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Wilke SK, Al-Rubkhi A, Benmore CJ, Byrn SR, Weber R. Modeling the Structure of Ketoprofen-Poly(vinylpyrrolidone) Amorphous Solid Dispersions with Empirical Potential Structure Refinements of X-ray Scattering Data. Mol Pharm 2024; 21:3967-3978. [PMID: 39018110 DOI: 10.1021/acs.molpharmaceut.4c00313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/19/2024]
Abstract
The metastability of amorphous formulations poses barriers to their safe and widespread commercialization. The propensity of amorphous solid dispersions (ASDs) to crystallize is directly linked to their molecular structure. Amorphous structures are inherently complex and thus difficult to fully characterize by experiments, which makes structural simulations an attractive route for investigating which structural characteristics correlate with ASD stability. In this study, we use empirical potential structure refinement (EPSR) to create molecular models of ketoprofen-poly(vinylpyrrolidone) (KTP/PVP) ASDs with 0-75 wt % drug loading. The EPSR technique uses X-ray total scattering measurements as constraints, yielding models that are consistent with the X-ray data. We perform several simulations to assess the sensitivity of the EPSR approach to input parameters such as intramolecular bond rotations, PVP molecule length, and PVP tacticity. Even at low drug loading (25 wt %), ∼40% of KTP molecules participate in KTP-KTP hydrogen bonding. The extent of KTP-PVP hydrogen bonding does not decrease significantly at higher drug loadings. However, the models' relative uncertainties are too large to conclude whether ASDs' lower stabilities at high drug loadings are due to changes in drug-excipient hydrogen bonding or a decrease in steric hindrance of KTP molecules. This study illustrates how EPSR, combined with total scattering measurements, can be a powerful tool for investigating structural characteristics in amorphous formulations and developing ASDs with improved stability.
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Affiliation(s)
- Stephen K Wilke
- Materials Development, Inc., Arlington Heights, Illinois 60004, United States
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | | | - Chris J Benmore
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Stephen R Byrn
- Improved Pharma, West Lafayette, Indiana 47906, United States
| | - Richard Weber
- Materials Development, Inc., Arlington Heights, Illinois 60004, United States
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois 60439, United States
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2
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Cs Szabo B, Szabo M, Nagy P, Varga Z, Panyi G, Kovacs T, Zakany F. Novel insights into the modulation of the voltage-gated potassium channel K V1.3 activation gating by membrane ceramides. J Lipid Res 2024; 65:100596. [PMID: 39019344 PMCID: PMC11367112 DOI: 10.1016/j.jlr.2024.100596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 07/08/2024] [Accepted: 07/10/2024] [Indexed: 07/19/2024] Open
Abstract
Membrane lipids extensively modulate the activation gating of voltage-gated potassium channels (KV), however, much less is known about the mechanisms of ceramide and glucosylceramide actions including which structural element is the main intramolecular target and whether there is any contribution of indirect, membrane biophysics-related mechanisms to their actions. We used two-electrode voltage-clamp fluorometry capable of recording currents and fluorescence signals to simultaneously monitor movements of the pore domain (PD) and the voltage sensor domain (VSD) of the KV1.3 ion channel after attaching an MTS-TAMRA fluorophore to a cysteine introduced into the extracellular S3-S4 loop of the VSD. We observed rightward shifts in the conductance-voltage (G-V) relationship, slower current activation kinetics, and reduced current amplitudes in response to loading the membrane with C16-ceramide (Cer) or C16-glucosylceramide (GlcCer). When analyzing VSD movements, only Cer induced a rightward shift in the fluorescence signal-voltage (F-V) relationship and slowed fluorescence activation kinetics, whereas GlcCer exerted no such effects. These results point at a distinctive mechanism of action with Cer primarily targeting the VSD, while GlcCer only the PD of KV1.3. Using environment-sensitive probes and fluorescence-based approaches, we show that Cer and GlcCer similarly increase molecular order in the inner, hydrophobic regions of bilayers, however, Cer induces a robust molecular reorganization at the membrane-water interface. We propose that this unique ordering effect in the outermost membrane layer in which the main VSD rearrangement involving an outward sliding of the top of S4 occurs can explain the VSD targeting mechanism of Cer, which is unavailable for GlcCer.
