1
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Mukhaleva E, Yang T, Sadler F, Sivaramakrishnan S, Ma N, Vaidehi N. Cellular lipids regulate the conformational ensembles of the disordered intracellular loop 3 in β2-adrenergic receptor. iScience 2024; 27:110086. [PMID: 38947516 PMCID: PMC11214514 DOI: 10.1016/j.isci.2024.110086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 03/19/2024] [Accepted: 05/20/2024] [Indexed: 07/02/2024] Open
Abstract
The intracellular loops of G protein-coupled receptors (GPCRs) have been shown to play a key role in G protein coupling and selectivity. We recently showed that the intrinsically disordered third intracellular loop (ICL3) of β2-adrenergic receptor is dynamic and equilibrates between open and closed conformations to regulate the G protein coupling. In this study, using the extensive molecular dynamics simulations in multi-lipid bilayer models, we show that the lipid phosphatidylinositol 4,5-bisphosphate (PIP2) stabilizes the active state of β2-adrenergic receptor by keeping ICL3 in an open conformation. This stabilization results in a tilt of the receptor within the membrane. Additionally, the ganglioside lipid, GM3 interacts with extracellular loops, impacting the ligand binding site allosterically. This demonstrates the active role of the chemistry of lipids in stabilizing specific GPCR conformations.
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Affiliation(s)
- Elizaveta Mukhaleva
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA, USA
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Tianyi Yang
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Fredrik Sadler
- Biochemistry, Molecular Biology and Biophysics Graduate Program, University of Minnesota, Minneapolis, MN, USA
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Sivaraj Sivaramakrishnan
- Biochemistry, Molecular Biology and Biophysics Graduate Program, University of Minnesota, Minneapolis, MN, USA
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Ning Ma
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Nagarajan Vaidehi
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA, USA
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA, USA
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2
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Mukhaleva E, Yang T, Sadler F, Sivaramakrishnan S, Ma N, Vaidehi N. Cellular Lipids Regulate the Conformational Ensembles of the Disordered Intracellular Loop 3 in β2 Adrenergic Receptor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.28.569080. [PMID: 38077083 PMCID: PMC10705491 DOI: 10.1101/2023.11.28.569080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
The structurally disordered intracellular loops (ICLs) of G protein-coupled receptors (GPCRs) play a critical role in G protein coupling. In our previous work, we used a combination of FRET-based and computational methodologies to show that the third intracellular loop (ICL3) modulates the activity and G protein coupling selectivity in GPCRs. In the current study, we have uncovered the role of several lipid components in modulating the conformational ensemble of ICL3 of the β2-adrenergic receptor (β2AR). Our findings indicate that phosphatidylinositol 4,5-bisphosphate (PIP2) in the inner leaflet of the membrane bilayer acts as a stabilizing anchor for ICL3, opening the intracellular cavity to facilitate G protein coupling. This interaction between PIP2 and ICL3 causes tilting of β2AR within the cellular membrane. Notably, this tilting of the receptor is supported by ganglioside GM3 stabilizing the extracellular loops on the outer leaflet of the bilayer, thereby exerting an allosteric effect on the orthosteric ligand binding pocket. Our results underscore the significance of lipids in modulating GPCR activity, proposing an allosteric mechanism that occurs through the receptor's orientation within the membrane.
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Affiliation(s)
- Elizaveta Mukhaleva
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA, USA
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Tianyi Yang
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Fredrik Sadler
- Biochemistry, Molecular Biology and Biophysics Graduate Program, University of Minnesota, Minneapolis, MN, USA
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Sivaraj Sivaramakrishnan
- Biochemistry, Molecular Biology and Biophysics Graduate Program, University of Minnesota, Minneapolis, MN, USA
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Ning Ma
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Nagarajan Vaidehi
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA, USA
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA, USA
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3
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Mishra S, van Aalst EJ, Wylie BJ, Brady LJ. Cardiolipin occupancy profiles of YidC paralogs reveal the significance of respective TM2 helix residues in determining paralog-specific phenotypes. Front Mol Biosci 2023; 10:1264454. [PMID: 37867558 PMCID: PMC10588454 DOI: 10.3389/fmolb.2023.1264454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 09/22/2023] [Indexed: 10/24/2023] Open
Abstract
YidC belongs to an evolutionarily conserved family of insertases, YidC/Oxa1/Alb3, in bacteria, mitochondria, and chloroplasts, respectively. Unlike Gram-negative bacteria, Gram-positives including Streptococcus mutans harbor two paralogs of YidC. The mechanism for paralog-specific phenotypes of bacterial YidC1 versus YidC2 has been partially attributed to the differences in their cytoplasmic domains. However, we previously identified a W138R gain-of-function mutation in the YidC1 transmembrane helix 2. YidC1W138R mostly phenocopied YidC2, yet the mechanism remained unknown. Primary sequence comparison of streptococcal YidCs led us to identify and mutate the YidC1W138 analog, YidC2S152 to W/A, which resulted in a loss of YidC2- and acquisition of YidC1-like phenotype. The predicted lipid-facing side chains of YidC1W138/YidC2S152 led us to propose a role for membrane phospholipids in specific-residue dependent phenotypes of S. mutans YidC paralogs. Cardiolipin (CL), a prevalent phospholipid in the S. mutans cytoplasmic membrane during acid stress, is encoded by a single gene, cls. We show a concerted mechanism for cardiolipin and YidC2 under acid stress based on similarly increased promoter activities and similar elimination phenotypes. Using coarse grain molecular dynamics simulations with the Martini2.2 Forcefield, YidC1 and YidC2 wild-type and mutant interactions with CL were assessed in silico. We observed substantially increased CL interaction in dimeric versus monomeric proteins, and variable CL occupancy in YidC1 and YidC2 mutant constructs that mimicked characteristics of the other wild-type paralog. Hence, paralog-specific amino acid- CL interactions contribute to YidC1 and YidC2-associated phenotypes that can be exchanged by point mutation at positions 138 or 152, respectively.
