1
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Umegawa Y, Kato S, Seo S, Shinoda W, Kawatake S, Matsuoka S, Murata M. Protein-lipid acyl chain interactions: Depth-dependent changes of segmental mobility of phospholipid in contact with bacteriorhodopsin. Biophys Chem 2024; 308:107204. [PMID: 38412762 DOI: 10.1016/j.bpc.2024.107204] [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: 12/02/2023] [Revised: 01/31/2024] [Accepted: 02/20/2024] [Indexed: 02/29/2024]
Abstract
Boundary lipids surrounding membrane proteins play an essential role in protein function and structure. These protein-lipid interactions are mainly divided into electrostatic interactions between the polar amino acids of proteins and polar heads of phospholipids, and hydrophobic interactions between protein transmembrane sites and phospholipid acyl chains. Our previous report (Kawatake et al., Biochim. Biophys. Acta 1858 [2016] 2106-2115) covered a method for selectively analyzing boundary lipid interactions and showed differences in membrane protein-peripheral lipid interactions due to differences in their head group. Interactions in the hydrophobic acyl chains of phospholipids are relatively consistent among proteins, but the details of these interactions have not been elucidated. In this study, we reconstituted bacteriorhodopsin as a model protein into phospholipid membranes labeled with 2H and 13C for solid-state NMR measurement to investigate the depth-dependent effect of the head group structure on the lipid bilayer. The results showed that the position of the phospholipid near the carbonyl carbon was affected by the head group in terms of selectivity for protein surfaces, whereas in the deep interior of the bilayer near the leaflet interface, there was little difference between the head groups, indicating that the dependence of their interactions on the head group was much reduced.
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Affiliation(s)
- Yuichi Umegawa
- JST-ERATO, Lipid Active Structure Project, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan; Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan; Forefront Research Center, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan.
| | - Sho Kato
- JST-ERATO, Lipid Active Structure Project, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan; Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Sangjae Seo
- Department of Materials Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan; Division of Supercomputing, Korea Institute of Science and Technology Information, 245 Daehak-ro, Yuseong-gu, Daejeon 34141, South Korea
| | - Wataru Shinoda
- Department of Materials Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan; Research Institute for Interdisciplinary Science, Okayama University, 3-1-1, Tsushima-naka, Okayama 700-8530, Japan
| | - Satoshi Kawatake
- JST-ERATO, Lipid Active Structure Project, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan; Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan; Forefront Research Center, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Shigeru Matsuoka
- JST-ERATO, Lipid Active Structure Project, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan; Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan; Forefront Research Center, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Michio Murata
- JST-ERATO, Lipid Active Structure Project, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan; Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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2
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Kalinichenko L, Kornhuber J, Sinning S, Haase J, Müller CP. Serotonin Signaling through Lipid Membranes. ACS Chem Neurosci 2024; 15:1298-1320. [PMID: 38499042 PMCID: PMC10995955 DOI: 10.1021/acschemneuro.3c00823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/22/2024] [Accepted: 02/27/2024] [Indexed: 03/20/2024] Open
Abstract
Serotonin (5-HT) is a vital modulatory neurotransmitter responsible for regulating most behaviors in the brain. An inefficient 5-HT synaptic function is often linked to various mental disorders. Primarily, membrane proteins controlling the expression and activity of 5-HT synthesis, storage, release, receptor activation, and inactivation are critical to 5-HT signaling in synaptic and extra-synaptic sites. Moreover, these signals represent information transmission across membranes. Although the lipid membrane environment is often viewed as fairly stable, emerging research suggests significant functional lipid-protein interactions with many synaptic 5-HT proteins. These protein-lipid interactions extend to almost all the primary lipid classes that form the plasma membrane. Collectively, these lipid classes and lipid-protein interactions affect 5-HT synaptic efficacy at the synapse. The highly dynamic lipid composition of synaptic membranes suggests that these lipids and their interactions with proteins may contribute to the plasticity of the 5-HT synapse. Therefore, this broader protein-lipid model of the 5-HT synapse necessitates a reconsideration of 5-HT's role in various associated mental disorders.
