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Oftedal TF, Diep DB, Kjos M. Design of Novel Saposin-like Bacteriocins Using a Hybrid Approach. Probiotics Antimicrob Proteins 2024:10.1007/s12602-024-10264-w. [PMID: 38713419 DOI: 10.1007/s12602-024-10264-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/17/2024] [Indexed: 05/08/2024]
Abstract
A multitude of approaches will be required to respond to the threat posed by the emergence and spread of antibiotic resistant pathogens. Bacteriocins have gained increasing attention as a possible alternative to antibiotics, as such peptide antimicrobials have mechanisms of action different from antibiotics and are therefore equally potent against antibiotic resistant bacteria as their susceptible counterparts. A group of bacteriocins known as saposin-like bacteriocins is believed to act directly on the bacterial membrane. Based on seven saposin-like leaderless bacteriocins, we have constructed a library of hybrid peptides containing all combinations of the N- and C-terminal halves of the native bacteriocins. All hybrid peptides were synthesized using in vitro protein expression and assayed for antimicrobial activity towards several pathogens. Of the 42 hybrid peptides, antimicrobial activity was confirmed for 11 novel hybrid peptides. Furthermore, several of the hybrid peptides exhibited altered antimicrobial spectra and apparent increase in potency compared to the peptides from which they were derived. The most promising hybrid, termed ISP26, was then obtained synthetically and shown to inhibit most of the Gram-positive species tested, including opportunistic pathogens and food spoilage bacteria. Additionally, ISP26 was shown to inhibit Acinetobacter, a species of Gram-negative bacteria frequently isolated from nosocomial infections. The activity of the hybrid library provides valuable insights into the design and screening of new active bacteriocins.
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Affiliation(s)
- Thomas F Oftedal
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.
| | - Dzung B Diep
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Morten Kjos
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
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2
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Sawyer TK, Aral E, Staros JV, Bobst CE, Garman SC. Human Saposin B Ligand Binding and Presentation to α-Galactosidase A. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.04.584535. [PMID: 38617236 PMCID: PMC11014568 DOI: 10.1101/2024.04.04.584535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Sphingolipid activator protein B (saposin B; SapB) is an essential activator of globotriaosylceramide (Gb3) catabolism by α-galactosidase A. However, the manner by which SapB stimulates α-galactosidase A activity remains unknown. To uncover the molecular mechanism of SapB presenting Gb3 to α-galactosidase A, we subjected the fluorescent substrate globotriaosylceramide-nitrobenzoxidazole (Gb3-NBD) to a series of biochemical and structural assays involving SapB. First, we showed that SapB stably binds Gb3-NBD using a fluorescence equilibrium binding assay, isolates Gb3-NBD from micelles, and facilitates α-galactosidase A cleavage of Gb3-NBD in vitro. Second, we crystallized SapB in the presence of Gb3-NBD and validated the ligand-bound assembly. Third, we captured transient interactions between SapB and α-galactosidase A by chemical cross-linking. Finally, we determined the crystal structure of SapB bound to α-galactosidase A. These findings establish general principles for molecular recognition in saposin:hydrolase complexes and highlight the utility of NBD reporter lipids in saposin biochemistry and structural biology.
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Affiliation(s)
- Thomas K Sawyer
- Department of Biochemistry & Molecular Biology, Institute of Applied Life Sciences, University of Massachusetts, Amherst, Massachusetts 01003, USA
- Program in Molecular & Cellular Biology, Institute of Applied Life Sciences, University of Massachusetts, Amherst, Massachusetts 01003, USA
| | - Efecan Aral
- Department of Biochemistry & Molecular Biology, Institute of Applied Life Sciences, University of Massachusetts, Amherst, Massachusetts 01003, USA
- Program in Molecular & Cellular Biology, Institute of Applied Life Sciences, University of Massachusetts, Amherst, Massachusetts 01003, USA
| | - James V Staros
- Department of Biochemistry & Molecular Biology, Institute of Applied Life Sciences, University of Massachusetts, Amherst, Massachusetts 01003, USA
| | - Cedric E Bobst
- Mass Spectrometry Core Facility, Institute of Applied Life Sciences, University of Massachusetts, Amherst, Massachusetts 01003, USA
| | - Scott C Garman
- Department of Biochemistry & Molecular Biology, Institute of Applied Life Sciences, University of Massachusetts, Amherst, Massachusetts 01003, USA
- Program in Molecular & Cellular Biology, Institute of Applied Life Sciences, University of Massachusetts, Amherst, Massachusetts 01003, USA
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3
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Lameris R, Shahine A, Veth M, Westerman B, Godfrey DI, Lutje Hulsik D, Brouwer P, Rossjohn J, de Gruijl TD, van der Vliet HJ. Enhanced CD1d phosphatidylserine presentation using a single-domain antibody promotes immunomodulatory CD1d-TIM-3 interactions. J Immunother Cancer 2023; 11:e007631. [PMID: 38040419 PMCID: PMC10693867 DOI: 10.1136/jitc-2023-007631] [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] [Accepted: 11/05/2023] [Indexed: 12/03/2023] Open
Abstract
BACKGROUND CD1d is a monomorphic major histocompatibility complex class I-like molecule that presents lipid antigens to distinct T-cell subsets and can be expressed by various malignancies. Antibody-mediated targeting of CD1d on multiple myeloma cells was reported to induce apoptosis and could therefore constitute a novel therapeutic approach. METHODS To determine how a CD1d-specific single-domain antibody (VHH) enhances binding of the early apoptosis marker annexin V to CD1d+ tumor cells we use in vitro cell-based assays and CRISPR-Cas9-mediated gene editing, and to determine the structure of the VHH1D17-CD1d(endogenous lipid) complex we use X-ray crystallography. RESULTS Anti-CD1d VHH1D17 strongly enhances annexin V binding to CD1d+ tumor cells but this does not reflect induction of apoptosis. Instead, we show that VHH1D17 enhances presentation of phosphatidylserine (PS) in CD1d and that this is saposin dependent. The crystal structure of the VHH1D17-CD1d(endogenous lipid) complex demonstrates that VHH1D17 binds the A'-pocket of CD1d, leaving the lipid headgroup solvent exposed, and has an electro-negatively charged patch which could be involved in the enhanced PS presentation by CD1d. Presentation of PS in CD1d does not trigger phagocytosis but leads to greatly enhanced binding of T-cell immunoglobulin and mucin domain containing molecules (TIM)-1 to TIM-3, TIM-4 and induces TIM-3 signaling. CONCLUSION Our findings reveal the existence of an immune modulatory CD1d(PS)-TIM axis with potentially unexpected implications for immune regulation in both physiological and pathological conditions.
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Affiliation(s)
- Roeland Lameris
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC Location VUmc, Amsterdam, The Netherlands
| | - Adam Shahine
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Myrthe Veth
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC Location VUmc, Amsterdam, The Netherlands
| | - Bart Westerman
- Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam UMC Location VUmc, Amsterdam, The Netherlands
| | - Dale I Godfrey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | | | | | - Jamie Rossjohn
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - Tanja D de Gruijl
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC Location VUmc, Amsterdam, The Netherlands
| | - Hans J van der Vliet
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC Location VUmc, Amsterdam, The Netherlands
- LAVA Therapeutics, Utrecht, The Netherlands
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4
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Sandhoff R, Sandhoff K. Neuronal Ganglioside and Glycosphingolipid (GSL) Metabolism and Disease : Cascades of Secondary Metabolic Errors Can Generate Complex Pathologies (in LSDs). ADVANCES IN NEUROBIOLOGY 2023; 29:333-390. [PMID: 36255681 DOI: 10.1007/978-3-031-12390-0_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Glycosphingolipids (GSLs) are a diverse group of membrane components occurring mainly on the surfaces of mammalian cells. They and their metabolites have a role in intercellular communication, serving as versatile biochemical signals (Kaltner et al, Biochem J 476(18):2623-2655, 2019) and in many cellular pathways. Anionic GSLs, the sialic acid containing gangliosides (GGs), are essential constituents of neuronal cell surfaces, whereas anionic sulfatides are key components of myelin and myelin forming oligodendrocytes. The stepwise biosynthetic pathways of GSLs occur at and lead along the membranes of organellar surfaces of the secretory pathway. After formation of the hydrophobic ceramide membrane anchor of GSLs at the ER, membrane-spanning glycosyltransferases (GTs) of the Golgi and Trans-Golgi network generate cell type-specific GSL patterns for cellular surfaces. GSLs of the cellular plasma membrane can reach intra-lysosomal, i.e. luminal, vesicles (ILVs) by endocytic pathways for degradation. Soluble glycoproteins, the glycosidases, lipid binding and transfer proteins and acid ceramidase are needed for the lysosomal catabolism of GSLs at ILV-membrane surfaces. Inherited mutations triggering a functional loss of glycosylated lysosomal hydrolases and lipid binding proteins involved in GSL degradation cause a primary lysosomal accumulation of their non-degradable GSL substrates in lysosomal storage diseases (LSDs). Lipid binding proteins, the SAPs, and the various lipids of the ILV-membranes regulate GSL catabolism, but also primary storage compounds such as sphingomyelin (SM), cholesterol (Chol.), or chondroitin sulfate can effectively inhibit catabolic lysosomal pathways of GSLs. This causes cascades of metabolic errors, accumulating secondary lysosomal GSL- and GG- storage that can trigger a complex pathology (Breiden and Sandhoff, Int J Mol Sci 21(7):2566, 2020).
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Affiliation(s)
- Roger Sandhoff
- Lipid Pathobiochemistry Group, German Cancer Research Center, Heidelberg, Germany
| | - Konrad Sandhoff
- LIMES, c/o Kekule-Institute for Organic Chemistry and Biochemistry, University of Bonn, Bonn, Germany.