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Affiliation(s)
- Surabhi Mishra
- Department of Oral Biology, University of Florida, Gainesville, FL, United States
| | - Evan J. van Aalst
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, United States
| | - Benjamin J. Wylie
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, United States
| | - L. Jeannine Brady
- Department of Oral Biology, University of Florida, Gainesville, FL, United States
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4
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Das T, Mukhopadhyay C. Comparison and Possible Binding Orientations of SARS-CoV-2 Spike N-Terminal Domain for Gangliosides GM3 and GM1. J Phys Chem B 2023; 127:6940-6948. [PMID: 37523476 DOI: 10.1021/acs.jpcb.3c02286] [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: 08/02/2023]
Abstract
SARS-CoV-2 spike glycoprotein is anchored by gangliosides. The sialic acid in the ganglioside headgroup is responsible for virus attachment and entry into host cells. We used coarse-grained (CG) molecular dynamics simulations to expand on our previous study of GM1 interaction with two different orientations of the SARS-CoV-2 S1 subunit N-terminal domain (NTD) and to confirm the role of sialic acid receptors in driving the viral receptor; GM3 was used as another ganglioside on the membrane. Because of the smaller headgroup, sialic acid is crucial in GM3 interactions, whereas GM1 interacts with NTD via both the sialic acid and external galactose. In line with our previous findings for NTD orientations in GM1 binding, we identified two orientations, "compact" and "distributed", comprising sugar receptor-interacting residues in GM3-embedded lipid bilayers. Gangliosides in closer proximity to the compact NTD orientation might cause relatively greater restrictions to penetrate the bilayer. However, the attachment of a distributed NTD orientation with more negative interaction energies appears to facilitate GM1/GM3 to move quickly across the membrane. Our findings likely shed some light on the orientations that the NTD receptor acquires during the early phases of interaction with GM1 and GM3 in a membrane environment.
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Affiliation(s)
- Tanushree Das
- Department of Chemistry, University of Calcutta, 92, A.P.C. Road, Kolkata 700009, India
| | - Chaitali Mukhopadhyay
- Department of Chemistry, University of Calcutta, 92, A.P.C. Road, Kolkata 700009, India
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5
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van Aalst EJ, McDonald CJ, Wylie BJ. Cholesterol Biases the Conformational Landscape of the Chemokine Receptor CCR3: A MAS SSNMR-Filtered Molecular Dynamics Study. J Chem Inf Model 2023; 63:3068-3085. [PMID: 37127541 PMCID: PMC10208230 DOI: 10.1021/acs.jcim.2c01546] [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: 12/07/2022] [Indexed: 05/03/2023]
Abstract
Cholesterol directs the pathway of ligand-induced G protein-coupled receptor (GPCR) signal transduction. The GPCR C-C motif chemokine receptor 3 (CCR3) is the principal chemotactic receptor for eosinophils, with roles in cancer metastasis and autoinflammatory conditions. Recently, we discovered a direct correlation between bilayer cholesterol and increased agonist-triggered CCR3 signal transduction. However, the allosteric molecular mechanism escalating ligand affinity and G protein coupling is unknown. To study cholesterol-guided CCR3 conformational selection, we implement comparative, objective measurement of protein architectures by scoring shifts (COMPASS) to grade model structures from molecular dynamics simulations. In this workflow, we scored predicted chemical shifts against 2-dimensional solid-state NMR 13C-13C correlation spectra of U-15N,13C-CCR3 samples prepared with and without cholesterol. Our analysis of trajectory model structures uncovers that cholesterol induces site-specific conformational restraint of extracellular loop (ECL) 2 and conserved motion in transmembrane helices and ECL3 not observed in simulations of bilayers with only phosphatidylcholine lipids. PyLipID analysis implicates direct cholesterol agency in CCR3 conformational selection and dynamics. Residue-residue contact scoring shows that cholesterol biases the conformational selection of the orthosteric pocket involving Y411.39, Y1133.32, and E2877.39. Lastly, we observe contact remodeling in activation pathway residues centered on the initial transmission switch, Na+ pocket, and R3.50 in the DRY motif. Our observations have unique implications for understanding of CCR3 ligand recognition and specificity and provide mechanistic insight into how cholesterol functions as an allosteric regulator of CCR3 signal transduction.
