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Sharma KD, Doktorova M, Waxham MN, Heberle FA. Cryo-EM images of phase-separated lipid bilayer vesicles analyzed with a machine-learning approach. Biophys J 2024; 123:2877-2891. [PMID: 38689500 DOI: 10.1016/j.bpj.2024.04.029] [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: 12/22/2023] [Revised: 03/08/2024] [Accepted: 04/26/2024] [Indexed: 05/02/2024] Open
Abstract
Lateral lipid heterogeneity (i.e., raft formation) in biomembranes plays a functional role in living cells. Three-component mixtures of low- and high-melting lipids plus cholesterol offer a simplified experimental model for raft domains in which a liquid-disordered (Ld) phase coexists with a liquid-ordered (Lo) phase. Using such models, we recently showed that cryogenic electron microscopy (cryo-EM) can detect phase separation in lipid vesicles based on differences in bilayer thickness. However, the considerable noise within cryo-EM data poses a significant challenge for accurately determining the membrane phase state at high spatial resolution. To this end, we have developed an image-processing pipeline that utilizes machine learning (ML) to predict the bilayer phase in projection images of lipid vesicles. Importantly, the ML method exploits differences in both the thickness and molecular density of Lo compared to Ld, which leads to improved phase identification. To assess accuracy, we used artificial images of phase-separated lipid vesicles generated from all-atom molecular dynamics simulations of Lo and Ld phases. Synthetic ground-truth data sets mimicking a series of compositions along a tieline of Ld + Lo coexistence were created and then analyzed with various ML models. For all tieline compositions, we find that the ML approach can correctly identify the bilayer phase with >90% accuracy, thus providing a means to isolate the intensity profiles of coexisting Ld and Lo phases, as well as accurately determine domain-size distributions, number of domains, and phase-area fractions. The method described here provides a framework for characterizing nanoscopic lateral heterogeneities in membranes and paves the way for a more detailed understanding of raft properties in biological contexts.
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Affiliation(s)
- Karan D Sharma
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee
| | - Milka Doktorova
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia
| | - M Neal Waxham
- Department of Neurobiology and Anatomy, University of Texas Health Science Center, Houston, Texas
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2
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Wu D, Tang H, Qiu X, Song S, Chen S, Robinson CV. Native MS-guided lipidomics to define endogenous lipid microenvironments of eukaryotic receptors and transporters. Nat Protoc 2024:10.1038/s41596-024-01037-4. [PMID: 39174660 DOI: 10.1038/s41596-024-01037-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 06/06/2024] [Indexed: 08/24/2024]
Abstract
The mammalian membrane is composed of various eukaryotic lipids interacting with extensively post-translationally modified proteins. Probing interactions between these mammalian membrane proteins and their diverse and heterogeneous lipid cohort remains challenging. Recently, native mass spectrometry (MS) combined with bottom-up 'omics' approaches has provided valuable information to relate structural and functional lipids to membrane protein assemblies in eukaryotic membranes. Here we provide a step-by-step protocol to identify and provide relative quantification for endogenous lipids bound to mammalian membrane proteins and their complexes. Using native MS to guide our lipidomics strategies, we describe the necessary sample preparation steps, followed by native MS data acquisition, tailored lipidomics and data interpretation. We also highlight considerations for the integration of different levels of information from native MS and lipidomics and how to deal with the various challenges that arise during the experiments. This protocol begins with the preparation of membrane proteins from mammalian cells and tissues for native MS. The results enable not only direct assessment of copurified endogenous lipids but also determination of the apparent affinities of specific lipids. Detailed sample preparation for lipidomics analysis is also covered, along with comprehensive settings for liquid chromatography-MS analysis. This protocol is suitable for the identification and quantification of endogenous lipids, including fatty acids, sterols, glycerolipids, phospholipids and glycolipids and can be used to interrogate proteins from recombinant sources to native membranes.
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Affiliation(s)
- Di Wu
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Haiping Tang
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Xingyu Qiu
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Siyuan Song
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Siyun Chen
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, Oxford, UK.