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Affiliation(s)
- Bence Cs Szabo
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Mate Szabo
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Peter Nagy
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Zoltan Varga
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Gyorgy Panyi
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Tamas Kovacs
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.
| | - Florina Zakany
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.
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3
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Zhu Y, Cho K, Lacin H, Zhu Y, DiPaola JT, Wilson BA, Patti GJ, Skeath JB. Loss of dihydroceramide desaturase drives neurodegeneration by disrupting endoplasmic reticulum and lipid droplet homeostasis in glial cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.01.573836. [PMID: 38260379 PMCID: PMC10802327 DOI: 10.1101/2024.01.01.573836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Dihydroceramide desaturases convert dihydroceramides to ceramides, the precursors of all complex sphingolipids. Reduction of DEGS1 dihydroceramide desaturase function causes pediatric neurodegenerative disorder hypomyelinating leukodystrophy-18 (HLD-18). We discovered that infertile crescent (ifc), the Drosophila DEGS1 homolog, is expressed primarily in glial cells to promote CNS development by guarding against neurodegeneration. Loss of ifc causes massive dihydroceramide accumulation and severe morphological defects in cortex glia, including endoplasmic reticulum (ER) expansion, failure of neuronal ensheathment, and lipid droplet depletion. RNAi knockdown of the upstream ceramide synthase schlank in glia of ifc mutants rescues ER expansion, suggesting dihydroceramide accumulation in the ER drives this phenotype. RNAi knockdown of ifc in glia but not neurons drives neuronal cell death, suggesting that ifc function in glia promotes neuronal survival. Our work identifies glia as the primary site of disease progression in HLD-18 and may inform on juvenile forms of ALS, which also feature elevated dihydroceramide levels.
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Affiliation(s)
- Yuqing Zhu
- Department of Genetics, Washington University School of Medicine, 4523 Clayton Avenue, St. Louis, MO 63110, USA
| | - Kevin Cho
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, St. Louis, MO 63130, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Mass Spectrometry and Metabolic Tracing, Washington University in St. Louis, One Brookings Drive, St. Louis, MO 63130, USA
| | - Haluk Lacin
- Division of Biological and Biomedical Systems, University of Missouri-Kansas City, Kansas City, MO 64110, USA
| | - Yi Zhu
- Department of Genetics, Washington University School of Medicine, 4523 Clayton Avenue, St. Louis, MO 63110, USA
| | - Jose T DiPaola
- Department of Genetics, Washington University School of Medicine, 4523 Clayton Avenue, St. Louis, MO 63110, USA
| | - Beth A Wilson
- Department of Genetics, Washington University School of Medicine, 4523 Clayton Avenue, St. Louis, MO 63110, USA
| | - Gary J Patti
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, St. Louis, MO 63130, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Mass Spectrometry and Metabolic Tracing, Washington University in St. Louis, One Brookings Drive, St. Louis, MO 63130, USA
| | - James B Skeath
- Department of Genetics, Washington University School of Medicine, 4523 Clayton Avenue, St. Louis, MO 63110, USA
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González-Ramírez EJ, Etxaniz A, Alonso A, Goñi FM. Phase behaviour of C18-N-acyl sphingolipids, the prevalent species in human brain. Colloids Surf B Biointerfaces 2022; 219:112855. [PMID: 36137336 DOI: 10.1016/j.colsurfb.2022.112855] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 09/10/2022] [Accepted: 09/14/2022] [Indexed: 10/31/2022]
Abstract
Lipidomic analysis of the N-acyl components of sphingolipids in different mammalian tissues had revealed that brain tissue differed from all the other samples in that SM contained mainly C18:0 and C24:1N-acyl chains, and that the most abundant Cer species was C18:0. Only in the nervous system was C18:0 found in sizable proportions. The high levels of C18:0 and C16:0, respectively in brain and non-brain SM, were important because SM is by far the most abundant sphingolipid in the plasma membrane. In view of these observations, the present paper is devoted to a comparative study of the properties of C16:0 and C18:0 sphingolipids (SM and Cer) pure and in mixtures of increasing complexities, using differential scanning calorimetry, confocal microscopy of giant unilamellar vesicles, and correlative fluorescence microscopy and atomic force microscopy of supported lipid bilayers. Membrane rigidity was measured by force spectroscopy. It was found that in mixtures containing dioleoyl phosphatidylcholine, sphingomyelin and cholesterol, i.e. representing the lipids predominant in the outer monolayer of cell membranes, lateral inhomogeneities occurred, with the formation of rigid domains within a continuous fluid phase. Inclusion of saturated Cer in the system was always found to increase the rigidity of the segregated domains. C18:0-based sphingolipids exhibit hydrocarbon chain-length asymmetry, and some singularities observed with this N-acyl chain, e.g. complex calorimetric endotherms, could be attributed to this property. Moreover, C18:0-based sphingolipids, that are typical of the excitable cells, were less miscible with the fluid phase than their C16:0 counterparts. The results could be interpreted as suggesting that the predominance of C18:0 Cer in the nervous system would contribute to the tightness of its plasma membranes, thus facilitating maintenance of the ion gradients.