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Affiliation(s)
- Evan J. van Aalst
- Department of Chemistry and
Biochemistry, Texas Tech University, Lubbock, Texas 79415, United States
| | - Corey J. McDonald
- Department of Chemistry and
Biochemistry, Texas Tech University, Lubbock, Texas 79415, United States
| | - Benjamin J. Wylie
- Department of Chemistry and
Biochemistry, Texas Tech University, Lubbock, Texas 79415, United States
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6
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Kjølbye LR, Sørensen L, Yan J, Berglund NA, Ferkinghoff-Borg J, Robinson CV, Schiøtt B. Lipid Modulation of a Class B GPCR: Elucidating the Modulatory Role of PI(4,5)P 2 Lipids. J Chem Inf Model 2022; 62:6788-6802. [PMID: 36036575 DOI: 10.1021/acs.jcim.2c00635] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) lipids have been shown to stabilize an active conformation of class A G-protein coupled receptors (GPCRs) through a conserved binding site, not present in class B GPCRs. For class B GPCRs, previous molecular dynamics (MD) simulation studies have shown PI(4,5)P2 interacting with the Glucagon receptor (GCGR), which constitutes an important target for diabetes and obesity therapeutics. In this work, we applied MD simulations supported by native mass spectrometry (nMS) to study lipid interactions with GCGR. We demonstrate how tail composition plays a role in modulating the binding of PI(4,5)P2 lipids to GCGR. Specifically, we find the PI(4,5)P2 lipids to have a higher affinity toward the inactive conformation of GCGR. Interestingly, we find that in contrast to class A GPCRs, PI(4,5)P2 appear to stabilize the inactive conformation of GCGR through a binding site conserved across class B GPCRs but absent in class A GPCRs. This suggests differences in the regulatory function of PI(4,5)P2 between class A and class B GPCRs.
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Affiliation(s)
- Lisbeth R Kjølbye
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark.,Novo Nordisk A/S, Novo Nordisk Park 1, 2760 Måløv, Denmark
| | - Lars Sørensen
- Novo Nordisk A/S, Novo Nordisk Park 1, 2760 Måløv, Denmark
| | - Jun Yan
- Novo Nordisk A/S, Novo Nordisk Park 1, 2760 Måløv, Denmark
| | - Nils A Berglund
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | | | - Carol V Robinson
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Birgit Schiøtt
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark.,Interdisciplinary Nanoscience Center, Aarhus University, Gustav Wieds vej 14, 8000 Aarhus C, Denmark
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7
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Yekefallah M, Rasberry CA, van Aalst EJ, Browning HP, Amani R, Versteeg DB, Wylie BJ. Mutational Insight into Allosteric Regulation of Kir Channel Activity. ACS OMEGA 2022; 7:43621-43634. [PMID: 36506180 PMCID: PMC9730464 DOI: 10.1021/acsomega.2c04456] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 11/10/2022] [Indexed: 06/08/2023]
Abstract
Potassium (K+) channels are regulated in part by allosteric communication between the helical bundle crossing, or inner gate, and the selectivity filter, or outer gate. This network is triggered by gating stimuli. In concert, there is an allosteric network which is a conjugated set of interactions which correlate long-range structural rearrangements necessary for channel function. Inward-rectifier K+ (Kir) channels favor inward K+ conductance, are ligand-gated, and help establish resting membrane potentials. KirBac1.1 is a bacterial Kir (KirBac) channel homologous to human Kir (hKir) channels. Additionally, KirBac1.1 is gated by the anionic phospholipid ligand phosphatidylglycerol (PG). In this study, we use site-directed mutagenesis to investigate residues involved in the KirBac1.1 gating mechanism and allosteric network we previously proposed using detailed solid-state NMR (SSNMR) measurements. Using fluorescence-based K+ and sodium (Na+) flux assays, we identified channel mutants with impaired function that do not alter selectivity of the channel. In tandem, we performed coarse grain molecular dynamics simulations, observing changes in PG-KirBac1.1 interactions correlated with mutant channel activity and contacts between the two transmembrane helices and pore helix tied to this behavior. Lipid affinity is closely tied to the proximity of two tryptophan residues on neighboring subunits which lure anionic lipids to a cationic pocket formed by a cluster of arginine residues. Thus, these simulations establish a structural and functional basis for the role of each mutated site in the proposed allosteric network. The experimental and simulated data provide insight into key functional residues involved in gating and lipid allostery of K+ channels. Our findings also have direct implications on the physiology of hKir channels due to conservation of many of the residues identified in this work from KirBac1.1.
