1
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Sankaran SV, Saiba R, Sikdar S, Vemparala S. Correlation Between Antimicrobial Structural Classes and Membrane Partitioning: Role of Emerging Lipid Packing Defects. J Membr Biol 2024:10.1007/s00232-024-00318-z. [PMID: 39037449 DOI: 10.1007/s00232-024-00318-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Accepted: 07/09/2024] [Indexed: 07/23/2024]
Abstract
In this study, a combination of bioinformatics and molecular dynamics simulations is employed to investigate the partitioning behavior of different classes of antimicrobial peptides (AMPs) into model membranes. The main objective is to identify any correlations between the structural characteristics of AMPs and their membrane identification and early-stage partitioning mechanisms. The simulation results reveal distinct membrane interactions among the various structural classes of AMPs, particularly in relation to the generation and subsequent interaction with lipid packing defects. Notably, AMPs with a structure-less coil conformation generate a higher number of deep and shallow defects, which are larger in size compared to other classes of AMPs. AMPs with helical component demonstrated the deepest insertion into the membrane. On the other hand, AMPs with a significant percentage of beta sheets tend to adsorb onto the membrane surface, suggesting a potentially distinct partitioning mechanism attributed to their structural rigidity. These findings highlight the diverse membrane interactions and partitioning mechanisms exhibited by different structural classes of AMPs.
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Affiliation(s)
- S V Sankaran
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai, Tamil Nadu, 600113, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
| | - Roni Saiba
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai, Tamil Nadu, 600113, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
| | - Samapan Sikdar
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai, Tamil Nadu, 600113, India.
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India.
| | - Satyavani Vemparala
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai, Tamil Nadu, 600113, India.
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India.
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2
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de Jesus M, Settle AH, Vorselen D, Gaetjens TK, Galiano M, Romin Y, Lee E, Wong YY, Fu TM, Santosa E, Winer BY, Tamzalit F, Wang MS, Santella A, Bao Z, Sun JC, Shah P, Theriot JA, Abel SM, Huse M. Single-cell topographical profiling of the immune synapse reveals a biomechanical signature of cytotoxicity. Sci Immunol 2024; 9:eadj2898. [PMID: 38941478 DOI: 10.1126/sciimmunol.adj2898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 06/05/2024] [Indexed: 06/30/2024]
Abstract
Immune cells have intensely physical lifestyles characterized by structural plasticity and force exertion. To investigate whether specific immune functions require stereotyped mechanical outputs, we used super-resolution traction force microscopy to compare the immune synapses formed by cytotoxic T cells with contacts formed by other T cell subsets and by macrophages. T cell synapses were globally compressive, which was fundamentally different from the pulling and pinching associated with macrophage phagocytosis. Spectral decomposition of force exertion patterns from each cell type linked cytotoxicity to compressive strength, local protrusiveness, and the induction of complex, asymmetric topography. These features were validated as cytotoxic drivers by genetic disruption of cytoskeletal regulators, live imaging of synaptic secretion, and in silico analysis of interfacial distortion. Synapse architecture and force exertion were sensitive to target stiffness and size, suggesting that the mechanical potentiation of killing is biophysically adaptive. We conclude that cellular cytotoxicity and, by implication, other effector responses are supported by specialized patterns of efferent force.
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Affiliation(s)
- Miguel de Jesus
- Louis V. Gerstner, Jr., Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexander H Settle
- Louis V. Gerstner, Jr., Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daan Vorselen
- Cell Biology and Immunology Group, Wageningen University & Research, Wageningen, Netherlands
- Department of Biology, University of Washington, Seattle, WA, USA
| | - Thomas K Gaetjens
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN, USA
| | - Michael Galiano
- Molecular Cytology Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yevgeniy Romin
- Molecular Cytology Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Esther Lee
- Immunology & Molecular Pathogenesis Program, Weill Cornell Medicine Graduate School of Medical Sciences, New York, NY, USA
| | - Yung Yu Wong
- Louis V. Gerstner, Jr., Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tian-Ming Fu
- Department of Electrical and Computer Engineering, Princeton University, Princeton, NJ, USA
| | - Endi Santosa
- Immunology & Molecular Pathogenesis Program, Weill Cornell Medicine Graduate School of Medical Sciences, New York, NY, USA
| | - Benjamin Y Winer
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fella Tamzalit
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mitchell S Wang
- Pharmacology Program, Weill Cornell Medicine Graduate School of Medical Sciences, New York, NY, USA
| | - Anthony Santella
- Molecular Cytology Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zhirong Bao
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joseph C Sun
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Pavak Shah
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Julie A Theriot
- Department of Biology, University of Washington, Seattle, WA, USA
| | - Steven M Abel
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN, USA
| | - Morgan Huse
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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3
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Fujimoto T. Nuclear lipid droplet: Guardian of nuclear membrane lipid homeostasis? Curr Opin Cell Biol 2024; 88:102370. [PMID: 38744005 DOI: 10.1016/j.ceb.2024.102370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 04/22/2024] [Indexed: 05/16/2024]
Abstract
Lipid droplets (LDs) are cytoplasmic organelles, but they are also found within the nucleus in small numbers. Nuclear LDs that form at the inner nuclear membrane (INM) often increase in response to perturbation in phosphatidic acid (PA) and/or diacylglycerol (DAG), both implicated in various INM functions. Nuclear LDs also increase upon downregulation of seipin, a protein that can trap PA and DAG in the endoplasmic reticulum. Notably, both PA and DAG appear to be more densely distributed on the surface of nuclear LDs than in the INM. I propose that nuclear LDs play a role in regulating the PA and DAG level in the INM, thereby contributing to the lipid homeostasis in this compartment.
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Affiliation(s)
- Toyoshi Fujimoto
- Laboratory of Molecular Cell Biology, Research Institute for Diseases of Old Age, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan. mailto:
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4
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Levintov L, Gorai B, Vashisth H. Spontaneous Dimerization and Distinct Packing Modes of Transmembrane Domains in Receptor Tyrosine Kinases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.09.593448. [PMID: 38798363 PMCID: PMC11118388 DOI: 10.1101/2024.05.09.593448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
The insulin receptor (IR) and the insulin-like growth factor-1 receptor (IGF1R) are homodimeric transmembrane glycoproteins that transduce signals across the membrane on binding of extracellular peptide ligands. The structures of IR/IGF1R fragments in apo and liganded states have revealed that the extracellular subunits of these receptors adopt Λ-shaped configurations to which are connected the intracellular tyrosine kinase (TK) domains. The binding of peptide ligands induces structural transitions in the extracellular subunits leading to potential dimerization of transmembrane domains (TMDs) and autophosphorylation in TKs. However, the activation mechanisms of IR/IGF1R, especially the role of TMDs in coordinating signal-inducing structural transitions, remain poorly understood, in part due to the lack of structures of full-length receptors in apo or liganded states. While atomistic simulations of IR/IGF1R TMDs showed that these domains can dimerize in single component membranes, spontaneous unbiased dimerization in a plasma membrane having physiologically representative lipid composition has not been observed. We address this limitation by employing coarse-grained (CG) molecular dynamics simulations to probe the dimerization propensity of IR/IGF1R TMDs. We observed that TMDs in both receptors spontaneously dimerized independent of their initial orientations in their dissociated states, signifying their natural propensity for dimerization. In the dimeric state, IR TMDs predominantly adopted X-shaped configurations with asymmetric helical packing and significant tilt relative to the membrane normal, while IGF1R TMDs adopted symmetric V-shaped or parallel configurations with either no tilt or a small tilt relative to the membrane normal. Our results suggest that IR/IGF1R TMDs spontaneously dimerize and adopt distinct dimerized configurations.
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Affiliation(s)
- Lev Levintov
- Department of Chemical Engineering and Bioengineering, University of New Hampshire, Durham 03824, New Hampshire, USA
| | - Biswajit Gorai
- Institute of Chemistry, Technical University of Berlin, Berlin 10623, Germany
| | - Harish Vashisth
- Department of Chemical Engineering and Bioengineering, University of New Hampshire, Durham 03824, New Hampshire, USA
- Department of Chemistry, University of New Hampshire, Durham 03824, New Hampshire, USA
- Integrated Applied Mathematics Program, University of New Hampshire, Durham 03824, New Hampshire, USA
- Molecular and Cellular Biotechnology Program, University of New Hampshire, Durham 03824, New Hampshire, USA
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5
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Osetrova M, Tkachev A, Mair W, Guijarro Larraz P, Efimova O, Kurochkin I, Stekolshchikova E, Anikanov N, Foo JC, Cazenave-Gassiot A, Mitina A, Ogurtsova P, Guo S, Potashnikova DM, Gulin AA, Vasin AA, Sarycheva A, Vladimirov G, Fedorova M, Kostyukevich Y, Nikolaev E, Wenk MR, Khrameeva EE, Khaitovich P. Lipidome atlas of the adult human brain. Nat Commun 2024; 15:4455. [PMID: 38796479 PMCID: PMC11127996 DOI: 10.1038/s41467-024-48734-y] [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: 12/15/2022] [Accepted: 05/07/2024] [Indexed: 05/28/2024] Open
Abstract
Lipids are the most abundant but poorly explored components of the human brain. Here, we present a lipidome map of the human brain comprising 75 regions, including 52 neocortical ones. The lipidome composition varies greatly among the brain regions, affecting 93% of the 419 analyzed lipids. These differences reflect the brain's structural characteristics, such as myelin content (345 lipids) and cell type composition (353 lipids), but also functional traits: functional connectivity (76 lipids) and information processing hierarchy (60 lipids). Combining lipid composition and mRNA expression data further enhances functional connectivity association. Biochemically, lipids linked with structural and functional brain features display distinct lipid class distribution, unsaturation extent, and prevalence of omega-3 and omega-6 fatty acid residues. We verified our conclusions by parallel analysis of three adult macaque brains, targeted analysis of 216 lipids, mass spectrometry imaging, and lipidome assessment of sorted murine neurons.
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Affiliation(s)
- Maria Osetrova
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Anna Tkachev
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Waltraud Mair
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | | | - Olga Efimova
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Ilia Kurochkin
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | | | | | - Juat Chin Foo
- Singapore Lipidomics Incubator, Life Sciences Institute and Precision Medicine Translational Research Program, Department of Biochemistry, Yong Loo Lin School of Medicine; National University of Singapore, Singapore, Singapore
| | - Amaury Cazenave-Gassiot
- Singapore Lipidomics Incubator, Life Sciences Institute and Precision Medicine Translational Research Program, Department of Biochemistry, Yong Loo Lin School of Medicine; National University of Singapore, Singapore, Singapore
| | | | | | - Song Guo
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Daria M Potashnikova
- Department of Cell Biology and Histology, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Alexander A Gulin
- N. N. Semenov Federal Research Center for Chemical Physics Russian Academy of Sciences, Moscow, Russia
| | - Alexander A Vasin
- N. N. Semenov Federal Research Center for Chemical Physics Russian Academy of Sciences, Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | | | - Gleb Vladimirov
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | | | | | - Evgeny Nikolaev
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Markus R Wenk
- Singapore Lipidomics Incubator, Life Sciences Institute and Precision Medicine Translational Research Program, Department of Biochemistry, Yong Loo Lin School of Medicine; National University of Singapore, Singapore, Singapore.
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6
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Stollmann A, Garcia-Guirado J, Hong JS, Rüedi P, Im H, Lee H, Ortega Arroyo J, Quidant R. Molecular fingerprinting of biological nanoparticles with a label-free optofluidic platform. Nat Commun 2024; 15:4109. [PMID: 38750038 PMCID: PMC11096335 DOI: 10.1038/s41467-024-48132-4] [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: 09/22/2023] [Accepted: 04/22/2024] [Indexed: 05/18/2024] Open
Abstract
Label-free detection of multiple analytes in a high-throughput fashion has been one of the long-sought goals in biosensing applications. Yet, for all-optical approaches, interfacing state-of-the-art label-free techniques with microfluidics tools that can process small volumes of sample with high throughput, and with surface chemistry that grants analyte specificity, poses a critical challenge to date. Here, we introduce an optofluidic platform that brings together state-of-the-art digital holography with PDMS microfluidics by using supported lipid bilayers as a surface chemistry building block to integrate both technologies. Specifically, this platform fingerprints heterogeneous biological nanoparticle populations via a multiplexed label-free immunoaffinity assay with single particle sensitivity. First, we characterise the robustness and performance of the platform, and then apply it to profile four distinct ovarian cell-derived extracellular vesicle populations over a panel of surface protein biomarkers, thus developing a unique biomarker fingerprint for each cell line. We foresee that our approach will find many applications where routine and multiplexed characterisation of biological nanoparticles are required.
