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Talandashti R, Moqadam M, Reuter N. Model Mechanism for Lipid Uptake by the Human STARD2/PC-TP Phosphatidylcholine Transfer Protein. J Phys Chem Lett 2024; 15:8287-8295. [PMID: 39143857 DOI: 10.1021/acs.jpclett.4c01743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2024]
Abstract
The human StAR-related lipid transfer domain protein 2 (STARD2), also known as phosphatidylcholine (PC) transfer protein, is a single-domain lipid transfer protein thought to transfer PC lipids between intracellular membranes. We performed extensive μs-long molecular dynamics simulations of STARD2 of its apo and holo forms in the presence or absence of complex lipid bilayers. The simulations in water reveal ligand-dependent conformational changes. In the 2 μs-long simulations of apo STARD2 in the presence of a lipid bilayer, we observed spontaneous reproducible PC lipid uptake into the protein hydrophobic cavity. We propose that the lipid extraction mechanism involves one to two metastable states stabilized by choline-tyrosine or choline-tryptophane cation-π interactions. Using free energy perturbation, we evaluate that PC-tyrosine cation-π interactions contribute 1.8 and 2.5 kcal/mol to the affinity of a PC-STARD2 metastable state, thus potentially providing a significant decrease of the energy barrier required for lipid desorption.
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Affiliation(s)
- Reza Talandashti
- Department of Chemistry, University of Bergen, Bergen 5020, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen 5020, Norway
| | - Mahmoud Moqadam
- Department of Chemistry, University of Bergen, Bergen 5020, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen 5020, Norway
| | - Nathalie Reuter
- Department of Chemistry, University of Bergen, Bergen 5020, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen 5020, Norway
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2
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Moqadam M, Gartan P, Talandashti R, Chiapparino A, Titeca K, Gavin AC, Reuter N. A Membrane-Assisted Mechanism for the Release of Ceramide from the CERT START Domain. J Phys Chem B 2024; 128:6338-6351. [PMID: 38903016 PMCID: PMC11228987 DOI: 10.1021/acs.jpcb.4c02398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/26/2024] [Accepted: 06/11/2024] [Indexed: 06/22/2024]
Abstract
Ceramide transfer protein CERT is the mediator of nonvesicular transfer of ceramide from the ER to Golgi. In CERT, START is the domain responsible for the binding and transport of ceramide. A wealth of structural data has revealed a helix-grip fold surrounding a large hydrophobic cavity holding the ceramide. Yet, little is known about the mechanisms by which START releases the ceramide through the polar region and into the packed environment of cellular membranes. As such events do not lend themselves easily to experimental investigations, we used multiple unbiased microsecond-long molecular simulations. We propose a membrane-assisted mechanism in which the membrane acts as an allosteric effector initiating the release of ceramide and where the passage of the ceramide acyl chains is facilitated by the intercalation of a single phosphatidylcholine lipid in the cavity, practically greasing the ceramide way out. We verify using free energy calculation and experimental lipidomics data that CERT forms stable complexes with phosphatidylcholine lipids, in addition to ceramide, thus providing validation for the proposed mechanism.