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8
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McGlone ER, Ansell TB, Dunsterville C, Song W, Carling D, Tomas A, Bloom SR, Sansom MSP, Tan T, Jones B. Hepatocyte cholesterol content modulates glucagon receptor signalling. Mol Metab 2022; 63:101530. [PMID: 35718339 PMCID: PMC9254120 DOI: 10.1016/j.molmet.2022.101530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 06/13/2022] [Indexed: 11/24/2022] Open
Abstract
OBJECTIVE To determine whether glucagon receptor (GCGR) actions are modulated by cellular cholesterol levels. METHODS We determined the effects of experimental cholesterol depletion and loading on glucagon-mediated cAMP production, ligand internalisation and glucose production in human hepatoma cells, mouse and human hepatocytes. GCGR interactions with lipid bilayers were explored using coarse-grained molecular dynamic simulations. Glucagon responsiveness was measured in mice fed a high cholesterol diet with or without simvastatin to modulate hepatocyte cholesterol content. RESULTS GCGR cAMP signalling was reduced by higher cholesterol levels across different cellular models. Ex vivo glucagon-induced glucose output from mouse hepatocytes was enhanced by simvastatin treatment. Mice fed a high cholesterol diet had increased hepatic cholesterol and a blunted hyperglycaemic response to glucagon, both of which were partially reversed by simvastatin. Simulations identified likely membrane-exposed cholesterol binding sites on the GCGR, including a site where cholesterol is a putative negative allosteric modulator. CONCLUSIONS Our results indicate that cellular cholesterol content influences glucagon sensitivity and indicate a potential molecular basis for this phenomenon. This could be relevant to the pathogenesis of non-alcoholic fatty liver disease, which is associated with both hepatic cholesterol accumulation and glucagon resistance.
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Affiliation(s)
- Emma Rose McGlone
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London W12 0NN, United Kingdom; Department of Surgery and Cancer, Imperial College London, London W12 0NN, United Kingdom.
| | - T Bertie Ansell
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom.
| | - Cecilia Dunsterville
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London W12 0NN, United Kingdom.
| | - Wanling Song
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom.
| | - David Carling
- Cellular Stress Research Group, MRC London Institute of Medical Sciences, Imperial College London, London W12 0NN, United Kingdom.
| | - Alejandra Tomas
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London W12 0NN, United Kingdom.
| | - Stephen R Bloom
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London W12 0NN, United Kingdom.
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom.
| | - Tricia Tan
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London W12 0NN, United Kingdom.
| | - Ben Jones
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London W12 0NN, United Kingdom.
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9
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Understanding the functional role of membrane confinements in TNF-mediated signaling by multiscale simulations. Commun Biol 2022; 5:228. [PMID: 35277586 PMCID: PMC8917213 DOI: 10.1038/s42003-022-03179-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 02/17/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractThe interaction between TNFα and TNFR1 is essential in maintaining tissue development and immune responses. While TNFR1 is a cell surface receptor, TNFα exists in both soluble and membrane-bound forms. Interestingly, it was found that the activation of TNFR1-mediated signaling pathways is preferentially through the soluble form of TNFα, which can also induce the clustering of TNFR1 on plasma membrane of living cells. We developed a multiscale simulation framework to compare receptor clustering induced by soluble and membrane-bound ligands. Comparing with the freely diffusive soluble ligands, we hypothesize that the conformational dynamics of membrane-bound ligands are restricted, which affects the clustering of ligand-receptor complexes at cell-cell interfaces. Our simulation revealed that only small clusters can form if TNFα is bound on cell surface. In contrast, the clustering triggered by soluble TNFα is more dynamic, and the size of clusters is statistically larger. We therefore demonstrated the impact of membrane-bound ligand on dynamics of receptor clustering. Moreover, considering that larger TNFα-TNFR1 clusters is more likely to provide spatial platform for downstream signaling pathway, our studies offer new mechanistic insights about why the activation of TNFR1-mediated signaling pathways is not preferred by membrane-bound form of TNFα.