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5
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Zhang Y, Deng P, Dai C, Wu M, Liu X, Li L, Pan X, Yuan J. Investigation of putative antimicrobial peptides in Carassius gibel, revealing a practical approach to screening antimicrobials. FISH & SHELLFISH IMMUNOLOGY 2022; 121:254-264. [PMID: 34990806 DOI: 10.1016/j.fsi.2021.12.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 12/22/2021] [Accepted: 12/28/2021] [Indexed: 06/14/2023]
Abstract
Antimicrobial peptides (AMPs) and their mimics are rapidly gaining attention as a new class of antimicrobials due to their clinical potential. AMPs are widely distributed throughout nature and participate in the innate host defense. In this study, 18 AMPs, including 3 β-defensins, 3 hepcidins, 4 liver-expressed antimicrobial peptide 2 (LEAP-2) compounds, 4 g-type lysozymes, 2 c-type lysozymes, and 2 NK-lysins, were identified from the genome of Carassius auratus by a homologous search and were further classified based on their fundamental structural features and molecular phylogeny. C. auratus AMPs were found to be ubiquitously distributed in all tested tissues and showed similar expression profiles, with the exception of β-defensins, when RT-qPCR was used to investigate the tissue distribution of AMPs in healthy Carassius gibel. In addition, the expression levels of NK-lysin genes in the tested tissues tended to be upregulated upon bacterial and viral infection when representative NK-lysins were chosen to examine their relative expression levels in various tissues. Importantly, the synthetic peptide caNKL2102-119, which targets the functional domain of saposin B in caNK-lysins, could effectively counter Aeromonas hydrophila, Staphylococcus aureus, and Escherichia coli with minimum inhibitory concentration (MIC) values of 3-6 μg/mL, as well as inhibit the proliferation of spring viraemia of carp virus (SVCV). These results provide potential targets for antibiotic-free breeding in the aquaculture industry.
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Affiliation(s)
- Yujun Zhang
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China; Hubei Engineering Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, 430070, People's Republic of China
| | - Ping Deng
- Wuhan Academy of Agricultural Sciences, Wuhan, 430070, People's Republic of China
| | - Caijiao Dai
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Mengke Wu
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Xueqin Liu
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China; Hubei Engineering Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, 430070, People's Republic of China
| | - Lijuan Li
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China; Hubei Engineering Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, 430070, People's Republic of China
| | - Xiaoyi Pan
- Key Laboratory of Healthy Freshwater Aquaculture, Ministry of Agriculture, Key Laboratory of Fish Health and Nutrition of Zhejiang Province, Zhejiang Institute of Freshwater Fisheries, Huzhou, 313001, People's Republic of China.
| | - Junfa Yuan
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China; Hubei Engineering Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, 430070, People's Republic of China.
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6
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Abstract
Membrane proteins (MPs) play essential roles in numerous cellular processes. Because around 70% of the currently marketed drugs target MPs, a detailed understanding of their structure, binding properties, and functional dynamics in a physiologically relevant environment is crucial for a more detailed understanding of this important protein class. We here summarize the benefits of using lipid nanodiscs for NMR structural investigations and provide a detailed overview of the currently used lipid nanodisc systems as well as their applications in solution-state NMR. Despite the increasing use of other structural methods for the structure determination of MPs in lipid nanodiscs, solution NMR turns out to be a versatile tool to probe a wide range of MP features, ranging from the structure determination of small to medium-sized MPs to probing ligand and partner protein binding as well as functionally relevant dynamical signatures in a lipid nanodisc setting. We will expand on these topics by discussing recent NMR studies with lipid nanodiscs and work out a key workflow for optimizing the nanodisc incorporation of an MP for subsequent NMR investigations. With this, we hope to provide a comprehensive background to enable an informed assessment of the applicability of lipid nanodiscs for NMR studies of a particular MP of interest.
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Affiliation(s)
- Umut Günsel
- Bavarian NMR Center (BNMRZ) at the Department of Chemistry, Technical University of Munich, Ernst-Otto-Fischer-Strasse 2, 85748 Garching, Germany
| | - Franz Hagn
- Bavarian NMR Center (BNMRZ) at the Department of Chemistry, Technical University of Munich, Ernst-Otto-Fischer-Strasse 2, 85748 Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
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Kurgan KW, Chen B, Brown KA, Falco Cobra P, Ye X, Ge Y, Gellman SH. Stable Picodisc Assemblies from Saposin Proteins and Branched Detergents. Biochemistry 2021; 60:1108-1119. [PMID: 33755420 DOI: 10.1021/acs.biochem.0c00924] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Methods for maintaining membrane proteins in their native state after removal from the lipid bilayer are essential for the study of this important class of biomacromolecules. Common solubilization strategies range from the use of detergents to more complex systems that involve a polypeptide working in concert with lipids or detergents, such as nanodiscs, picodiscs, and peptidiscs, in which an engineered protein or synthetic peptide surrounds the membrane protein along with a lipid sheath. Picodiscs employ the protein saposin A, which naturally functions to facilitate lipid degradation in the lysozome. Saposin A-amphiphile complexes therefore tend to be most stable at acidic pH, which is not optimal for most membrane protein applications. In search of new picodisc assemblies, we have explored pairings of saposin A or other saposin proteins with a range of detergents, and we have identified a number of combinations that spontaneously co-assemble at neutral pH. The resulting picodiscs are stable for weeks and have been characterized by size-exclusion chromatography, native mass spectrometry, and small angle X-ray scattering. The new assemblies are formed by double-tail detergents rather than more traditional single-tail detergents; the double-tail detergents can be seen as structurally intermediate between single-tail detergents and common lipids. In addition to saposin A, an engineered variant of saposin B (designated saposin BW) forms picodisc assemblies. These findings provide a framework for future efforts to solubilize membrane proteins with multiple picodisc systems that were previously unknown.
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8
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Sowa ST, Moilanen A, Biterova E, Saaranen MJ, Lehtiö L, Ruddock LW. High-resolution Crystal Structure of Human pERp1, A Saposin-like Protein Involved in IgA, IgM and Integrin Maturation in the Endoplasmic Reticulum. J Mol Biol 2021; 433:166826. [PMID: 33453188 DOI: 10.1016/j.jmb.2021.166826] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 01/05/2021] [Accepted: 01/05/2021] [Indexed: 01/24/2023]
Abstract
The folding of disulfide bond containing proteins in the endoplasmic reticulum (ER) is a complex process that requires protein folding factors, some of which are protein-specific. The ER resident saposin-like protein pERp1 (MZB1, CNPY5) is crucial for the correct folding of IgA, IgM and integrins. pERp1 also plays a role in ER calcium homeostasis and plasma cell mobility. As an important factor for proper IgM maturation and hence immune function, pERp1 is upregulated in many auto-immune diseases. This makes it a potential therapeutic target. pERp1 belongs to the CNPY family of ER resident saposin-like proteins. To date, five of these proteins have been identified. All are implicated in protein folding and all contain a saposin-like domain. All previously structurally characterized saposins are involved in lipid binding. However, there are no reports of CNPY family members interacting with lipids, suggesting a novel function for the saposin fold. However, the molecular mechanisms of their function remain elusive. To date, no structure of any CNPY protein has been reported. Here, we present the high-resolution (1.4 Å) crystal structure of human pERp1 and confirm that it has a saposin-fold with unique structural elements not present in other saposin-fold structures. The implications for the role of CNPY proteins in protein folding in the ER are discussed.
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Affiliation(s)
- Sven T Sowa
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7, 90220 Oulu, Finland; Biocenter Oulu, Aapistie 5, 90220 Oulu, Finland.
| | - Antti Moilanen
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7, 90220 Oulu, Finland.
| | - Ekaterina Biterova
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7, 90220 Oulu, Finland
| | - Mirva J Saaranen
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7, 90220 Oulu, Finland.
| | - Lari Lehtiö
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7, 90220 Oulu, Finland; Biocenter Oulu, Aapistie 5, 90220 Oulu, Finland.
| | - Lloyd W Ruddock
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7, 90220 Oulu, Finland.
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Shamin M, Spratley SJ, Graham SC, Deane JE. A Tetrameric Assembly of Saposin A: Increasing Structural Diversity in Lipid Transfer Proteins. CONTACT (THOUSAND OAKS (VENTURA COUNTY, CALIF.)) 2021; 4:251525642110523. [PMID: 37143956 PMCID: PMC7614494 DOI: 10.1177/25152564211052382] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Saposins are lipid transfer proteins required for the degradation of sphingolipids in the lysosome. These small proteins bind lipids by transitioning from a closed, monomeric state to an open conformation exposing a hydrophobic surface that binds and shields hydrophobic lipid tails from the aqueous environment. Saposins form a range of multimeric assemblies to encompass these bound lipids and present them to hydrolases in the lysosome. This lipid-binding property of human saposin A has been exploited to form lipoprotein nanodiscs suitable for structural studies of membrane proteins. Here we present the crystal structure of a unique tetrameric assembly of murine saposin A produced serendipitously, following modifications of published protocols for making lipoprotein nanodiscs. The structure of this new saposin oligomer highlights the diversity of tertiary arrangement that can be adopted by these important lipid transfer proteins.
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Affiliation(s)
- Maria Shamin
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
| | - Samantha J. Spratley
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
| | - Stephen C. Graham
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK
| | - Janet E. Deane
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
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10
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The interplay between Glucocerebrosidase, α-synuclein and lipids in human models of Parkinson's disease. Biophys Chem 2020; 273:106534. [PMID: 33832803 DOI: 10.1016/j.bpc.2020.106534] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 12/18/2020] [Accepted: 12/18/2020] [Indexed: 12/25/2022]
Abstract
Mutations in the gene GBA, encoding glucocerebrosidase (GCase), are the highest genetic risk factor for Parkinson's disease (PD). GCase is a lysosomal glycoprotein responsible for the hydrolysis of glucosylceramide into glucose and ceramide. Mutations in GBA cause a decrease in GCase activity, stability and protein levels which in turn lead to the accumulation of GCase lipid substrates as well as α-synuclein (αS) in vitro and in vivo. αS is the main constituent of Lewy bodies found in the brain of PD patients and an increase in its levels was found to be associated with a decrease in GCase activity/protein levels in vitro and in vivo. In this review, we describe the reported biophysical and biochemical changes that GBA mutations can induce in GCase activity and stability as well as the current overview of the levels of GCase protein/activity, αS and lipids measured in patient-derived samples including post-mortem brains, stem cell-derived neurons, cerebrospinal fluid, blood and fibroblasts as well as in SH-SY5Y cells. In particular, we report how the levels of αS and lipids are affected by/correlated to significant changes in GCase activity/protein levels and which cellular pathways are activated or disrupted by these changes in each model. Finally, we review the current strategies used to revert the changes in the levels of GCase activity/protein, αS and lipids in the context of PD.