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Affiliation(s)
- Emilio J González-Ramírez
- Instituto Biofisika (CSIC, UPV/EHU) and Department of Biochemistry, University of the Basque Country, 48940 Leioa, Spain
| | - Asier Etxaniz
- Instituto Biofisika (CSIC, UPV/EHU) and Department of Biochemistry, University of the Basque Country, 48940 Leioa, Spain
| | - Alicia Alonso
- Instituto Biofisika (CSIC, UPV/EHU) and Department of Biochemistry, University of the Basque Country, 48940 Leioa, Spain.
| | - Félix M Goñi
- Instituto Biofisika (CSIC, UPV/EHU) and Department of Biochemistry, University of the Basque Country, 48940 Leioa, Spain
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6
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Zhao L, Liao C, Chen D, Zhang D, Li G, Zhang X. Stiffening Effect of Ceramide on Lipid Membranes Provides Non-Sacrificial Protection against Potent Chemical Damage. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:3522-3529. [PMID: 35263105 DOI: 10.1021/acs.langmuir.1c03427] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Ceramide is a sphingolipid that constitutes only a small fraction of membrane biomolecules but plays a central role in regulating many biological processes. The ceramide level in cell membranes can drastically increase in response to external damage, which has been hypothesized to involve ceramide's biophysical role that increases the membrane packing density and lowers the membrane permeability. However, direct observation of the consequent influence on membrane chemistry resulting from these ceramide-induced physical properties has been absent. Using our unique field-induced droplet ionization mass spectrometry technique combined with molecular dynamics simulations, here we report that the addition of ceramide to POPC monolayer membranes at the air-water interface greatly reduces the chemical damage from potent chemicals, •OH radicals, and HCl vapor, by stiffening the membrane packing and lowering the permeability. These results shed new light on the underlying chemoprotective role of ceramide in lipid membranes, which might serve as a previously unknown protection mechanism in response to external stimuli that cause cell stress or death.
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Affiliation(s)
- Lingling Zhao
- College of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), Renewable Energy Conversion and Storage Center (ReCAST), Haihe Laboratory of Sustainable Chemical Transformations, Beijing National Laboratory for Molecular Sciences, Shenzhen Research Institute, Frontiers Science Center for New Organic Matter, Nankai University, Tianjin 300071, China
| | - Chenyi Liao
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Danye Chen
- College of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), Renewable Energy Conversion and Storage Center (ReCAST), Haihe Laboratory of Sustainable Chemical Transformations, Beijing National Laboratory for Molecular Sciences, Shenzhen Research Institute, Frontiers Science Center for New Organic Matter, Nankai University, Tianjin 300071, China
| | - Dongmei Zhang
- College of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), Renewable Energy Conversion and Storage Center (ReCAST), Haihe Laboratory of Sustainable Chemical Transformations, Beijing National Laboratory for Molecular Sciences, Shenzhen Research Institute, Frontiers Science Center for New Organic Matter, Nankai University, Tianjin 300071, China
| | - Guohui Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Xinxing Zhang
- College of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), Renewable Energy Conversion and Storage Center (ReCAST), Haihe Laboratory of Sustainable Chemical Transformations, Beijing National Laboratory for Molecular Sciences, Shenzhen Research Institute, Frontiers Science Center for New Organic Matter, Nankai University, Tianjin 300071, China
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7
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Dingjan T, Futerman AH. The role of the 'sphingoid motif' in shaping the molecular interactions of sphingolipids in biomembranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183701. [PMID: 34302797 DOI: 10.1016/j.bbamem.2021.183701] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 07/16/2021] [Indexed: 12/28/2022]
Abstract