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10
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Smith NA, Wardak AZ, Cowan AD, Colman PM, Czabotar PE, Smith BJ. The Bak core dimer focuses triacylglycerides in the membrane. Biophys J 2022; 121:347-360. [PMID: 34973947 PMCID: PMC8822611 DOI: 10.1016/j.bpj.2021.12.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/15/2021] [Accepted: 12/28/2021] [Indexed: 02/03/2023] Open
Abstract
Apoptosis, the intrinsic programmed cell death process, is mediated by the Bcl-2 family members Bak and Bax. Activation via formation of symmetric core dimers and oligomerization on the mitochondrial outer membrane (MOM) leads to permeabilization and cell death. Although this process is linked to the MOM, the role of the membrane in facilitating such pores is poorly understood. We recently described Bak core domain dimers, revealing lipid binding sites and an initial role of lipids in oligomerization. Here we describe simulations that identified localized clustering and interaction of triacylglycerides (TAGs) with a minimized Bak dimer construct. Coalescence of TAGs occurred beneath this Bak dimer, mitigating dimer-induced local membrane thinning and curvature in representative coarse-grain MOM and model membrane systems. Furthermore, the effects observed as a result of coarse-grain TAG cluster formation was concentration dependent, scaling from low physiological MOM concentrations to those found in other organelles. We find that increasing the TAG concentration in liposomes mimicking the MOM decreased the ability of activated Bak to permeabilize these liposomes. These results suggest that the presence of TAGs within a Bak-lipid membrane preserves membrane integrity and is associated with reduced membrane stress, suggesting a possible role of TAGs in Bak-mediated apoptosis.
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Affiliation(s)
- Nicholas A. Smith
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
| | - Ahmad Z. Wardak
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Angus D. Cowan
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia,Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Peter M. Colman
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia,Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Peter E. Czabotar
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia,Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Brian J. Smith
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia,Corresponding author
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11
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Ansell TB, Curran L, Horrell MR, Pipatpolkai T, Letham SC, Song W, Siebold C, Stansfeld PJ, Sansom MSP, Corey RA. Relative Affinities of Protein-Cholesterol Interactions from Equilibrium Molecular Dynamics Simulations. J Chem Theory Comput 2021; 17:6548-6558. [PMID: 34523933 PMCID: PMC8515805 DOI: 10.1021/acs.jctc.1c00547] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Indexed: 12/18/2022]
Abstract
Specific interactions of lipids with membrane proteins contribute to protein stability and function. Multiple lipid interactions surrounding a membrane protein are often identified in molecular dynamics (MD) simulations and are, increasingly, resolved in cryo-electron microscopy (cryo-EM) densities. Determining the relative importance of specific interaction sites is aided by determination of lipid binding affinities using experimental or simulation methods. Here, we develop a method for determining protein-lipid binding affinities from equilibrium coarse-grained MD simulations using binding saturation curves, designed to mimic experimental protocols. We apply this method to directly obtain affinities for cholesterol binding to multiple sites on a range of membrane proteins and compare our results with free energies obtained from density-based equilibrium methods and with potential of mean force calculations, getting good agreement with respect to the ranking of affinities for different sites. Thus, our binding saturation method provides a robust, high-throughput alternative for determining the relative consequence of individual sites seen in, e.g., cryo-EM derived membrane protein structures surrounded by an array of ancillary lipid densities.
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Affiliation(s)
- T. Bertie Ansell
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
| | - Luke Curran
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
| | - Michael R. Horrell
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
| | - Tanadet Pipatpolkai
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
- Department
of Physiology, Anatomy & Genetics, University
of Oxford, South Parks
Road, Oxford, OX1 3PT, U.K.
| | - Suzanne C. Letham
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
- Sir
William Dunn School of Pathology, University
of Oxford, South Parks
Road, Oxford, OX1 3RE, U.K.
| | - Wanling Song
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
| | - Christian Siebold
- Division
of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, U.K.
| | - Phillip J. Stansfeld
- School
of Life Sciences and Department of Chemistry, University of Warwick, Coventry, CV4 7AL, U.K.
| | - Mark S. P. Sansom
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
| | - Robin A. Corey
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
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12
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Yokoyama N, Hanafusa K, Hotta T, Oshima E, Iwabuchi K, Nakayama H. Multiplicity of Glycosphingolipid-Enriched Microdomain-Driven Immune Signaling. Int J Mol Sci 2021; 22:9565. [PMID: 34502474 PMCID: PMC8430928 DOI: 10.3390/ijms22179565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/29/2021] [Accepted: 09/01/2021] [Indexed: 11/16/2022] Open
Abstract
Glycosphingolipids (GSLs), together with cholesterol, sphingomyelin (SM), and glycosylphosphatidylinositol (GPI)-anchored and membrane-associated signal transduction molecules, form GSL-enriched microdomains. These specialized microdomains interact in a cis manner with various immune receptors, affecting immune receptor-mediated signaling. This, in turn, results in the regulation of a broad range of immunological functions, including phagocytosis, cytokine production, antigen presentation and apoptosis. In addition, GSLs alone can regulate immunological functions by acting as ligands for immune receptors, and exogenous GSLs can alter the organization of microdomains and microdomain-associated signaling. Many pathogens, including viruses, bacteria and fungi, enter host cells by binding to GSL-enriched microdomains. Intracellular pathogens survive inside phagocytes by manipulating intracellular microdomain-driven signaling and/or sphingolipid metabolism pathways. This review describes the mechanisms by which GSL-enriched microdomains regulate immune signaling.