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK.
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3
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Sandberg JW, Santiago-McRae E, Ennis J, Brannigan G. The density-threshold affinity: Calculating lipid binding affinities from unbiased coarse-grained molecular dynamics simulations. Methods Enzymol 2024; 701:47-82. [PMID: 39025580 DOI: 10.1016/bs.mie.2024.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Many membrane proteins are sensitive to their local lipid environment. As structural methods for membrane proteins have improved, there is growing evidence of direct, specific binding of lipids to protein surfaces. Unfortunately the workhorse of understanding protein-small molecule interactions, the binding affinity for a given site, is experimentally inaccessible for these systems. Coarse-grained molecular dynamics simulations can be used to bridge this gap, and are relatively straightforward to learn. Such simulations allow users to observe spontaneous binding of lipids to membrane proteins and quantify localized densities of individual lipids or lipid fragments. In this chapter we outline a protocol for extracting binding affinities from these localized distributions, known as the "density threshold affinity." The density threshold affinity uses an adaptive and flexible definition of site occupancy that alleviates the need to distinguish between "bound'' lipids and bulk lipids that are simply diffusing through the site. Furthermore, the method allows "bead-level" resolution that is suitable for the case where lipids share binding sites, and circumvents ambiguities about a relevant reference state. This approach provides a convenient and straightforward method for comparing affinities of a single lipid species for multiple sites, multiple lipids for a single site, and/or a single lipid species modeled using multiple forcefields.
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Affiliation(s)
- Jesse W Sandberg
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ, United States
| | - Ezry Santiago-McRae
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ, United States
| | - Jahmal Ennis
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ, United States
| | - Grace Brannigan
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ, United States; Department of Physics, Rutgers University, Camden, NJ, United States.
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Thakur GCN, Uday A, Cebecauer M, Roos WH, Cwiklik L, Hof M, Jurkiewicz P, Melcrová A. Charge of a transmembrane peptide alters its interaction with lipid membranes. Colloids Surf B Biointerfaces 2024; 235:113765. [PMID: 38309153 DOI: 10.1016/j.colsurfb.2024.113765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 01/19/2024] [Accepted: 01/21/2024] [Indexed: 02/05/2024]
Abstract
Transmembrane (TM) proteins interact closely with the surrounding membrane lipids. Lipids in the vicinity of TM proteins were reported to have hindered mobility, which has been associated with lipids being caught up in the rough surface of the TM domains. These reports, however, neglect one important factor that largely influences the membrane behavior - electrostatics of the TM peptides that are usually positively charged at their cytosolic end. Here, we study on the example of a neutral and a positively charged WALP peptide, how the charge of a TM peptide influences the membrane. We investigate both its dynamics and mechanics by: (i) time dependent fluorescent shift in combination with classical and FRET generalized polarization to evaluate the mobility of lipids at short and long-range distance from the peptide, (ii) atomic force microscopy to observe the mechanical stability of the peptide-containing membranes, and (iii) molecular dynamics simulations to analyze the peptide-lipid interactions. We show that both TM peptides lower lipid mobility in their closest surroundings. The peptides cause lateral heterogeneity in lipid mobility, which in turn prevents free lipid rearrangement and lowers the membrane ability to seal ruptures after mechanical indentations. Introduction of a positive charge to the peptide largely enhances these effects, affecting the whole membrane. We thus highlight that unspecific peptide-lipid interactions, especially the electrostatics, should not be overlooked as they have a great impact on the mechanics and dynamics of the whole membrane.
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Affiliation(s)
- Garima C N Thakur
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, 182 23 Prague 8, Czech Republic; University of Chemical and Technology, Technická 5, Dejvice, 160 00 Prague 6, Czech Republic
| | - Arunima Uday
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, 182 23 Prague 8, Czech Republic; University of Chemical and Technology, Technická 5, Dejvice, 160 00 Prague 6, Czech Republic
| | - Marek Cebecauer
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, 182 23 Prague 8, Czech Republic
| | - Wouter H Roos
- Zernike Institute for Advanced Materials, Rijksuniversiteit Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands
| | - Lukasz Cwiklik
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, 182 23 Prague 8, Czech Republic; Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 166 10 Prague 6, Czech Republic
| | - Martin Hof
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, 182 23 Prague 8, Czech Republic
| | - Piotr Jurkiewicz
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, 182 23 Prague 8, Czech Republic.
| | - Adéla Melcrová
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, 182 23 Prague 8, Czech Republic; Zernike Institute for Advanced Materials, Rijksuniversiteit Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands.