Sphingolipids can be differentiated from other membrane lipids by the distinctive chemistry of the sphingoid long chain base (LCB), which is generated by the condensation of an amino acid (normally but not always serine) and a fatty acyl CoA (normally palmitoyl CoA) by the pyridoxal phosphate-dependent enzyme, serine palmitoyl transferase (SPT). The first five carbon atoms of the sphingoid LCB, herein defined as the 'sphingoid motif', are largely responsible for the unique chemical and biophysical properties of sphingolipids since they can undergo a relatively large number (compared to other lipid species) of molecular interactions with other membrane lipids, via hydrogen-bonding, charge-pairing, hydrophobic and van der Waals interactions. These interactions are responsible, for instance, for the association of sphingolipids with cholesterol in the membrane lipid bilayer. Here, we discuss some of the unique properties of this sphingoid motif, and in addition to outlining how this structural motif drives intra-bilayer interactions, discuss the atomic details of the interactions with two critical players in the biosynthetic pathway, namely SPT, and the ceramide transport protein, CERT. In the former, the selectivity of sphingolipid synthesis relies on a hydrogen bond interaction between Lys379 of SPTLC2 and the l-serine sidechain hydroxyl moiety. In the latter, the entire sphingoid motif is stereoselectively recognized by a hydrogen-bonding network involving all three sphingoid motif heteroatoms. The remarkable selectivity of these interactions, and the subtle means by which these interactions are modified and regulated in eukaryotic cells raises a number of challenging questions about the generation of these proteins, and of their interactions with the sphingoid motif in evolutionary history.
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Affiliation(s)
- Tamir Dingjan
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Anthony H Futerman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel.
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8
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de la Arada I, González-Ramírez EJ, Alonso A, Goñi FM, Arrondo JLR. Exploring polar headgroup interactions between sphingomyelin and ceramide with infrared spectroscopy. Sci Rep 2020; 10:17606. [PMID: 33077787 PMCID: PMC7573612 DOI: 10.1038/s41598-020-74781-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 09/22/2020] [Indexed: 01/11/2023] Open
Abstract
Ceramide is a major actor in the sphingolipid signaling pathway elicited by various kinds of cell stress. Under those conditions ceramide (Cer) is produced in the plasma membrane as a product of sphingomyelin (SM) hydrolysis, and this may lead to apoptosis. Thus, SM and Cer coexist in the membrane for some time, and they are known to separate laterally from the (more abundant) glycerolipids, giving rise to highly rigid domains or platforms. The properties of these domains/platforms are rather well understood, but the underlying SM:Cer molecular interactions have not been explored in detail. Infrared (IR) spectroscopy is a powerful analytical technique that provides information on all the chemical groupings in a molecule, and that can be applied to membranes and lipid bilayers in aqueous media. IR spectra can be conveniently retrieved as a function of temperature, thus revealing the thermotropic transitions of SM and its mixtures with Cer. Four regions of the IR spectrum of these sphingolipids have been examined, two of them dominated by the hydrophobic regions in the molecules, namely the C–H stretching vibrations (2800–3000 cm−1), and the CH2 scissoring vibrations (1455–1485 cm−1), and two others arising from chemical groups at the lipid-water interface, the sphingolipid amide I band (1600–1680 cm−1), and the phosphate vibrations in the 1000–1110 cm−1 region. The latter two regions have been rarely studied in the past. The IR data from the hydrophobic components show a gel (or ripple)-fluid transition of SM at 40 °C, that is shifted up to about 70 °C when Cer is added to the bilayers, in agreement with previous studies using a variety of techniques. IR information concerning the polar parts is more interesting. The amide I (carbonyl) band of pure SM exhibits a maximum at 1638 cm−1 at room temperature, and its position is shifted by about 10 cm−1 in the presence of Cer. Cer causes also a change in the overall band shape, but no signs of band splitting are seen, suggesting that SM and Cer carbonyl groups are interacting tightly, presumably through H-bonds. The 1086 cm−1 band, corresponding to PO2− vibrations, appears more stable in SM than in DPPC, and it is further stabilized by Cer, again suggesting an important role of H-bonds in the formation of SM:Cer clusters. Thus, SM and Cer can interact through their polar headgroups, in a way that is not accessible to other lipid classes.
