) and has been open to the public since June 1996. It contains a public and a private area. The public area includes published DNA and protein sequence data for ORs, links to OR models and data on their expression, chromosomal localization and source organism, as well as (i) links to bibliography through PubMed and (ii) interactive WWW-based tools, such as BLAST homology searching. The private area functions as a service to laboratories that are actively cloning receptors. Source laboratories enter the sequences of the receptor clones they have characterized to the private database and can search for identical or near identical OR sequences in both public and private databases. If another laboratory has cloned and deposited an identical or closely matching sequence there are means for communication between the laboratories to help avoid duplication of work. ORDB is available via the WWW at http://crepe.med.yale.edu/ORDB/HTML
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Affiliation(s)
- E Skoufos
- Center for Medical Informatics and Section of Neurobiology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06511,
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Shepherd GM, Mirsky JS, Healy MD, Singer MS, Skoufos E, Hines MS, Nadkarni PM, Miller PL. The Human Brain Project: neuroinformatics tools for integrating, searching and modeling multidisciplinary neuroscience data. Trends Neurosci 1998; 21:460-8. [PMID: 9829685 DOI: 10.1016/s0166-2236(98)01300-9] [Citation(s) in RCA: 88] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
What is neuroinformatics? What is the Human Brain Project? Why should you care? Supported by a consortium of US funding agencies, the Human Brain Project aims to bring to the analysis of brain function the same advantages of Internet-accessible databases and database tools that have been crucial to the development of molecular biology and the Human Genome Project. The much greater complexity of neural data, however, makes this a far more challenging task. As a pilot project in this new initiative, we review some of the progress that has been made and indicate some of the problems, challenges and opportunities that lie ahead.
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Affiliation(s)
- G M Shepherd
- Section of Neurobiology, Yale University School of Medicine, New Haven, CT 06510, USA
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Mirsky JS, Nadkarni PM, Healy MD, Miller PL, Shepherd GM. Database tools for integrating and searching membrane property data correlated with neuronal morphology. J Neurosci Methods 1998; 82:105-21. [PMID: 10223520 DOI: 10.1016/s0165-0270(98)00049-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A critical problem in neuroscience is the lack of database tools for integrating neuronal property data. We report here the development of a combined object oriented-relational database (NeuronDB, http://senselab.med.yale.edu/neurondb) that meets these needs by providing tools for integrating data within neurons and comparing data across neurons. It focuses on three types of neuronal properties voltage-gated channels, neurotransmitter receptors, and neurotransmitters. The data are organized in relation to different regions of neurons as represented in canonical forms; using simple canonical models of complex cells as a vehicle for indexing information permits the database to be searchable across different neurons. Using these multidimensional search tools, users can locate specific properties in specific regions of a neuron; obtain integrated summaries of all properties within a region; and carry out searches to compare properties across equivalent compartments in different neurons. These tools thus permit searches of the multidimensional neuron property space equivalent to homology searches of sequence databases. NeuronDB is accessible over the Internet; it provides immediate links to citation indexes and abstracts supporting the deposited data, and annotations that indicate the state of acceptance of the data. Users are encouraged to contribute data. The ability to input the data from NeuronDB directly to NEURON and GENESIS is being developed. As a shared Web resource, NeuronDB should enhance the efforts of neuroscientists and neuronal modellers to analyze and compare the functional operations of different types of neurons.
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Affiliation(s)
- J S Mirsky
- Section of Neurobiology, Yale University School of Medicine, New Haven, CT 06510, USA.
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Healy MD, Smith JE, Singer MS, Nadkarni PM, Skoufos E, Miller PL, Shepherd GM. Olfactory receptor database (ORDB): a resource for sharing and analyzing published and unpublished data. Chem Senses 1997; 22:321-6. [PMID: 9218144 DOI: 10.1093/chemse/22.3.321] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
An olfactory receptor database (ORDB) is being developed to facilitate analysis of this large gene family. ORDB currently contains over 400 olfactory receptor sequences and related information, and is available via the World Wide Web. We plan to incorporate functional data, structural models, spatial localization and other categories of information, toward an integrated model of olfactory receptor function.