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11
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Dupuis JH, Wang S, Song C, Yada RY. The role of disulfide bonds in a Solanum tuberosum saposin-like protein investigated using molecular dynamics. PLoS One 2020; 15:e0237884. [PMID: 32841243 PMCID: PMC7447066 DOI: 10.1371/journal.pone.0237884] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 08/04/2020] [Indexed: 01/31/2023] Open
Abstract
The Solanum tuberosum plant specific insert (StPSI) has a defensive role in potato plants, with the requirements of acidic pH and anionic lipids. The StPSI contains a set of three highly conserved disulfide bonds that bridge the protein’s helical domains. Removal of these bonds leads to enhanced membrane interactions. This work examined the effects of their sequential removal, both individually and in combination, using all-atom molecular dynamics to elucidate the role of disulfide linkages in maintaining overall protein tertiary structure. The tertiary structure was found to remain stable at both acidic (active) and neutral (inactive) pH despite the removal of disulfide linkages. The findings include how the dimer structure is stabilized and the impact on secondary structure on a residue-basis as a function of disulfide bond removal. The StPSI possesses an extensive network of inter-monomer hydrophobic interactions and intra-monomer hydrogen bonds, which is likely the key to the stability of the StPSI by stabilizing local secondary structure and the tertiary saposin-fold, leading to a robust association between monomers, regardless of the disulfide bond state. Removal of disulfide bonds did not significantly impact secondary structure, nor lead to quaternary structural changes. Instead, disulfide bond removal induces regions of amino acids with relatively higher or lower variation in secondary structure, relative to when all the disulfide bonds are intact. Although disulfide bonds are not required to preserve overall secondary structure, they may have an important role in maintaining a less plastic structure within plant cells in order to regulate membrane affinity or targeting.
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Affiliation(s)
- John H. Dupuis
- Food, Nutrition, and Health Program, Faculty of Land and Food Systems, University of British Columbia, Vancouver, British Columbia, Canada
| | - Shenlin Wang
- College of Chemistry and Molecular Engineering and Beijing NMR Center, Peking University, Beijing, People's Republic of China
| | - Chen Song
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, People’s Republic of China
| | - Rickey Y. Yada
- Food, Nutrition, and Health Program, Faculty of Land and Food Systems, University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail:
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12
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The Droserasin 1 PSI: A Membrane-Interacting Antimicrobial Peptide from the Carnivorous Plant Drosera capensis. Biomolecules 2020; 10:biom10071069. [PMID: 32709016 PMCID: PMC7407137 DOI: 10.3390/biom10071069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 07/08/2020] [Accepted: 07/13/2020] [Indexed: 12/11/2022] Open
Abstract
The Droserasins, aspartic proteases from the carnivorous plant Drosera capensis, contain a 100-residue plant-specific insert (PSI) that is post-translationally cleaved and independently acts as an antimicrobial peptide. PSIs are of interest not only for their inhibition of microbial growth, but also because they modify the size of lipid vesicles and strongly interact with biological membranes. PSIs may therefore be useful for modulating lipid systems in NMR studies of membrane proteins. Here we present the expression and biophysical characterization of the Droserasin 1 PSI (D1 PSI.) This peptide is monomeric in solution and maintains its primarily α-helical secondary structure over a wide range of temperatures and pH values, even under conditions where its three disulfide bonds are reduced. Vesicle fusion assays indicate that the D1 PSI strongly interacts with bacterial and fungal lipids at pH 5 and lower, consistent with the physiological pH of D. capensis mucilage. It binds lipids with a variety of head groups, highlighting its versatility as a potential stabilizer for lipid nanodiscs. Solid-state NMR spectra collected at a field strength of 36 T, using a unique series-connected hybrid magnet, indicate that the peptide is folded and strongly bound to the membrane. Molecular dynamics simulations indicate that the peptide is stable as either a monomer or a dimer in a lipid bilayer. Both the monomer and the dimer allow the passage of water through the membrane, albeit at different rates.
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13
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Cheung LKY, Dupuis JH, Dee DR, Bryksa BC, Yada RY. Roles of Plant-Specific Inserts in Plant Defense. TRENDS IN PLANT SCIENCE 2020; 25:682-694. [PMID: 32526173 DOI: 10.1016/j.tplants.2020.02.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 02/10/2020] [Accepted: 02/14/2020] [Indexed: 06/11/2023]
Abstract
Ubiquitously expressed in plants, the plant-specific insert (PSI) of typical plant aspartic proteases (tpAPs) has been associated with plant development, stress response, and defense processes against invading pathogens. Despite sharing high sequence identity, structural studies revealed possible different mechanisms of action among species. The PSI induces signaling pathways of defense hormones in vivo and demonstrates broad-spectrum activity against phytopathogens in vitro. Recent characterization of the PSI-tpAP relationship uncovered novel, nonconventional intracellular protein transport pathways and improved tpAP production yields for industrial applications. In spite of research to date, relatively little is known about the structure-function relationships of PSIs. A comprehensive understanding of their biological roles may benefit plant protection strategies against virulent phytopathogens.
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Affiliation(s)
- Lennie K Y Cheung
- Faculty of Land and Food Systems, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - John H Dupuis
- Faculty of Land and Food Systems, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Derek R Dee
- Faculty of Land and Food Systems, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Brian C Bryksa
- Faculty of Land and Food Systems, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Rickey Y Yada
- Faculty of Land and Food Systems, University of British Columbia, Vancouver, BC V6T 1Z4, Canada. @ubc.ca
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14
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Klöpfer K, Hagn F. Beyond detergent micelles: The advantages and applications of non-micellar and lipid-based membrane mimetics for solution-state NMR. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2019; 114-115:271-283. [PMID: 31779883 DOI: 10.1016/j.pnmrs.2019.08.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/20/2019] [Accepted: 08/22/2019] [Indexed: 06/10/2023]
Abstract
Membrane proteins are important players in signal transduction and the exchange of metabolites within or between cells. Thus, this protein class is the target of around 60 % of currently marketed drugs, emphasizing their essential biological role. Besides functional assays, structural and dynamical investigations on this protein class are crucial to fully understanding their functionality. Even though X-ray crystallography and electron microscopy are the main methods to determine structures of membrane proteins and their complexes, NMR spectroscopy can contribute essential information on systems that (a) do not crystallize and (b) are too small for EM. Furthermore, NMR is a versatile tool for monitoring functional dynamics of biomolecules at various time scales. A crucial aspect of such studies is the use of a membrane mimetic that resembles a native environment and thus enables the extraction of functional insights. In recent decades, the membrane protein NMR community has moved from rather harsh detergents to membrane systems having more native-like properties. In particular, most recently phospholipid nanodiscs have been developed and optimized mainly for solution-state NMR but are now also being used for solid-state NMR spectroscopy. Nanodiscs consist of a patch of a planar lipid bilayer that is encircled by different (bio-)polymers to form particles of defined and tunable size. In this review, we provide an overview of available membrane mimetics, including nanodiscs, amphipols and bicelles, that are suitable for high-resolution NMR spectroscopy and describe how these advanced membrane mimetics can facilitate NMR studies on the structure and dynamics of membrane proteins. Since the stability of membrane proteins depends critically on the chosen membrane mimetic, we emphasize the importance of a suitable system that is not necessarily developed for solution-state NMR applications and hence requires optimization for each membrane protein. However, lipid-based membrane mimetics offer the possibility of performing NMR experiments at elevated temperatures and studying ligand and partner protein complexes as well as their functional dynamics in a realistic membrane environment. In order to be able to make an informed decision during the selection of a suitable membrane system, we provide a detailed overview of the available options for various membrane protein classes and thereby facilitate this often-difficult selection process for a broad range of desired NMR applications.
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Affiliation(s)
- Kai Klöpfer
- Bavarian NMR Center at the Department of Chemistry, Technical University of Munich, Ernst-Otto-Fischer-Str. 2, 85747 Garching, Germany; Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Franz Hagn
- Bavarian NMR Center at the Department of Chemistry, Technical University of Munich, Ernst-Otto-Fischer-Str. 2, 85747 Garching, Germany; Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany.
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15
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Autzen HE, Julius D, Cheng Y. Membrane mimetic systems in CryoEM: keeping membrane proteins in their native environment. Curr Opin Struct Biol 2019; 58:259-268. [PMID: 31279500 DOI: 10.1016/j.sbi.2019.05.022] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 05/24/2019] [Accepted: 05/27/2019] [Indexed: 01/02/2023]
Abstract
Advances in electron microscopes, detectors and data processing algorithms have greatly facilitated the structural determination of many challenging integral membrane proteins that have been evasive to crystallization. These breakthroughs facilitate the application and development of various membrane protein solubilization approaches for structural studies, including reconstitution into lipid nanoparticles. In this review, we discuss various approaches for preparing transmembrane proteins for structural determination with single-particle electron cryo microscopy (cryoEM).
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Affiliation(s)
- Henriette E Autzen
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143, USA; Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - David Julius
- Department of Physiology, University of California, San Francisco, CA 94143, USA.
| | - Yifan Cheng
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143, USA; Howard Hughes Medical Institute, University of California, San Francisco, CA 94143, USA.
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16
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Abstract
Glycosphingolipids are cell-type-specific components of the outer leaflet of mammalian plasma membranes. Gangliosides, sialic acid–containing glycosphingolipids, are especially enriched on neuronal surfaces. As amphi-philic molecules, they comprise a hydrophilic oligosaccharide chain attached to a hydrophobic membrane anchor, ceramide. Whereas glycosphingolipid formation is catalyzed by membrane-bound enzymes along the secretory pathway, degradation takes place at the surface of intralysosomal vesicles of late endosomes and lysosomes catalyzed in a stepwise fashion by soluble hydrolases and assisted by small lipid-binding glycoproteins. Inherited defects of lysosomal hydrolases or lipid-binding proteins cause the accumulation of undegradable material in lysosomal storage diseases (GM1 and GM2 gangliosidosis; Fabry, Gaucher, and Krabbe diseases; and metachromatic leukodystrophy). The catabolic processes are strongly modified by the lipid composition of the substrate-carrying membranes, and the pathological accumulation of primary storage compounds can trigger an accumulation of secondary storage compounds (e.g., small glycosphingolipids and cholesterol in Niemann-Pick disease).