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Affiliation(s)
- Igor de la Arada
- Instituto Biofisika (CSIC, UPV/EHU), and Departamento de Bioquímica, Universidad del País Vasco, 48940, Leioa, Spain
| | - Emilio J González-Ramírez
- Instituto Biofisika (CSIC, UPV/EHU), and Departamento de Bioquímica, Universidad del País Vasco, 48940, Leioa, Spain
| | - Alicia Alonso
- Instituto Biofisika (CSIC, UPV/EHU), and Departamento de Bioquímica, Universidad del País Vasco, 48940, Leioa, Spain
| | - Félix M Goñi
- Instituto Biofisika (CSIC, UPV/EHU), and Departamento de Bioquímica, Universidad del País Vasco, 48940, Leioa, Spain.
| | - José-Luis R Arrondo
- Instituto Biofisika (CSIC, UPV/EHU), and Departamento de Bioquímica, Universidad del País Vasco, 48940, Leioa, Spain
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9
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Ceramide Domains in Health and Disease: A Biophysical Perspective. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1159:79-108. [DOI: 10.1007/978-3-030-21162-2_6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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10
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Effect of Ceramide Tail Length on the Structure of Model Stratum Corneum Lipid Bilayers. Biophys J 2019; 114:113-125. [PMID: 29320678 DOI: 10.1016/j.bpj.2017.10.031] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 10/18/2017] [Accepted: 10/19/2017] [Indexed: 12/22/2022] Open
Abstract
Lipid bilayers composed of non-hydroxy sphingosine ceramide (CER NS), cholesterol (CHOL), and free fatty acids (FFAs), which are components of the human skin barrier, are studied via molecular dynamics simulations. Since mixtures of these lipids exist in dense gel phases with little molecular mobility at physiological conditions, care must be taken to ensure that the simulations become decorrelated from the initial conditions. Thus, we propose and validate an equilibration protocol based on simulated tempering, in which the simulation takes a random walk through temperature space, allowing the system to break out of metastable configurations and hence become decorrelated from its initial configuration. After validating the equilibration protocol, which we refer to as random-walk molecular dynamics, the effects of the lipid composition and ceramide tail length on bilayer properties are studied. Systems containing pure CER NS, CER NS + CHOL, and CER NS + CHOL + FFA, with the CER NS fatty acid tail length varied within each CER NS-CHOL-FFA composition, are simulated. The bilayer thickness is found to depend on the structure of the center of the bilayer, which arises as a result of the tail-length asymmetry between the lipids studied. The hydrogen bonding between the lipid headgroups and with water is found to change with the overall lipid composition, but is mostly independent of the CER fatty acid tail length. Subtle differences in the lateral packing of the lipid tails are also found as a function of CER tail length. Overall, these results provide insight into the experimentally observed trend of altered barrier properties in skin systems where there are more CERs with shorter tails present.
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11
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Rhys NH, Duffy IB, Sowden CL, Lorenz CD, McLain SE. On the hydration of DOPE in solution. J Chem Phys 2019; 150:115104. [PMID: 30902020 DOI: 10.1063/1.5085736] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The atomic-scale hydration structure around the 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE) headgroup in a chloroform/water solution has been investigated using neutron diffraction enhanced by isotopic substitution and NMR, coupled with empirical potential structure refinement and molecular dynamics simulations. The results obtained show the preferential binding sites for water molecules on the DOPE headgroups, with the most predominant interactions being with the ammonium and phosphate groups. Interestingly, the level of hydration, as well as the association of DOPE molecules, varies according to the simulation method used. The results here suggest the presence of a tight water network around these lipid headgroups that could affect the permeability of the membrane for lipid-mediated diffusion.
