1
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Meredith SA, Kusunoki Y, Evans SD, Morigaki K, Connell SD, Adams PG. Evidence for a transfer-to-trap mechanism of fluorophore concentration quenching in lipid bilayers. Biophys J 2024:S0006-3495(24)00485-5. [PMID: 39039794 DOI: 10.1016/j.bpj.2024.07.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 05/30/2024] [Accepted: 07/19/2024] [Indexed: 07/24/2024] Open
Abstract
It is important to understand the behaviors of fluorescent molecules because, firstly, they are often utilized as probes in biophysical experiments and, secondly, they are crucial cofactors in biological processes such as photosynthesis. A phenomenon called "fluorescence quenching" occurs when fluorophores are present at high concentrations, but the mechanisms for quenching are debated. Here, we used a technique called "in-membrane electrophoresis" to generate concentration gradients of fluorophores within a supported lipid bilayer, across which quenching was expected to occur. Fluorescence lifetime imaging microscopy (FLIM) provides images where the fluorescence intensity in each pixel is correlated to fluorescence lifetime: the intensity provides information about the location and concentration of fluorophores and the lifetime reveals the occurrence of energy-dissipative processes. FLIM was used to compare the quenching behavior of three commonly used fluorophores: Texas Red (TR), nitrobenzoaxadiazole (NBD), and 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY). FLIM images provided evidence of quenching in regions where the fluorophores accumulated, but the degree of quenching varied between the different fluorophores. The relationship between quenching and concentration was quantified and the "critical radius for trap formation," representing the relative quenching strength, was calculated as 2.70, 2.02, and 1.14 nm, for BODIPY, TR, and NBD, respectively. The experimental data support the theory that quenching takes place via a "transfer-to-trap" mechanism which proposes, firstly, that excitation energy is transferred between fluorophores and may reach a "trap site," resulting in immediate energy dissipation, and, secondly, that trap sites are formed in a concentration-dependent manner. Some previous work suggested that quenching occurs only when fluorophores aggregate, or form long-lived dimers, but our data and this theory argue that traps may be "statistical pairs" of fluorophores that exist only transiently. Our findings should inspire future work to assess whether these traps can be charge-transfer states, excited-state dimers, or something else.
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Affiliation(s)
- Sophie A Meredith
- School of Physics and Astronomy, University of Leeds, Leeds, UK; Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Yuka Kusunoki
- Graduate School of Agricultural Science and Biosignal Research Center, Kobe University, Kobe, Japan
| | - Stephen D Evans
- School of Physics and Astronomy, University of Leeds, Leeds, UK
| | - Kenichi Morigaki
- Graduate School of Agricultural Science and Biosignal Research Center, Kobe University, Kobe, Japan
| | - Simon D Connell
- School of Physics and Astronomy, University of Leeds, Leeds, UK; Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Peter G Adams
- School of Physics and Astronomy, University of Leeds, Leeds, UK; Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK.
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2
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Mallick S, Agmon N. Lateral diffusion of ions near membrane surface. Phys Chem Chem Phys 2024; 26:19433-19449. [PMID: 38973628 DOI: 10.1039/d3cp04112c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2024]
Abstract
Biological membranes isolate living cells from their environment, while allowing selective molecular transport between the inner and outer realms. For example, Na+ and K+ permeability through ionic channels contributes to neural conduction. Whether the ionic currents arise directly from cations in the bulk, or from the interface, is currently unclear. There are only scant results concerning lateral diffusion of ions on aquated membrane surfaces (and strong belief that this occurs through binding to a diffusing lipid). We performed classical molecular dynamics (MD) simulations of monovalent ions, Na+, K+, and Cl-, near the surface of the zwitterionic palmitoyl-oleoyl-phosphatidylcholine (POPC) membrane. Realistic force-fields for lipids (Amber's Lipid17 and Lipid21) and water (TIP4P-Ew) are tested for the mass and charge densities and the electrostatic potential across the membrane. These calculations reveal that the chloride can bind to the choline moiety through an intervening water molecule by forming a CH⋯OH hydrogen bond, while cations bind to both the phosphatic and carbonyl oxygens of phosphatidylcholine moieties. Upon transitioning from the bulk to the interface, a cation sheds some of its hydration water, which are replaced by headgroup atoms. Notably, an interfacial cation can bind 1-4 headgroup atoms, which is a key to understanding its surface hopping mechanism. We find that cation binding to three headgroup atoms immobilizes it, while binding to four energizes it. Consequently, the lateral cation diffusion rate is only 15-25 times slower than in the bulk, and 4-5 times faster than lipid self-diffusion. K+ diffusion is notably more anomalous than Na+, switching from sub- to super-diffusion after about 2 ns.