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Affiliation(s)
- Bernadette Breiden
- LIMES Institute, Membrane Biology and Lipid Biochemistry Unit, Universität Bonn, D-53121 Bonn, Germany;,
| | - Konrad Sandhoff
- LIMES Institute, Membrane Biology and Lipid Biochemistry Unit, Universität Bonn, D-53121 Bonn, Germany;,
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17
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Inherited monogenic defects of ceramide metabolism: Molecular bases and diagnoses. Clin Chim Acta 2019; 495:457-466. [PMID: 31128082 DOI: 10.1016/j.cca.2019.05.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 05/20/2019] [Accepted: 05/21/2019] [Indexed: 02/07/2023]
Abstract
Ceramides are membrane lipids implicated in the regulation of numerous biological functions. Recent evidence suggests that specific subsets of molecular species of ceramide may play distinct physiological roles. The importance of this family of molecules in vertebrates is witnessed by the deleterious consequences of genetic alterations in ceramide metabolism. This brief review summarizes the clinical presentation of human disorders due to the deficiency of enzymes involved either in the biosynthesis or the degradation of ceramides. Information on the possible underlying pathophysiological mechanisms is also provided, based on knowledge gathered from animal models of these inherited rare conditions. When appropriate, tools for chemical and molecular diagnosis of these disorders and therapeutic options are also presented.
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18
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Mechanism of glucocerebrosidase activation and dysfunction in Gaucher disease unraveled by molecular dynamics and deep learning. Proc Natl Acad Sci U S A 2019; 116:5086-5095. [PMID: 30808805 DOI: 10.1073/pnas.1818411116] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The lysosomal enzyme glucocerebrosidase-1 (GCase) catalyzes the cleavage of a major glycolipid glucosylceramide into glucose and ceramide. The absence of fully functional GCase leads to the accumulation of its lipid substrates in lysosomes, causing Gaucher disease, an autosomal recessive disorder that displays profound genotype-phenotype nonconcordance. More than 250 disease-causing mutations in GBA1, the gene encoding GCase, have been discovered, although only one of these, N370S, causes 70% of disease. Here, we have used a knowledge-based docking protocol that considers experimental data of protein-protein binding to generate a complex between GCase and its known facilitator protein saposin C (SAPC). Multiscale molecular-dynamics simulations were used to study lipid self-assembly, membrane insertion, and the dynamics of the interactions between different components of the complex. Deep learning was applied to propose a model that explains the mechanism of GCase activation, which requires SAPC. Notably, we find that conformational changes in the loops at the entrance of the substrate-binding site are stabilized by direct interactions with SAPC and that the loss of such interactions induced by N370S and another common mutation, L444P, result in destabilization of the complex and reduced GCase activation. Our findings provide an atomistic-level explanation for GCase activation and the precise mechanism through which N370S and L444P cause Gaucher disease.
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19
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Johansson J, Curstedt T. Synthetic surfactants with SP-B and SP-C analogues to enable worldwide treatment of neonatal respiratory distress syndrome and other lung diseases. J Intern Med 2019; 285:165-186. [PMID: 30357986 DOI: 10.1111/joim.12845] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Treatment of neonatal respiratory distress syndrome (RDS) using animal-derived lung surfactant preparations has reduced the mortality of handling premature infants with RDS to a 50th of that in the 1960s. The supply of animal-derived lung surfactants is limited and only a part of the preterm babies is treated. Thus, there is a need to develop well-defined synthetic replicas based on key components of natural surfactant. A synthetic product that equals natural-derived surfactants would enable cost-efficient production and could also facilitate the development of the treatments of other lung diseases than neonatal RDS. Recently the first synthetic surfactant that contains analogues of the two hydrophobic surfactant proteins B (SP-B) and SP-C entered clinical trials for the treatment of neonatal RDS. The development of functional synthetic analogues of SP-B and SP-C, however, is considerably more challenging than anticipated 30 years ago when the first structural information of the native proteins became available. For SP-B, a complex three-dimensional dimeric structure stabilized by several disulphides has necessitated the design of miniaturized analogues. The main challenge for SP-C has been the pronounced amyloid aggregation propensity of its transmembrane region. The development of a functional non-aggregating SP-C analogue that can be produced synthetically was achieved by designing the amyloidogenic native sequence so that it spontaneously forms a stable transmembrane α-helix.
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Affiliation(s)
- J Johansson
- Department of Neurobiology, Care Sciences and Society, Section for Neurogeriatrics, Karolinska Institutet, Huddinge, Sweden
| | - T Curstedt
- Laboratory for Surfactant Research, Department of Molecular Medicine and Surgery, Karolinska Institutet at Karolinska University Hospital, Stockholm, Sweden
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20
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An Isoprene Lipid-Binding Protein Promotes Eukaryotic Coenzyme Q Biosynthesis. Mol Cell 2019; 73:763-774.e10. [PMID: 30661980 DOI: 10.1016/j.molcel.2018.11.033] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 10/16/2018] [Accepted: 11/27/2018] [Indexed: 02/06/2023]
Abstract
The biosynthesis of coenzyme Q presents a paradigm for how cells surmount hydrophobic barriers in lipid biology. In eukaryotes, CoQ precursors-among nature's most hydrophobic molecules-must somehow be presented to a series of enzymes peripherally associated with the mitochondrial inner membrane. Here, we reveal that this process relies on custom lipid-binding properties of COQ9. We show that COQ9 repurposes the bacterial TetR fold to bind aromatic isoprenes with high specificity, including CoQ intermediates that likely reside entirely within the bilayer. We reveal a process by which COQ9 associates with cardiolipin-rich membranes and warps the membrane surface to access this cargo. Finally, we identify a molecular interface between COQ9 and the hydroxylase COQ7, motivating a model whereby COQ9 presents intermediates directly to CoQ enzymes. Overall, our results provide a mechanism for how a lipid-binding protein might access, select, and deliver specific cargo from a membrane to promote biosynthesis.
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21
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Davidson BA, Hassan S, Garcia EJ, Tayebi N, Sidransky E. Exploring genetic modifiers of Gaucher disease: The next horizon. Hum Mutat 2018; 39:1739-1751. [PMID: 30098107 PMCID: PMC6240360 DOI: 10.1002/humu.23611] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 08/01/2018] [Accepted: 08/03/2018] [Indexed: 12/26/2022]
Abstract
Gaucher disease is an autosomal recessive lysosomal storage disorder resulting from mutations in the gene GBA1 that lead to a deficiency in the enzyme glucocerebrosidase. Accumulation of the enzyme's substrates, glucosylceramide and glucosylsphingosine, results in symptoms ranging from skeletal and visceral involvement to neurological manifestations. Nonetheless, there is significant variability in clinical presentations amongst patients, with limited correlation between genotype and phenotype. Contributing to this clinical variation are genetic modifiers that influence the phenotypic outcome of the disorder. In this review, we explore the role of genetic modifiers in Mendelian disorders and describe methods to facilitate their discovery. In addition, we provide examples of candidate modifiers of Gaucher disease, explore their relevance in the development of potential therapeutics, and discuss the impact of GBA1 and modifying mutations on other more common diseases like Parkinson disease. Identifying these important modulators of Gaucher phenotype may ultimately unravel the complex relationship between genotype and phenotype and lead to improved counseling and treatments.
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Affiliation(s)
- Brad A. Davidson
- Section on Molecular Neurogenetics, Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Shahzeb Hassan
- Section on Molecular Neurogenetics, Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Eric Joshua Garcia
- Section on Molecular Neurogenetics, Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Nahid Tayebi
- Section on Molecular Neurogenetics, Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Ellen Sidransky
- Section on Molecular Neurogenetics, Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
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22
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Gebai A, Gorelik A, Nagar B. Crystal structure of saposin D in an open conformation. J Struct Biol 2018; 204:145-150. [PMID: 30026085 DOI: 10.1016/j.jsb.2018.07.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 07/10/2018] [Accepted: 07/16/2018] [Indexed: 11/30/2022]
Abstract
Saposins are accessory proteins that aid in the degradation of sphingolipids by hydrolytic enzymes. Their structure usually comprises four α-helices arranged in various conformations including an open, V-shaped form that is generally associated with the ability to interact with membranes and/or enzymes to accentuate activity. Saposin D is required by the lysosomal hydrolase, acid ceramidase, which breaks down ceramide into sphingosine and free fatty acid, to display optimal activity. The structure of saposin D was previously determined in an inactive conformation, revealing a monomeric, closed and compact form. Here, we present the crystal structure of the open, V-shaped form of saposin D. The overall shape is similar to the open conformation found in other saposins with slight differences in the angles between the α-helices. The structure forms a dimer that serves to stabilize the hydrophobic surface exposed in the open form, which results in an internal, hydrophobic cavity that could be used to carry extracted membrane lipids.
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Affiliation(s)
- Ahmad Gebai
- Department of Biochemistry and Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montreal, QC H3G 0B1, Canada
| | - Alexei Gorelik
- Department of Biochemistry and Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montreal, QC H3G 0B1, Canada
| | - Bhushan Nagar
- Department of Biochemistry and Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montreal, QC H3G 0B1, Canada.
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23
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Sandhoff R, Sandhoff K. Emerging concepts of ganglioside metabolism. FEBS Lett 2018; 592:3835-3864. [PMID: 29802621 DOI: 10.1002/1873-3468.13114] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 05/15/2018] [Accepted: 05/17/2018] [Indexed: 11/12/2022]
Abstract
Gangliosides (GGs) are sialic acid-containing glycosphingolipids (GSLs) and major membrane components enriched on cellular surfaces. Biosynthesis of mammalian GGs starts at the cytosolic leaflet of endoplasmic reticulum (ER) membranes with the formation of their hydrophobic ceramide anchors. After intracellular ceramide transfer to Golgi and trans-Golgi network (TGN) membranes, anabolism of GGs, as well as of other GSLs, is catalyzed by membrane-spanning glycosyltransferases (GTs) along the secretory pathway. Combined activity of only a few promiscuous GTs allows for the formation of cell-type-specific glycolipid patterns. Following an exocytotic vesicle flow to the cellular plasma membranes, GGs can be modified by metabolic reactions at or near the cellular surface. For degradation, GGs are endocytosed to reach late endosomes and lysosomes. Whereas membrane-spanning enzymes of the secretory pathway catalyze GSL and GG formation, a cooperation of soluble glycosidases, lipases and lipid-binding cofactors, namely the sphingolipid activator proteins (SAPs), act as the main players of GG and GSL catabolism at intralysosomal luminal vesicles (ILVs).