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Affiliation(s)
- Liubov
S. Kalinichenko
- Department
of Psychiatry and Psychotherapy, University
Clinic, Friedrich-Alexander-University of Erlangen-Nürnberg, Schwabachanlage 6, 91054, Erlangen, Germany
| | - Johannes Kornhuber
- Department
of Psychiatry and Psychotherapy, University
Clinic, Friedrich-Alexander-University of Erlangen-Nürnberg, Schwabachanlage 6, 91054, Erlangen, Germany
| | - Steffen Sinning
- Department
of Forensic Medicine, Aarhus University, Palle Juul-Jensens Boulevard 99, 8200 Aarhus N, Denmark
| | - Jana Haase
- School
of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - Christian P. Müller
- Department
of Psychiatry and Psychotherapy, University
Clinic, Friedrich-Alexander-University of Erlangen-Nürnberg, Schwabachanlage 6, 91054, Erlangen, Germany
- Institute
of Psychopharmacology, Central Institute of Mental Health, Medical
Faculty Mannheim, Heidelberg University, 69047, Mannheim, Germany
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3
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Pöhnl M, Trollmann MFW, Böckmann RA. Nonuniversal impact of cholesterol on membranes mobility, curvature sensing and elasticity. Nat Commun 2023; 14:8038. [PMID: 38081812 PMCID: PMC10713574 DOI: 10.1038/s41467-023-43892-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023] Open
Abstract
Biological membranes, composed mainly of phospholipids and cholesterol, play a vital role as cellular barriers. They undergo localized reshaping in response to environmental cues and protein interactions, with the energetics of deformations crucial for exerting biological functions. This study investigates the non-universal role of cholesterol on the structure and elasticity of saturated and unsaturated lipid membranes. Our study uncovers a highly cooperative relationship between thermal membrane bending and local cholesterol redistribution, with cholesterol showing a strong preference for the compressed membrane leaflet. Remarkably, in unsaturated membranes, increased cholesterol mobility enhances cooperativity, resulting in membrane softening despite membrane thickening and lipid compression caused by cholesterol. These findings elucidate the intricate interplay between thermodynamic forces and local molecular interactions that govern collective properties of membranes.
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Affiliation(s)
- Matthias Pöhnl
- Computational Biology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Marius F W Trollmann
- Computational Biology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- Erlangen National High Perfomance Computing Center (NHR@FAU), Erlangen, Germany
| | - Rainer A Böckmann
- Computational Biology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.
- Erlangen National High Perfomance Computing Center (NHR@FAU), Erlangen, Germany.
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4
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Gahbauer S, DeLeon C, Braz JM, Craik V, Kang HJ, Wan X, Huang XP, Billesbølle CB, Liu Y, Che T, Deshpande I, Jewell M, Fink EA, Kondratov IS, Moroz YS, Irwin JJ, Basbaum AI, Roth BL, Shoichet BK. Docking for EP4R antagonists active against inflammatory pain. Nat Commun 2023; 14:8067. [PMID: 38057319 PMCID: PMC10700596 DOI: 10.1038/s41467-023-43506-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 11/12/2023] [Indexed: 12/08/2023] Open
Abstract
The lipid prostaglandin E2 (PGE2) mediates inflammatory pain by activating G protein-coupled receptors, including the prostaglandin E2 receptor 4 (EP4R). Nonsteroidal anti-inflammatory drugs (NSAIDs) reduce nociception by inhibiting prostaglandin synthesis, however, the disruption of upstream prostanoid biosynthesis can lead to pleiotropic effects including gastrointestinal bleeding and cardiac complications. In contrast, by acting downstream, EP4R antagonists may act specifically as anti-inflammatory agents and, to date, no selective EP4R antagonists have been approved for human use. In this work, seeking to diversify EP4R antagonist scaffolds, we computationally dock over 400 million compounds against an EP4R crystal structure and experimentally validate 71 highly ranked, de novo synthesized molecules. Further, we show how structure-based optimization of initial docking hits identifies a potent and selective antagonist with 16 nanomolar potency. Finally, we demonstrate favorable pharmacokinetics for the discovered compound as well as anti-allodynic and anti-inflammatory activity in several preclinical pain models in mice.