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Affiliation(s)
- Subhasish Mallick
- The Fritz Haber Research Center, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel.
| | - Noam Agmon
- The Fritz Haber Research Center, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel.
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3
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Smith RS, Weaver DR, King GM, Kosztin I. Chain-Length Dependence of Peptide-Lipid Bilayer Interaction Strength and Binding Kinetics: A Combined Theoretical and Experimental Approach. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:14467-14475. [PMID: 38963062 DOI: 10.1021/acs.langmuir.4c01218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
Physical interactions between polypeptide chains and lipid membranes underlie critical cellular processes. Yet, despite fundamental importance, key mechanistic aspects of these interactions remain elusive. Bulk experiments have revealed a linear relationship between free energy and peptide chain length in a model system, but does this linearity extend to the interaction strength and to the kinetics of lipid binding? To address these questions, we utilized a combination of coarse-grained molecular dynamics (CG MD) simulations, analytical modeling, and atomic force microscopy (AFM)-based single molecule force spectroscopy. Following previous bulk experiments, we focused on interactions between short hydrophobic peptides (WLn, n = 1, ..., 5) with 1-palmitoyl-2-oleoyl-glycero-3-phosphocholine (POPC) bilayers, a simple system that probes peptide primary structure effects. Potentials of mean force extracted from CG MD recapitulated the linearity of free energy with the chain length. Simulation results were quantitatively connected to bulk biochemical experiments via a single scaling factor of order unity, corroborating the methodology. Additionally, CG MD revealed an increase in the distance to the transition state, a result that weakens the dependence of the dissociation force on the peptide chain length. AFM experiments elucidated rupture force distributions and, through modeling, intrinsic dissociation rates. Taken together, the analysis indicates a rupture force plateau in the WLn-POPC system, suggesting that the final rupture event involves the last 2 or 3 residues. In contrast, the linear dependence on chain length was preserved in the intrinsic dissociation rate. This study advances the understanding of peptide-lipid interactions and provides potentially useful insights for the design of peptides with tailored membrane-interacting properties.
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Affiliation(s)
- Ryan S Smith
- Department of Physics & Astronomy, University of Missouri, Columbia, Missouri 65211, United States
| | - Dylan R Weaver
- Department of Physics & Astronomy, University of Missouri, Columbia, Missouri 65211, United States
| | - Gavin M King
- Department of Physics & Astronomy, University of Missouri, Columbia, Missouri 65211, United States
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Ioan Kosztin
- Department of Physics & Astronomy, University of Missouri, Columbia, Missouri 65211, United States
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4
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Correa Y, Ravel M, Imbert M, Waldie S, Clifton L, Terry A, Roosen‐Runge F, Lagerstedt JO, Moir M, Darwish T, Cárdenas M, Del Giudice R. Lipid exchange of apolipoprotein A-I amyloidogenic variants in reconstituted high-density lipoprotein with artificial membranes. Protein Sci 2024; 33:e4987. [PMID: 38607188 PMCID: PMC11010956 DOI: 10.1002/pro.4987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/13/2024]
Abstract
High-density lipoproteins (HDLs) are responsible for removing cholesterol from arterial walls, through a process known as reverse cholesterol transport. The main protein in HDL, apolipoprotein A-I (ApoA-I), is essential to this process, and changes in its sequence significantly alter HDL structure and functions. ApoA-I amyloidogenic variants, associated with a particular hereditary degenerative disease, are particularly effective at facilitating cholesterol removal, thus protecting carriers from cardiovascular disease. Thus, it is conceivable that reconstituted HDL (rHDL) formulations containing ApoA-I proteins with functional/structural features similar to those of amyloidogenic variants hold potential as a promising therapeutic approach. Here we explored the effect of protein cargo and lipid composition on the function of rHDL containing one of the ApoA-I amyloidogenic variants G26R or L174S by Fourier transformed infrared spectroscopy and neutron reflectometry. Moreover, small-angle x-ray scattering uncovered the structural and functional differences between rHDL particles, which could help to comprehend higher cholesterol efflux activity and apparent lower phospholipid (PL) affinity. Our findings indicate distinct trends in lipid exchange (removal vs. deposition) capacities of various rHDL particles, with the rHDL containing the ApoA-I amyloidogenic variants showing a markedly lower ability to remove lipids from artificial membranes compared to the rHDL containing the native protein. This effect strongly depends on the level of PL unsaturation and on the particles' ultrastructure. The study highlights the importance of the protein cargo, along with lipid composition, in shaping rHDL structure, contributing to our understanding of lipid-protein interactions and their behavior.