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Affiliation(s)
- Roger Sandhoff
- Lipid Pathobiochemistry Group (G131), German Cancer Research Center, Heidelberg, Germany
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24
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Gebai A, Gorelik A, Li Z, Illes K, Nagar B. Structural basis for the activation of acid ceramidase. Nat Commun 2018; 9:1621. [PMID: 29692406 PMCID: PMC5915598 DOI: 10.1038/s41467-018-03844-2] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 03/14/2018] [Indexed: 01/21/2023] Open
Abstract
Acid ceramidase (aCDase, ASAH1) hydrolyzes lysosomal membrane ceramide into sphingosine, the backbone of all sphingolipids, to regulate many cellular processes. Abnormal function of aCDase leads to Farber disease, spinal muscular atrophy with progressive myoclonic epilepsy, and is associated with Alzheimer’s, diabetes, and cancer. Here, we present crystal structures of mammalian aCDases in both proenzyme and autocleaved forms. In the proenzyme, the catalytic center is buried and protected from solvent. Autocleavage triggers a conformational change exposing a hydrophobic channel leading to the active site. Substrate modeling suggests distinct catalytic mechanisms for substrate hydrolysis versus autocleavage. A hydrophobic surface surrounding the substrate binding channel appears to be a site of membrane attachment where the enzyme accepts substrates facilitated by the accessory protein, saposin-D. Structural mapping of disease mutations reveals that most would destabilize the protein fold. These results will inform the rational design of aCDase inhibitors and recombinant aCDase for disease therapeutics. Acid ceramidase (aCDase) hydrolyzes lysosomal membrane ceramide into sphingosine and its dysfunction leads to a variety of disease phenotypes. Here, the authors present structures of aCDase in its proenzyme and autocleaved forms, which provides insight into its mechanism of action.
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Affiliation(s)
- Ahmad Gebai
- Department of Biochemistry and Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montreal, QC, H3G 0B1, Canada
| | - Alexei Gorelik
- Department of Biochemistry and Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montreal, QC, H3G 0B1, Canada
| | - Zixian Li
- Department of Biochemistry and Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montreal, QC, H3G 0B1, Canada
| | - Katalin Illes
- Department of Biochemistry and Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montreal, QC, H3G 0B1, Canada
| | - Bhushan Nagar
- Department of Biochemistry and Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montreal, QC, H3G 0B1, Canada.
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25
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Garrido-Arandia M, Cuevas-Zuviría B, Díaz-Perales A, Pacios LF. A Comparative Study of Human Saposins. Molecules 2018; 23:molecules23020422. [PMID: 29443946 PMCID: PMC6017893 DOI: 10.3390/molecules23020422] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 02/12/2018] [Accepted: 02/13/2018] [Indexed: 12/02/2022] Open
Abstract
Saposins are small proteins implicated in trafficking and loading of lipids onto Cluster of Differentiation 1 (CD1) receptor proteins that in turn present lipid antigens to T cells and a variety of T-cell receptors, thus playing a crucial role in innate and adaptive immune responses in humans. Despite their low sequence identity, the four types of human saposins share a similar folding pattern consisting of four helices linked by three conserved disulfide bridges. However, their lipid-binding abilities as well as their activities in extracting, transporting and loading onto CD1 molecules a variety of sphingo- and phospholipids in biological membranes display two striking characteristics: a strong pH-dependence and a structural change between a compact, closed conformation and an open conformation. In this work, we present a comparative computational study of structural, electrostatic, and dynamic features of human saposins based upon their available experimental structures. By means of structural alignments, surface analyses, calculation of pH-dependent protonation states, Poisson-Boltzmann electrostatic potentials, and molecular dynamics simulations at three pH values representative of biological media where saposins fulfill their function, our results shed light into their intrinsic features. The similarities and differences in this class of proteins depend on tiny variations of local structural details that allow saposins to be key players in triggering responses in the human immune system.
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MESH Headings
- Amino Acid Sequence
- Antigens, CD/chemistry
- Antigens, CD/immunology
- Antigens, CD1/chemistry
- Antigens, CD1/immunology
- Cell Membrane/chemistry
- Cell Membrane/immunology
- Humans
- Immunity, Innate
- Lipids/chemistry
- Lipids/immunology
- Molecular Dynamics Simulation
- Phospholipids/chemistry
- Phospholipids/immunology
- Protein Binding/immunology
- Protein Structure, Secondary
- Receptors, Antigen, T-Cell/chemistry
- Receptors, Antigen, T-Cell/immunology
- Saposins/chemistry
- Saposins/immunology
- T-Lymphocytes/immunology
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Affiliation(s)
- María Garrido-Arandia
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Campus de Montegancedo-UPM, 28223 Madrid, Spain.
| | - Bruno Cuevas-Zuviría
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Campus de Montegancedo-UPM, 28223 Madrid, Spain.
| | - Araceli Díaz-Perales
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Campus de Montegancedo-UPM, 28223 Madrid, Spain.
- Departamento de Biotecnología-Biología Vegetal, ETSIAAB, Universidad Politécnica de Madrid (UPM), Ciudad Universitaria, 28040 Madrid, Spain.
| | - Luis F Pacios
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Campus de Montegancedo-UPM, 28223 Madrid, Spain.
- Departamento de Biotecnología-Biología Vegetal, ETSIAAB, Universidad Politécnica de Madrid (UPM), Ciudad Universitaria, 28040 Madrid, Spain.
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26
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Simões ICM, Coimbra JTS, Neves RPP, Costa IPD, Ramos MJ, Fernandes PA. Properties that rank protein:protein docking poses with high accuracy. Phys Chem Chem Phys 2018; 20:20927-20942. [DOI: 10.1039/c8cp03888k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The development of docking algorithms to predict near-native structures of protein:protein complexes from the structure of the isolated monomers is of paramount importance for molecular biology and drug discovery.
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Affiliation(s)
- Inês C. M. Simões
- UCIBIO
- REQUIMTE
- Departamento de Química e Bioquímica
- Faculdade de Ciências
- Universidade do Porto
| | - João T. S. Coimbra
- UCIBIO
- REQUIMTE
- Departamento de Química e Bioquímica
- Faculdade de Ciências
- Universidade do Porto
| | - Rui P. P. Neves
- UCIBIO
- REQUIMTE
- Departamento de Química e Bioquímica
- Faculdade de Ciências
- Universidade do Porto
| | - Inês P. D. Costa
- UCIBIO
- REQUIMTE
- Departamento de Química e Bioquímica
- Faculdade de Ciências
- Universidade do Porto
| | - Maria J. Ramos
- UCIBIO
- REQUIMTE
- Departamento de Química e Bioquímica
- Faculdade de Ciências
- Universidade do Porto
| | - Pedro A. Fernandes
- UCIBIO
- REQUIMTE
- Departamento de Química e Bioquímica
- Faculdade de Ciências
- Universidade do Porto
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27
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Bryksa BC, Yada RY. Protein Structure Insights into the Bilayer Interactions of the Saposin-Like Domain of Solanum tuberosum Aspartic Protease. Sci Rep 2017; 7:16911. [PMID: 29208977 PMCID: PMC5717070 DOI: 10.1038/s41598-017-16734-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 11/16/2017] [Indexed: 12/26/2022] Open
Abstract
Many plant aspartic proteases contain a saposin-like domain whose principal functions are intracellular sorting and host defence. Its structure is characterised by helical segments cross-linked by three highly conserved cystines. The present study on the saposin-like domain of Solanum tuberosum aspartic protease revealed that acidification from inactive to active conditions causes dimerisation and a strand-to-helix secondary structure transition independent of bilayer interaction. Bilayer fusion was shown to occur under reducing conditions yielding a faster shift to larger vesicle sizes relative to native conditions, implying that a lower level structural motif might be bilayer-active. Characterisation of peptide sequences based on the domain’s secondary structural regions showed helix-3 to be active (~4% of the full domain’s activity), and mutation of its sole positively charged residue resulted in loss of activity and disordering of structure. Also, the peptides’ respective circular dichroism spectra suggested that native folding within the full domain is dependent on surrounding structure. Overall, the present study reveals that the aspartic protease saposin-like domain active structure is an open saposin fold dimer whose formation is pH-dependent, and that a bilayer-active motif shared among non-saposin membrane-active proteins including certain plant defence proteins is nested within an overall structure essential for native functionality.
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Affiliation(s)
- Brian C Bryksa
- Ontario Agricultural College, University of Guelph, N1G 2W1, Guelph, Ontario, Canada
| | - Rickey Y Yada
- Faculty of Land and Food Systems, University of British Columbia, Vancouver, V6T 1Z4, British Columbia, Canada.
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28
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Krishnamoorthy A, Witkowski A, Tran JJ, Weers PMM, Ryan RO. Characterization of secondary structure and lipid binding behavior of N-terminal saposin like subdomain of human Wnt3a. Arch Biochem Biophys 2017; 630:38-46. [PMID: 28754322 DOI: 10.1016/j.abb.2017.07.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 07/14/2017] [Accepted: 07/24/2017] [Indexed: 02/06/2023]
Abstract
Wnt signaling is essential for embryonic development and adult homeostasis in multicellular organisms. A conserved feature among Wnt family proteins is the presence of two structural domains. Within the N-terminal (NT) domain there exists a motif that is superimposable upon saposin-like protein (SAPLIP) family members. SAPLIPs are found in plants, microbes and animals and possess lipid surface seeking activity. To investigate the function of the Wnt3a saposin-like subdomain (SLD), recombinant SLD was studied in isolation. Bacterial expression of this Wnt fragment was achieved only when the core SLD included 82 NT residues of Wnt3a (NT-SLD). Unlike SAPLIPs, NT-SLD required the presence of detergent to achieve solubility at neutral pH. Deletion of two hairpin loop extensions present in NT-SLD, but not other SAPLIPs, had no effect on the solubility properties of NT-SLD. Far UV circular dichroism spectroscopy of NT-SLD yielded 50-60% α-helix secondary structure. Limited proteolysis of isolated NT-SLD in buffer and detergent micelles showed no differences in cleavage kinetics. Unlike prototypical saposins, NT-SLD exhibited weak membrane-binding affinity and lacked cell lytic activity. In cell-based canonical Wnt signaling assays, NT-SLD was unable to induce stabilization of β-catenin or modulate the extent of β-catenin stabilization induced by full-length Wnt3a. Taken together, the results indicate neighboring structural elements within full-length Wnt3a affect SLD conformational stability. Moreover, SLD function(s) in Wnt proteins appear to have evolved away from those commonly attributed to SAPLIP family members.