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Affiliation(s)
- Mahmoud Moqadam
- Department
of Chemistry, University of Bergen, Bergen 5020, Norway
- Computational
Biology Unit, Department of Informatics, University of Bergen, Bergen 5020, Norway
| | - Parveen Gartan
- Department
of Chemistry, University of Bergen, Bergen 5020, Norway
- Computational
Biology Unit, Department of Informatics, University of Bergen, Bergen 5020, Norway
| | - Reza Talandashti
- Department
of Chemistry, University of Bergen, Bergen 5020, Norway
- Computational
Biology Unit, Department of Informatics, University of Bergen, Bergen 5020, Norway
| | - Antonella Chiapparino
- European
Molecular Biology Laboratory, EMBL, Meyerhofstrasse 1, Heidelberg D-69117, Germany
| | - Kevin Titeca
- European
Molecular Biology Laboratory, EMBL, Meyerhofstrasse 1, Heidelberg D-69117, Germany
- Department
of Cell Physiology and Metabolism, University
of Geneva, CMU Rue Michel-Servet 1, Genève 4 1211, Switzerland
| | - Anne-Claude Gavin
- Department
of Cell Physiology and Metabolism, University
of Geneva, CMU Rue Michel-Servet 1, Genève 4 1211, Switzerland
| | - Nathalie Reuter
- Department
of Chemistry, University of Bergen, Bergen 5020, Norway
- Computational
Biology Unit, Department of Informatics, University of Bergen, Bergen 5020, Norway
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Talandashti R, van Ek L, Gehin C, Xue D, Moqadam M, Gavin AC, Reuter N. Membrane specificity of the human cholesterol transfer protein STARD4. J Mol Biol 2024; 436:168572. [PMID: 38615744 DOI: 10.1016/j.jmb.2024.168572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 03/28/2024] [Accepted: 04/09/2024] [Indexed: 04/16/2024]
Abstract
STARD4 regulates cholesterol homeostasis by transferring cholesterol between the plasma membrane and endoplasmic reticulum. The STARD4 structure features a helix-grip fold surrounding a large hydrophobic cavity holding the sterol. Its access is controlled by a gate formed by the Ω1 and Ω4 loops and the C-terminal α-helix. Little is known about the mechanisms by which STARD4 binds to membranes and extracts/releases cholesterol. All available structures of STARD4 are without a bound sterol and display the same closed conformation of the gate. The cholesterol transfer activity of the mouse STARD4 is enhanced in the presence of anionic lipids, and in particular of phosphatidylinositol biphosphates (PIP2) for which two binding sites were proposed on the mouse STARD4 surface. Yet only one of these sites is conserved in human STARD4. We here report the results of a liposome microarray-based assay and microseconds-long molecular dynamics simulations of human STARD4 with complex lipid bilayers mimicking the composition of the donor and acceptor membranes. We show that the binding of apo form of human STARD4 is sensitive to the presence of PIP2 through two specific binding sites, one of which was not identified on mouse STARD4. We report two novel conformations of the gate in holo-STARD4: a yet-unobserved close conformation and an open conformation of Ω4 shedding light on the opening/closure mechanism needed for cholesterol uptake/release. Overall, the modulation of human STARD4 membrane-binding by lipid composition, and by the presence of the cargo supports the capacity of human STARD4 to achieve directed transfer between specific organelle membranes.
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Affiliation(s)
- Reza Talandashti
- Department of Chemistry, University of Bergen, Bergen 5020, Norway; Computational Biology Unit, Department of Informatics, University of Bergen, Bergen 5020, Norway
| | - Larissa van Ek
- Department of Cellular Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland; Diabetes Center, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Charlotte Gehin
- École Polytechnique Fédérale de Lausanne EPFL, Lausanne, Switzerland
| | - Dandan Xue
- Department of Chemistry, University of Bergen, Bergen 5020, Norway; Computational Biology Unit, Department of Informatics, University of Bergen, Bergen 5020, Norway
| | - Mahmoud Moqadam
- Department of Chemistry, University of Bergen, Bergen 5020, Norway; Computational Biology Unit, Department of Informatics, University of Bergen, Bergen 5020, Norway
| | - Anne-Claude Gavin
- Department of Cellular Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland; Diabetes Center, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Nathalie Reuter
- Department of Chemistry, University of Bergen, Bergen 5020, Norway; Computational Biology Unit, Department of Informatics, University of Bergen, Bergen 5020, Norway.