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Affiliation(s)
- Stefan Gahbauer
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Chelsea DeLeon
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27514, USA
| | - Joao M Braz
- Department of Anatomy, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Veronica Craik
- Department of Anatomy, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Hye Jin Kang
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27514, USA
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Xiaobo Wan
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Xi-Ping Huang
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27514, USA
| | - Christian B Billesbølle
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Yongfeng Liu
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27514, USA
| | - Tao Che
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27514, USA
- Center of Clinical Pharmacology, Department of Anesthesiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Ishan Deshpande
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Madison Jewell
- Department of Anatomy, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Elissa A Fink
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Ivan S Kondratov
- Enamine Ltd., Kyiv, Ukraine
- V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Yurii S Moroz
- Chemspace LLC, Kyiv, Ukraine
- National Taras Shevchenko University of Kyiv, Kyiv, Ukraine
| | - John J Irwin
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Allan I Basbaum
- Department of Anatomy, University of California San Francisco, San Francisco, CA, 94158, USA.
| | - Bryan L Roth
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27514, USA.
- National Institute of Mental Health Psychoactive Drug Screening Program, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27514, USA.
- Division of Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill Eshelman School of Pharmacy, Chapel Hill, NC, 27514, USA.
| | - Brian K Shoichet
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94158, USA.
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5
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Di Marino D, Conflitti P, Motta S, Limongelli V. Structural basis of dimerization of chemokine receptors CCR5 and CXCR4. Nat Commun 2023; 14:6439. [PMID: 37833254 PMCID: PMC10575954 DOI: 10.1038/s41467-023-42082-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are prominent drug targets responsible for extracellular-to-intracellular signal transduction. GPCRs can form functional dimers that have been poorly characterized so far. Here, we show the dimerization mechanism of the chemokine receptors CCR5 and CXCR4 by means of an advanced free-energy technique named coarse-grained metadynamics. Our results reproduce binding events between the GPCRs occurring in the minute timescale, revealing a symmetric and an asymmetric dimeric structure for each of the three investigated systems, CCR5/CCR5, CXCR4/CXCR4, and CCR5/CXCR4. The transmembrane helices TM4-TM5 and TM6-TM7 are the preferred binding interfaces for CCR5 and CXCR4, respectively. The identified dimeric states differ in the access to the binding sites of the ligand and G protein, indicating that dimerization may represent a fine allosteric mechanism to regulate receptor activity. Our study offers structural basis for the design of ligands able to modulate the formation of CCR5 and CXCR4 dimers and in turn their activity, with therapeutic potential against HIV, cancer, and immune-inflammatory diseases.
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Affiliation(s)
- Daniele Di Marino
- Department of Life and Environmental Sciences - New York-Marche Structural Biology Centre (NY-MaSBiC), Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy
- Neuronal Death and Neuroprotection Unit, Department of Neuroscience, Mario Negri Institute for Pharmacological Research-IRCCS, Via Mario Negri 2, 20156, Milan, Italy
- National Biodiversity Future Center (NBFC), Palermo, Italy
| | - Paolo Conflitti
- Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Euler Institute, Via G. Buffi 13, CH-6900, Lugano, Switzerland
| | - Stefano Motta
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126, Milan, Italy
| | - Vittorio Limongelli
- Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Euler Institute, Via G. Buffi 13, CH-6900, Lugano, Switzerland.