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Affiliation(s)
- Alexia Stollmann
- Nanophotonic Systems Laboratory, Department of Mechanical and Process Engineering, ETH Zurich, 8092, Zurich, Switzerland
| | - Jose Garcia-Guirado
- Nanophotonic Systems Laboratory, Department of Mechanical and Process Engineering, ETH Zurich, 8092, Zurich, Switzerland
| | - Jae-Sang Hong
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Pascal Rüedi
- Nanophotonic Systems Laboratory, Department of Mechanical and Process Engineering, ETH Zurich, 8092, Zurich, Switzerland
| | - Hyungsoon Im
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Hakho Lee
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Jaime Ortega Arroyo
- Nanophotonic Systems Laboratory, Department of Mechanical and Process Engineering, ETH Zurich, 8092, Zurich, Switzerland.
| | - Romain Quidant
- Nanophotonic Systems Laboratory, Department of Mechanical and Process Engineering, ETH Zurich, 8092, Zurich, Switzerland.
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7
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Griseti E, Bello AA, Bieth E, Sabbagh B, Iacovoni JS, Bigay J, Laurell H, Čopič A. Molecular mechanisms of perilipin protein function in lipid droplet metabolism. FEBS Lett 2024; 598:1170-1198. [PMID: 38140813 DOI: 10.1002/1873-3468.14792] [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: 10/21/2023] [Revised: 11/27/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023]
Abstract
Perilipins are abundant lipid droplet (LD) proteins present in all metazoans and also in Amoebozoa and fungi. Humans express five perilipins, which share a similar domain organization: an amino-terminal PAT domain and an 11-mer repeat region, which can fold into amphipathic helices that interact with LDs, followed by a structured carboxy-terminal domain. Variations of this organization that arose during vertebrate evolution allow for functional specialization between perilipins in relation to the metabolic needs of different tissues. We discuss how different features of perilipins influence their interaction with LDs and their cellular targeting. PLIN1 and PLIN5 play a direct role in lipolysis by regulating the recruitment of lipases to LDs and LD interaction with mitochondria. Other perilipins, particularly PLIN2, appear to protect LDs from lipolysis, but the molecular mechanism is not clear. PLIN4 stands out with its long repetitive region, whereas PLIN3 is most widely expressed and is used as a nascent LD marker. Finally, we discuss the genetic variability in perilipins in connection with metabolic disease, prominent for PLIN1 and PLIN4, underlying the importance of understanding the molecular function of perilipins.
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Affiliation(s)
- Elena Griseti
- Institut des Maladies Métaboliques et Cardiovasculaires - I2MC, Université de Toulouse, Inserm, Université Toulouse III - Paul Sabatier (UPS), France
| | - Abdoul Akim Bello
- Institut de Pharmacologie Moléculaire et Cellulaire - IPMC, Université Côte d'Azur, CNRS, Valbonne, France
| | - Eric Bieth
- Institut des Maladies Métaboliques et Cardiovasculaires - I2MC, Université de Toulouse, Inserm, Université Toulouse III - Paul Sabatier (UPS), France
- Departement de Génétique Médicale, Centre Hospitalier Universitaire de Toulouse, France
| | - Bayane Sabbagh
- Centre de Recherche en Biologie Cellulaire de Montpellier - CRBM, Université de Montpellier, CNRS, France
| | - Jason S Iacovoni
- Institut des Maladies Métaboliques et Cardiovasculaires - I2MC, Université de Toulouse, Inserm, Université Toulouse III - Paul Sabatier (UPS), France
| | - Joëlle Bigay
- Institut de Pharmacologie Moléculaire et Cellulaire - IPMC, Université Côte d'Azur, CNRS, Valbonne, France
| | - Henrik Laurell
- Institut des Maladies Métaboliques et Cardiovasculaires - I2MC, Université de Toulouse, Inserm, Université Toulouse III - Paul Sabatier (UPS), France
| | - Alenka Čopič
- Centre de Recherche en Biologie Cellulaire de Montpellier - CRBM, Université de Montpellier, CNRS, France
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8
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Gunwant V, Gahtori P, Varanasi SR, Pandey R. Protein-Mediated Changes in Membrane Fluidity and Ordering: Insights into the Molecular Mechanism and Implications for Cellular Function. J Phys Chem Lett 2024; 15:4408-4415. [PMID: 38625684 DOI: 10.1021/acs.jpclett.3c03627] [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: 04/17/2024]
Abstract
Probing protein-membrane interactions is vital for understanding biological functionality for various applications such as drug development, targeted drug delivery, and creation of functional biomaterials for medical and industrial purposes. In this study, we have investigated interaction of Human Serum Albumin (HSA) with two different lipids, dipalmitoylphosphatidylglycerol (dDPPG) and dipalmitoylphosphatidylcholine (dDPPC), using Vibrational Sum Frequency Generation spectroscopy at different membrane fluidity values. In the liquid-expanded (LE) state of the lipid, HSA (at pH 3.5) deeply intercalated lipid chains through a combination of electrostatic and hydrophobic interactions, which resulted in more ordering of the lipid chains. However, in the liquid-condensed (LC) state, protein intercalation is decreased due to tighter lipid packing. Moreover, our findings revealed distinct differences in HSA's interaction with dDPPG and dDPPC lipids. The interaction with dDPPC remained relatively weak compared to dDPPG. These results shed light on the significance of protein mediated changes in lipid characteristics, which hold considerable implications for understanding membrane protein behavior, lipid-mediated cellular processes, and lipid-based biomaterial design.
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Affiliation(s)
- Vineet Gunwant
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Preeti Gahtori
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Srinivasa Rao Varanasi
- Department of Physics, Sultan Qaboos University, P.O. Box 36, Al-Khoud 123, Muscat, Oman
| | - Ravindra Pandey
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
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9
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van der Pol RI, Brinkmann BW, Sevink GJA. Analyzing Lipid Membrane Defects via a Coarse-Grained to Triangulated Surface Map: The Role of Lipid Order and Local Curvature in Molecular Binding. J Chem Theory Comput 2024; 20:2888-2900. [PMID: 38537131 PMCID: PMC11008102 DOI: 10.1021/acs.jctc.4c00082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/14/2024] [Accepted: 03/14/2024] [Indexed: 04/10/2024]
Abstract
Lipid packing defects are known to serve as quantitative indicators for protein binding to lipid membranes. This paper presents a protocol for mapping molecular lipid detail onto a triangulated continuum leaflet representation. Besides establishing the desired forward counterpart to the existing inverse TS2CG map, this coarse-grained to triangulated surface (CG2TS) map enables straightforward extraction of the defect characteristics for any membrane geometry found in nature. We have applied our protocol to investigate the role of local curvature and varying lipid packing on the defect constant π. We find that the defect size is greatly influenced by both factors, arguing strongly against the usual assignment of a single defect constant in the case of more realistic membrane conditions. An important discovery is that lipids in the gel phase produce larger defects, or a higher π, in domains of high (local) curvature than the same lipid in a liquid phase of any curvature. This finding suggests that membranes featuring very ordered lipid packing can bind proteins via large defects in curved regions. Finally, we propose a route for estimating defect constants directly from the standard membrane properties. Identifying the precise role of composition, lipid (tail) order, and (local) curvature in defects for the irregular lipid structures that are (temporally) present in many biological processes is instrumental for obtaining fundamental insight as well as for a rational design of membrane binding targets.
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Affiliation(s)
- Rianne
W. I. van der Pol
- Leiden
Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Bregje W. Brinkmann
- Institute
of Environmental Sciences, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - G. J. Agur Sevink
- Leiden
Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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10
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Kang C, Fujioka K, Sun R. Atomistic Insight into the Lipid Nanodomains of Synaptic Vesicles. J Phys Chem B 2024; 128:2707-2716. [PMID: 38325816 DOI: 10.1021/acs.jpcb.3c07982] [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: 02/09/2024]
Abstract
Membrane curvature, once regarded as a passive consequence of membrane composition and cellular architecture, has been shown to actively modulate various properties of the cellular membrane. These changes could also lead to segregation of the constituents of the membrane, generating nanodomains with precise biological properties. Proteins often linked with neurodegeneration (e.g., tau, alpha-synuclein) exhibit an unintuitive affinity for synaptic vesicles in neurons, which are reported to lack distinct, ordered nanodomains based on their composition. In this study, all-atom molecular dynamics simulations are used to study a full-scale synaptic vesicle of realistic Gaussian curvature and its effect on the membrane dynamics and lipid nanodomain organization. Compelling indicators of nanodomain formation, from the perspective of composition, surface areas per lipid, order parameter, and domain lifetime, are identified in the vesicle membrane, which are absent in a flat bilayer of the same lipid composition. Therefore, our study supports the idea that curvature may induce phase separation in an otherwise fluid, disordered membrane.
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Affiliation(s)
- Christopher Kang
- Department of Chemistry, The University of Hawai'i, Ma̅noa, 2545 McCarthy Mall, Honolulu, Hawaii 96822, United States
| | - Kazuumi Fujioka
- Department of Chemistry, The University of Hawai'i, Ma̅noa, 2545 McCarthy Mall, Honolulu, Hawaii 96822, United States
| | - Rui Sun
- Department of Chemistry, The University of Hawai'i, Ma̅noa, 2545 McCarthy Mall, Honolulu, Hawaii 96822, United States
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11
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Papadopoulou P, van der Pol R, van Hilten N, van Os WL, Pattipeiluhu R, Arias-Alpizar G, Knol RA, Noteborn W, Moradi MA, Ferraz MJ, Aerts JMFG, Sommerdijk N, Campbell F, Risselada HJ, Sevink GJA, Kros A. Phase-Separated Lipid-Based Nanoparticles: Selective Behavior at the Nano-Bio Interface. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2310872. [PMID: 37988682 DOI: 10.1002/adma.202310872] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Indexed: 11/23/2023]
Abstract
The membrane-protein interface on lipid-based nanoparticles influences their in vivo behavior. Better understanding may evolve current drug delivery methods toward effective targeted nanomedicine. Previously, the cell-selective accumulation of a liposome formulation in vivo is demonstrated, through the recognition of lipid phase-separation by triglyceride lipases. This exemplified how liposome morphology and composition can determine nanoparticle-protein interactions. Here, the lipase-induced compositional and morphological changes of phase-separated liposomes-which bear a lipid droplet in their bilayer- are investigated, and the mechanism upon which lipases recognize and bind to the particles is unravelled. The selective lipolytic degradation of the phase-separated lipid droplet is observed, while nanoparticle integrity remains intact. Next, the Tryptophan-rich loop of the lipase is identified as the region with which the enzymes bind to the particles. This preferential binding is due to lipid packing defects induced on the liposome surface by phase separation. In parallel, the existing knowledge that phase separation leads to in vivo selectivity, is utilized to generate phase-separated mRNA-LNPs that target cell-subsets in zebrafish embryos, with subsequent mRNA delivery and protein expression. Together, these findings can expand the current knowledge on selective nanoparticle-protein communications and in vivo behavior, aspects that will assist to gain control of lipid-based nanoparticles.