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Al Saedi A, Yacoub AS, Awad K, Karasik D, Brotto M, Duque G. The Interplay of Lipid Signaling in Musculoskeletal Cross Talk: Implications for Health and Disease. Methods Mol Biol 2024; 2816:1-11. [PMID: 38977583 DOI: 10.1007/978-1-0716-3902-3_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
The intricate interplay between the muscle and bone tissues is a fundamental aspect of musculoskeletal physiology. Over the past decades, emerging research has highlighted the pivotal role of lipid signaling in mediating communication between these tissues. This chapter delves into the multifaceted mechanisms through which lipids, particularly phospholipids, sphingolipids, and eicosanoids, participate in orchestrating cellular responses and metabolic pathways in both muscle and bone. Additionally, we examine the clinical implications of disrupted lipid signaling in musculoskeletal disorders, offering insights into potential therapeutic avenues. This chapter aims to shed light on the complex lipid-driven interactions between the muscle and bone tissues, paving the way for a deeper understanding of musculoskeletal health and disease.
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Affiliation(s)
- Ahmed Al Saedi
- Division of Endocrinology, Boston Children's Hospital, Boston, MA, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
| | - Ahmed S Yacoub
- Bone-Muscle Research Center, College of Nursing and Health Innovation, The University of Texas at Arlington, Arlington, TX, USA
| | - Kamal Awad
- Bone-Muscle Research Center, College of Nursing and Health Innovation, The University of Texas at Arlington, Arlington, TX, USA
| | - David Karasik
- The Musculoskeletal Genetics Laboratory, The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Marco Brotto
- Bone-Muscle Research Center, College of Nursing and Health Innovation, The University of Texas at Arlington, Arlington, TX, USA
| | - Gustavo Duque
- Research Institute of McGill University Health Center, Department of Medicine, McGill University, Québec, Canada
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Xie H, Weinstein H. Allosterically coupled conformational dynamics in solution prepare the sterol transfer protein StarD4 to release its cargo upon interaction with target membranes. Front Mol Biosci 2023; 10:1197154. [PMID: 37275961 PMCID: PMC10232897 DOI: 10.3389/fmolb.2023.1197154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/04/2023] [Indexed: 06/07/2023] Open
Abstract
Complex mechanisms regulate the cellular distribution of cholesterol, a critical component of eukaryote membranes involved in regulation of membrane protein functions directly and through the physiochemical properties of membranes. StarD4, a member of the steroidogenic acute regulator-related lipid-transfer (StART) domain (StARD)-containing protein family, is a highly efficient sterol-specific transfer protein involved in cholesterol homeostasis. Its mechanism of cargo loading and release remains unknown despite recent insights into the key role of phosphatidylinositol phosphates in modulating its interactions with target membranes. We have used large-scale atomistic Molecular dynamics (MD) simulations to study how the dynamics of cholesterol bound to the StarD4 protein can affect interaction with target membranes, and cargo delivery. We identify the two major cholesterol (CHL) binding modes in the hydrophobic pocket of StarD4, one near S136&S147 (the Ser-mode), and another closer to the putative release gate located near W171, R92&Y117 (the Trp-mode). We show that conformational changes of StarD4 associated directly with the transition between these binding modes facilitate the opening of the gate. To understand the dynamics of this connection we apply a machine-learning algorithm for the detection of rare events in MD trajectories (RED), which reveals the structural motifs involved in the opening of a front gate and a back corridor in the StarD4 structure occurring together with the spontaneous transition of CHL from the Ser-mode of binding to the Trp-mode. Further analysis of MD trajectory data with the information-theory based NbIT method reveals the allosteric network connecting the CHL binding site to the functionally important structural components of the gate and corridor. Mutations of residues in the allosteric network are shown to affect the performance of the allosteric connection. These findings outline an allosteric mechanism which prepares the CHL-bound StarD4 to release and deliver the cargo when it is bound to the target membrane.