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6
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Girych M, Kulig W, Enkavi G, Vattulainen I. How Neuromembrane Lipids Modulate Membrane Proteins: Insights from G-Protein-Coupled Receptors (GPCRs) and Receptor Tyrosine Kinases (RTKs). Cold Spring Harb Perspect Biol 2023; 15:a041419. [PMID: 37487628 PMCID: PMC10547395 DOI: 10.1101/cshperspect.a041419] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
Lipids play a diverse and critical role in cellular processes in all tissues. The unique lipid composition of nerve membranes is particularly interesting because it contains, among other things, polyunsaturated lipids, such as docosahexaenoic acid, which the body only gets through the diet. The crucial role of lipids in neurological processes, especially in receptor-mediated cell signaling, is emphasized by the fact that in many neuropathological diseases there are significant deviations in the lipid composition of nerve membranes compared to healthy individuals. The lipid composition of neuromembranes can significantly affect the function of receptors by regulating the physical properties of the membrane or by affecting specific interactions between receptors and lipids. In addition, it is worth noting that the ligand-binding pocket of many receptors is located inside the cell membrane, due to which lipids can even modulate the binding of ligands to their receptors. These mechanisms highlight the importance of lipids in the regulation of membrane receptor activation and function. In this article, we focus on two major protein families: G-protein-coupled receptors (GPCRs) and receptor tyrosine kinases (RTKs) and discuss how lipids affect their function in neuronal membranes, elucidating the basic mechanisms underlying neuronal function and dysfunction.
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Affiliation(s)
- Mykhailo Girych
- Department of Physics, University of Helsinki, FI-00014 Helsinki, Finland
| | - Waldemar Kulig
- Department of Physics, University of Helsinki, FI-00014 Helsinki, Finland
| | - Giray Enkavi
- Department of Physics, University of Helsinki, FI-00014 Helsinki, Finland
| | - Ilpo Vattulainen
- Department of Physics, University of Helsinki, FI-00014 Helsinki, Finland
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7
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Mohole M, Sengupta D, Chattopadhyay A. Synergistic and Competitive Lipid Interactions in the Serotonin 1A Receptor Microenvironment. ACS Chem Neurosci 2022; 13:3403-3415. [PMID: 36351047 DOI: 10.1021/acschemneuro.2c00422] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The interaction of lipids with G-protein-coupled receptors (GPCRs) has been shown to modulate and dictate several aspects of GPCR organization and function. Diverse lipid interaction sites have been identified from structural biology, bioinformatics, and molecular dynamics studies. For example, multiple cholesterol interaction sites have been identified in the serotonin1A receptor, along with distinct and overlapping sphingolipid interaction sites. How these lipids interact with each other and what is the resultant effect on the receptor is still not clear. In this work, we have analyzed lipid-lipid crosstalk at the receptor of the serotonin1A receptor embedded in a membrane bilayer that mimics the neuronal membrane composition by long coarse-grain simulations. Using a set of similarity coefficients, we classified lipids that bind at the receptor together as synergistic cobinding, and those that bind individually as competitive. Our results show that certain lipids interact with the serotonin1A receptor in synergy with each other. Not surprisingly, the ganglioside GM1 and cholesterol show a synergistic cobinding, along with the relatively uncommon GM1-phosphatidylethanolamine (PE) and cholesterol-PE synergy. In contrast, certain lipid pairs such as cholesterol and sphingomyelin appear to be in competition at several sites, despite their coexistence in lipid nanodomains. In addition, we observed intralipid competition between two lipid tails, with the receptor exhibiting increased interactions with the unsaturated lipid tails. We believe our work represents an important step in understanding the diversity of GPCR-lipid interactions and exploring synergistic cobinding and competition in natural membranes.
