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Hu M, Zhang X, Latham A, Šali A, Ideker T, Lundberg E. Tools for assembling the cell: Towards the era of cell structural bioinformatics. Pac Symp Biocomput 2024; 29:661-665. [PMID: 38160316] [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: 01/03/2024]
Abstract
Cells consist of large components, such as organelles, that recursively factor into smaller systems, such as condensates and protein complexes, forming a dynamic multi-scale structure of the cell. Recent technological innovations have paved the way for systematic interrogation of subcellular structures, yielding unprecedented insights into their roles and interactions. In this workshop, we discuss progress, challenges, and collaboration to marshal various computational approaches toward assembling an integrated structural map of the human cell.
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Affiliation(s)
- Mengzhou Hu
- Department of Medicine, University of California San Diego, San Diego, CA, USA†These authors contributed equally
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Gaber A, Kim SJ, Kaake RM, Benčina M, Krogan N, Šali A, Pavšič M, Lenarčič B. EpCAM homo-oligomerization is not the basis for its role in cell-cell adhesion. Sci Rep 2018; 8:13269. [PMID: 30185875 PMCID: PMC6125409 DOI: 10.1038/s41598-018-31482-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 08/20/2018] [Indexed: 01/01/2023] Open
Abstract
Cell-surface tumor marker EpCAM plays a key role in proliferation, differentiation and adhesion processes in stem and epithelial cells. It is established as a cell-cell adhesion molecule, forming intercellular interactions through homophilic association. However, the mechanism by which such interactions arise has not yet been fully elucidated. Here, we first show that EpCAM monomers do not associate into oligomers that would resemble an inter-cellular homo-oligomer, capable of mediating cell-cell adhesion, by using SAXS, XL-MS and bead aggregation assays. Second, we also show that EpCAM forms stable dimers on the surface of a cell with pre-formed cell-cell contacts using FLIM-FRET; however, no inter-cellular homo-oligomers were detectable. Thus, our study provides clear evidence that EpCAM indeed does not function as a homophilic cell adhesion molecule and therefore calls for a significant revision of its role in both normal and cancerous tissues. In the light of this, we strongly support the previously suggested name Epithelial Cell Activating Molecule instead of the Epithelial Cell Adhesion Molecule.
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Affiliation(s)
- Aljaž Gaber
- Department of Chemistry and Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, Ljubljana, SI 1000, Slovenia
| | - Seung Joong Kim
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, 1700 4th Street, Suite 503B, San Francisco, CA, 94158, USA
| | - Robyn M Kaake
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
| | - Mojca Benčina
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, Ljubljana, SI 1000, Slovenia
| | - Nevan Krogan
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute, QBI, Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Andrej Šali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, 1700 4th Street, Suite 503B, San Francisco, CA, 94158, USA
| | - Miha Pavšič
- Department of Chemistry and Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, Ljubljana, SI 1000, Slovenia.
| | - Brigita Lenarčič
- Department of Chemistry and Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, Ljubljana, SI 1000, Slovenia.
- Department of Biochemistry, Molecular and Structural Biology, Institute Jožef Stefan, Jamova 39, Ljubljana, SI 1000, Slovenia.
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Puizdar V, Zajc T, Žerovnik E, Renko M, Pieper U, Eswar N, Šali A, Dolenc I, Turk V. Biochemical characterization and structural modeling of human cathepsin E variant 2 in comparison to the wild-type protein. Biol Chem 2012; 393:177-86. [PMID: 22718633 PMCID: PMC4111641 DOI: 10.1515/hsz-2011-0219] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [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: 09/20/2011] [Accepted: 12/19/2011] [Indexed: 11/15/2022]
Abstract
Cathepsin E splice variant 2 appears in a number of gastric carcinomas. Here we report detecting this variant in HeLa cells using polyclonal antibodies and biotinylated inhibitor pepstatin A. An overexpression of GFP fusion proteins of cathepsin E and its splice variant within HEK-293T cells was performed to show their localization. Their distribution under a fluorescence microscope showed that they are colocalized. We also expressed variants 1 and 2 of cathepsins E, with propeptide and without it, in Escherichia coli. After refolding from the inclusion bodies, the enzymatic activity and circular dichroism spectra of the splice variant 2 were compared to those of the wild-type mature active cathepsins E. While full-length cathepsin E variant 1 is activated at acid pH, the splice variant remains inactive. In contrast to the active cathepsin E, the splice variant 2 predominantly assumes β-sheet structure, prone to oligomerization, at least under in vitro conditions, as shown by atomic force microscopy as shallow disk-like particles. A comparative structure model of splice variant 2 was computed based on its alignment to the known structure of cathepsin E intermediate (Protein Data Bank code 1TZS) and used to rationalize its conformational properties and loss of activity.