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Affiliation(s)
- Noriko Yokoyama
- Institute for Environmental and Gender-Specific Medicine, Juntendo University, Graduate School of Medicine, Urayasu, Chiba 279-0021, Japan; (N.Y.); (K.H.); (T.H.); (E.O.); (K.I.)
| | - Kei Hanafusa
- Institute for Environmental and Gender-Specific Medicine, Juntendo University, Graduate School of Medicine, Urayasu, Chiba 279-0021, Japan; (N.Y.); (K.H.); (T.H.); (E.O.); (K.I.)
| | - Tomomi Hotta
- Institute for Environmental and Gender-Specific Medicine, Juntendo University, Graduate School of Medicine, Urayasu, Chiba 279-0021, Japan; (N.Y.); (K.H.); (T.H.); (E.O.); (K.I.)
| | - Eriko Oshima
- Institute for Environmental and Gender-Specific Medicine, Juntendo University, Graduate School of Medicine, Urayasu, Chiba 279-0021, Japan; (N.Y.); (K.H.); (T.H.); (E.O.); (K.I.)
| | - Kazuhisa Iwabuchi
- Institute for Environmental and Gender-Specific Medicine, Juntendo University, Graduate School of Medicine, Urayasu, Chiba 279-0021, Japan; (N.Y.); (K.H.); (T.H.); (E.O.); (K.I.)
- Laboratory of Biochemistry, Juntendo University Faculty of Health Care and Nursing, Urayasu, Chiba 279-0023, Japan
- Infection Control Nursing, Juntendo University Graduate School of Health Care and Nursing, Urayasu, Chiba 279-0023, Japan
| | - Hitoshi Nakayama
- Institute for Environmental and Gender-Specific Medicine, Juntendo University, Graduate School of Medicine, Urayasu, Chiba 279-0021, Japan; (N.Y.); (K.H.); (T.H.); (E.O.); (K.I.)
- Laboratory of Biochemistry, Juntendo University Faculty of Health Care and Nursing, Urayasu, Chiba 279-0023, Japan
- Infection Control Nursing, Juntendo University Graduate School of Health Care and Nursing, Urayasu, Chiba 279-0023, Japan
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13
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Insights into the Role of Membrane Lipids in the Structure, Function and Regulation of Integral Membrane Proteins. Int J Mol Sci 2021; 22:ijms22169026. [PMID: 34445730 PMCID: PMC8396450 DOI: 10.3390/ijms22169026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/15/2021] [Accepted: 08/17/2021] [Indexed: 02/07/2023] Open
Abstract
Membrane proteins exist within the highly hydrophobic membranes surrounding cells and organelles, playing key roles in cellular function. It is becoming increasingly clear that the membrane does not just act as an appropriate environment for these proteins, but that the lipids that make up these membranes are essential for membrane protein structure and function. Recent technological advances in cryogenic electron microscopy and in advanced mass spectrometry methods, as well as the development of alternative membrane mimetic systems, have allowed experimental study of membrane protein–lipid complexes. These have been complemented by computational approaches, exploiting the ability of Molecular Dynamics simulations to allow exploration of membrane protein conformational changes in membranes with a defined lipid content. These studies have revealed the importance of lipids in stabilising the oligomeric forms of membrane proteins, mediating protein–protein interactions, maintaining a specific conformational state of a membrane protein and activity. Here we review some of the key recent advances in the field of membrane protein–lipid studies, with major emphasis on respiratory complexes, transporters, channels and G-protein coupled receptors.