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Affiliation(s)
- Panagiota Papadopoulou
- Department of Supramolecular & Biomaterials Chemistry, Leiden Institute of Chemistry (LIC), Leiden University, P. O. Box 9502, Leiden, 2300 RA, The Netherlands
| | - Rianne van der Pol
- Department of Supramolecular & Biomaterials Chemistry, Leiden Institute of Chemistry (LIC), Leiden University, P. O. Box 9502, Leiden, 2300 RA, The Netherlands
| | - Niek van Hilten
- Department of Supramolecular & Biomaterials Chemistry, Leiden Institute of Chemistry (LIC), Leiden University, P. O. Box 9502, Leiden, 2300 RA, The Netherlands
| | - Winant L van Os
- Department of Supramolecular & Biomaterials Chemistry, Leiden Institute of Chemistry (LIC), Leiden University, P. O. Box 9502, Leiden, 2300 RA, The Netherlands
| | - Roy Pattipeiluhu
- Department of Supramolecular & Biomaterials Chemistry, Leiden Institute of Chemistry (LIC), Leiden University, P. O. Box 9502, Leiden, 2300 RA, The Netherlands
| | - Gabriela Arias-Alpizar
- Department of Supramolecular & Biomaterials Chemistry, Leiden Institute of Chemistry (LIC), Leiden University, P. O. Box 9502, Leiden, 2300 RA, The Netherlands
| | - Renzo Aron Knol
- Department of Supramolecular & Biomaterials Chemistry, Leiden Institute of Chemistry (LIC), Leiden University, P. O. Box 9502, Leiden, 2300 RA, The Netherlands
| | - Willem Noteborn
- NeCEN, Leiden University, Einsteinweg 55, Leiden, 2333 AL, The Netherlands
| | - Mohammad-Amin Moradi
- Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, P. O. Box 513, Eindhoven, 5600 MB, The Netherlands
| | - Maria Joao Ferraz
- Department of Medical Biochemistry, Leiden Institute of Chemistry (LIC), Leiden University, P. O. Box 9502, Leiden, 2300 RA, The Netherlands
| | | | - Nico Sommerdijk
- Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, P. O. Box 513, Eindhoven, 5600 MB, The Netherlands
- Department of Medical BioSciences and Radboud Technology Center - Electron Microscopy, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
| | - Frederick Campbell
- Department of Supramolecular & Biomaterials Chemistry, Leiden Institute of Chemistry (LIC), Leiden University, P. O. Box 9502, Leiden, 2300 RA, The Netherlands
| | - Herre Jelger Risselada
- Department of Supramolecular & Biomaterials Chemistry, Leiden Institute of Chemistry (LIC), Leiden University, P. O. Box 9502, Leiden, 2300 RA, The Netherlands
- Department of Physics, Technical University Dortmund, 44221, Dortmund, Germany
| | - Geert Jan Agur Sevink
- Department of Biophysical Organic Chemistry, Leiden Institute of Chemistry (LIC), Leiden University, P. O. Box 9502, Leiden, 2300 RA, The Netherlands
| | - Alexander Kros
- Department of Supramolecular & Biomaterials Chemistry, Leiden Institute of Chemistry (LIC), Leiden University, P. O. Box 9502, Leiden, 2300 RA, The Netherlands
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12
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Pajtinka P, Vácha R. Amphipathic Helices Can Sense Both Positive and Negative Curvatures of Lipid Membranes. J Phys Chem Lett 2024; 15:175-179. [PMID: 38153203 PMCID: PMC10788957 DOI: 10.1021/acs.jpclett.3c02785] [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: 10/06/2023] [Revised: 12/09/2023] [Accepted: 12/19/2023] [Indexed: 12/29/2023]
Abstract
Curvature sensing is an essential ability of biomolecules to preferentially localize to membrane regions of a specific curvature. It has been shown that amphipathic helices (AHs), helical peptides with both hydrophilic and hydrophobic regions, could sense a positive membrane curvature. The origin of this AH sensing has been attributed to their ability to exploit lipid-packing defects that are enhanced in regions of positive curvature. In this study, we revisit an alternative framework where AHs act as sensors of local internal stress within the membrane, suggesting the possibility of an AH sensing a negative membrane curvature. Using molecular dynamics simulations, we gradually tuned the hydrophobicity of AHs, thereby adjusting their insertion depth so that the curvature preference of AHs is switched from positive to negative. This study suggests that highly hydrophobic AHs could preferentially localize proteins to regions of a negative membrane curvature.
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Affiliation(s)
- Peter Pajtinka
- CEITEC
− Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
- National
Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Robert Vácha
- CEITEC
− Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
- National
Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
- Department
of Condensed Matter Physics, Faculty of Science, Masaryk University, Kotlářská 267/2, 611 37 Brno, Czech
Republic
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13
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Li XH, Yu CWH, Gomez-Navarro N, Stancheva V, Zhu H, Murthy A, Wozny M, Malhotra K, Johnson CM, Blackledge M, Santhanam B, Liu W, Huang J, Freund SMV, Miller EA, Babu MM. Dynamic conformational changes of a tardigrade group-3 late embryogenesis abundant protein modulate membrane biophysical properties. PNAS NEXUS 2024; 3:pgae006. [PMID: 38269070 PMCID: PMC10808001 DOI: 10.1093/pnasnexus/pgae006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 12/26/2023] [Indexed: 01/26/2024]
Abstract
A number of intrinsically disordered proteins (IDPs) encoded in stress-tolerant organisms, such as tardigrade, can confer fitness advantage and abiotic stress tolerance when heterologously expressed. Tardigrade-specific disordered proteins including the cytosolic-abundant heat-soluble proteins are proposed to confer stress tolerance through vitrification or gelation, whereas evolutionarily conserved IDPs in tardigrades may contribute to stress tolerance through other biophysical mechanisms. In this study, we characterized the mechanism of action of an evolutionarily conserved, tardigrade IDP, HeLEA1, which belongs to the group-3 late embryogenesis abundant (LEA) protein family. HeLEA1 homologs are found across different kingdoms of life. HeLEA1 is intrinsically disordered in solution but shows a propensity for helical structure across its entire sequence. HeLEA1 interacts with negatively charged membranes via dynamic disorder-to-helical transition, mainly driven by electrostatic interactions. Membrane interaction of HeLEA1 is shown to ameliorate excess surface tension and lipid packing defects. HeLEA1 localizes to the mitochondrial matrix when expressed in yeast and interacts with model membranes mimicking inner mitochondrial membrane. Yeast expressing HeLEA1 shows enhanced tolerance to hyperosmotic stress under nonfermentative growth and increased mitochondrial membrane potential. Evolutionary analysis suggests that although HeLEA1 homologs have diverged their sequences to localize to different subcellular organelles, all homologs maintain a weak hydrophobic moment that is characteristic of weak and reversible membrane interaction. We suggest that such dynamic and weak protein-membrane interaction buffering alterations in lipid packing could be a conserved strategy for regulating membrane properties and represent a general biophysical solution for stress tolerance across the domains of life.
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Affiliation(s)
- Xiao-Han Li
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Conny W H Yu
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | | | | | - Hongni Zhu
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Andal Murthy
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Michael Wozny
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Ketan Malhotra
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | | | - Martin Blackledge
- Université Grenoble Alpes, CNRS, Commissariat à l’Energie Atomique et aux Energies Alternatives, Institut de Biologie Structurale, 38000 Grenoble, France
| | - Balaji Santhanam
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
- Department of Structural Biology, Center of Excellence for Data-Driven Discovery, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Wei Liu
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Jinqing Huang
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | | | | | - M Madan Babu
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
- Department of Structural Biology, Center of Excellence for Data-Driven Discovery, St Jude Children's Research Hospital, Memphis, TN 38105, USA
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14
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Lira RB, Hammond JCF, Cavalcanti RRM, Rous M, Riske KA, Roos WH. The underlying mechanical properties of membranes tune their ability to fuse. J Biol Chem 2023; 299:105430. [PMID: 37926280 PMCID: PMC10716014 DOI: 10.1016/j.jbc.2023.105430] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 10/16/2023] [Accepted: 10/23/2023] [Indexed: 11/07/2023] Open
Abstract
Membrane fusion is a ubiquitous process associated with a multitude of biological events. Although it has long been appreciated that membrane mechanics plays an important role in membrane fusion, the molecular interplay between mechanics and fusion has remained elusive. For example, although different lipids modulate membrane mechanics differently, depending on their composition, molar ratio, and complex interactions, differing lipid compositions may lead to similar mechanical properties. This raises the question of whether (i) the specific lipid composition or (ii) the average mesoscale mechanics of membranes acts as the determining factor for cellular function. Furthermore, little is known about the potential consequences of fusion on membrane disruption. Here, we use a combination of confocal microscopy, time-resolved imaging, and electroporation to shed light onto the underlying mechanical properties of membranes that regulate membrane fusion. Fusion efficiency follows a nearly universal behavior that depends on membrane fluidity parameters, such as membrane viscosity and bending rigidity, rather than on specific lipid composition. This helps explaining why the charged and fluid membranes of the inner leaflet of the plasma membrane are more fusogenic than their outer counterparts. Importantly, we show that physiological levels of cholesterol, a key component of biological membranes, has a mild effect on fusion but significantly enhances membrane mechanical stability against pore formation, suggesting that its high cellular levels buffer the membrane against disruption. The ability of membranes to efficiently fuse while preserving their integrity may have given evolutionary advantages to cells by enabling their function while preserving membrane stability.
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Affiliation(s)
- Rafael B Lira
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, Netherlands.
| | - Jayna C F Hammond
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, Netherlands
| | | | - Madelief Rous
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, Netherlands
| | - Karin A Riske
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Wouter H Roos
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, Netherlands.
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15
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Balleza D. Peptide Flexibility and the Hydrophobic Moment are Determinants to Evaluate the Clinical Potential of Magainins. J Membr Biol 2023; 256:317-330. [PMID: 37097306 DOI: 10.1007/s00232-023-00286-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 04/05/2023] [Indexed: 04/26/2023]
Abstract
Using a flexibility prediction algorithm and in silico structural modeling, we have calculated the intrinsic flexibility of several magainin derivatives. In the case of magainin-2 (Mag-2) and magainin H2 (MAG-H2) we have found that MAG-2 is more flexible than its hydrophobic analog, Mag-H2. This affects the degree of bending of both peptides, with a kink around two central residues (R10, R11), whereas, in Mag-H2, W10 stiffens the peptide. Moreover, this increases the hydrophobic moment of Mag-H2, which could explain its propensity to form pores in POPC model membranes, which exhibit near-to-zero spontaneous curvatures. Likewise, the protective effect described in DOPC membranes for this peptide regarding its facilitation in pore formation would be related to the propensity of this lipid to form membranes with negative spontaneous curvature. The flexibility of another magainin analog (MSI-78) is even greater than that of Mag-2. This facilitates the peptide to present a kind of hinge around the central F12 as well as a C-terminal end prone to be disordered. Such characteristics are key to understanding the broad-spectrum antimicrobial actions exhibited by this peptide. These data reinforce the hypothesis on the determinant role of spontaneous membrane curvature, intrinsic peptide flexibility, and specific hydrophobic moment in assessing the bioactivity of membrane-active antimicrobial peptides.
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Affiliation(s)
- Daniel Balleza
- Laboratorio de Microbiología, Unidad de Investigación y Desarrollo en Alimentos, Instituto Tecnológico de Veracruz, Tecnológico Nacional de México, Veracruz, Mexico.
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16
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Wilkins AA, Schwarz B, Torres-Escobar A, Castore R, Landry L, Latimer B, Bohrnsen E, Bosio CM, Dragoi AM, Ivanov SS. The intracellular growth of the vacuolar pathogen Legionella pneumophila is dependent on the acyl chain composition of host membranes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.19.567753. [PMID: 38045297 PMCID: PMC10690232 DOI: 10.1101/2023.11.19.567753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Legionella pneumophila is an accidental human bacterial pathogen that infects and replicates within alveolar macrophages causing a severe atypical pneumonia known as Legionnaires' disease. As a prototypical vacuolar pathogen L. pneumophila establishes a unique endoplasmic reticulum (ER)-derived organelle within which bacterial replication takes place. Bacteria-derived proteins are deposited in the host cytosol and in the lumen of the pathogen-occupied vacuole via a type IVb (T4bSS) and a type II (T2SS) secretion system respectively. These secretion system effector proteins manipulate multiple host functions to facilitate intracellular survival of the bacteria. Subversion of host membrane glycerophospholipids (GPLs) by the internalized bacteria via distinct mechanisms feature prominently in trafficking and biogenesis of the Legionella -containing vacuole (LCV). Conventional GPLs composed of a glycerol backbone linked to a polar headgroup and esterified with two fatty acids constitute the bulk of membrane lipids in eukaryotic cells. The acyl chain composition of GPLs dictates phase separation of the lipid bilayer and therefore determines the physiochemical properties of biological membranes - such as membrane disorder, fluidity and permeability. In mammalian cells, fatty acids esterified in membrane GPLs are sourced endogenously from de novo synthesis or via internalization from the exogenous pool of lipids present in serum and other interstitial fluids. Here, we exploited the preferential utilization of exogenous fatty acids for GPL synthesis by macrophages to reprogram the acyl chain composition of host membranes and investigated its impact on LCV homeostasis and L. pneumophila intracellular replication. Using saturated fatty acids as well as cis - and trans - isomers of monounsaturated fatty acids we discovered that under conditions promoting lipid packing and membrane rigidification L. pneumophila intracellular replication was significantly reduced. Palmitoleic acid - a C16:1 monounsaturated fatty acid - that promotes membrane disorder when enriched in GPLs significantly increased bacterial replication within human and murine macrophages but not in axenic growth assays. Lipidome analysis of infected macrophages showed that treatment with exogenous palmitoleic acid resulted in membrane acyl chain reprogramming in a manner that promotes membrane disorder and live-cell imaging revealed that the consequences of increasing membrane disorder impinge on several LCV homeostasis parameters. Collectively, we provide experimental evidence that L. pneumophila replication within its intracellular niche is a function of the lipid bilayer disorder and hydrophobic thickness.