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Affiliation(s)
- M D Healy
- Center for Medical Informatics, Yale University School of Medicine, New Haven, CT 06520-208009, USA
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Holt ND, Gould FK, Taylor CE, Harwood JF, Freeman R, Healy MD, Corris PA, Dark JH. Incidence and significance of noncytomegalovirus viral respiratory infection after adult lung transplantation. J Heart Lung Transplant 1997; 16:416-9. [PMID: 9154952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Lower respiratory tract infection is a major cause of morbidity and death after lung transplantation. The incidence and significance of noncytomegalovirus viral respiratory tract infections has not been reported to date. We report our center's experience with these infections.
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Affiliation(s)
- N D Holt
- Regional Cardiothoracic Centre, Freeman Hospital, Newcastle upon Tyne, United Kingdom
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15
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Peterson BE, Healy MD, Nadkarni PM, Miller PL, Shepherd GM. ModelDB: an environment for running and storing computational models and their results applied to neuroscience. J Am Med Inform Assoc 1996; 3:389-98. [PMID: 8930855 PMCID: PMC116323 DOI: 10.1136/jamia.1996.97084512] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Research groups within the Human Brain Project are developing technologies to help organize and make accessible the vast quantities of information being accumulated in the neurosciences. The goal of this work is to provide systems that enable this complex information from many diverse sources to be synthesized into a coherent theory of nervous system function. Our initial approach to this problem has been to create several small databases. While addressing the issues of each individual database, we are also considering how each might be incorporated into an integrated cluster of databases. In this paper, we describe a pilot project in which we construct a database of computational models of neuronal function. This database allows models to be created and run and their results reviewed through a World Wide Web interface. Because models encapsulate knowledge in a formal manner about how neuronal systems function, we also discuss how this database forms a natural center for our initial attempts at creating a cluster of related databases. General issues of database development in the context of the Web are also discussed.
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Affiliation(s)
- B E Peterson
- Yale University School of Medicine, New Haven, CT, USA.
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16
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Murray JJ, Healy MD. Drug-mineral interactions: a new responsibility for the hospital dietitian. J Am Diet Assoc 1991; 91:66-70, 73. [PMID: 1869762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Recent hospital accreditation guidelines encourage hospital dietitians to monitor patient drug therapy and provide education regarding drug-food interactions. However, information concerning these interactions is lacking, even though they can occur frequently. Minerals in foods can complex with drugs and/or alter the gastrointestinal environment to affect the normal absorption processes of drugs and minerals. There are three types of drug-mineral interactions: (a) malabsorption of the mineral and/or drug; (b) mineral depletion and retention; and (c) drug-mineral interactions induced by simultaneous antacid ingestion. It is recommended that oral drugs be administered on an empty stomach 1 hour before or 2 hours after a meal and at least 2 hours before or after antacid use. A small snack of refined carbohydrates with low nutrient density can be consumed with drugs that cause gastric upset when given on an empty stomach.
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Affiliation(s)
- J J Murray
- Department of Nutrition, Incarnate Word College, San Antonio, TX 78209
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Healy MD, Malluche HH, Goldstein DA, Singer FR, Massry SG. Effects of long-term therapy with calcitriol in patients with moderate renal failure. Arch Intern Med 1980; 140:1030-3. [PMID: 6893118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Since abnormalities in divalent ion metabolism occur early in renal insufficiency, treatment of patients with moderate renal failure with calcitriol could halt and/or reverse these disturbances. The effects of long-term treatment with calcitriol (0.5 microgram/day) in three such patients were evaluated. Serum calcium level rose from 0.3 to 0.7 mg/dL. Blood parathyroid hormone levels were mildly elevated and fell to normal. Intestinal absorption of calcium increased. The patients had hypocalciuria and the urinary calcium level increased. Creatinine clearance remained stable in all patients. Iliac crest biopsy specimens obtained after double tetracycline hydrochloride labeling revealed mild osteomalacia and hyperparathyroid bone disease that healed after therapy. The data show that a small dose of calcitriol is safe and effective for the management of the derangements of divalent ion metabolism in patients with moderate renal failure.