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Affiliation(s)
- Madhura Mohole
- CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune411 008, India.,Academy of Scientific and Innovative Research, Ghaziabad201 002, India
| | - Durba Sengupta
- CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune411 008, India.,Academy of Scientific and Innovative Research, Ghaziabad201 002, India
| | - Amitabha Chattopadhyay
- Academy of Scientific and Innovative Research, Ghaziabad201 002, India.,CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad500 007, India
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8
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López-Martín M, Renault P, Giraldo J, Vázquez-Ibar JL, Perálvarez-Marín A. In Silico Assessment of the Lipid Fingerprint Signature of ATP2, the Essential P4-ATPase of Malaria Parasites. MEMBRANES 2022; 12:membranes12070702. [PMID: 35877905 PMCID: PMC9325222 DOI: 10.3390/membranes12070702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/05/2022] [Accepted: 07/08/2022] [Indexed: 02/04/2023]
Abstract
ATP2, a putative type 4 P-type ATPase, is a phosphatidylinositol-4-phosphate (PI4P)-regulated phospholipid transporter with an interesting potential as an antimalarial drug target due to its conservation across Plasmodium species and its essential role in the life cycle of Plasmodium falciparum. Despite its importance, the exact mechanism of its action and regulation is still not fully understood. In this study we used coarse-grained molecular dynamics (CG-MD) to elucidate the lipid–protein interactions between a heterogeneous lipid membrane containing phosphatidylinositol and Plasmodium chabaudi ATP2 (PcATP2), an ortholog of P. falciparum ATP2. Our study reveals structural information of the lipid fingerprint of ATP2, and provides structural information on the potential phosphatidylinositol allosteric binding site. Moreover, we identified a set of evolutionary conserved residues that may play a key role in the binding and stabilization of lipids in the binding pocket.
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Affiliation(s)
- Mario López-Martín
- Biophysics Unit, Department of Biochemistry and Molecular Biology, School of Medicine, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain;
- Institut de Neurociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; (P.R.); (J.G.)
| | - Pedro Renault
- Institut de Neurociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; (P.R.); (J.G.)
- Laboratory of Molecular Neuropharmacology and Bioinformatics, Unitat de Bioestadística, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
- Unitat de Neurociència Traslacional, Parc Taulí Hospital Universitari, Institut d’Investigació i Innovació Parc Taulí (I3PT), Institut de Neurociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
- Instituto de Salud Carlos III, Centro de Investigación Biomédica en Red de Salud Mental, CIBERSAM, 08193 Bellaterra, Spain
| | - Jesus Giraldo
- Institut de Neurociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; (P.R.); (J.G.)
- Laboratory of Molecular Neuropharmacology and Bioinformatics, Unitat de Bioestadística, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
- Unitat de Neurociència Traslacional, Parc Taulí Hospital Universitari, Institut d’Investigació i Innovació Parc Taulí (I3PT), Institut de Neurociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
- Instituto de Salud Carlos III, Centro de Investigación Biomédica en Red de Salud Mental, CIBERSAM, 08193 Bellaterra, Spain
| | - José Luis Vázquez-Ibar
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France
- Correspondence: (J.L.V.-I.); (A.P.-M.); Tel.: +33-1-69-08-89-44 (J.L.V.-I.); +34-93-581-4504 (A.P.-M.)
| | - Alex Perálvarez-Marín
- Biophysics Unit, Department of Biochemistry and Molecular Biology, School of Medicine, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain;
- Institut de Neurociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; (P.R.); (J.G.)
- Correspondence: (J.L.V.-I.); (A.P.-M.); Tel.: +33-1-69-08-89-44 (J.L.V.-I.); +34-93-581-4504 (A.P.-M.)
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9
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Alavizargar A, Elting A, Wedlich-Söldner R, Heuer A. Lipid-Mediated Association of the Slg1 Transmembrane Domains in Yeast Plasma Membranes. J Phys Chem B 2022; 126:3240-3256. [PMID: 35446028 DOI: 10.1021/acs.jpcb.2c00192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Clustering of transmembrane proteins underlies a multitude of fundamental biological processes at the plasma membrane (PM) such as receptor activation, lateral domain formation, and mechanotransduction. The self-association of the respective transmembrane domains (TMDs) has also been suggested to be responsible for the micron-scaled patterns seen for integral membrane proteins in the budding yeast PM. However, the underlying interplay between the local lipid composition and the TMD identity is still not mechanistically understood. In this work, we combined coarse-grained molecular dynamics simulations of simplified bilayer systems with high-resolution live-cell microscopy to analyze the distribution of a representative helical yeast TMD from the PM sensor Slg1 within different lipid environments. In our simulations, we specifically evaluated the effects of acyl chain saturation and anionic lipid head groups on the association of two TMDs. We found that weak lipid-protein interactions significantly affect the configuration of TMD dimers and the free energy of association. Increased amounts of unsaturated phospholipids (PLs) strongly reduced the helix-helix interaction, while the presence of anionic phosphatidylserine (PS) hardly affected the dimer formation. We could experimentally confirm this surprising lack of effect of PS using the network factor, a mesoscopic measure of PM pattern formation in yeast cells. Simulations also showed that the formation of TMD dimers in turn increased the order parameter of the surrounding lipids and induced long-range perturbations in lipid organization. In summary, our results shed new light on the mechanisms of lipid-mediated dimerization of TMDs in complex lipid mixtures.