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5
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Hawes E, Claxton D, Oeser J, O’Brien R. Identification of structural motifs critical for human G6PC2 function informed by sequence analysis and an AlphaFold2-predicted model. Biosci Rep 2024; 44:BSR20231851. [PMID: 38095063 PMCID: PMC10776900 DOI: 10.1042/bsr20231851] [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: 10/26/2023] [Revised: 11/22/2023] [Accepted: 12/12/2023] [Indexed: 01/10/2024] Open
Abstract
G6PC2 encodes a glucose-6-phosphatase (G6Pase) catalytic subunit, primarily expressed in pancreatic islet β cells, which modulates the sensitivity of insulin secretion to glucose and thereby regulates fasting blood glucose (FBG). Mutational analyses were conducted to validate an AlphaFold2 (AF2)-predicted structure of human G6PC2 in conjunction with a novel method to solubilize and purify human G6PC2 from a heterologous expression system. These analyses show that residues forming a predicted intramolecular disulfide bond are essential for G6PC2 expression and that residues forming part of a type 2 phosphatidic acid phosphatase (PAP2) motif are critical for enzyme activity. Additional mutagenesis shows that residues forming a predicted substrate cavity modulate enzyme activity and substrate specificity and residues forming a putative cholesterol recognition amino acid consensus (CRAC) motif influence protein expression or enzyme activity. This CRAC motif begins at residue 219, the site of a common G6PC2 non-synonymous single-nucleotide polymorphism (SNP), rs492594 (Val219Leu), though the functional impact of this SNP is disputed. In microsomal membrane preparations, the L219 variant has greater activity than the V219 variant, but this difference disappears when G6PC2 is purified in detergent micelles. We hypothesize that this was due to a differential association of the two variants with cholesterol. This concept was supported by the observation that the addition of cholesteryl hemi-succinate to the purified enzymes decreased the Vmax of the V219 and L219 variants ∼8-fold and ∼3 fold, respectively. We anticipate that these observations should support the rational development of G6PC2 inhibitors designed to lower FBG.
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Affiliation(s)
- Emily M. Hawes
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, U.S.A
| | - Derek P. Claxton
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, U.S.A
| | - James K. Oeser
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, U.S.A
| | - Richard M. O’Brien
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, U.S.A
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Gobet A, Moissonnier L, Chaptal V. CryoEM Data Analysis of Membrane Proteins. Practical Considerations on Amphipathic Belts, Ligands, and Variability Analysis. Methods Mol Biol 2024; 2715:471-483. [PMID: 37930545 DOI: 10.1007/978-1-0716-3445-5_28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
Membrane proteins data analysis by cryoEM shows some specificities, as can be found in other typical investigations such as biochemistry, biophysics, or X-ray crystallography. Membrane proteins are typically surrounded by an amphipathic belt that will have some degree of influence on the 3D reconstruction and analysis. In this chapter, we review our experience with the ABC transporter BmrA, as well as our statistical analysis of amphipathic belts around membrane proteins, to bring awareness on some particular features of membrane protein investigations by cryoEM.
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Affiliation(s)
- Alexia Gobet
- Molecular Microbiology and Structural Biochemistry, UMR5086 CNRS University Lyon 1, Lyon, France
| | - Loïck Moissonnier
- Molecular Microbiology and Structural Biochemistry, UMR5086 CNRS University Lyon 1, Lyon, France
| | - Vincent Chaptal
- Molecular Microbiology and Structural Biochemistry, UMR5086 CNRS University Lyon 1, Lyon, France.