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Affiliation(s)
- Natasha H Rhys
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Imogen B Duffy
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Christopher L Sowden
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Christian D Lorenz
- Department of Physics, King's College London, London WC2R 2LS, United Kingdom
| | - Sylvia E McLain
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
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12
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Abstract
Ceramides are sphingolipids containing a sphingosine or a related base, to which a fatty acid is linked through an amide bond. When incorporated into a lipid bilayer, ceramides exhibit a number of properties not shared by almost any other membrane lipid: Ceramides ( a) are extremely hydrophobic and thus cannot exist in suspension in aqueous media; ( b) increase the molecular order (rigidity) of phospholipids in membranes; ( c) give rise to lateral phase separation and domain formation in phospholipid bilayers; ( d) possess a marked intrinsic negative curvature that facilitates formation of inverted hexagonal phases; ( e) make bilayers and cell membranes permeable to small and large (i.e., protein-size) solutes; and ( f) promote transmembrane (flip-flop) lipid motion. Unfortunately, there is hardly any link between the physical studies reviewed here and the mass of biological and clinical studies on the effects of ceramides in health and disease.
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Affiliation(s)
- Alicia Alonso
- Instituto Biofisika [University of the Basque Country and Spanish National Research Council (CSIC)], 48940 Leioa, Spain
- Department of Biochemistry and Molecular Biology, University of the Basque Country, 48940 Leioa, Spain;,
| | - Félix M. Goñi
- Instituto Biofisika [University of the Basque Country and Spanish National Research Council (CSIC)], 48940 Leioa, Spain
- Department of Biochemistry and Molecular Biology, University of the Basque Country, 48940 Leioa, Spain;,
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13
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Ingram DJ, Headen TF, Skipper NT, Callear SK, Billing M, Sella A. Dihydrogen vs. hydrogen bonding in the solvation of ammonia borane by tetrahydrofuran and liquid ammonia. Phys Chem Chem Phys 2018; 20:12200-12209. [DOI: 10.1039/c7cp08220g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The solvation structures of two systems rich in hydrogen and dihydrogen bonding interactions have been studied in detail experimentally through neutron diffraction with hydrogen/deuterium isotopic substitution.
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Affiliation(s)
- David J. Ingram
- Department of Physics & Astronomy
- University College London
- London
- UK
- Department of Chemistry
| | | | - Neal T. Skipper
- Department of Physics & Astronomy
- University College London
- London
- UK
- London Centre for Nanotechnology
| | | | | | - Andrea Sella
- Department of Chemistry
- University College London
- London
- UK
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14
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Gillams RJ, Lorenz CD, McLain SE. Comparative atomic-scale hydration of the ceramide and phosphocholine headgroup in solution and bilayer environments. J Chem Phys 2017; 144:225101. [PMID: 27306021 DOI: 10.1063/1.4952444] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Previous studies have used neutron diffraction to elucidate the hydration of the ceramide and the phosphatidylcholine headgroup in solution. These solution studies provide bond-length resolution information on the system, but are limited to liquid samples. The work presented here investigates how the hydration of ceramide and phosphatidylcholine headgroups in a solution compares with that found in a lipid bilayer. This work shows that the hydration patterns seen in the solution samples provide valuable insight into the preferential location of hydrating water molecules in the bilayer. There are certain subtle differences in the distribution, which result from a combination of the lipid conformation and the lipid-lipid interactions within the bilayer environment. The lipid-lipid interactions in the bilayer will be dependent on the composition of the bilayer, whereas the restricted exploration of conformational space is likely to be applicable in all membrane environments. The generalized description of hydration gathered from the neutron diffraction studies thus provides good initial estimation for the hydration pattern, but this can be further refined for specific systems.
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Affiliation(s)
- Richard J Gillams
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Christian D Lorenz
- Department of Physics, King's College London, London WC2R 2LS, United Kingdom
| | - Sylvia E McLain
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
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15
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Maugeri L, Busch S, McLain SE, Pardo LC, Bruni F, Ricci MA. Structure-activity relationships in carbohydrates revealed by their hydration. Biochim Biophys Acta Gen Subj 2016; 1861:1486-1493. [PMID: 28011302 DOI: 10.1016/j.bbagen.2016.12.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 12/13/2016] [Accepted: 12/17/2016] [Indexed: 11/25/2022]
Abstract
One of the more intriguing aspects of carbohydrate chemistry is that despite having very similar molecular structures, sugars have very different properties. For instance, there is a sensible difference in sweet taste between glucose and trehalose, even though trehalose is a disaccharide that comprised two glucose units, suggesting a different ability of these two carbohydrates to bind to sweet receptors. Here we have looked at the hydration of specific sites and at the three-dimensional configuration of water molecules around three carbohydrates (glucose, cellobiose, and trehalose), combining neutron diffraction data with computer modelling. Results indicate that identical chemical groups can have radically different hydration patterns depending on their location on a given molecule. These differences can be linked with the specific activity of glucose, cellobiose, and trehalose as a sweet substance, as building block of cellulose fiber, and as a bioprotective agent, respectively. This article is part of a Special Issue entitled "Recent Advances in Bionanomaterials" Guest Editors: Dr. Marie-Louise Saboungi and Dr. Samuel D. Bader.