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Affiliation(s)
- Yubexi Correa
- Biofilm – Research Center for Biointerfaces and Department of Biomedical Science, Faculty of Health and SocietyMalmö UniversityMalmöSweden
| | - Mathilde Ravel
- Biofilm – Research Center for Biointerfaces and Department of Biomedical Science, Faculty of Health and SocietyMalmö UniversityMalmöSweden
| | - Marie Imbert
- Biofilm – Research Center for Biointerfaces and Department of Biomedical Science, Faculty of Health and SocietyMalmö UniversityMalmöSweden
| | - Sarah Waldie
- Biofilm – Research Center for Biointerfaces and Department of Biomedical Science, Faculty of Health and SocietyMalmö UniversityMalmöSweden
| | - Luke Clifton
- ISIS Pulsed Neutron and Muon Source, Science and Technology Facilities CouncilRutherford Appleton Laboratory, Harwell Science and Innovation CampusDidcotUK
| | - Ann Terry
- MAX IV LaboratoryCoSAXS Beamline, Lund UniversityLundSweden
| | - Felix Roosen‐Runge
- Biofilm – Research Center for Biointerfaces and Department of Biomedical Science, Faculty of Health and SocietyMalmö UniversityMalmöSweden
| | - Jens O. Lagerstedt
- Islet Cell Exocytosis, Department of Clinical Sciences in Malmö, Lund University Diabetes CentreLund UniversityMalmöSweden
- Rare Endocrine Disorders, Research and Early DevelopmentNovo NordiskCopenhagenDenmark
| | - Michael Moir
- National Deuteration FacilityAustralian Nuclear Science and Technology Organization (ANSTO)Lucas HeightsNew South WalesAustralia
| | - Tamim Darwish
- National Deuteration FacilityAustralian Nuclear Science and Technology Organization (ANSTO)Lucas HeightsNew South WalesAustralia
- Faculty of Science and TechnologyUniversity of CanberraCanberraAustralian Capital TerritoryAustralia
| | - Marité Cárdenas
- Biofilm – Research Center for Biointerfaces and Department of Biomedical Science, Faculty of Health and SocietyMalmö UniversityMalmöSweden
- Ikerbasque, Basque Foundation for ScienceBilbaoSpain
- Biofisika Institute (University of Basque Country and Consejo Superior de Investigaciones Científicas (UPV/EHU, CSIC))LeioaSpain
| | - Rita Del Giudice
- Biofilm – Research Center for Biointerfaces and Department of Biomedical Science, Faculty of Health and SocietyMalmö UniversityMalmöSweden
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5
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Thakur GCN, Uday A, Jurkiewicz P. FRET-GP - A Local Measure of the Impact of Transmembrane Peptide on Lipids. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:18390-18402. [PMID: 38048524 DOI: 10.1021/acs.langmuir.3c02505] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/06/2023]
Abstract
Reconstitution of a transmembrane protein in model lipid systems allows studying its structure and dynamics in isolation from the complexity of the natural environment. This approach also provides a well-defined environment for studying the interactions of proteins with lipids. In this work, we describe the FRET-GP method, which utilizes Förster resonance energy transfer (FRET) to specifically probe the nanoenvironment of a transmembrane domain. The tryptophan residues flanking this domain act as efficient FRET donors, while Laurdan acts as acceptor. The fluorescence of this solvatochromic probe is quantified using generalized polarization (GP) to report on lipid mobility in the vicinity of the transmembrane domain. We applied FRET-GP to study the transmembrane peptide WALP incorporated in liposomes. We found that the direct excitation of Laurdan to its second singlet state strongly contributes to GP values measured in FRET conditions. Removal of this parasitic contribution was essential for proper determination of GPFRET - the local analogue of classical GP parameter. The presence of WALP significantly increased both parameters but the local effects were considerably stronger (GPFRET ≫ GP). We conclude that WALP restricts lipid movement in its vicinity, inducing lateral inhomogeneity in membrane fluidity. WALP was also found to influence lipid phase transition. Our findings demonstrated that FRET-GP simultaneously provides local and global results, thereby enhancing the depth of information obtained from the measurement. We highlight the simplicity and sensitivity of the method, but also discuss its potential and limitations in studying protein-lipid interactions.