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Affiliation(s)
- Hengyi Xie
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, United States
| | - Harel Weinstein
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, United States
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, United States
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Rogers JR, Geissler PL. Ceramide-1-phosphate transfer protein enhances lipid transport by disrupting hydrophobic lipid-membrane contacts. PLoS Comput Biol 2023; 19:e1010992. [PMID: 37036851 PMCID: PMC10085062 DOI: 10.1371/journal.pcbi.1010992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 03/03/2023] [Indexed: 04/11/2023] Open
Abstract
Cellular distributions of the sphingolipid ceramide-1-phosphate (C1P) impact essential biological processes. C1P levels are spatiotemporally regulated by ceramide-1-phosphate transfer protein (CPTP), which efficiently shuttles C1P between organelle membranes. Yet, how CPTP rapidly extracts and inserts C1P into a membrane remains unknown. Here, we devise a multiscale simulation approach to elucidate biophysical details of CPTP-mediated C1P transport. We find that CPTP binds a membrane poised to extract and insert C1P and that membrane binding promotes conformational changes in CPTP that facilitate C1P uptake and release. By significantly disrupting a lipid's local hydrophobic environment in the membrane, CPTP lowers the activation free energy barrier for passive C1P desorption and enhances C1P extraction from the membrane. Upon uptake of C1P, further conformational changes may aid membrane unbinding in a manner reminiscent of the electrostatic switching mechanism used by other lipid transfer proteins. Insertion of C1P into an acceptor membrane, eased by a decrease in membrane order by CPTP, restarts the transfer cycle. Most notably, we provide molecular evidence for CPTP's ability to catalyze C1P extraction by breaking hydrophobic C1P-membrane contacts with compensatory hydrophobic lipid-protein contacts. Our work, thus, provides biophysical insights into how CPTP efficiently traffics C1P between membranes to maintain sphingolipid homeostasis and, additionally, presents a simulation method aptly suited for uncovering the catalytic mechanisms of other lipid transfer proteins.
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Affiliation(s)
- Julia R Rogers
- Department of Chemistry, University of California, Berkeley, California, United States of America
| | - Phillip L Geissler
- Department of Chemistry, University of California, Berkeley, California, United States of America
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
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Hong Z, Adlakha J, Wan N, Guinn E, Giska F, Gupta K, Melia TJ, Reinisch KM. Mitoguardin-2-mediated lipid transfer preserves mitochondrial morphology and lipid droplet formation. J Cell Biol 2022; 221:e202207022. [PMID: 36282247 PMCID: PMC9597353 DOI: 10.1083/jcb.202207022] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 09/12/2022] [Accepted: 10/04/2022] [Indexed: 12/15/2022] Open
Abstract
Lipid transport proteins at membrane contacts, where organelles are closely apposed, are critical in redistributing lipids from the endoplasmic reticulum (ER), where they are made, to other cellular membranes. Such protein-mediated transfer is especially important for maintaining organelles disconnected from secretory pathways, like mitochondria. We identify mitoguardin-2, a mitochondrial protein at contacts with the ER and/or lipid droplets (LDs), as a lipid transporter. An x-ray structure shows that the C-terminal domain of mitoguardin-2 has a hydrophobic cavity that binds lipids. Mass spectrometry analysis reveals that both glycerophospholipids and free-fatty acids co-purify with mitoguardin-2 from cells, and that each mitoguardin-2 can accommodate up to two lipids. Mitoguardin-2 transfers glycerophospholipids between membranes in vitro, and this transport ability is required for roles both in mitochondrial and LD biology. While it is not established that protein-mediated transfer at contacts plays a role in LD metabolism, our findings raise the possibility that mitoguardin-2 functions in transporting fatty acids and glycerophospholipids at mitochondria-LD contacts.
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Affiliation(s)
- Zhouping Hong
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT
| | - Jyoti Adlakha
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT
| | - Neng Wan
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT
| | - Emily Guinn
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT
| | - Fabian Giska
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT
- Nanobiology Institute, Yale University, West Haven, CT
| | - Kallol Gupta
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT
- Nanobiology Institute, Yale University, West Haven, CT
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD
| | - Thomas J. Melia
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT
| | - Karin M. Reinisch
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD
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