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Affiliation(s)
- Aparna Krishnamoorthy
- Department of Nutritional Sciences and Toxicology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Andrzej Witkowski
- Children's Hospital Oakland Research Institute, 5700 Martin Luther King Jr. Way, Oakland, CA 94609, USA
| | - Jesse J Tran
- Department of Chemistry and Biochemistry, California State University, Long Beach, CA 90840, USA
| | - Paul M M Weers
- Department of Chemistry and Biochemistry, California State University, Long Beach, CA 90840, USA
| | - Robert O Ryan
- Department of Nutritional Sciences and Toxicology, University of California Berkeley, Berkeley, CA 94720, USA; Children's Hospital Oakland Research Institute, 5700 Martin Luther King Jr. Way, Oakland, CA 94609, USA.
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29
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Bonjack-Shterengartz M, Avnir D. The enigma of the near-symmetry of proteins: Domain swapping. PLoS One 2017; 12:e0180030. [PMID: 28708874 PMCID: PMC5510828 DOI: 10.1371/journal.pone.0180030] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 06/08/2017] [Indexed: 01/25/2023] Open
Abstract
The majority of proteins form oligomers which have rotational symmetry. Literature has suggested many functional advantages that the symmetric packing offers. Yet, despite these advantages, the vast majority of protein oligomers are only nearly symmetric. A key question in the field of proteins structure is therefore, if symmetry is so advantageous, why do oligomers settle for aggregates that do not maximize that structural property? The answer to that question is apparently multi-parametric, and involves distortions at the interaction zones of the monomer units of the oligomer in order to minimize the free energy, the dynamics of the protein, the effects of surroundings parameters, and the mechanism of oligomerization. The study of this problem is in its infancy: Only the first parameter has been explored so far. Here we focus on the last parameter-the mechanism of formation. To test this effect we have selected to focus on the domain swapping mechanism of oligomerization, by which oligomers form in a mechanism that swaps identical portions of monomeric units, resulting in an interwoven oligomer. We are using continuous symmetry measures to analyze in detail the oligomer formed by this mechanism, and found, that without exception, in all analyzed cases, perfect symmetry is given away, and we are able to identify that the main burden of distortion lies in the hinge regions that connect the swapped portions. We show that the continuous symmetry analysis method clearly identifies the hinge region of swapped domain proteins-considered to be a non-trivial task. We corroborate our conclusion about the central role of the hinge region in affecting the symmetry of the oligomers, by a special probability analysis developed particularly for that purpose.
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Affiliation(s)
- Maayan Bonjack-Shterengartz
- Institute of Chemistry and the Lise Meitner Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - David Avnir
- Institute of Chemistry and the Lise Meitner Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
- * E-mail:
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30
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Graf CGF, Schulz C, Schmälzlein M, Heinlein C, Mönnich M, Perkams L, Püttner M, Boos I, Hessefort M, Lombana Sanchez JN, Weyand M, Steegborn C, Breiden B, Ross K, Schwarzmann G, Sandhoff K, Unverzagt C. Synthetic Glycoforms Reveal Carbohydrate-Dependent Bioactivity of Human Saposin D. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701362] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
| | - Christian Schulz
- Bioorg. Chemie, Gebäude NWI; Universität Bayreuth; 95440 Bayreuth Germany
| | - Marina Schmälzlein
- Bioorg. Chemie, Gebäude NWI; Universität Bayreuth; 95440 Bayreuth Germany
| | - Christian Heinlein
- Bioorg. Chemie, Gebäude NWI; Universität Bayreuth; 95440 Bayreuth Germany
| | - Manuel Mönnich
- Bioorg. Chemie, Gebäude NWI; Universität Bayreuth; 95440 Bayreuth Germany
| | - Lukas Perkams
- Bioorg. Chemie, Gebäude NWI; Universität Bayreuth; 95440 Bayreuth Germany
| | - Markus Püttner
- Bioorg. Chemie, Gebäude NWI; Universität Bayreuth; 95440 Bayreuth Germany
| | - Irene Boos
- Bioorg. Chemie, Gebäude NWI; Universität Bayreuth; 95440 Bayreuth Germany
| | - Markus Hessefort
- Bioorg. Chemie, Gebäude NWI; Universität Bayreuth; 95440 Bayreuth Germany
| | | | - Michael Weyand
- Department of Biochemistry; Universität Bayreuth; Germany
| | | | | | | | | | | | - Carlo Unverzagt
- Bioorg. Chemie, Gebäude NWI; Universität Bayreuth; 95440 Bayreuth Germany
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31
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Graf CGF, Schulz C, Schmälzlein M, Heinlein C, Mönnich M, Perkams L, Püttner M, Boos I, Hessefort M, Lombana Sanchez JN, Weyand M, Steegborn C, Breiden B, Ross K, Schwarzmann G, Sandhoff K, Unverzagt C. Synthetic Glycoforms Reveal Carbohydrate-Dependent Bioactivity of Human Saposin D. Angew Chem Int Ed Engl 2017; 56:5252-5257. [DOI: 10.1002/anie.201701362] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Indexed: 12/15/2022]
Affiliation(s)
| | - Christian Schulz
- Bioorg. Chemie, Gebäude NWI; Universität Bayreuth; 95440 Bayreuth Germany
| | - Marina Schmälzlein
- Bioorg. Chemie, Gebäude NWI; Universität Bayreuth; 95440 Bayreuth Germany
| | - Christian Heinlein
- Bioorg. Chemie, Gebäude NWI; Universität Bayreuth; 95440 Bayreuth Germany
| | - Manuel Mönnich
- Bioorg. Chemie, Gebäude NWI; Universität Bayreuth; 95440 Bayreuth Germany
| | - Lukas Perkams
- Bioorg. Chemie, Gebäude NWI; Universität Bayreuth; 95440 Bayreuth Germany
| | - Markus Püttner
- Bioorg. Chemie, Gebäude NWI; Universität Bayreuth; 95440 Bayreuth Germany
| | - Irene Boos
- Bioorg. Chemie, Gebäude NWI; Universität Bayreuth; 95440 Bayreuth Germany
| | - Markus Hessefort
- Bioorg. Chemie, Gebäude NWI; Universität Bayreuth; 95440 Bayreuth Germany
| | | | - Michael Weyand
- Department of Biochemistry; Universität Bayreuth; Germany
| | | | | | | | | | | | - Carlo Unverzagt
- Bioorg. Chemie, Gebäude NWI; Universität Bayreuth; 95440 Bayreuth Germany
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32
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Malinina L, Patel DJ, Brown RE. How α-Helical Motifs Form Functionally Diverse Lipid-Binding Compartments. Annu Rev Biochem 2017; 86:609-636. [PMID: 28375742 DOI: 10.1146/annurev-biochem-061516-044445] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Lipids are produced site-specifically in cells and then distributed nonrandomly among membranes via vesicular and nonvesicular trafficking mechanisms. The latter involves soluble amphitropic proteins extracting specific lipids from source membranes to function as molecular solubilizers that envelope their insoluble cargo before transporting it to destination sites. Lipid-binding and lipid transfer structural motifs range from multi-β-strand barrels, to β-sheet cups and baskets covered by α-helical lids, to multi-α-helical bundles and layers. Here, we focus on how α-helical proteins use amphipathic helical layering and bundling to form modular lipid-binding compartments and discuss the functional consequences. Preformed compartments generally rely on intramolecular disulfide bridging to maintain conformation (e.g., albumins, nonspecific lipid transfer proteins, saposins, nematode polyprotein allergens/antigens). Insights into nonpreformed hydrophobic compartments that expand and adapt to accommodate a lipid occupant are few and provided mostly by the three-layer, α-helical ligand-binding domain of nuclear receptors. The simple but elegant and nearly ubiquitous two-layer, α-helical glycolipid transfer protein (GLTP)-fold now further advances understanding.
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Affiliation(s)
- Lucy Malinina
- The Hormel Institute, University of Minnesota, Austin, Minnesota 55912; ,
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065;
| | - Rhoderick E Brown
- The Hormel Institute, University of Minnesota, Austin, Minnesota 55912; ,
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33
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Towle KM, Vederas JC. Structural features of many circular and leaderless bacteriocins are similar to those in saposins and saposin-like peptides. MEDCHEMCOMM 2017; 8:276-285. [PMID: 30108744 PMCID: PMC6072434 DOI: 10.1039/c6md00607h] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 12/09/2016] [Indexed: 12/14/2022]
Abstract
Bacteriocins are potent antimicrobial peptides that are ribosomally produced and exported by bacteria, presumably to aid elimination of competing microorganisms. Many circular and linear leaderless bacteriocins have a recuring three dimensional structural motif known as a saposin-like fold. Although these bacteriocin sizes and sequences are often quite different, and their mechanisms of action vary, this conserved motif of multiple helices appears critical for activity and may enable peptide-lipid and peptide-receptor interactions in target bacterial cell membranes. Comparisons between electrostatic surfaces and hydrophobic surface maps of different bacteriocins are discussed emphasizing similarities and differences in the context of proposed modes of action.
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Affiliation(s)
- K M Towle
- Department of Chemistry , University of Alberta , Edmonton , Alberta , T6G 2G2 Canada .
| | - J C Vederas
- Department of Chemistry , University of Alberta , Edmonton , Alberta , T6G 2G2 Canada .
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34
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All-atom molecular dynamics simulations of lung surfactant protein B: Structural features of SP-B promote lipid reorganization. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:3082-3092. [DOI: 10.1016/j.bbamem.2016.09.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 08/30/2016] [Accepted: 09/20/2016] [Indexed: 01/07/2023]
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35
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Xiong ZJ, Huang J, Poda G, Pomès R, Privé GG. Structure of Human Acid Sphingomyelinase Reveals the Role of the Saposin Domain in Activating Substrate Hydrolysis. J Mol Biol 2016; 428:3026-42. [PMID: 27349982 DOI: 10.1016/j.jmb.2016.06.012] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Revised: 06/14/2016] [Accepted: 06/16/2016] [Indexed: 11/29/2022]
Abstract
Acid sphingomyelinase (ASM) is a lysosomal phosphodiesterase that catalyzes the hydrolysis of sphingomyelin to produce ceramide and phosphocholine. While other lysosomal sphingolipid hydrolases require a saposin activator protein for full activity, the ASM polypeptide incorporates a built-in N-terminal saposin domain and does not require an external activator protein. Here, we report the crystal structure of human ASM and describe the organization of the three main regions of the enzyme: the N-terminal saposin domain, the proline-rich connector, and the catalytic domain. The saposin domain is tightly associated along an edge of the large, bowl-shaped catalytic domain and adopts an open form that exposes a hydrophobic concave surface approximately 30Å from the catalytic center. The calculated electrostatic potential of the enzyme is electropositive at the acidic pH of the lysosome, consistent with the strict requirement for the presence of acidic lipids in target membranes. Docking studies indicate that sphingomyelin binds with the ceramide-phosphate group positioned at the binuclear zinc center and molecular dynamic simulations indicate that the intrinsic flexibility of the saposin domain is important for monomer-dimer exchange and for membrane interactions. Overall, ASM uses a combination of electrostatic and hydrophobic interactions to cause local disruptions of target bilayers in order to bring the lipid headgroup to the catalytic center in a membrane-bound reaction.