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Affiliation(s)
- Laura Maugeri
- Dipartimento di Scienze, Università degli Studi Roma Tre, Via della Vasca Navale 84, Roma 00146, Italy
| | - Sebastian Busch
- German Engineering Materials Science Centre (GEMS) at Heinz Maier-Leibnitz Zentrum (MLZ), Helmholtz-Zentrum Geesthacht GmbH, Lichtenbergstr. Garching bei München 1 85747, Germany
| | - Sylvia E McLain
- Department of Biochemistry, University of Oxford, South Park Road, Oxford, Oxfordshire OX1 3QU, UK
| | - Luis Carlos Pardo
- Departament de Física i Enginyeria Nuclear, Universitat Politècnica de Catalunya Barcelona 08028, Catalonia, Spain
| | - Fabio Bruni
- Dipartimento di Scienze, Università degli Studi Roma Tre, Via della Vasca Navale 84, Roma 00146, Italy
| | - Maria Antonietta Ricci
- Dipartimento di Scienze, Università degli Studi Roma Tre, Via della Vasca Navale 84, Roma 00146, Italy.
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16
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Rhys NH, Gillams RJ, Collins LE, Callear SK, Lawrence MJ, McLain SE. On the structure of an aqueous propylene glycol solution. J Chem Phys 2016; 145:224504. [DOI: 10.1063/1.4971208] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Natasha H. Rhys
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Richard J. Gillams
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Louise E. Collins
- King’s College London, Institute of Pharmaceutical Science, London SE1 9NH, United Kingdom
| | - Samantha K. Callear
- STFC, ISIS Facility, Rutherford Appleton Laboratory, Didcot OX11 0QU United Kingdom
| | - M. Jayne Lawrence
- King’s College London, Institute of Pharmaceutical Science, London SE1 9NH, United Kingdom
| | - Sylvia E. McLain
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
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17
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Das S, Paul S. Mechanism of Hydrotropic Action of Hydrotrope Sodium Cumene Sulfonate on the Solubility of Di-t-Butyl-Methane: A Molecular Dynamics Simulation Study. J Phys Chem B 2016; 120:173-83. [PMID: 26684411 DOI: 10.1021/acs.jpcb.5b09668] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydrotropes are special class of amphiphilic molecules that have an ability to solubilize the insoluble or sparingly soluble molecules in water. To find out the mechanism of hydrotropic action of hydrotropes on hydrophobic molecules, we have carried out classical molecular dynamics simulation of hydrophobic solute di-t-butyl-methane (DTBM) and hydrotrope sodium cumene sulfonate (SCS) in water with a regime of SCS concentrations. Our study demonstrates that, above the minimum hydrotrope concentration (MHC), the self-aggregation of SCS starts, and it creates a micellar-like environment in which the hydrophobic tail part of SCS points inward while its hydrophilic sulfonate group points outward to make favorable contact with water molecules. The formation of the hydrophobic core of SCS cluster creates a hydrophobic environment where the hydrophobic DTBM molecules are encapsulated. Interestingly, the determination of average water-SCS hydrogen bonds further suggests that the aggregate formation of SCS molecules has a negligible influence on it. Moreover, the calculations of Flory-Huggins interaction parameters also reveal favorable interactions between hydrotrope SCS and solute DTBM molecules. The implications of these findings on the mechanism of hydrotrope assisted enhanced solubility of hydrophobic molecules are discussed.