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14
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van Aalst E, Koneri J, Wylie BJ. In Silico Identification of Cholesterol Binding Motifs in the Chemokine Receptor CCR3. MEMBRANES 2021; 11:570. [PMID: 34436333 PMCID: PMC8401243 DOI: 10.3390/membranes11080570] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 07/21/2021] [Accepted: 07/22/2021] [Indexed: 01/14/2023]
Abstract
CC motif chemokine receptor 3 (CCR3) is a Class A G protein-coupled receptor (GPCR) mainly responsible for the cellular trafficking of eosinophils. As such, it plays key roles in inflammatory conditions, such as asthma and arthritis, and the metastasis of many deadly forms of cancer. However, little is known about how CCR3 functionally interacts with its bilayer environment. Here, we investigate cholesterol binding sites in silico through Coarse-Grained Molecular Dynamics (MD) and Pylipid analysis using an extensively validated homology model based on the crystal structure of CCR5. These simulations identified several cholesterol binding sites containing Cholesterol Recognition/Interaction Amino Acid Consensus motif (CRAC) and its inversion CARC motifs in CCR3. One such site, a CARC site in TM1, in conjunction with aliphatic residues in TM7, emerged as a candidate for future investigation based on the cholesterol residency time within the binding pocket. This site forms the core of a cholesterol binding site previously observed in computational studies of CCR2 and CCR5. Most importantly, these cholesterol binding sites are conserved in other chemokine receptors and may provide clues to cholesterol regulation mechanisms in this subfamily of Class A GPCRs.
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Affiliation(s)
| | | | - Benjamin J. Wylie
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79423, USA; (E.v.A.); (J.K.)
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15
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Damian M, Louet M, Gomes AAS, M'Kadmi C, Denoyelle S, Cantel S, Mary S, Bisch PM, Fehrentz JA, Catoire LJ, Floquet N, Banères JL. Allosteric modulation of ghrelin receptor signaling by lipids. Nat Commun 2021; 12:3938. [PMID: 34168117 PMCID: PMC8225672 DOI: 10.1038/s41467-021-23756-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 05/07/2021] [Indexed: 02/05/2023] Open
Abstract
The membrane is an integral component of the G protein-coupled receptor signaling machinery. Here we demonstrate that lipids regulate the signaling efficacy and selectivity of the ghrelin receptor GHSR through specific interactions and bulk effects. We find that PIP2 shifts the conformational equilibrium of GHSR away from its inactive state, favoring basal and agonist-induced G protein activation. This occurs because of a preferential binding of PIP2 to specific intracellular sites in the receptor active state. Another lipid, GM3, also binds GHSR and favors G protein activation, but mostly in a ghrelin-dependent manner. Finally, we find that not only selective interactions but also the thickness of the bilayer reshapes the conformational repertoire of GHSR, with direct consequences on G protein selectivity. Taken together, this data illuminates the multifaceted role of the membrane components as allosteric modulators of how ghrelin signal could be propagated.
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Affiliation(s)
- Marjorie Damian
- IBMM, UMR 5247, CNRS, Université de Montpellier, ENSCM, Montpellier, France
| | - Maxime Louet
- IBMM, UMR 5247, CNRS, Université de Montpellier, ENSCM, Montpellier, France
| | - Antoniel Augusto Severo Gomes
- IBMM, UMR 5247, CNRS, Université de Montpellier, ENSCM, Montpellier, France
- Laboratório de Física Biológica, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Céline M'Kadmi
- IBMM, UMR 5247, CNRS, Université de Montpellier, ENSCM, Montpellier, France
| | - Séverine Denoyelle
- IBMM, UMR 5247, CNRS, Université de Montpellier, ENSCM, Montpellier, France
| | - Sonia Cantel
- IBMM, UMR 5247, CNRS, Université de Montpellier, ENSCM, Montpellier, France
| | - Sophie Mary
- IBMM, UMR 5247, CNRS, Université de Montpellier, ENSCM, Montpellier, France
| | - Paulo M Bisch
- Laboratório de Física Biológica, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | | | - Laurent J Catoire
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR 7099, CNRS, Université de Paris, Institut de Biologie Physico-Chimique (FRC 550), Paris, France
| | - Nicolas Floquet
- IBMM, UMR 5247, CNRS, Université de Montpellier, ENSCM, Montpellier, France
| | - Jean-Louis Banères
- IBMM, UMR 5247, CNRS, Université de Montpellier, ENSCM, Montpellier, France.
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16
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Overduin M, Trieber C, Prosser RS, Picard LP, Sheff JG. Structures and Dynamics of Native-State Transmembrane Protein Targets and Bound Lipids. MEMBRANES 2021; 11:451. [PMID: 34204456 PMCID: PMC8235241 DOI: 10.3390/membranes11060451] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 06/08/2021] [Accepted: 06/15/2021] [Indexed: 02/06/2023]
Abstract
Membrane proteins work within asymmetric bilayers of lipid molecules that are critical for their biological structures, dynamics and interactions. These properties are lost when detergents dislodge lipids, ligands and subunits, but are maintained in native nanodiscs formed using styrene maleic acid (SMA) and diisobutylene maleic acid (DIBMA) copolymers. These amphipathic polymers allow extraction of multicomponent complexes of post-translationally modified membrane-bound proteins directly from organ homogenates or membranes from diverse types of cells and organelles. Here, we review the structures and mechanisms of transmembrane targets and their interactions with lipids including phosphoinositides (PIs), as resolved using nanodisc systems and methods including cryo-electron microscopy (cryo-EM) and X-ray diffraction (XRD). We focus on therapeutic targets including several G protein-coupled receptors (GPCRs), as well as ion channels and transporters that are driving the development of next-generation native nanodiscs. The design of new synthetic polymers and complementary biophysical tools bodes well for the future of drug discovery and structural biology of native membrane:protein assemblies (memteins).