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Affiliation(s)
- Zi-Jian Xiong
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Jingjing Huang
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Gennady Poda
- Drug Discovery, Ontario Institute for Cancer Research, Toronto, Ontario, Canada; Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Régis Pomès
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Gilbert G Privé
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada; Princess Margaret Cancer Centre, Toronto, Ontario, Canada.
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36
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Frauenfeld J, Löving R, Armache JP, Sonnen AFP, Guettou F, Moberg P, Zhu L, Jegerschöld C, Flayhan A, Briggs JAG, Garoff H, Löw C, Cheng Y, Nordlund P. A saposin-lipoprotein nanoparticle system for membrane proteins. Nat Methods 2016; 13:345-51. [PMID: 26950744 PMCID: PMC4894539 DOI: 10.1038/nmeth.3801] [Citation(s) in RCA: 183] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 01/21/2016] [Indexed: 12/11/2022]
Abstract
A limiting factor in membrane protein research is the ability to solubilize and stabilize such proteins. Detergents are used most often for solubilizing membrane proteins, but they are associated with protein instability and poor compatibility with structural and biophysical studies. Here we present a saposin-lipoprotein nanoparticle system, Salipro, which allows for the reconstitution of membrane proteins in a lipid environment that is stabilized by a scaffold of saposin proteins. We demonstrate the applicability of the method on two purified membrane protein complexes as well as by the direct solubilization and nanoparticle incorporation of a viral membrane protein complex from the virus membrane. Our approach facilitated high-resolution structural studies of the bacterial peptide transporter PeptTSo2 by single-particle cryo-electron microscopy (cryo-EM) and allowed us to stabilize the HIV envelope glycoprotein in a functional state.
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Affiliation(s)
- Jens Frauenfeld
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Robin Löving
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Jean-Paul Armache
- Keck Advanced Microscopy Laboratory, Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
| | - Andreas F-P Sonnen
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory-Universitätsklinikum Heidelberg, Heidelberg, Germany
| | - Fatma Guettou
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Per Moberg
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Lin Zhu
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.,School of Technology and Health, Royal Institute of Technology, Novum, Huddinge, Sweden
| | - Caroline Jegerschöld
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.,School of Technology and Health, Royal Institute of Technology, Novum, Huddinge, Sweden
| | | | - John A G Briggs
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory-Universitätsklinikum Heidelberg, Heidelberg, Germany
| | - Henrik Garoff
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Christian Löw
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,EMBL Hamburg, Hamburg, Germany
| | - Yifan Cheng
- Keck Advanced Microscopy Laboratory, Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA.,Howard Hughes Medical Institute, University of California San Francisco, San Francisco, California, USA
| | - Pär Nordlund
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
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37
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Vadlamudi Y, Muthu K, M. SK. Structural exploration of acid sphingomyelinase at different physiological pH through molecular dynamics and docking studies. RSC Adv 2016. [DOI: 10.1039/c6ra16584b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Acid sphingomyelinase (ASM) hydrolysis the sphingomyelin at physiological pH 5.0 and subsequently leads to ceramide production.
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Affiliation(s)
| | - Kannan Muthu
- Centre for Bioinformatics
- Pondicherry University
- Pondicherry 605014
- India
| | - Suresh Kumar M.
- Centre for Bioinformatics
- Pondicherry University
- Pondicherry 605014
- India
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38
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The effects of chemically synthesized saposin C on glucosylceramide-β-glucosidase. Clin Biochem 2015; 48:1177-80. [DOI: 10.1016/j.clinbiochem.2015.06.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2015] [Revised: 05/27/2015] [Accepted: 06/01/2015] [Indexed: 11/20/2022]
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39
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Hill CH, Read RJ, Deane JE. Structure of human saposin A at lysosomal pH. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2015; 71:895-900. [PMID: 26144235 PMCID: PMC4498711 DOI: 10.1107/s2053230x15008584] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 05/01/2015] [Indexed: 11/10/2022]
Abstract
The saposins are essential cofactors for the normal lysosomal degradation of complex glycosphingolipids by acid hydrolase enzymes; defects in either saposin or hydrolase function lead to severe metabolic diseases. Saposin A (SapA) activates the enzyme β-galactocerebrosidase (GALC), which catalyzes the breakdown of β-D-galactocerebroside, the principal lipid component of myelin. SapA is known to bind lipids and detergents in a pH-dependent manner; this is accompanied by a striking transition from a `closed' to an `open' conformation. However, previous structures were determined at non-lysosomal pH. This work describes a 1.8 Å resolution X-ray crystal structure determined at the physiologically relevant lysosomal pH 4.8. In the absence of lipid or detergent at pH 4.8, SapA is observeed to adopt a conformation closely resembling the previously determined `closed' conformation, showing that pH alone is not sufficient for the transition to the `open' conformation. Structural alignments reveal small conformational changes, highlighting regions of flexibility.
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Affiliation(s)
- Chris H Hill
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, England
| | - Randy J Read
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, England
| | - Janet E Deane
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, England
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40
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Olmeda B, García‐Álvarez B, Gómez MJ, Martínez‐Calle M, Cruz A, Pérez‐Gil J. A model for the structure and mechanism of action of pulmonary surfactant protein B. FASEB J 2015; 29:4236-47. [DOI: 10.1096/fj.15-273458] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 06/15/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Bárbara Olmeda
- Departmento de Bioquímica, Facultad de BiologíaUniversidad ComplutenseMadridSpain
| | | | - Manuel J. Gómez
- Centro de Astrobiología (INTA‐CSIC), Torrejón de ArdozMadridSpain
| | - Marta Martínez‐Calle
- Departmento de Bioquímica, Facultad de BiologíaUniversidad ComplutenseMadridSpain
| | - Antonio Cruz
- Departmento de Bioquímica, Facultad de BiologíaUniversidad ComplutenseMadridSpain
| | - Jesús Pérez‐Gil
- Departmento de Bioquímica, Facultad de BiologíaUniversidad ComplutenseMadridSpain
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41
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Michalek M, Leippe M. Mechanistic insights into the lipid interaction of an ancient saposin-like protein. Biochemistry 2015; 54:1778-86. [PMID: 25715682 DOI: 10.1021/acs.biochem.5b00094] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The members of the expanding family of saposin-like proteins (SAPLIPs) have various biological functions in plants, animals, and humans. In addition to a similar protein backbone, these proteins have in common the fact that they interact with lipid membranes. According to their phylogenetic position, it has long been thought that amoeboid protozoans produce archetypes of SAPLIPs and that these are lytic proteins that can perforate membranes of prokaryotic and eukaryotic target cells. Here, we show that an amoebic SAPLIP from Entamoeba invadens does not form lytic pores in membranes but displays several characteristics that are known from human saposins. The protein named invaposin changes the conformation from a closed to an open form in the presence of lipid membranes, acts in a pH-dependent manner, selectively binds anionic lipids, aggregates lipid vesicles of the preferred composition, and dimerizes upon acidification. Our data indicate that the principal features of the lipid-binding saposins evolved long before the appearance of the vertebrate lineage and push the origin of saposins even deeper down the phylogenetic tree to unicellular organisms.
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Affiliation(s)
- Matthias Michalek
- Zoological Institute, Comparative Immunobiology, University of Kiel , Olshausenstrasse 40, 24098 Kiel, Germany
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42
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Ghasriani H, Kwok JKC, Sherratt AR, Foo ACY, Qureshi T, Goto NK. Micelle-Catalyzed Domain Swapping in the GlpG Rhomboid Protease Cytoplasmic Domain. Biochemistry 2014; 53:5907-15. [DOI: 10.1021/bi500919v] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Houman Ghasriani
- Department of Chemistry and ‡Department of Biochemistry, Microbiology
and
Immunology, University of Ottawa, Ottawa, Ontario, Canada K1N 6N5
| | - Jason K. C. Kwok
- Department of Chemistry and ‡Department of Biochemistry, Microbiology
and
Immunology, University of Ottawa, Ottawa, Ontario, Canada K1N 6N5
| | - Allison R. Sherratt
- Department of Chemistry and ‡Department of Biochemistry, Microbiology
and
Immunology, University of Ottawa, Ottawa, Ontario, Canada K1N 6N5
| | - Alexander C. Y. Foo
- Department of Chemistry and ‡Department of Biochemistry, Microbiology
and
Immunology, University of Ottawa, Ottawa, Ontario, Canada K1N 6N5
| | - Tabussom Qureshi
- Department of Chemistry and ‡Department of Biochemistry, Microbiology
and
Immunology, University of Ottawa, Ottawa, Ontario, Canada K1N 6N5
| | - Natalie K. Goto
- Department of Chemistry and ‡Department of Biochemistry, Microbiology
and
Immunology, University of Ottawa, Ottawa, Ontario, Canada K1N 6N5
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43
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De Moura DC, Bryksa BC, Yada RY. In silico insights into protein-protein interactions and folding dynamics of the saposin-like domain of Solanum tuberosum aspartic protease. PLoS One 2014; 9:e104315. [PMID: 25188221 PMCID: PMC4154668 DOI: 10.1371/journal.pone.0104315] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 06/09/2014] [Indexed: 12/29/2022] Open
Abstract
The plant-specific insert is an approximately 100-residue domain found exclusively within the C-terminal lobe of some plant aspartic proteases. Structurally, this domain is a member of the saposin-like protein family, and is involved in plant pathogen defense as well as vacuolar targeting of the parent protease molecule. Similar to other members of the saposin-like protein family, most notably saposins A and C, the recently resolved crystal structure of potato (Solanum tuberosum) plant-specific insert has been shown to exist in a substrate-bound open conformation in which the plant-specific insert oligomerizes to form homodimers. In addition to the open structure, a closed conformation also exists having the classic saposin fold of the saposin-like protein family as observed in the crystal structure of barley (Hordeum vulgare L.) plant-specific insert. In the present study, the mechanisms of tertiary and quaternary conformation changes of potato plant-specific insert were investigated in silico as a function of pH. Umbrella sampling and determination of the free energy change of dissociation of the plant-specific insert homodimer revealed that increasing the pH of the system to near physiological levels reduced the free energy barrier to dissociation. Furthermore, principal component analysis was used to characterize conformational changes at both acidic and neutral pH. The results indicated that the plant-specific insert may adopt a tertiary structure similar to the characteristic saposin fold and suggest a potential new structural motif among saposin-like proteins. To our knowledge, this acidified PSI structure presents the first example of an alternative saposin-fold motif for any member of the large and diverse SAPLIP family.