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Affiliation(s)
- Azadeh Alavizargar
- Institute of Physical Chemistry, University of Muenster, Corrensstr. 28/30, 48149 Muenster, Germany
| | - Annegret Elting
- Institute of Cell Dynamics and Imaging, University of Muenster, Von-Esmarch-Str. 56, 48149 Muenster, Germany
| | - Roland Wedlich-Söldner
- Institute of Cell Dynamics and Imaging, University of Muenster, Von-Esmarch-Str. 56, 48149 Muenster, Germany
| | - Andreas Heuer
- Institute of Physical Chemistry, University of Muenster, Corrensstr. 28/30, 48149 Muenster, Germany
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10
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Song W, Duncan AL, Sansom MSP. Modulation of adenosine A2a receptor oligomerization by receptor activation and PIP 2 interactions. Structure 2021; 29:1312-1325.e3. [PMID: 34270937 PMCID: PMC8581623 DOI: 10.1016/j.str.2021.06.015] [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: 04/06/2021] [Revised: 05/28/2021] [Accepted: 06/25/2021] [Indexed: 11/23/2022]
Abstract
GPCRs have been shown to form oligomers, which generate distinctive signaling outcomes. However, the structural nature of the oligomerization process remains uncertain. We have characterized oligomeric configurations of the adenosine A2a receptor (A2aR) by combining large-scale molecular dynamics simulations with Markov state models. These oligomeric structures may also serve as templates for studying oligomerization of other class A GPCRs. Our simulation data revealed that receptor activation results in enhanced oligomerization, more diverse oligomer populations, and a more connected oligomerization network. The active state conformation of the A2aR shifts protein-protein association interfaces to those involving intracellular loop ICL3 and transmembrane helix TM6. Binding of PIP2 to A2aR stabilizes protein-protein interactions via PIP2-mediated association interfaces. These results indicate that A2aR oligomerization is responsive to the local membrane lipid environment. This, in turn, suggests a modulatory effect on A2aR whereby a given oligomerization profile favors the dynamic formation of specific supramolecular signaling complexes.
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Affiliation(s)
- Wanling Song
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Anna L Duncan
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
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11
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Vickery ON, Stansfeld PJ. CG2AT2: an Enhanced Fragment-Based Approach for Serial Multi-scale Molecular Dynamics Simulations. J Chem Theory Comput 2021; 17:6472-6482. [PMID: 34492188 PMCID: PMC8515810 DOI: 10.1021/acs.jctc.1c00295] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
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Coarse-grained molecular
dynamics provides a means for simulating
the assembly and interactions of macromolecular complexes at a reduced
level of representation, thereby allowing both longer timescale and
larger sized simulations. Here, we describe an enhanced fragment-based
protocol for converting macromolecular complexes from coarse-grained
to atomistic resolution, for further refinement and analysis. While
the focus is upon systems that comprise an integral membrane protein
embedded in a phospholipid bilayer, the technique is also suitable
for membrane-anchored and soluble protein/nucleotide complexes. Overall,
this provides a method for generating an accurate and well-equilibrated
atomic-level description of a macromolecular complex. The approach
is evaluated using a diverse test set of 11 system configurations
of varying size and complexity. Simulations are assessed in terms
of protein stereochemistry, conformational drift, lipid/protein interactions,
and lipid dynamics.