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Affiliation(s)
- Vida Puizdar
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Tajana Zajc
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Eva Žerovnik
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Miha Renko
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Ursula Pieper
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences at UCSF, Department of Pharmaceutical Chemistry, University of California, San Francisco, UCSF MC 2552, Byers Hall, 1700 4th Street, Suite 503 B, San Francisco, CA 94158, USA
| | - Narayanan Eswar
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences at UCSF, Department of Pharmaceutical Chemistry, University of California, San Francisco, UCSF MC 2552, Byers Hall, 1700 4th Street, Suite 503 B, San Francisco, CA 94158, USA
| | - Andrej Šali
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences at UCSF, Department of Pharmaceutical Chemistry, University of California, San Francisco, UCSF MC 2552, Byers Hall, 1700 4th Street, Suite 503 B, San Francisco, CA 94158, USA
| | - Iztok Dolenc
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Vito Turk
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
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Liedtke W, Choe Y, Martí-Renom MA, Bell AM, Denis CS, Šali A, Hudspeth AJ, Friedman JM, Heller S. Vanilloid receptor-related osmotically activated channel (VR-OAC), a candidate vertebrate osmoreceptor. Cell 2000; 103:525-35. [PMID: 11081638 PMCID: PMC2211528 DOI: 10.1016/s0092-8674(00)00143-4] [Citation(s) in RCA: 1032] [Impact Index Per Article: 43.0] [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: 01/20/2023]
Abstract
The detection of osmotic stimuli is essential for all organisms, yet few osmoreceptive proteins are known, none of them in vertebrates. By employing a candidate-gene approach based on genes encoding members of the TRP superfamily of ion channels, we cloned cDNAs encoding the vanilloid receptor-related osmotically activated channel (VR-OAC) from the rat, mouse, human, and chicken. This novel cation-selective channel is gated by exposure to hypotonicity within the physiological range. In the central nervous system, the channel is expressed in neurons of the circumventricular organs, neurosensory cells responsive to systemic osmotic pressure. The channel also occurs in other neurosensory cells, including inner-ear hair cells, sensory neurons, and Merkel cells.
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MESH Headings
- Amino Acid Sequence
- Animals
- Ankyrin Repeat/genetics
- Ankyrin Repeat/physiology
- Brain/cytology
- Brain/metabolism
- Brain/physiology
- CHO Cells
- Calcium Signaling
- Cations/metabolism
- Chickens/genetics
- Chromosomes, Human, Pair 12/genetics
- Chromosomes, Human, Pair 17/genetics
- Cloning, Molecular
- Cricetinae
- Electrophysiology
- Gene Expression Profiling
- Hair Cells, Auditory, Inner/chemistry
- Hair Cells, Auditory, Inner/metabolism
- Hair Cells, Auditory, Inner/physiology
- Humans
- Hypotonic Solutions
- In Situ Hybridization
- Ion Channel Gating
- Merkel Cells/chemistry
- Merkel Cells/metabolism
- Mice
- Molecular Sequence Data
- Neurons, Afferent/chemistry
- Neurons, Afferent/metabolism
- Neurons, Afferent/physiology
- Osmolar Concentration
- Osmotic Pressure
- Phylogeny
- RNA, Messenger/analysis
- RNA, Messenger/genetics
- Radiation Hybrid Mapping
- Rats
- Receptors, Drug/chemistry
- Receptors, Drug/genetics
- Receptors, Drug/metabolism
- Sequence Alignment
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Affiliation(s)
- Wolfgang Liedtke
- Laboratory of Molecular Genetics, The Rockefeller University, New York, NY 10021
| | - Yong Choe
- Laboratory of Sensory Neuroscience, The Rockefeller University, New York, NY 10021
| | - Marc A. Martí-Renom
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10021
| | - Andrea M. Bell
- Laboratory of Sensory Neuroscience, The Rockefeller University, New York, NY 10021
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10021
| | - Charlotte S. Denis
- Laboratory of Sensory Neuroscience, The Rockefeller University, New York, NY 10021
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10021
| | - Andrej Šali
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10021
| | - A. J. Hudspeth
- Laboratory of Sensory Neuroscience, The Rockefeller University, New York, NY 10021
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10021
| | - Jeffrey M. Friedman
- Laboratory of Molecular Genetics, The Rockefeller University, New York, NY 10021
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10021
| | - Stefan Heller
- Laboratory of Sensory Neuroscience, The Rockefeller University, New York, NY 10021
- To whom correspondence should be addressed ()
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Dinner A, Šali A, Karplus M, Shakhnovich E. Phase diagram of a model protein derived by exhaustive enumeration of the conformations. J Chem Phys 1994. [DOI: 10.1063/1.467769] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Michel H, Johnson MS, Overington J, Šali A, Zhu Z, Donnelly D, Thomas P, McCleod A, Goold R, Topham C, Blundell TL, Alber T, Goldenberg DP, Kollman P. Symposium 1: Structure and engineering of proteins: New developments. Anal Bioanal Chem 1990. [DOI: 10.1007/bf00325709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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