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17
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Lee S, Carrasquillo Rodríguez JW, Merta H, Bahmanyar S. A membrane-sensing mechanism links lipid metabolism to protein degradation at the nuclear envelope. J Cell Biol 2023; 222:e202304026. [PMID: 37382667 PMCID: PMC10309186 DOI: 10.1083/jcb.202304026] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/22/2023] [Accepted: 06/02/2023] [Indexed: 06/30/2023] Open
Abstract
Lipid composition determines organelle identity; however, whether the lipid composition of the inner nuclear membrane (INM) domain of the ER contributes to its identity is not known. Here, we show that the INM lipid environment of animal cells is under local control by CTDNEP1, the master regulator of the phosphatidic acid phosphatase lipin 1. Loss of CTDNEP1 reduces association of an INM-specific diacylglycerol (DAG) biosensor and results in a decreased percentage of polyunsaturated containing DAG species. Alterations in DAG metabolism impact the levels of the resident INM protein Sun2, which is under local proteasomal regulation. We identify a lipid-binding amphipathic helix (AH) in the nucleoplasmic domain of Sun2 that prefers membrane packing defects. INM dissociation of the Sun2 AH is linked to its proteasomal degradation. We suggest that direct lipid-protein interactions contribute to sculpting the INM proteome and that INM identity is adaptable to lipid metabolism, which has broad implications on disease mechanisms associated with the nuclear envelope.
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Affiliation(s)
- Shoken Lee
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | | | - Holly Merta
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Shirin Bahmanyar
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT, USA
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18
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Tripathy M, Srivastava A. Lipid packing in biological membranes governs protein localization and membrane permeability. Biophys J 2023; 122:2727-2743. [PMID: 37254482 PMCID: PMC10397809 DOI: 10.1016/j.bpj.2023.05.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 04/18/2023] [Accepted: 05/25/2023] [Indexed: 06/01/2023] Open
Abstract
Plasma membrane (PM) heterogeneity has long been implicated in various cellular functions. However, mechanistic principles governing functional regulations of lipid environment are not well understood due to the inherent complexities associated with the relevant length and timescales that limit both direct experimental measurements and their interpretation. In this context, computer simulations hold immense potential to investigate molecular-level interactions and mechanisms that lead to PM heterogeneity and its functions. Herein, we investigate spatial and dynamic heterogeneity in model membranes with coexisting liquid ordered and liquid disordered phases and characterize the membrane order in terms of the local topological changes in lipid environment using the nonaffine deformation framework. Furthermore, we probe the packing defects in these membranes, which can be considered as the conjugate of membrane order assessed in terms of the nonaffine parameter. In doing so, we formalize the connection between membrane packing and local membrane order and use that to explore the mechanistic principles behind their functions. Our observations suggest that heterogeneity in mixed phase membranes is a consequence of local lipid topology and its temporal evolution, which give rise to disparate lipid packing in ordered and disordered domains. This in turn governs the distinct nature of packing defects in these domains that can play a crucial role in preferential localization of proteins in mixed phase membranes. Furthermore, we observe that lipid packing also leads to contrasting distribution of free volume in the membrane core region in ordered and disordered membranes, which can lead to distinctive membrane permeability of small molecules. Our results, thus, indicate that heterogeneity in mixed phase membranes closely governs the membrane functions that may emerge from packing-related basic design principles.
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Affiliation(s)
- Madhusmita Tripathy
- Molecular Biophysics Unit, Indian Institute of Science Bangalore, Bangalore, Karnataka, India.
| | - Anand Srivastava
- Molecular Biophysics Unit, Indian Institute of Science Bangalore, Bangalore, Karnataka, India.
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19
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Zhukov A, Popov V. Eukaryotic Cell Membranes: Structure, Composition, Research Methods and Computational Modelling. Int J Mol Sci 2023; 24:11226. [PMID: 37446404 DOI: 10.3390/ijms241311226] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/03/2023] [Accepted: 07/06/2023] [Indexed: 07/15/2023] Open
Abstract
This paper deals with the problems encountered in the study of eukaryotic cell membranes. A discussion on the structure and composition of membranes, lateral heterogeneity of membranes, lipid raft formation, and involvement of actin and cytoskeleton networks in the maintenance of membrane structure is included. Modern methods for the study of membranes and their constituent domains are discussed. Various simplified models of biomembranes and lipid rafts are presented. Computer modelling is considered as one of the most important methods. This is stated that from the study of the plasma membrane structure, it is desirable to proceed to the diverse membranes of all organelles of the cell. The qualitative composition and molar content of individual classes of polar lipids, free sterols and proteins in each of these membranes must be considered. A program to create an open access electronic database including results obtained from the membrane modelling of individual cell organelles and the key sites of the membranes, as well as models of individual molecules composing the membranes, has been proposed.
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Affiliation(s)
- Anatoly Zhukov
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street 35, 127276 Moscow, Russia
| | - Valery Popov
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street 35, 127276 Moscow, Russia
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20
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Sosa Ponce ML, Remedios MH, Moradi-Fard S, Cobb JA, Zaremberg V. SIR telomere silencing depends on nuclear envelope lipids and modulates sensitivity to a lysolipid. J Cell Biol 2023; 222:e202206061. [PMID: 37042812 PMCID: PMC10103788 DOI: 10.1083/jcb.202206061] [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: 06/13/2022] [Revised: 11/29/2022] [Accepted: 03/24/2023] [Indexed: 04/13/2023] Open
Abstract
The nuclear envelope (NE) is important in maintaining genome organization. The role of lipids in communication between the NE and telomere regulation was investigated, including how changes in lipid composition impact gene expression and overall nuclear architecture. Yeast was treated with the non-metabolizable lysophosphatidylcholine analog edelfosine, known to accumulate at the perinuclear ER. Edelfosine induced NE deformation and disrupted telomere clustering but not anchoring. Additionally, the association of Sir4 at telomeres decreased. RNA-seq analysis showed altered expression of Sir-dependent genes located at sub-telomeric (0-10 kb) regions, consistent with Sir4 dispersion. Transcriptomic analysis revealed that two lipid metabolic circuits were activated in response to edelfosine, one mediated by the membrane sensing transcription factors, Spt23/Mga2, and the other by a transcriptional repressor, Opi1. Activation of these transcriptional programs resulted in higher levels of unsaturated fatty acids and the formation of nuclear lipid droplets. Interestingly, cells lacking Sir proteins displayed resistance to unsaturated-fatty acids and edelfosine, and this phenotype was connected to Rap1.
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Affiliation(s)
| | | | - Sarah Moradi-Fard
- Departments of Biochemistry and Molecular Biology and Oncology, Cumming School of Medicine, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Calgary, Canada
| | - Jennifer A. Cobb
- Departments of Biochemistry and Molecular Biology and Oncology, Cumming School of Medicine, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Calgary, Canada
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, Canada
| | - Vanina Zaremberg
- Department of Biological Sciences, University of Calgary, Calgary, Canada
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21
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Choi YM, Ajjaji D, Fleming KD, Borbat PP, Jenkins ML, Moeller BE, Fernando S, Bhatia SR, Freed JH, Burke JE, Thiam AR, Airola MV. Structural insights into perilipin 3 membrane association in response to diacylglycerol accumulation. Nat Commun 2023; 14:3204. [PMID: 37268630 PMCID: PMC10238389 DOI: 10.1038/s41467-023-38725-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 05/12/2023] [Indexed: 06/04/2023] Open
Abstract
Lipid droplets (LDs) are dynamic organelles that contain an oil core mainly composed of triglycerides (TAG) that is surrounded by a phospholipid monolayer and LD-associated proteins called perilipins (PLINs). During LD biogenesis, perilipin 3 (PLIN3) is recruited to nascent LDs as they emerge from the endoplasmic reticulum. Here, we analyze how lipid composition affects PLIN3 recruitment to membrane bilayers and LDs, and the structural changes that occur upon membrane binding. We find that the TAG precursors phosphatidic acid and diacylglycerol (DAG) recruit PLIN3 to membrane bilayers and define an expanded Perilipin-ADRP-Tip47 (PAT) domain that preferentially binds DAG-enriched membranes. Membrane binding induces a disorder to order transition of alpha helices within the PAT domain and 11-mer repeats, with intramolecular distance measurements consistent with the expanded PAT domain adopting a folded but dynamic structure upon membrane binding. In cells, PLIN3 is recruited to DAG-enriched ER membranes, and this requires both the PAT domain and 11-mer repeats. This provides molecular details of PLIN3 recruitment to nascent LDs and identifies a function of the PAT domain of PLIN3 in DAG binding.
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Affiliation(s)
- Yong Mi Choi
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Dalila Ajjaji
- Laboratoire de Physique de l'École normale supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université Paris Cité, F-75005, Paris, France
| | - Kaelin D Fleming
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8N 1A1, Canada
| | - Peter P Borbat
- National Biomedical Resource for Advanced Electron Spin Resonance Technology (ACERT), Cornell University, Ithaca, NY, 14853, USA
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Meredith L Jenkins
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8N 1A1, Canada
| | - Brandon E Moeller
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8N 1A1, Canada
| | - Shaveen Fernando
- Department of Chemistry, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Surita R Bhatia
- Department of Chemistry, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Jack H Freed
- National Biomedical Resource for Advanced Electron Spin Resonance Technology (ACERT), Cornell University, Ithaca, NY, 14853, USA
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8N 1A1, Canada.
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada.
| | - Abdou Rachid Thiam
- Laboratoire de Physique de l'École normale supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université Paris Cité, F-75005, Paris, France.
| | - Michael V Airola
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, 11794, USA.
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22
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Kawano K, Kamasaka K, Yokoyama F, Kawamoto J, Ogawa T, Kurihara T, Matsuzaki K. Structural factors governing binding of curvature-sensing peptides to bacterial extracellular vesicles covered with hydrophilic polysaccharide chains. Biophys Chem 2023; 299:107039. [PMID: 37209609 DOI: 10.1016/j.bpc.2023.107039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/27/2023] [Accepted: 05/08/2023] [Indexed: 05/22/2023]
Abstract
Extracellular vesicles (EVs) have attracted an attention as important targets in the fields of biology and medical science because they contain physiologically active molecules. Curvature-sensing peptides are currently used as novel tools for marker-independent EV detection techniques. A structure-activity correlation study demonstrated that the α-helicity of the peptides is prominently involved in peptide binding to vesicles. However, whether a flexible structure changing from a random coil to an α-helix upon binding to vesicles or a restricted α-helical structure is an important factor in the detection of biogenic vesicles is still unclear. To address this issue, we compared the binding affinities of stapled and unstapled peptides for bacterial EVs with different surface polysaccharide chains. We found that unstapled peptides showed similar binding affinities for bacterial EVs regardless of surface polysaccharide chains, whereas stapled peptides showed substantially decreased binding affinities for bacterial EVs covered with capsular polysaccharides. This is probably because curvature-sensing peptides must pass through the layer of hydrophilic polysaccharide chains prior to binding to the hydrophobic membrane surface. While stapled peptides with restricted structures cannot easily pass through the layer of polysaccharide chains, unstapled peptides with flexible structures can easily approach the membrane surface. Therefore, we concluded that the structural flexibility of curvature-sensing peptides is a key factor for governing the highly sensitive detection of bacterial EVs.
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Affiliation(s)
- Kenichi Kawano
- Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan.
| | - Kouhei Kamasaka
- Institute for Chemical Research, Kyoto University, Gokasho, Uji 611-0011, Japan
| | - Fumiaki Yokoyama
- Institute for Chemical Research, Kyoto University, Gokasho, Uji 611-0011, Japan; Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Jun Kawamoto
- Institute for Chemical Research, Kyoto University, Gokasho, Uji 611-0011, Japan
| | - Takuya Ogawa
- Institute for Chemical Research, Kyoto University, Gokasho, Uji 611-0011, Japan
| | - Tatsuo Kurihara
- Institute for Chemical Research, Kyoto University, Gokasho, Uji 611-0011, Japan
| | - Katsumi Matsuzaki
- Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
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23
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Sikdar S, Rani G, Vemparala S. Role of Lipid Packing Defects in Determining Membrane Interactions of Antimicrobial Polymers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:4406-4412. [PMID: 36920370 DOI: 10.1021/acs.langmuir.3c00031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Understanding the emergence and role of lipid packing defects in the detection and subsequent partitioning of antimicrobial agents into bacterial membranes is essential for gaining insights into general antimicrobial mechanisms. Herein, using methacrylate polymers as a model platform, we investigate the effects of inclusion of various functional groups in the biomimetic antimicrobial polymer design on the aspects of lipid packing defects in model bacterial membranes. Two antimicrobial polymers are considered: ternary polymers composed of cationic, hydrophobic, and polar moieties and binary polymers with only cationic and hydrophobic moieties. We find that differing modes of insertion of these two polymers lead to different packing defects in the bacterial membrane. While insertion of both binary and ternary polymers leads to an enhanced number of deep defects in the upper leaflet, shallow defects are moderately enhanced upon interaction with ternary polymers only. We provide conclusive evidence that insertion of antimicrobial polymers in bacterial membrane is preceded by sensing of interfacial lipid packing defects. Our simulation results show that the hydrophobic groups are inserted at a single colocalized deep defect site for both binary and ternary polymers. However, the presence of polar groups in the ternary polymers use the shallow defects close to the lipid-water interface, in addition, to insert into the membrane, which leads to a more folded conformation of the ternary polymer in the membrane environment, and hence a different membrane partitioning mechanism compared to the binary polymer, which acquires an amphiphilic conformation.