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Blumenkrantz MJ, Kopple JD, Koffler A, Kamdar AK, Healy MD, Feinstein EI, Massry SG. Total parenteral nutrition in the management of acute renal failure. Am J Clin Nutr 1978; 31:1831-40. [PMID: 101071 DOI: 10.1093/ajcn/31.10.1831] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Malnutrition is frequently present in patients with acute renal failure and may affect morbidity and mortality in this condition. When adequate nourishment cannot be given through the gastrointestinal tract, total parental nutrition with amino acids and hypertonic glucose may have beneficial results. Total parenteral nutrition has been reported to stabilize or reduce serum urea nitrogen, potassium and phosphorus levels, improve wound healing, enhance survival from acute renal failure, and possibly increase the rate of recovery of renal function. The optimal composition of the total parenteral nutrition infusate is unknown. Preliminary results of a double-blind study are reported in which one man received hypertonic glucose alone, two received glucose with essential amino acids (21 g/day), and three received glucose with essential (21 g/day) and nonessential (21 g/day) amino acids. All infusates were isocaloric. No differences were observed in serum urea nitrogen levels, serum urea nitrogen/creatinine ratios or urea appearance rates. Nitrogen balance was negative in all patients. The ratio of essential amino acids/nonessential amino acids were higher and the tyrosine/phenylalanine ratios were lower in plasma in the two patients receiving glucose with essential amino acids. No patient survived the hospitalization. In view of the markedly negative nitrogen balance frequently observed in these and earlier studies, the use of a different composition or quantity of amino acids, a higher energy intake, and anabolic hormones deserve further investigation.
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Fulton SC, Healy MD. Comparison of the effectiveness of deserpidine, reserpine, and alpha-methyltyrosine on brain biogenic amines. Fed Proc 1976; 35:2558-62. [PMID: 11134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Ramirez SG, Carrier O, Turlapaty PD, Healy MD. The influence of reserpine on the responsiveness to norepinephrine and electrolyte contents of rabbit atria. Arch Int Pharmacodyn Ther 1976; 223:324-32. [PMID: 999413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
This study was designed to investigate the relationships between reserpine-induced supersensitivity and electrolyte levels in isolated rabbit atria. Atria from reserpine-treated (1, 3 or 4 mg/kg 24 hr before) and untreated rabbits were placed in an isolated organ bath for determination of dose-response relationships for norepinephrine, or were used for electrolyte assay. Reserpine-treated atria had greater resting and maximum rates of beat than did untreated atria. However, the ED50 concentrations of norepinephrine producing a rate response were similar. Atria pretreated with 1 or 3 mg/kg reserpine were supersensitive to the inotropic effect of norepinephrine. 4 mg/kg reserpine did not induce inotropic supersensitivity. Atrial sodium contents were significantly increased by 3 mg/kg reserpine. Potassium contents were increased by 1 and 4 mg/kg reserpine. Calcium contents were significantly decreased by 4 mg/kg reserpine, while magnesium contents were increased by 1 and 4 mg/kg. Reserpine induced supersensitivity to the inotropic effects of norepinephrine but did not alter the sensitivity to the chronotropic effect of the drug. This supersensitivity may be linked to alterations in the tissue's homeostatic mechanisms for calcium.
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Healy MD. Seven-year review of maternal and perinatal deaths. J Iowa Med Soc 1970; 60:329-31. [PMID: 5451713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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