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Affiliation(s)
- Shubhadip Das
- Department of Chemistry, Indian Institute of Technology , Guwahati, Assam 781039, India
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology , Guwahati, Assam 781039, India
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18
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Sridhar A, Johnston AJ, Varathan L, McLain SE, Biggin PC. The solvation structure of alprazolam. Phys Chem Chem Phys 2016; 18:22416-25. [DOI: 10.1039/c6cp02645a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Alprazolam is a benzodiazepine that is commonly prescribed for the treatment of anxiety and other related disorders.
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19
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Henao A, Johnston AJ, Guàrdia E, McLain SE, Pardo LC. On the positional and orientational order of water and methanol around indole: a study on the microscopic origin of solubility. Phys Chem Chem Phys 2016; 18:23006-16. [DOI: 10.1039/c6cp04183c] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The increase in solubility for indole in methanol water solutions relative to pure water is a result methanol −OH–π interactions. In addition, excess entropy calculations suggest that this process is enthalpically rather than entropically driven.
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Affiliation(s)
- Andres Henao
- Grup de Caracterització de Materials
- Departament de Física
- ETSEIB
- Universitat Politècnica de Catalunya
- E-08028 Barcelona
| | | | - Elvira Guàrdia
- Grup de Simulació per Ordinador en Matèria Condensada
- Departament de Física
- B4-B5 Campus Nord
- Universitat Politècnica de Catalunya
- E-08034 Barcelona
| | | | - Luis Carlos Pardo
- Grup de Caracterització de Materials
- Departament de Física
- ETSEIB
- Universitat Politècnica de Catalunya
- E-08028 Barcelona
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20
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Johnston AJ, Busch S, Pardo LC, Callear SK, Biggin PC, McLain SE. On the atomic structure of cocaine in solution. Phys Chem Chem Phys 2016; 18:991-9. [DOI: 10.1039/c5cp06090g] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A combination of neutron diffraction and computation has been used to investigate the atomic scale structure of cocaine in aqueous solutions.
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Affiliation(s)
| | - Sebastian Busch
- German Engineering Materials Science Centre (GEMS) at Heinz Maier-Leibnitz Zentrum (MLZ)
- Helmholtz-Zentrum Geesthacht GmbH
- 85747 Garching bei München
- Germany
| | - Luis Carlos Pardo
- Departament de Física i Enginyeria Nuclear
- Escola Tècnica Superior d'Enginyeria Industrial de Barcelona (ETSEIB)
- Universitat Politècnica de Catalunya
- 08028 Barcelona
- Spain
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21
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Biswas S, Mallik BS. Aqueous solvation of an amide molecule from first principles molecular simulations: Structure, hydrogen bond dynamics and spectral signature. J Mol Liq 2015. [DOI: 10.1016/j.molliq.2015.11.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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22
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Johnston AJ, Zhang YR, Busch S, Pardo LC, Imberti S, McLain SE. Amphipathic solvation of indole: implications for the role of tryptophan in membrane proteins. J Phys Chem B 2015; 119:5979-87. [PMID: 25893741 DOI: 10.1021/acs.jpcb.5b02476] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The microscopic structure of the tryptophan side chain, indole, in an amphiphilic environment has been investigated using a combination of neutron diffraction measurements and simulations in solution. The results show that indole is preferentially solvated by hydrogen bonding interactions between water and alcohol -OH groups rather than the interaction being dominated by indole-methyl interactions. This has implications for understanding how tryptophan interacts with the amphipathic membrane environment to anchor proteins into membranes, where the results here suggest that the benzene ring of tryptophan interacts directly with the interfacial water at the membrane surface rather than being buried into the hydrophobic regions of the membrane bilayer.
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Affiliation(s)
| | - Yapei Rosie Zhang
- ‡Department of Biochemistry, Princeton University, Princeton, New Jersey, United States
| | - Sebastian Busch
- ⊥German Engineering Materials Science Centre (GEMS), Heinz Maier-Leibnitz Zentrum (MLZ), Helmholtz-Zentrum Geesthacht GmbH Lichtenbergstrasse 1, 85747 Garching bei München, Germany
| | - Luis Carlos Pardo
- §Departament de Física i Enginyeria Nuclear, Universitat Politècnica de Catalunya, Barcelona, Catalonia, Spain
| | - Silvia Imberti
- ∥ISIS Facility, Rutherford Appleton Laboratory, Didcot, Chilton, U.K
| | - Sylvia E McLain
- †Department of Biochemistry, University of Oxford, Oxford, U.K
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