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Affiliation(s)
- Samapan Sikdar
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai 600113, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India
| | - Garima Rani
- Department of Physics and Materials Science, University of Luxembourg, Luxembourg City L-1511, Luxembourg
| | - Satyavani Vemparala
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai 600113, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India
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24
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Zhu J, Meng W, Man Lam S, Shui G, Huang X. Phosphatidylcholine deficiency increases ferroptosis susceptibility in the C. elegans germline. J Genet Genomics 2023; 50:318-329. [PMID: 36933794 DOI: 10.1016/j.jgg.2023.03.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 02/15/2023] [Accepted: 03/06/2023] [Indexed: 03/18/2023]
Abstract
Ferroptosis, a regulated and iron-dependent form of cell death characterized by peroxidation of membrane phospholipids, has tremendous potential for the therapy of human diseases. The causal link between phospholipid homeostasis and ferroptosis is incompletely understood. Here, we reveal that spin-4, a previously identified regulator of the "B12-one-carbon cycle-phosphatidylcholine (PC)" pathway, sustains germline development and fertility by ensuring PC sufficiency in the nematode Caenorhabditis elegans. Mechanistically, SPIN-4 regulates lysosomal activity which is required for B12-associated PC synthesis. PC deficiency-induced sterility can be rescued by reducing the levels of polyunsaturated fatty acids (PUFAs), reactive oxygen species (ROS) , and redox-active iron, which indicates that the sterility is mediated by germline ferroptosis. These results highlight the critical role of PC homeostasis in ferroptosis susceptibility and offer a new target for pharmacological approaches.
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Affiliation(s)
- Jinglin Zhu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Meng
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Sin Man Lam
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Guanghou Shui
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xun Huang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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25
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van Hilten N, Methorst J, Verwei N, Risselada HJ. Physics-based generative model of curvature sensing peptides; distinguishing sensors from binders. SCIENCE ADVANCES 2023; 9:eade8839. [PMID: 36930719 PMCID: PMC10022891 DOI: 10.1126/sciadv.ade8839] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 02/09/2023] [Indexed: 06/18/2023]
Abstract
Proteins can specifically bind to curved membranes through curvature-induced hydrophobic lipid packing defects. The chemical diversity among such curvature "sensors" challenges our understanding of how they differ from general membrane "binders" that bind without curvature selectivity. Here, we combine an evolutionary algorithm with coarse-grained molecular dynamics simulations (Evo-MD) to resolve the peptide sequences that optimally recognize the curvature of lipid membranes. We subsequently demonstrate how a synergy between Evo-MD and a neural network (NN) can enhance the identification and discovery of curvature sensing peptides and proteins. To this aim, we benchmark a physics-trained NN model against experimental data and show that we can correctly identify known sensors and binders. We illustrate that sensing and binding are phenomena that lie on the same thermodynamic continuum, with only subtle but explainable differences in membrane binding free energy, consistent with the serendipitous discovery of sensors.
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Affiliation(s)
- Niek van Hilten
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden, 2333 CC, Netherlands
| | - Jeroen Methorst
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden, 2333 CC, Netherlands
| | - Nino Verwei
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden, 2333 CC, Netherlands
| | - Herre Jelger Risselada
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden, 2333 CC, Netherlands
- Department of Physics, Technical University Dortmund, Otto-Hahn-Strasse 4, Dortmund, 44227, Germany
- Institute of Theoretical Physics, Georg-August-University Göttingen, Friedrich-Hund-Platz 1, Göttingen, 37077, Germany
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26
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Tiwari A, Pradhan S, Sannigrahi A, Mahakud AK, Jha S, Chattopadhyay K, Biswas M, Saleem M. “Interplay of lipid-head group and packing defects in driving Amyloid-beta mediated myelin-like model membrane deformation”. J Biol Chem 2023; 299:104653. [PMID: 36990217 PMCID: PMC10148160 DOI: 10.1016/j.jbc.2023.104653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 02/24/2023] [Accepted: 03/21/2023] [Indexed: 03/29/2023] Open
Abstract
Accumulating evidence suggests that amyloid plaque associated myelin lipid loss as a result of elevated amyloid burden might also contribute to Alzheimer's disease. The amyloid fibrils though closely associated with lipids under physiological conditions, however, the progression of membrane remodeling events leading to lipid-fibril assembly remains unknown. Here we first reconstitute the interaction of Aβ-40 with myelin-like model membrane and show that the binding of Aβ-40 induces extensive tubulation. To look into the mechanism of membrane tubulation we chose a set of membrane conditions varying in lipid packing density and net charge that allows us to dissect the contribution of lipid specificity of Aβ-40 binding, aggregation kinetics, and subsequent changes in membrane parameters such as fluidity, diffusion, and compressibility modulus. We show that the binding of Aβ-40 depends predominantly on the lipid packing defect densities and electrostatic interactions and results in rigidification of the myelin-like model membrane during the early phase of amyloid aggregation. Furthermore, elongation of Aβ-40 into higher oligomeric and fibrillar species leads to eventual fluidization of the model membrane followed by extensive lipid membrane tubulation observed in the late phase. Taken together, our results capture mechanistic insights into snapshots of temporal dynamics of Aβ-40 - myelin-like model membrane interaction and demonstrate how short timescale, local phenomena of binding, and fibril-mediated load generation results in the consequent association of lipids with growing amyloid fibrils.
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27
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Moss FR, Lincoff J, Tucker M, Mohammed A, Grabe M, Frost A. Brominated lipid probes expose structural asymmetries in constricted membranes. Nat Struct Mol Biol 2023; 30:167-175. [PMID: 36624348 PMCID: PMC9935397 DOI: 10.1038/s41594-022-00898-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 11/11/2022] [Indexed: 01/11/2023]
Abstract
Lipids in biological membranes are thought to be functionally organized, but few experimental tools can probe nanoscale membrane structure. Using brominated lipids as contrast probes for cryo-EM and a model ESCRT-III membrane-remodeling system composed of human CHMP1B and IST1, we observed leaflet-level and protein-localized structural lipid patterns within highly constricted and thinned membrane nanotubes. These nanotubes differed markedly from protein-free, flat bilayers in leaflet thickness, lipid diffusion rates and lipid compositional and conformational asymmetries. Simulations and cryo-EM imaging of brominated stearoyl-docosahexanenoyl-phosphocholine showed how a pair of phenylalanine residues scored the outer leaflet with a helical hydrophobic defect where polyunsaturated docosahexaenoyl tails accumulated at the bilayer surface. Combining cryo-EM of halogenated lipids with molecular dynamics thus enables new characterizations of the composition and structure of membranes on molecular length scales.
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Affiliation(s)
- Frank R Moss
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
- SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Altos Labs, Redwood City, CA, USA
| | - James Lincoff
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California San Francisco (UCSF), San Francisco, CA, USA
| | - Maxwell Tucker
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California San Francisco (UCSF), San Francisco, CA, USA
| | - Arshad Mohammed
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
- University of California Berkeley, Berkeley, CA, USA
- Altos Labs, Redwood City, CA, USA
| | - Michael Grabe
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA.
- Cardiovascular Research Institute, University of California San Francisco (UCSF), San Francisco, CA, USA.
| | - Adam Frost
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA.
- Altos Labs, Redwood City, CA, USA.
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28
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Li L, Ji J, Song F, Hu J. Intercellular Receptor-ligand Binding: Effect of Protein-membrane Interaction. J Mol Biol 2023; 435:167787. [PMID: 35952805 DOI: 10.1016/j.jmb.2022.167787] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/03/2022] [Accepted: 08/04/2022] [Indexed: 02/04/2023]
Abstract
Gaining insights into the intercellular receptor-ligand binding is of great importance for understanding numerous physiological and pathological processes, and stimulating new strategies in drug design and discovery. In contrast to the in vitro protein interaction in solution, the anchored receptor and ligand molecules interact with membrane in situ, which affects the intercellular receptor-ligand binding. Here, we review theoretical, simulation and experimental works regarding the regulatory effects of protein-membrane interactions on intercellular receptor-ligand binding mainly from the following aspects: membrane fluctuations, membrane curvature, glycocalyx, and lipid raft. In addition, we discuss biomedical significances and possible research directions to advance the field and highlight the importance of understanding of coupling effects of these factors in pharmaceutical development.
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Affiliation(s)
- Long Li
- Kuang Yaming Honors School and Institute for Brain Sciences, Nanjing University, 210023 Nanjing, China; State Key Laboratory of Nonlinear Mechanics and Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, 100190 Beijing, China
| | - Jing Ji
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education Beijing Advanced Innovation Center for Biomedical Engineering School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China.
| | - Fan Song
- State Key Laboratory of Nonlinear Mechanics and Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, 100190 Beijing, China; School of Engineering Science, University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Jinglei Hu
- Kuang Yaming Honors School and Institute for Brain Sciences, Nanjing University, 210023 Nanjing, China.
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29
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Gahan CG, Van Lehn RC, Blackwell HE, Lynn DM. Interactions of Bacterial Quorum Sensing Signals with Model Lipid Membranes: Influence of Membrane Composition on Membrane Remodeling. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:295-307. [PMID: 36534123 PMCID: PMC10038191 DOI: 10.1021/acs.langmuir.2c02506] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
We report the influence of membrane composition on the multiscale remodeling of multicomponent lipid bilayers initiated by contact with the amphiphilic bacterial quorum sensing signal N-(3-oxo)-dodecanoyl-l-homoserine lactone (3-oxo-C12-AHL) and its anionic headgroup hydrolysis product, 3-oxo-C12-HS. We used fluorescence microscopy and quartz crystal microbalance with dissipation (QCM-D) to characterize membrane reformation that occurs when these amphiphiles are placed in contact with supported lipid bilayers (SLBs) composed of (i) 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) containing varying amounts of cholesterol or (ii) mixtures of DOPC and either 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE, a conical zwitterionic lipid) or 1,2-dioleoyl-sn-glycero-3-phospho-l-serine (DOPS, a model anionic lipid). In general, we observe these mixed-lipid membranes to undergo remodeling events, including the formation and subsequent collapse of long tubules and the formation of hemispherical caps, upon introduction to biologically relevant concentrations of 3-oxo-C12-AHL and 3-oxo-C12-HS in ways that differ substantially from those observed in single-component DOPC membranes. These differences in bilayer reformation and their associated dynamics can be understood in terms of the influence of membrane composition on the time scales of molecular flip-flop, lipid packing defects, and lipid phase segregation in these materials. The lipid components investigated here are representative of classes of lipids that comprise both naturally occurring cell membranes and many useful synthetic soft materials. These studies thus represent a first step toward understanding the ways in which membrane composition can impact interactions with this important class of bacterial signaling molecules.