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Affiliation(s)
- Dref C. De Moura
- Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada
- Department of Food Science, University of Guelph, Guelph, Ontario, Canada
| | - Brian C. Bryksa
- Department of Food Science, University of Guelph, Guelph, Ontario, Canada
| | - Rickey Y. Yada
- Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada
- Department of Food Science, University of Guelph, Guelph, Ontario, Canada
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Hu H, Zhang H, Gao Z, Wang D, Liu G, Xu J, Lan K, Dong Y. Structure of the type VI secretion phospholipase effector Tle1 provides insight into its hydrolysis and membrane targeting. ACTA ACUST UNITED AC 2014; 70:2175-85. [DOI: 10.1107/s1399004714012899] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 06/03/2014] [Indexed: 08/30/2023]
Abstract
A diverse superfamily of phospholipases consisting of the type VI lipase effectors Tle1–Tle5 secreted by the bacterial type VI secretion system (T6SS) have recently been identified as antibacterial effectors that hydrolyze membrane phospholipids. These effectors show no significant homology to known lipases, and their mechanism of membrane targeting and hydrolysis of phospholipids remains unknown. Here, the crystal structure of Tle1 (∼96.5 kDa) fromPseudomonas aeruginosarefined to 2.0 Å resolution is reported, representing the first structure of this superfamily. Its overall structure can be divided into two distinct parts, the phospholipase catalytic module and the putative membrane-anchoring module; this arrangement has not previously been observed in known lipase structures. The phospholipase catalytic module has a canonical α/β-hydrolase fold and mutation of any residue in the Ser-Asp-His catalytic triad abolishes its toxicity. The putative membrane-anchoring module adopts an open conformation composed of three amphipathic domains, and its partial folds are similar to those of several periplasmic or membrane proteins. A cell-toxicity assay revealed that the putative membrane-anchoring module is critical to Tle1 antibacterial activity. A molecular-dynamics (MD) simulation system in which the putative membrane-anchoring module embedded into a bilayer was stable over 50 ns. These structure–function studies provide insight into the hydrolysis and membrane-targeting process of the unique phospholipase Tle1.
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Rebollido-Rios R, Bandari S, Wilms C, Jakuschev S, Vortkamp A, Grobe K, Hoffmann D. Signaling domain of Sonic Hedgehog as cannibalistic calcium-regulated zinc-peptidase. PLoS Comput Biol 2014; 10:e1003707. [PMID: 25033298 PMCID: PMC4102407 DOI: 10.1371/journal.pcbi.1003707] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2013] [Accepted: 05/22/2014] [Indexed: 12/30/2022] Open
Abstract
Sonic Hedgehog (Shh) is a representative of the evolutionary closely related class of Hedgehog proteins that have essential signaling functions in animal development. The N-terminal domain (ShhN) is also assigned to the group of LAS proteins (LAS = Lysostaphin type enzymes, D-Ala-D-Ala metalloproteases, Sonic Hedgehog), of which all members harbor a structurally well-defined Zn2+ center; however, it is remarkable that ShhN so far is the only LAS member without proven peptidase activity. Another unique feature of ShhN in the LAS group is a double-Ca2+ center close to the zinc. We have studied the effect of these calcium ions on ShhN structure, dynamics, and interactions. We find that the presence of calcium has a marked impact on ShhN properties, with the two calcium ions having different effects. The more strongly bound calcium ion significantly stabilizes the overall structure. Surprisingly, the binding of the second calcium ion switches the putative catalytic center from a state similar to LAS enzymes to a state that probably is catalytically inactive. We describe in detail the mechanics of the switch, including the effect on substrate co-ordinating residues and on the putative catalytic water molecule. The properties of the putative substrate binding site suggest that ShhN could degrade other ShhN molecules, e.g. by cleavage at highly conserved glycines in ShhN. To test experimentally the stability of ShhN against autodegradation, we compare two ShhN mutants in vitro: (1) a ShhN mutant unable to bind calcium but with putative catalytic center intact, and thus, according to our hypothesis, a constitutively active peptidase, and (2) a mutant carrying additionally mutation E177A, i.e., with the putative catalytically active residue knocked out. The in vitro results are consistent with ShhN being a cannibalistic zinc-peptidase. These experiments also reveal that the peptidase activity depends on pH.
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Affiliation(s)
- Rocio Rebollido-Rios
- Research Group Bioinformatics, Faculty of Biology, Center of Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Shyam Bandari
- Institute of Physiological Chemistry and Pathobiochemistry, Faculty of Medicine, University of Münster, Münster, Germany
| | - Christoph Wilms
- Research Group Bioinformatics, Faculty of Biology, Center of Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Stanislav Jakuschev
- Research Group Bioinformatics, Faculty of Biology, Center of Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Andrea Vortkamp
- Department of Developmental Biology, Faculty of Biology, Center of Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Kay Grobe
- Institute of Physiological Chemistry and Pathobiochemistry, Faculty of Medicine, University of Münster, Münster, Germany
| | - Daniel Hoffmann
- Research Group Bioinformatics, Faculty of Biology, Center of Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
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Mason L, Amani P, Cross M, Baker J, Bailey UM, Jones MK, Gasser RB, Hofmann A. The Relevance of Structural Biology in Studying Molecules Involved in Parasite–Host Interactions: Potential for Designing New Interventions. Aust J Chem 2014. [DOI: 10.1071/ch14304] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
New interventions against infectious diseases require a detailed knowledge and understanding of pathogen–host interactions and pathogeneses at the molecular level. The combination of the considerable advances in systems biology research with methods to explore the structural biology of molecules is poised to provide new insights into these areas. Importantly, exploring three-dimensional structures of proteins is central to understanding disease processes, and establishing structure–function relationships assists in identification and assessment of new drug and vaccine targets. Frequently, the molecular arsenal deployed by invading pathogens, and in particular parasites, reveals a common theme whereby families of proteins with conserved three-dimensional folds play crucial roles in infectious processes, but individual members of such families show high levels of specialisation, which is often achieved through grafting particular structural features onto the shared overall fold. Accordingly, the applicability of predictive methodologies based on the primary structure of proteins or genome annotations is limited, particularly when thorough knowledge of molecular-level mechanisms is required. Such instances exemplify the need for experimental three-dimensional structures provided by protein crystallography, which remain an essential component of this area of research. In the present article, we review two examples of key protein families recently investigated in our laboratories, which could represent intervention targets in the metabolome or secretome of parasites.
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Yap TL, Gruschus JM, Velayati A, Sidransky E, Lee JC. Saposin C protects glucocerebrosidase against α-synuclein inhibition. Biochemistry 2013; 52:7161-3. [PMID: 24070323 PMCID: PMC3833811 DOI: 10.1021/bi401191v] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mutations in GBA1, the gene for glucocerebrosidase (GCase), are genetic risk factors for Parkinson disease (PD). α-Synuclein (α-Syn), a protein implicated in PD, interacts with GCase and efficiently inhibits enzyme activity. GCase deficiency causes the lysosomal storage disorder Gaucher disease (GD). We show that saposin C (Sap C), a protein vital for GCase activity in vivo, protects GCase against α-syn inhibition. Using nuclear magnetic resonance spectroscopy, site-specific fluorescence, and Förster energy transfer probes, Sap C was observed to displace α-syn from GCase in solution and on lipid vesicles. Our results suggest that Sap C might play a crucial role in GD-related PD.
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Affiliation(s)
- Thai Leong Yap
- Laboratory of Molecular Biophysics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, Bethesda, Maryland 20892, United States
| | - James M. Gruschus
- Laboratory of Molecular Biophysics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, Bethesda, Maryland 20892, United States
| | - Arash Velayati
- Section on Molecular Neurogenetics, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Ellen Sidransky
- Section on Molecular Neurogenetics, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Jennifer C. Lee
- Laboratory of Molecular Biophysics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, Bethesda, Maryland 20892, United States
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Ishibashi Y, Kohyama-Koganeya A, Hirabayashi Y. New insights on glucosylated lipids: metabolism and functions. Biochim Biophys Acta Mol Cell Biol Lipids 2013; 1831:1475-85. [PMID: 23770033 DOI: 10.1016/j.bbalip.2013.06.001] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Revised: 06/01/2013] [Accepted: 06/04/2013] [Indexed: 01/05/2023]
Abstract
Ceramide, cholesterol, and phosphatidic acid are major basic structures for cell membrane lipids. These lipids are modified with glucose to generate glucosylceramide (GlcCer), cholesterylglucoside (ChlGlc), and phosphatidylglucoside (PtdGlc), respectively. Glucosylation dramatically changes the functional properties of lipids. For instance, ceramide acts as a strong tumor suppressor that causes apoptosis and cell cycle arrest, while GlcCer has an opposite effect, downregulating ceramide activities. All glucosylated lipids are enriched in lipid rafts or microdomains and play fundamental roles in a variety of cellular processes. In this review, we discuss the biological functions and metabolism of these three glucosylated lipids.
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Affiliation(s)
- Yohei Ishibashi
- Laboratory for Molecular Membrane Neuroscience, RIKEN Brain Science Institute, Wako, Saitama, Japan
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Abstract
The crystal structure of a Wnt morphogen bound to its Frizzled receptor ectodomain provides insights into the evolutionary provenance of this complex fold and offers an explanation for why Wnts utilize both lipid- and protein-mediated contacts to engage Frizzleds.
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50
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Olmeda B, García-Álvarez B, Pérez-Gil J. Structure–function correlations of pulmonary surfactant protein SP-B and the saposin-like family of proteins. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2012; 42:209-22. [DOI: 10.1007/s00249-012-0858-9] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 08/18/2012] [Accepted: 09/03/2012] [Indexed: 02/06/2023]
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