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Affiliation(s)
- Owen N Vickery
- School of Life Sciences & Department of Chemistry, University of Warwick, Gibbet Hill Campus, Coventry CV4 7AL, U.K
| | - Phillip J Stansfeld
- School of Life Sciences & Department of Chemistry, University of Warwick, Gibbet Hill Campus, Coventry CV4 7AL, U.K
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12
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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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13
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Hanser F, Marsol C, Valencia C, Villa P, Klymchenko AS, Bonnet D, Karpenko J. Nile Red-Based GPCR Ligands as Ultrasensitive Probes of the Local Lipid Microenvironment of the Receptor. ACS Chem Biol 2021; 16:651-660. [PMID: 33733725 DOI: 10.1021/acschembio.0c00897] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The local lipid microenvironment of transmembrane receptors is an essential factor in G protein coupled receptor (GPCR) signaling. However, tools are currently missing for studying endogenously expressed GPCRs in primary cells and tissues. Here, we introduce fluorescent environment-sensitive GPCR ligands for probing the microenvironment of the receptor in living cells using fluorescence microscopy under no-wash conditions. We designed and synthesized antagonist ligands of the oxytocin receptor (OTR) by conjugating a high-affinity nonpeptidic OTR ligand PF-3274167 to the environment-sensitive fluorescent dye Nile Red. The length of the polar PEG spacer between the pharmacophore and the fluorophore was adjusted to lower the nonspecific interactions of the probe while preserving a strong fluorogenic response. We demonstrated that the new probes embed into the lipid bilayer in the vicinity of the receptor and convey information about the local polarity and the lipid order via the wavelength-shifting emission of the Nile Red fluorophore.
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Affiliation(s)
- Fabien Hanser
- Laboratoire d’Innovation Thérapeutique, UMR7200 CNRS/Université de Strasbourg, Strasbourg Drug Discovery and Development Institute (IMS), 74 route du Rhin, 67401 Illkirch-Graffenstaden, France
| | - Claire Marsol
- Laboratoire d’Innovation Thérapeutique, UMR7200 CNRS/Université de Strasbourg, Strasbourg Drug Discovery and Development Institute (IMS), 74 route du Rhin, 67401 Illkirch-Graffenstaden, France
- Plate-forme de chimie biologique intégrative de Strasbourg (PCBiS), UMS 3286 CNRS/Université de Strasbourg, Strasbourg Drug Discovery and Development Institute (IMS), ESBS Pôle API, Bld Sébastien Brant, 67412 Illkirch-Graffenstaden, France
| | - Christel Valencia
- Plate-forme de chimie biologique intégrative de Strasbourg (PCBiS), UMS 3286 CNRS/Université de Strasbourg, Strasbourg Drug Discovery and Development Institute (IMS), ESBS Pôle API, Bld Sébastien Brant, 67412 Illkirch-Graffenstaden, France
| | - Pascal Villa
- Plate-forme de chimie biologique intégrative de Strasbourg (PCBiS), UMS 3286 CNRS/Université de Strasbourg, Strasbourg Drug Discovery and Development Institute (IMS), ESBS Pôle API, Bld Sébastien Brant, 67412 Illkirch-Graffenstaden, France
| | - Andrey S. Klymchenko
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS/Université de Strasbourg, 74 route du Rhin, 67401 Illkirch-Graffenstaden, France
| | - Dominique Bonnet
- Laboratoire d’Innovation Thérapeutique, UMR7200 CNRS/Université de Strasbourg, Strasbourg Drug Discovery and Development Institute (IMS), 74 route du Rhin, 67401 Illkirch-Graffenstaden, France
| | - Julie Karpenko
- Laboratoire d’Innovation Thérapeutique, UMR7200 CNRS/Université de Strasbourg, Strasbourg Drug Discovery and Development Institute (IMS), 74 route du Rhin, 67401 Illkirch-Graffenstaden, France
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14
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Bochicchio A, Brandner AF, Engberg O, Huster D, Böckmann RA. Spontaneous Membrane Nanodomain Formation in the Absence or Presence of the Neurotransmitter Serotonin. Front Cell Dev Biol 2020; 8:601145. [PMID: 33330494 PMCID: PMC7734319 DOI: 10.3389/fcell.2020.601145] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/06/2020] [Indexed: 11/23/2022] Open
Abstract