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Affiliation(s)
- Curran G. Gahan
- Department of Chemical and Biological Engineering, University of Wisconsin–Madison, 1415 Engineering Dr., Madison, WI 53706, USA
| | - Reid C. Van Lehn
- Department of Chemical and Biological Engineering, University of Wisconsin–Madison, 1415 Engineering Dr., Madison, WI 53706, USA
| | - Helen E. Blackwell
- Department of Chemistry, University of Wisconsin–Madison, 1101 University Ave., Madison, WI 53706, USA
| | - David M. Lynn
- Department of Chemical and Biological Engineering, University of Wisconsin–Madison, 1415 Engineering Dr., Madison, WI 53706, USA
- Department of Chemistry, University of Wisconsin–Madison, 1101 University Ave., Madison, WI 53706, USA
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30
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Wu H, Huang H, Zhang Y, Lu X, Majewski PW, Feng X. Stabilizing Differential Interfacial Curvatures by Mismatched Molecular Geometries: Toward Polymers with Percolating 1 nm Channels of Gyroid Minimal Surfaces. ACS NANO 2022; 16:21139-21151. [PMID: 36516967 DOI: 10.1021/acsnano.2c09103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Soft materials with self-assembled networks possess saddle-shaped interfaces with distributed negative Gaussian curvatures. The ability to stabilize such a geometry is critically important for various applications but can be challenging due to the possibly "deficient" packing of the building blocks. This nontrivial challenge has been manifested, for example, by the limited availability of cross-linkable bicontinuous cubic (Q) liquid crystals (LCs), which can be utilized to fabricate compelling polymers with networked nanochannels uniformly sized at ∼1 nm. Here, we devise a facile approach to stabilizing cross-linkable Q mesophases by leveraging the synergistic self-assembly from pairs of scalably synthesized polymerizable amphiphiles. Hybridization of the molecular geometries by mixing significantly increases the propensity of the local deviations in the interfacial curvature specifically required for Q assemblies. "Normal" (type 1) double gyroid LCs possessing 1 nm ionic channels conforming to minimal surfaces can be formulated by simultaneous hydration of the amphiphile mixtures, as opposed to the formation of hexagonal or lamellar mesophases exhibited by the single-amphiphile systems, respectively. Fixation of the bicontinuous network in polymers via radical polymerization has been efficaciously facilitated by the presence of the bifunctional polymerizable groups in one of the employed amphiphiles. High-fidelity lock-in of the ordered continuous 1 nm channels has been unambiguously confirmed by the observation of single-crystal-like diffraction patterns from synchrotron small-angle X-ray scattering and large-area periodicities by transmission electron microscopy. The produced polymeric materials exhibit the required mechanical integrity as well as chemical robustness in a variety of organic solvents that benefit their practical applications for selective transport of ions and molecules.
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Affiliation(s)
- Hanyu Wu
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Center for Advanced Low-Dimension Materials, and College of Materials Sciences and Engineering, Donghua University, Shanghai201620, People's Repubic of China
| | - Hairui Huang
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Center for Advanced Low-Dimension Materials, and College of Materials Sciences and Engineering, Donghua University, Shanghai201620, People's Repubic of China
| | - Yizhou Zhang
- Key Laboratory of Organic Compound Pollution Control Engineering, Ministry of Education, and School of Environmental and Chemical Engineering, Shanghai University, Shanghai200444, People's Repubic of China
| | - Xinglin Lu
- CAS Key Laboratory of Urban Pollutant Conversion, University of Science and Technology of China, Hefei, Anhui230026, People's Repubic of China
| | - Pawel W Majewski
- Department of Chemistry, University of Warsaw, Warsaw02089, Poland
| | - Xunda Feng
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Center for Advanced Low-Dimension Materials, and College of Materials Sciences and Engineering, Donghua University, Shanghai201620, People's Repubic of China
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31
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Jensen LE, Rao S, Schuschnig M, Cada AK, Martens S, Hummer G, Hurley JH. Membrane curvature sensing and stabilization by the autophagic LC3 lipidation machinery. SCIENCE ADVANCES 2022; 8:eadd1436. [PMID: 36516251 PMCID: PMC9750143 DOI: 10.1126/sciadv.add1436] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 11/10/2022] [Indexed: 05/28/2023]
Abstract
How the highly curved phagophore membrane is stabilized during autophagy initiation is a major open question in autophagosome biogenesis. Here, we use in vitro reconstitution on membrane nanotubes and molecular dynamics simulations to investigate how core autophagy proteins in the LC3 (Microtubule-associated proteins 1A/1B light chain 3) lipidation cascade interact with curved membranes, providing insight into their possible roles in regulating membrane shape during autophagosome biogenesis. ATG12(Autophagy-related 12)-ATG5-ATG16L1 was up to 100-fold enriched on highly curved nanotubes relative to flat membranes. At high surface density, ATG12-ATG5-ATG16L1 binding increased the curvature of the nanotubes. While WIPI2 (WD repeat domain phosphoinositide-interacting protein 2) binding directs membrane recruitment, the amphipathic helix α2 of ATG16L1 is responsible for curvature sensitivity. Molecular dynamics simulations revealed that helix α2 of ATG16L1 inserts shallowly into the membrane, explaining its curvature-sensitive binding to the membrane. These observations show how the binding of the ATG12-ATG5-ATG16L1 complex to the early phagophore rim could stabilize membrane curvature and facilitate autophagosome growth.
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Affiliation(s)
- Liv E. Jensen
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Shanlin Rao
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Martina Schuschnig
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria
| | - A. King Cada
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA
| | - Sascha Martens
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria
| | - Gerhard Hummer
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
- Institute of Biophysics, Goethe University Frankfurt, Frankfurt am Main 60438, Germany
| | - James H. Hurley
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA 94720, USA
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32
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Ivanova KA, Bashkirov PV. Noise in Ultrashort Elastic Membrane Nanotube. BIOCHEMISTRY (MOSCOW), SUPPLEMENT SERIES A: MEMBRANE AND CELL BIOLOGY 2022. [DOI: 10.1134/s1990747822050063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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33
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Rogers S, Gui L, Kovalenko A, Zoni V, Carpentier M, Ramji K, Ben Mbarek K, Bacle A, Fuchs P, Campomanes P, Reetz E, Speer NO, Reynolds E, Thiam AR, Vanni S, Nicastro D, Henne WM. Triglyceride lipolysis triggers liquid crystalline phases in lipid droplets and alters the LD proteome. J Cell Biol 2022; 221:213472. [PMID: 36112368 PMCID: PMC9485706 DOI: 10.1083/jcb.202205053] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 08/10/2022] [Accepted: 08/22/2022] [Indexed: 01/08/2023] Open
Abstract
Lipid droplets (LDs) are reservoirs for triglycerides (TGs) and sterol-esters (SEs), but how these lipids are organized within LDs and influence their proteome remain unclear. Using in situ cryo-electron tomography, we show that glucose restriction triggers lipid phase transitions within LDs generating liquid crystalline lattices inside them. Mechanistically this requires TG lipolysis, which decreases the LD's TG:SE ratio, promoting SE transition to a liquid crystalline phase. Molecular dynamics simulations reveal TG depletion promotes spontaneous TG and SE demixing in LDs, additionally altering the lipid packing of the PL monolayer surface. Fluorescence imaging and proteomics further reveal that liquid crystalline phases are associated with selective remodeling of the LD proteome. Some canonical LD proteins, including Erg6, relocalize to the ER network, whereas others remain LD-associated. Model peptide LiveDrop also redistributes from LDs to the ER, suggesting liquid crystalline phases influence ER-LD interorganelle transport. Our data suggests glucose restriction drives TG mobilization, which alters the phase properties of LD lipids and selectively remodels the LD proteome.
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Affiliation(s)
- Sean Rogers
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Long Gui
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Anastasiia Kovalenko
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Valeria Zoni
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Maxime Carpentier
- Laboratoire de Physique de l'École Normale Supérieure, École normale supérieure, Université Paris Sciences et Lettres, Centre national de la recherche scientifique, Sorbonne Université, Université de Paris, Paris, France
| | - Kamran Ramji
- Laboratoire de Physique de l'École Normale Supérieure, École normale supérieure, Université Paris Sciences et Lettres, Centre national de la recherche scientifique, Sorbonne Université, Université de Paris, Paris, France
| | - Kalthoum Ben Mbarek
- Laboratoire de Physique de l'École Normale Supérieure, École normale supérieure, Université Paris Sciences et Lettres, Centre national de la recherche scientifique, Sorbonne Université, Université de Paris, Paris, France
| | - Amelie Bacle
- Institute Jacques Monod, Centre national de la recherche scientifique, University of Paris, Paris, France
| | - Patrick Fuchs
- Laboratoire des Biomolécules, Paris, France.,Université de Paris, UFR Sciences du Vivant, Paris, France
| | - Pablo Campomanes
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Evan Reetz
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Natalie Ortiz Speer
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Emma Reynolds
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Abdou Rachid Thiam
- Laboratoire de Physique de l'École Normale Supérieure, École normale supérieure, Université Paris Sciences et Lettres, Centre national de la recherche scientifique, Sorbonne Université, Université de Paris, Paris, France
| | - Stefano Vanni
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Daniela Nicastro
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX
| | - W Mike Henne
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX
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34
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Hybrid bilayer membranes as platforms for biomimicry and catalysis. Nat Rev Chem 2022; 6:862-880. [PMID: 37117701 DOI: 10.1038/s41570-022-00433-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/20/2022] [Indexed: 11/08/2022]
Abstract
Hybrid bilayer membrane (HBM) platforms represent an emerging nanoscale bio-inspired interface that has broad implications in energy catalysis and smart molecular devices. An HBM contains multiple modular components that include an underlying inorganic surface with a biological layer appended on top. The inorganic interface serves as a support with robust mechanical properties that can also be decorated with functional moieties, sensing units and catalytic active sites. The biological layer contains lipids and membrane-bound entities that facilitate or alter the activity and selectivity of the embedded functional motifs. With their structural complexity and functional flexibility, HBMs have been demonstrated to enhance catalytic turnover frequency and regulate product selectivity of the O2 and CO2 reduction reactions, which have applications in fuel cells and electrolysers. HBMs can also steer the mechanistic pathways of proton-coupled electron transfer (PCET) reactions of quinones and metal complexes by tuning electron and proton delivery rates. Beyond energy catalysis, HBMs have been equipped with enzyme mimics and membrane-bound redox agents to recapitulate natural energy transport chains. With channels and carriers incorporated, HBM sensors can quantify transmembrane events. This Review serves to summarize the major accomplishments achieved using HBMs in the past decade.
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Bozelli JC, Yune J, Aulakh SS, Cao Z, Fernandes A, Seitova A, Tong Y, Schreier S, Epand RM. Human Diacylglycerol Kinase ε N-Terminal Segment Regulates the Phosphatidylinositol Cycle, Controlling the Rate but Not the Acyl Chain Composition of Its Lipid Intermediates. ACS Chem Biol 2022; 17:2495-2506. [PMID: 35767833 DOI: 10.1021/acschembio.2c00387] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Diacylglycerol kinase ε (DGKε), an enzyme of the phosphatidylinositol (PI) cycle, bears a highly conserved hydrophobic N-terminal segment, which was proposed to anchor the enzyme into the membrane. However, the importance of this segment to the DGKε function remains to be determined. To address this question, it is here reported an in silico and in vitro combined research strategy. Capitalizing on the AlphaFold 2.0 predicted structure of human DGKε, it is shown that its hydrophobic N-terminal segment anchors it into the membrane via a transmembrane α-helix. Coarse-grained based elastic network model studies showed that a conformational change in the hydrophobic N-terminal segment determines the proximity between the active site of DGKε and the membrane-water interface, likely regulating its kinase activity. In vitro studies with a purified DGKε construct lacking the hydrophobic N-terminal segment (His-SUMO*-Δ50-DGKε) corroborated the role of the N-terminus in regulating DGKε enzymatic properties. The comparison between the enzymatic properties of DGKε and His-SUMO*-Δ50-DGKε showed that the conserved N-terminal segment markedly inhibits the enzyme activity and its sensitivity to membrane intrinsic negative curvature, while also playing a role in the modulation of the enzyme by phosphatidylserine. On the other hand, this segment did not strongly affect its diacylglycerol acyl chain specificity, the modulation of the enzyme by membrane morphological changes, or the activation by phosphatidic acid-rich lipid domains. Hence, these results suggest that the conservation of the hydrophobic N-terminal segment of DGKε throughout evolution guaranteed not only membrane anchorage but also an efficient and elegant manner to regulate the rate of the PI cycle.