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Chen C, Zhu Z. Recent Advances in the Nanoshells Approach for Encapsulation of Single Probiotics. Drug Des Devel Ther 2023; 17:2763-2774. [PMID: 37705759 PMCID: PMC10497064 DOI: 10.2147/dddt.s419897] [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: 05/04/2023] [Accepted: 08/16/2023] [Indexed: 09/15/2023] Open
Abstract
The intestine, often referred to as the "second brain" of the human body, houses a vast microbial community that plays a crucial role in maintaining the host's balance and directly impacting overall health. Probiotics, a type of beneficial microorganism, offer various health benefits when consumed. However, probiotics face challenges such as acidic conditions in the stomach, bile acids, enzymes, and other adverse factors before they can colonize the intestinal tissues. At present, pills, dry powder, encapsulation, chemically modified bacteria, and genetically engineered bacteria have emerged as the preferred method for the stable and targeted delivery of probiotics. In particular, the use of nanoshells on the surface of single probiotics has shown promise in regulating their growth and differentiation. These nanoshells can detach from the probiotics' surface upon reaching the intestine, facilitating direct contact between the probiotics and intestinal mucosa. In this perspective, we provide an overview of the current developments in the formation of nanoshells mediated by single probiotics. We also discuss the advantages and disadvantages of different nanocoating strategies and explore future trends in probiotic protection.
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Affiliation(s)
- Cheng Chen
- The People’s Hospital of Danyang, Affiliated Danyang Hospital of Nantong University, Danyang, Jiangsu Province, 212300, People’s Republic of China
| | - Ziyu Zhu
- The Affiliated Huai’an Hospital of Xuzhou Medical University and the Second People’s Hospital of Huai’an, Huai’an, 223002, People’s Republic of China
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Nyenhuis SB, Wu X, Strub MP, Yim YI, Stanton AE, Baena V, Syed ZA, Canagarajah B, Hammer JA, Hinshaw JE. OPA1 helical structures give perspective to mitochondrial dysfunction. Nature 2023; 620:1109-1116. [PMID: 37612506 DOI: 10.1038/s41586-023-06462-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 07/19/2023] [Indexed: 08/25/2023]
Abstract
Dominant optic atrophy is one of the leading causes of childhood blindness. Around 60-80% of cases1 are caused by mutations of the gene that encodes optic atrophy protein 1 (OPA1), a protein that has a key role in inner mitochondrial membrane fusion and remodelling of cristae and is crucial for the dynamic organization and regulation of mitochondria2. Mutations in OPA1 result in the dysregulation of the GTPase-mediated fusion process of the mitochondrial inner and outer membranes3. Here we used cryo-electron microscopy methods to solve helical structures of OPA1 assembled on lipid membrane tubes, in the presence and absence of nucleotide. These helical assemblies organize into densely packed protein rungs with minimal inter-rung connectivity, and exhibit nucleotide-dependent dimerization of the GTPase domains-a hallmark of the dynamin superfamily of proteins4. OPA1 also contains several unique secondary structures in the paddle domain that strengthen its membrane association, including membrane-inserting helices. The structural features identified in this study shed light on the effects of pathogenic point mutations on protein folding, inter-protein assembly and membrane interactions. Furthermore, mutations that disrupt the assembly interfaces and membrane binding of OPA1 cause mitochondrial fragmentation in cell-based assays, providing evidence of the biological relevance of these interactions.
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Affiliation(s)
- Sarah B Nyenhuis
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD, USA
| | - Xufeng Wu
- Light Microscopy Facility, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | - Marie-Paule Strub
- Protein Expression Facility, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | - Yang-In Yim
- Cell and Developmental Biology Center, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | - Abigail E Stanton
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD, USA
- Molecular Biology Department, Princeton University, Princeton, NJ, USA
| | - Valentina Baena
- Electron Microscopy Core, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | - Zulfeqhar A Syed
- Electron Microscopy Core, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | - Bertram Canagarajah
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD, USA
| | - John A Hammer
- Cell and Developmental Biology Center, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | - Jenny E Hinshaw
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD, USA.
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