Detailed knowledge on the formation of biomembrane domains, their structure, composition, and physical characteristics is scarce. Despite its frequently discussed importance in signaling, e.g., in obtaining localized non-homogeneous receptor compositions in the plasma membrane, the nanometer size as well as the dynamic and transient nature of domains impede their experimental characterization. In turn, atomistic molecular dynamics (MD) simulations combine both, high spatial and high temporal resolution. Here, using microsecond atomistic MD simulations, we characterize the spontaneous and unbiased formation of nano-domains in a plasma membrane model containing phosphatidylcholine (POPC), palmitoyl-sphingomyelin (PSM), and cholesterol (Chol) in the presence or absence of the neurotransmitter serotonin at different temperatures. In the ternary mixture, highly ordered and highly disordered domains of similar composition coexist at 303 K. The distinction of domains by lipid acyl chain order gets lost at lower temperatures of 298 and 294 K, suggesting a phase transition at ambient temperature. By comparison of domain ordering and composition, we demonstrate how the domain-specific binding of the neurotransmitter serotonin results in a modified domain lipid composition and a substantial downward shift of the phase transition temperature. Our simulations thus suggest a novel mode of action of neurotransmitters possibly of importance in neuronal signal transmission.
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Affiliation(s)
- Anna Bochicchio
- Computational Biology, Department Biology, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Astrid F Brandner
- Computational Biology, Department Biology, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Oskar Engberg
- Institute for Medical Physics and Biophysics, University of Leipzig, Leipzig, Germany
| | - Daniel Huster
- Institute for Medical Physics and Biophysics, University of Leipzig, Leipzig, Germany.,Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Rainer A Böckmann
- Computational Biology, Department Biology, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
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15
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The Interplay among Subunit Composition, Cardiolipin Content, and Aggregation State of Bovine Heart Cytochrome c Oxidase. Cells 2020; 9:cells9122588. [PMID: 33287231 PMCID: PMC7761698 DOI: 10.3390/cells9122588] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 11/24/2020] [Accepted: 12/01/2020] [Indexed: 02/07/2023] Open
Abstract
Mitochondrial cytochrome c oxidase (CcO) is a multisubunit integral membrane complex consisting of 13 dissimilar subunits, as well as three to four tightly bound molecules of cardiolipin (CL). The monomeric unit of CcO is able to form a dimer and participate in the formation of supercomplexes in the inner mitochondrial membrane. The structural and functional integrity of the enzyme is crucially dependent on the full subunit complement and the presence of unperturbed bound CL. A direct consequence of subunit loss, CL removal, or its oxidative modification is the destabilization of the quaternary structure, loss of the activity, and the inability to dimerize. Thus, the intimate interplay between individual components of the complex is imperative for regulation of the CcO aggregation state. While it appears that the aggregation state of CcO might affect its conformational stability, the functional role of the aggregation remains unclear as both monomeric and dimeric forms of CcO seem to be fully active. Here, we review the current status of our knowledge with regard to the role of dimerization in the function and stability of CcO and factors, such as subunit composition, amphiphilic environment represented by phospholipids/detergents, and posttranslational modifications that play a role in the regulation of the CcO aggregation state.
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16
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Marrink SJ, Levental I. Computational and Experimental Advances in Biomembranes: Resolving Their Complexity. J Phys Chem B 2020; 124:9975-9976. [PMID: 33176427 DOI: 10.1021/acs.jpcb.0c09401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Ilya Levental
- University of Virginia, Charlottesville, Virginia 22903, United States
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