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Affiliation(s)
- José Carlos Bozelli
- Department of Biochemistry and Biomedical Sciences, McMaster University, Health Sciences Centre, Hamilton, ON L8S 3L8, Canada
| | - Jenny Yune
- Department of Biochemistry and Biomedical Sciences, McMaster University, Health Sciences Centre, Hamilton, ON L8S 3L8, Canada
| | - Sukhvershjit S Aulakh
- Department of Biochemistry and Biomedical Sciences, McMaster University, Health Sciences Centre, Hamilton, ON L8S 3L8, Canada
| | - Zihao Cao
- Department of Biochemistry and Biomedical Sciences, McMaster University, Health Sciences Centre, Hamilton, ON L8S 3L8, Canada
| | - Alexia Fernandes
- Department of Biochemistry and Biomedical Sciences, McMaster University, Health Sciences Centre, Hamilton, ON L8S 3L8, Canada
| | - Alma Seitova
- Structural Genomics Consortium, University of Toronto, Toronto, ON N5G 1L7, Canada
| | - Yufeng Tong
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - Shirley Schreier
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo 05508-000, Brazil
| | - Richard M Epand
- Department of Biochemistry and Biomedical Sciences, McMaster University, Health Sciences Centre, Hamilton, ON L8S 3L8, Canada
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36
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Abstract
Some dividing cells sense their shape by becoming polarized along their long axis. Cell polarity is controlled in part by polarity proteins, like Rho GTPases, cycling between active membrane-bound forms and inactive cytosolic forms, modeled as a "wave-pinning" reaction-diffusion process. Does shape sensing emerge from wave pinning? We show that wave pinning senses the cell's long axis. Simulating wave pinning on a curved surface, we find that high-activity domains migrate to peaks and troughs of the surface. For smooth surfaces, a simple rule of minimizing the domain perimeter while keeping its area fixed predicts the final position of the domain and its shape. However, when we introduce roughness to our surfaces, shape sensing can be disrupted, and high-activity domains can become localized to locations other than the global peaks and valleys of the surface. On rough surfaces, the domains of the wave-pinning model are more robust in finding the peaks and troughs than the minimization rule, although both can become trapped in steady states away from the peaks and valleys. We can control the robustness of shape sensing by altering the Rho GTPase diffusivity and the domain size. We also find that the shape-sensing properties of cell polarity models can explain how domains localize to curved regions of deformed cells. Our results help to understand the factors that allow cells to sense their shape-and the limits that membrane roughness can place on this process.
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van Hilten N, Stroh KS, Risselada HJ. Efficient Quantification of Lipid Packing Defect Sensing by Amphipathic Peptides: Comparing Martini 2 and 3 with CHARMM36. J Chem Theory Comput 2022; 18:4503-4514. [PMID: 35709386 PMCID: PMC9281404 DOI: 10.1021/acs.jctc.2c00222] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In biological systems, proteins can be attracted to curved or stretched regions of lipid bilayers by sensing hydrophobic defects in the lipid packing on the membrane surface. Here, we present an efficient end-state free energy calculation method to quantify such sensing in molecular dynamics simulations. We illustrate that lipid packing defect sensing can be defined as the difference in mechanical work required to stretch a membrane with and without a peptide bound to the surface. We also demonstrate that a peptide's ability to concurrently induce excess leaflet area (tension) and elastic softening─a property we call the "characteristic area of sensing" (CHAOS)─and lipid packing sensing behavior are in fact two sides of the same coin. In essence, defect sensing displays a peptide's propensity to generate tension. The here-proposed mechanical pathway is equally accurate yet, computationally, about 40 times less costly than the commonly used alchemical pathway (thermodynamic integration), allowing for more feasible free energy calculations in atomistic simulations. This enabled us to directly compare the Martini 2 and 3 coarse-grained and the CHARMM36 atomistic force fields in terms of relative binding free energies for six representative peptides including the curvature sensor ALPS and two antiviral amphipathic helices (AH). We observed that Martini 3 qualitatively reproduces experimental trends while producing substantially lower (relative) binding free energies and shallower membrane insertion depths compared to atomistic simulations. In contrast, Martini 2 tends to overestimate (relative) binding free energies. Finally, we offer a glimpse into how our end-state-based free energy method can enable the inverse design of optimal lipid packing defect sensing peptides when used in conjunction with our recently developed evolutionary molecular dynamics (Evo-MD) method. We argue that these optimized defect sensors─aside from their biomedical and biophysical relevance─can provide valuable targets for the development of lipid force fields.
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Affiliation(s)
- Niek van Hilten
- Leiden Institute of Chemistry, Leiden University, Leiden 2300 RA, The Netherlands
| | - Kai Steffen Stroh
- Department of Physics, Technical University Dortmund, Dortmund 44221, Germany.,Institute for Theoretical Physics, Georg-August-University Göttingen, Göttingen 37077, Germany
| | - Herre Jelger Risselada
- Leiden Institute of Chemistry, Leiden University, Leiden 2300 RA, The Netherlands.,Department of Physics, Technical University Dortmund, Dortmund 44221, Germany.,Institute for Theoretical Physics, Georg-August-University Göttingen, Göttingen 37077, Germany
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38
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Tumor protein D54 binds intracellular nanovesicles via an extended amphipathic region. J Biol Chem 2022; 298:102136. [PMID: 35714773 PMCID: PMC9270247 DOI: 10.1016/j.jbc.2022.102136] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 11/22/2022] Open
Abstract
Tumor Protein D54 (TPD54) is an abundant cytosolic protein that belongs to the TPD52 family, a family of four proteins (TPD52, 53, 54 and 55) that are overexpressed in several cancer cells. Even though the functions of these proteins remain elusive, recent investigations indicate that TPD54 binds to very small cytosolic vesicles with a diameter of ca. 30 nm, half the size of classical (e.g. COPI and COPII) transport vesicles. Here, we investigated the mechanism of intracellular nanovesicle capture by TPD54. Bioinformatical analysis suggests that TPD54 contains a small coiled-coil followed by four amphipathic helices (AH1-4), which could fold upon binding to lipid membranes. Limited proteolysis, circular dichroism (CD) spectroscopy, tryptophan fluorescence, and cysteine mutagenesis coupled to covalent binding of a membrane sensitive probe showed that binding of TPD54 to small liposomes is accompanied by large structural changes in the amphipathic helix region. Furthermore, site-directed mutagenesis indicated that AH2 and AH3 have a predominant role in TPD54 binding to membranes both in cells and using model liposomes. We found that AH3 has the physicochemical features of an Amphipathic Lipid Packing Sensor (ALPS) motif, which, in other proteins, enables membrane binding in a curvature-dependent manner. Accordingly, we observed that binding of TPD54 to liposomes is very sensitive to membrane curvature and lipid unsaturation. We conclude that TPD54 recognizes nanovesicles through a combination of ALPS-dependent and -independent mechanisms.
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Scott JS, Nassar ZD, Swinnen JV, Butler LM. Monounsaturated fatty acids: key regulators of cell viability and intracellular signalling in cancer. Mol Cancer Res 2022; 20:1354-1364. [PMID: 35675039 DOI: 10.1158/1541-7786.mcr-21-1069] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 04/29/2022] [Accepted: 06/06/2022] [Indexed: 11/16/2022]
Abstract
Cancer cells feature increased macromolecular biosynthesis to support the formation of new organelles and membranes for cell division. In particular, lipids are key macromolecules that comprise cellular membrane components, substrates for energy generation and mediators of inter- and intracellular signalling. The emergence of more sensitive and accurate technology for profiling the "lipidome" of cancer cells has led to unprecedented leaps in understanding the complexity of cancer metabolism, but also highlighted promising therapeutic vulnerabilities. Notably, fatty acids, as lipid building blocks, are critical players in all stages of cancer development and progression and the importance of fatty acid desaturation and its impact on cancer cell biology has been well established. Recent years have seen the reports of new mechanistic insights into the role of monounsaturated fatty acids (MUFAs) in cancer, as regulators of cell death and lipid-related cellular signalling. This commentary aims to highlight these diverse roles of MUFAs in cancer cells which may yield new directions for therapeutic interventions involving these important fatty acids.
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Affiliation(s)
| | | | | | - Lisa M Butler
- University of Adelaide, School of Medicine and Freemasons Foundation Centre for Men's Health, Adelaide, SA, Australia
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40
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Shen Z, Lengyel M, Niethammer P. The yellow brick road to nuclear membrane mechanotransduction. APL Bioeng 2022; 6:021501. [PMID: 35382443 PMCID: PMC8967412 DOI: 10.1063/5.0080371] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 03/09/2022] [Indexed: 02/06/2023] Open
Abstract
The nuclear membrane may function as a mechanosensory surface alongside the plasma membrane. In this Review, we discuss how this idea emerged, where it currently stands, and point out possible implications, without any claim of comprehensiveness.
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Affiliation(s)
| | - Miklós Lengyel
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Philipp Niethammer
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
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41
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Kanehara K, Cho Y, Yu CY. A lipid viewpoint on the plant endoplasmic reticulum stress response. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2835-2847. [PMID: 35560195 DOI: 10.1093/jxb/erac063] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 02/15/2022] [Indexed: 06/15/2023]
Abstract
Organisms, including humans, seem to be constantly exposed to various changes, which often have undesirable effects, referred to as stress. To keep up with these changes, eukaryotic cells may have evolved a number of relevant cellular processes, such as the endoplasmic reticulum (ER) stress response. Owing to presumably intimate links between human diseases and the ER function, the ER stress response has been extensively investigated in various organisms for a few decades. Based on these studies, we now have a picture of the molecular mechanisms of the ER stress response, one of which, the unfolded protein response (UPR), is highly conserved among yeasts, mammals, higher plants, and green algae. In this review, we attempt to highlight the plant UPR from the perspective of lipids, especially membrane phospholipids. Phosphatidylcholine (PtdCho) and phosphatidylethanolamine (PtdEtn) are the most abundant membrane phospholipids in eukaryotic cells. The ratio of PtdCho to PtdEtn and the unsaturation of fatty acyl tails in both phospholipids may be critical factors for the UPR, but the pathways responsible for PtdCho and PtdEtn biosynthesis are distinct in animals and plants. We discuss the plant UPR in comparison with the system in yeasts and animals in the context of membrane phospholipids.
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Affiliation(s)
- Kazue Kanehara
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Yueh Cho
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Chao-Yuan Yu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
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42
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Molecular Mechanisms Underlying Caveolin-1 Mediated Membrane Curvature. J Membr Biol 2022; 255:225-236. [PMID: 35467110 DOI: 10.1007/s00232-022-00236-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 03/22/2022] [Indexed: 10/18/2022]
Abstract
Caveolin-1 is one of the main protein components of caveolae that acts as a mechanosensor at the cell membrane. The interactions of caveolin-1 with membranes have been shown to lead to complex effects such as curvature and the clustering of specific lipids. Here, we review the emerging concepts on the molecular interactions of caveolin-1, with a focus on insights from coarse-grain molecular dynamics simulations. Consensus structural models of caveolin-1 report a helix-turn-helix core motif with flanking domains of higher disorder that could be membrane composition dependent. Caveolin-1 appears to be mainly surface-bound and does not embed very deep in the membrane to which it is bound. The most interesting aspect of caveolin-1 membrane binding is the interplay of cholesterol clustering and membrane curvature. Although cholesterol has been reported to cluster in the vicinity of caveolin-1 by several approaches, simulations show that the clustering is maximal in membrane leaflet opposing the surface-bound caveolin-1. The intrinsic negative curvature of cholesterol appears to stabilize the negative curvature in the opposing leaflet. In fact, the simulations show that blocking cholesterol clustering (through artificial position restraints) blocks membrane curvature, and vice versa. Concomitant with cholesterol clustering is sphingomyelin clustering, again in the opposing leaflet, but in a concentration-dependent manner. The differential stress due to caveolin-1 binding and the inherent asymmetry of the membrane leaflets could be the determinant for membrane curvature and needs to be further probed. The review is an important step to reconcile the molecular level details emerging from simulations with the mesoscopic details provided by state of the art experimental approaches.
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43
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Beasley M, Frazee N, Groover S, Valentine SJ, Mertz B, Legleiter J. Physicochemical Properties Altered by the Tail Group of Lipid Membranes Influence Huntingtin Aggregation and Lipid Binding. J Phys Chem B 2022; 126:3067-3081. [PMID: 35439000 DOI: 10.1021/acs.jpcb.1c10254] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Huntington's disease is a neurodegenerative disorder caused by an expanded polyglutamine (polyQ) domain within the huntingtin protein (htt) that initiates toxic protein aggregation. Htt directly interacts with membranes, influencing aggregation and spurring membrane abnormalities. These interactions are facilitated by the 17 N-terminal residues (Nt17) that form an amphipathic α-helix implicated in both lipid binding and aggregation. Here, the impact of unsaturation in phospholipid tails on htt-lipid interaction and htt aggregation was determined. There was no correlation between the degree of htt-lipid complexation and the degree of htt aggregation in the presence of each lipid system, indicating that lipid systems with different properties uniquely alter the membrane-mediated aggregation mechanisms. Also, the association between Nt17 and membrane surfaces is determined by complementarity between hydrophobic residues and membrane defects and how easily the peptide can partition into the bilayer. Our results provide critical insights into how membrane physical properties influence downstream htt aggregation.