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Affiliation(s)
- Michael Overduin
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada;
| | - Catharine Trieber
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada;
| | - R. Scott Prosser
- Department of Chemistry, University of Toronto, UTM, Mississauga, ON L5L 1C6, Canada; (R.S.P.); (L.-P.P.)
| | - Louis-Philippe Picard
- Department of Chemistry, University of Toronto, UTM, Mississauga, ON L5L 1C6, Canada; (R.S.P.); (L.-P.P.)
| | - Joey G. Sheff
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON K1A 0R6, Canada;
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17
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Marzook A, Tomas A, Jones B. The Interplay of Glucagon-Like Peptide-1 Receptor Trafficking and Signalling in Pancreatic Beta Cells. Front Endocrinol (Lausanne) 2021; 12:678055. [PMID: 34040588 PMCID: PMC8143046 DOI: 10.3389/fendo.2021.678055] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 04/15/2021] [Indexed: 12/30/2022] Open
Abstract
The glucagon-like peptide 1 receptor (GLP-1R) is a class B G protein-coupled receptor (GPCR) which mediates the effects of GLP-1, an incretin hormone secreted primarily from L-cells in the intestine and within the central nervous system. The GLP-1R, upon activation, exerts several metabolic effects including the release of insulin and suppression of appetite, and has, accordingly, become an important target for the treatment for type 2 diabetes (T2D). Recently, there has been heightened interest in how the activated GLP-1R is trafficked between different endomembrane compartments, controlling the spatial origin and duration of intracellular signals. The discovery of "biased" GLP-1R agonists that show altered trafficking profiles and selective engagement with different intracellular effectors has added to the tools available to study the mechanisms and physiological importance of these processes. In this review we survey early and recent work that has shed light on the interplay between GLP-1R signalling and trafficking, and how it might be therapeutically tractable for T2D and related diseases.
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Affiliation(s)
- Amaara Marzook
- Section of Endocrinology and Investigative Medicine, Imperial College London, London, United Kingdom
| | - Alejandra Tomas
- Section of Cell Biology and Functional Genomics, Imperial College London, London, United Kingdom
| | - Ben Jones
- Section of Endocrinology and Investigative Medicine, Imperial College London, London, United Kingdom
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18
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Su Z, Dhusia K, Wu Y. A multiscale study on the mechanisms of spatial organization in ligand-receptor interactions on cell surfaces. Comput Struct Biotechnol J 2021; 19:1620-1634. [PMID: 33868599 PMCID: PMC8026753 DOI: 10.1016/j.csbj.2021.03.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 03/21/2021] [Accepted: 03/21/2021] [Indexed: 01/11/2023] Open
Abstract
The binding of cell surface receptors with extracellular ligands triggers distinctive signaling pathways, leading into the corresponding phenotypic variation of cells. It has been found that in many systems, these ligand-receptor complexes can further oligomerize into higher-order structures. This ligand-induced oligomerization of receptors on cell surfaces plays an important role in regulating the functions of cell signaling. The underlying mechanism, however, is not well understood. One typical example is proteins that belong to the tumor necrosis factor receptor (TNFR) superfamily. Using a generic multiscale simulation platform that spans from atomic to subcellular levels, we compared the detailed physical process of ligand-receptor oligomerization for two specific members in the TNFR superfamily: the complex formed between ligand TNFα and receptor TNFR1 versus the complex formed between ligand TNFβ and receptor TNFR2. Interestingly, although these two systems share high similarity on the tertiary and quaternary structural levels, our results indicate that their oligomers are formed with very different dynamic properties and spatial patterns. We demonstrated that the changes of receptor’s conformational fluctuations due to the membrane confinements are closely related to such difference. Consistent to previous experiments, our simulations also showed that TNFR can preassemble into dimers prior to ligand binding, while the introduction of TNF ligands induced higher-order oligomerization due to a multivalent effect. This study, therefore, provides the molecular basis to TNFR oligomerization and reveals new insights to TNFR-mediated signal transduction. Moreover, our multiscale simulation framework serves as a prototype that paves the way to study higher-order assembly of cell surface receptors in many other bio-systems.
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Affiliation(s)
- Zhaoqian Su
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, United States
| | - Kalyani Dhusia
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, United States
| | - Yinghao Wu
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, United States
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