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Affiliation(s)
- Maryssa Beasley
- The C. Eugene Bennett Department of Chemistry, West Virginia University, 217 Clark Hall, Morgantown, West Virginia 26506, United States
| | - Nicolas Frazee
- The C. Eugene Bennett Department of Chemistry, West Virginia University, 217 Clark Hall, Morgantown, West Virginia 26506, United States
| | - Sharon Groover
- The C. Eugene Bennett Department of Chemistry, West Virginia University, 217 Clark Hall, Morgantown, West Virginia 26506, United States
| | - Stephen J Valentine
- The C. Eugene Bennett Department of Chemistry, West Virginia University, 217 Clark Hall, Morgantown, West Virginia 26506, United States
| | - Blake Mertz
- The C. Eugene Bennett Department of Chemistry, West Virginia University, 217 Clark Hall, Morgantown, West Virginia 26506, United States.,WVU Cancer Institute, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Justin Legleiter
- The C. Eugene Bennett Department of Chemistry, West Virginia University, 217 Clark Hall, Morgantown, West Virginia 26506, United States.,Blanchette Rockefeller Neurosciences Institutes, West Virginia University, 1 Medical Center Drive, P.O. Box 9303, Morgantown, West Virginia 26505, United States.,Department of Neuroscience, West Virginia University, 1 Medical Center Drive, P.O. Box 9303, Morgantown, West Virginia 26505, United States
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44
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Kluge C, Pöhnl M, Böckmann RA. Spontaneous local membrane curvature induced by transmembrane proteins. Biophys J 2022; 121:671-683. [PMID: 35122737 PMCID: PMC8943716 DOI: 10.1016/j.bpj.2022.01.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 01/13/2022] [Accepted: 01/28/2022] [Indexed: 11/26/2022] Open
Abstract
The (local) curvature of cellular membranes acts as a driving force for the targeting of membrane-associated proteins to specific membrane domains, as well as a sorting mechanism for transmembrane proteins, e.g., by accumulation in regions of matching spontaneous curvature. The latter measure was previously experimentally employed to study the curvature induced by the potassium channel KvAP and by aquaporin AQP0. However, the direction of the reported spontaneous curvature levels as well as the molecular driving forces governing the membrane curvature induced by these integral transmembrane proteins could not be addressed experimentally. Here, using both coarse-grained and atomistic molecular dynamics (MD) simulations, we report induced spontaneous curvature values for the homologous potassium channel Kv 1.2/2.1 Chimera (KvChim) and AQP0 embedded in unrestrained lipid bicelles that are in very good agreement with experiment. Importantly, the direction of curvature could be directly assessed from our simulations: KvChim induces a strong positive membrane curvature (≈0.036 nm-1) whereas AQP0 causes a comparably small negative curvature (≈-0.019 nm-1). Analyses of protein-lipid interactions within the bicelle revealed that the potassium channel shapes the surrounding membrane via structural determinants. Differences in shape of the protein-lipid interface of the voltage-gating domains between the extracellular and cytosolic membrane leaflets induce membrane stress and thereby promote a protein-proximal membrane curvature. In contrast, the water pore AQP0 displayed a high structural stability and an only faint effect on the surrounding membrane environment that is connected to its wedge-like shape.
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Affiliation(s)
- Christoph Kluge
- Computational Biology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Matthias Pöhnl
- Computational Biology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Rainer A. Böckmann
- Computational Biology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany,National Center for High-Performance Computing Erlangen (NHR@FAU), Erlangen, Germany,Corresponding author
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45
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Sikdar S, Banerjee M, Vemparala S. Role of Disulphide Bonds in Membrane Partitioning of a Viral Peptide. J Membr Biol 2022; 255:129-142. [PMID: 35218393 PMCID: PMC8881898 DOI: 10.1007/s00232-022-00218-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 02/02/2022] [Indexed: 01/22/2023]
Abstract
The importance of disulphide bond in mediating viral peptide entry into host cells is well known. In the present work, we elucidate the role of disulphide (SS) bond in partitioning mechanism of membrane-active Hepatitis A Virus-2B (HAV-2B) peptide, which harbours three cysteine residues promoting formation of multiple SS-bonded states. The inclusion of SS-bond not only results in a compact conformation but also induces distorted α-helical hairpin geometry in comparison to SS-free state. Owing to these, the hydrophobic residues get buried, restricting the insertion of SS-bonded HAV-2B peptide into lipid packing defects and thus the partitioning of the peptide is completely or partly abolished. In this way, the disulphide bond can potentially regulate the partitioning of HAV-2B peptide such that the membrane remodelling effects of this viral peptide are significantly reduced. The current findings may have potential implications in drug designing, targeting the HAV-2B protein by promoting disulphide bond formation within its membrane-active region.
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Affiliation(s)
- Samapan Sikdar
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai, 600113, India. .,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
| | - Manidipa Banerjee
- Kusuma School of Biological Sciences, Indian Institute of Technology-Delhi, Hauz Khas, New Delhi, 110016, India.
| | - Satyavani Vemparala
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai, 600113, India. .,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
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46
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Cibulka J, Bisaccia F, Radisavljević K, Gudino Carrillo RM, Köhler A. Assembly principle of a membrane-anchored nuclear pore basket scaffold. SCIENCE ADVANCES 2022; 8:eabl6863. [PMID: 35148185 PMCID: PMC8836807 DOI: 10.1126/sciadv.abl6863] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Nuclear pore complexes (NPCs) are membrane-embedded gatekeepers of traffic between the nucleus and cytoplasm. Key features of the NPC symmetric core have been elucidated, but little is known about the NPC basket, a prominent structure with numerous roles in gene expression. Studying the basket was hampered by its instability and connection to the inner nuclear membrane (INM). Here, we reveal the assembly principle of the yeast NPC basket by reconstituting a recombinant Nup60-Mlp1-Nup2 scaffold on a synthetic membrane. Nup60 serves as the basket's flexible suspension cable, harboring an array of short linear motifs (SLiMs). These bind multivalently to the INM, the coiled-coil protein Mlp1, the FG-nucleoporin Nup2, and the NPC core. We suggest that SLiMs, embedded in disordered regions, allow the basket to adapt its structure in response to bulky cargo and changes in gene expression. Our study opens avenues for the higher-order reconstitution of basket-anchored NPC assemblies on membranes.
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47
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Sapp K, Sodt AJ. Observed steric crowding at modest coverage requires a particular membrane-binding scheme or a complementary mechanism. Biophys J 2022; 121:430-438. [PMID: 34971618 PMCID: PMC8822614 DOI: 10.1016/j.bpj.2021.12.036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 08/21/2021] [Accepted: 12/23/2021] [Indexed: 02/03/2023] Open
Abstract
Membrane shape transitions, including fusion and fission, play an important role in many biological processes. It is therefore essential to understand mechanisms of "curvature generation," the mathematical quantification of membrane shape. Among the different mechanisms is the effect of steric pressure between proteins crowded on a surface. At a higher curvature, there is more space for the crowders and less steric pressure. Currently, the physical model of curvature induction by crowding views the proteins as being bound to the surface as a whole rather than to the underlying lipids. Here, we split the previously understood model into two pieces: first, the reduction in steric pressure due to reduced collisions between proteins, and second, the increased area available to the protein that is independent of other crowders. The cases are distinguished by how the crowder is attached to the membrane. When a protein is attached to a specific lipid, as is the case in a typical crowding experiment, one should not model its lateral entropy; this has already been accounted for by the underlying lipid. The Carnahan-Starling pressure includes this lateral entropy. The revised theory predicts that a purely entropic crowding mechanism is inconsistent with observations of reshaping at the lower range of surface coverage, suggesting that an additional mechanism is at play.
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Affiliation(s)
- Kayla Sapp
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Alexander J. Sodt
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland,Corresponding author
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48
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A synergy between mechanosensitive calcium- and membrane-binding mediates tension-sensing by C2-like domains. Proc Natl Acad Sci U S A 2022; 119:2112390119. [PMID: 34969839 PMCID: PMC8740744 DOI: 10.1073/pnas.2112390119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/19/2021] [Indexed: 11/23/2022] Open
Abstract
A cell must be able to measure whether the lipid membranes that surround its insides are stretched. Currently, mechanosensitive ion channels are the best-studied class of membrane tension sensors, but recent work suggests that peripheral membrane enzymes that gauge nuclear confinement or swelling during cell migration or upon tissue injury constitute a second class. The mechanosensitivity of these enzymes derives from their calcium-dependent (“C2-like”) membrane-interaction domains. Although these can be found in many important signaling proteins, they have remained virtually unstudied as mechanotransducers. How membrane tension controls these domains and what features render them mechanosensitive is unclear. Here, we show that membrane tension-sensing by C2-like domains is mediated by a synergy between mechanosensitive calcium-binding and membrane insertion. When nuclear membranes are stretched, the peripheral membrane enzyme cytosolic phospholipase A2 (cPLA2) binds via its calcium-dependent C2 domain (cPLA2-C2) and initiates bioactive lipid signaling and tissue inflammation. More than 150 C2-like domains are encoded in vertebrate genomes. How many of them are mechanosensors and quantitative relationships between tension and membrane recruitment remain unexplored, leaving a knowledge gap in the mechanotransduction field. In this study, we imaged the mechanosensitive adsorption of cPLA2 and its C2 domain to nuclear membranes and artificial lipid bilayers, comparing it to related C2-like motifs. Stretch increased the Ca2+ sensitivity of all tested domains, promoting half-maximal binding of cPLA2 at cytoplasmic resting-Ca2+ concentrations. cPLA2-C2 bound up to 50 times tighter to stretched than to unstretched membranes. Our data suggest that a synergy of mechanosensitive Ca2+ interactions and deep, hydrophobic membrane insertion enables cPLA2-C2 to detect stretched membranes with antibody-like affinity, providing a quantitative basis for understanding mechanotransduction by C2-like domains.
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Srinivasan S, Vanni S. Computational Approaches to Investigate and Design Lipid-binding Domains for Membrane Biosensing. Chimia (Aarau) 2021; 75:1031-1036. [PMID: 34920773 DOI: 10.2533/chimia.2021.1031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Association of proteins with cellular membranes is critical for signaling and membrane trafficking processes. Many peripheral lipid-binding domains have been identified in the last few decades and have been investigated for their specific lipid-sensing properties using traditional in vivo and in vitro studies. However, several knowledge gaps remain owing to intrinsic limitations of these methodologies. Thus, novel approaches are necessary to further our understanding in lipid-protein biology. This review briefly discusses lipid-binding domains that act as specific lipid biosensors and provides a broad perspective on the computational approaches such as molecular dynamics (MD) simulations and machine learning (ML)-based techniques that can be used to study protein-membrane interactions. We also highlight the need for de novo design of proteins that elicit specific lipid-binding properties.
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Affiliation(s)
| | - Stefano Vanni
- Department of Biology, University of Fribourg, Switzerland;,
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Claxton DP, Overway EM, Oeser JK, O'Brien RM, Mchaourab HS. Biophysical and functional properties of purified glucose-6-phosphatase catalytic subunit 1. J Biol Chem 2021; 298:101520. [PMID: 34952005 PMCID: PMC8753184 DOI: 10.1016/j.jbc.2021.101520] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/10/2021] [Accepted: 12/17/2021] [Indexed: 11/18/2022] Open
Abstract
Glucose-6-phosphatase catalytic subunit 1 (G6PC1) plays a critical role in hepatic glucose production during fasting by mediating the terminal step of the gluconeogenesis and glycogenolysis pathways. In concert with accessory transport proteins, this membrane-integrated enzyme catalyzes glucose production from glucose-6-phosphate (G6P) to support blood glucose homeostasis. Consistent with its metabolic function, dysregulation of G6PC1 gene expression contributes to diabetes, and mutations that impair phosphohydrolase activity form the clinical basis of glycogen storage disease type 1a. Despite its relevance to health and disease, a comprehensive view of G6PC1 structure and mechanism has been limited by the absence of expression and purification strategies that isolate the enzyme in a functional form. In this report, we apply a suite of biophysical and biochemical tools to fingerprint the in vitro attributes of catalytically active G6PC1 solubilized in lauryl maltose neopentyl glycol (LMNG) detergent micelles. When purified from Sf9 insect cell membranes, the glycosylated mouse ortholog (mG6PC1) recapitulated functional properties observed previously in intact hepatic microsomes and displayed the highest specific activity reported to date. Additionally, our results establish a direct correlation between the catalytic and structural stability of mG6PC1, which is underscored by the enhanced thermostability conferred by phosphatidylcholine and the cholesterol analog cholesteryl hemisuccinate. In contrast, the N96A variant, which blocks N-linked glycosylation, reduced thermostability. The methodologies described here overcome long-standing obstacles in the field and lay the necessary groundwork for a detailed analysis of the mechanistic structural biology of G6PC1 and its role in complex metabolic disorders.
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Affiliation(s)
- Derek P Claxton
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA.
| | - Emily M Overway
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
| | - James K Oeser
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
| | - Richard M O'Brien
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
| | - Hassane S Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
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