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Affiliation(s)
- Garima C N Thakur
- J. Heyrovský Institute of Physical Chemistry of the Academy of Sciences of the Czech Republic, v.v.i., Prague 182 00, Czech Republic
| | - Arunima Uday
- J. Heyrovský Institute of Physical Chemistry of the Academy of Sciences of the Czech Republic, v.v.i., Prague 182 00, Czech Republic
| | - Piotr Jurkiewicz
- J. Heyrovský Institute of Physical Chemistry of the Academy of Sciences of the Czech Republic, v.v.i., Prague 182 00, Czech Republic
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6
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Balleza D. Peptide Flexibility and the Hydrophobic Moment are Determinants to Evaluate the Clinical Potential of Magainins. J Membr Biol 2023; 256:317-330. [PMID: 37097306 DOI: 10.1007/s00232-023-00286-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 04/05/2023] [Indexed: 04/26/2023]
Abstract
Using a flexibility prediction algorithm and in silico structural modeling, we have calculated the intrinsic flexibility of several magainin derivatives. In the case of magainin-2 (Mag-2) and magainin H2 (MAG-H2) we have found that MAG-2 is more flexible than its hydrophobic analog, Mag-H2. This affects the degree of bending of both peptides, with a kink around two central residues (R10, R11), whereas, in Mag-H2, W10 stiffens the peptide. Moreover, this increases the hydrophobic moment of Mag-H2, which could explain its propensity to form pores in POPC model membranes, which exhibit near-to-zero spontaneous curvatures. Likewise, the protective effect described in DOPC membranes for this peptide regarding its facilitation in pore formation would be related to the propensity of this lipid to form membranes with negative spontaneous curvature. The flexibility of another magainin analog (MSI-78) is even greater than that of Mag-2. This facilitates the peptide to present a kind of hinge around the central F12 as well as a C-terminal end prone to be disordered. Such characteristics are key to understanding the broad-spectrum antimicrobial actions exhibited by this peptide. These data reinforce the hypothesis on the determinant role of spontaneous membrane curvature, intrinsic peptide flexibility, and specific hydrophobic moment in assessing the bioactivity of membrane-active antimicrobial peptides.
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Affiliation(s)
- Daniel Balleza
- Laboratorio de Microbiología, Unidad de Investigación y Desarrollo en Alimentos, Instituto Tecnológico de Veracruz, Tecnológico Nacional de México, Veracruz, Mexico.
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7
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Meier S, Ridgway ZM, Picciano AL, Caputo GA. Impacts of Hydrophobic Mismatch on Antimicrobial Peptide Efficacy and Bilayer Permeabilization. Antibiotics (Basel) 2023; 12:1624. [PMID: 37998826 PMCID: PMC10669323 DOI: 10.3390/antibiotics12111624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/06/2023] [Accepted: 11/08/2023] [Indexed: 11/25/2023] Open
Abstract
Antimicrobial resistance continues to be a major threat to world health, with the continued emergence of resistant bacterial strains. Antimicrobial peptides have emerged as an attractive option for the development of novel antimicrobial compounds in part due to their ubiquity in nature and the general lack of resistance development to this class of molecules. In this work, we analyzed the antimicrobial peptide C18G and several truncated forms for efficacy and the underlying mechanistic effects of the sequence truncation. The peptides were screened for antimicrobial efficacy against several standard laboratory strains, and further analyzed using fluorescence spectroscopy to evaluate binding to model lipid membranes and bilayer disruption. The results show a clear correlation between the length of the peptide and the antimicrobial efficacy. Furthermore, there is a correlation between peptide length and the hydrophobic thickness of the bilayer, indicating that hydrophobic mismatch is likely a contributing factor to the loss of efficacy in shorter peptides.
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Affiliation(s)
- Steven Meier
- Department of Chemistry & Biochemistry, Rowan University, Glassboro, NJ 08028, USA (A.L.P.)
| | - Zachary M. Ridgway
- Department of Chemistry & Biochemistry, Rowan University, Glassboro, NJ 08028, USA (A.L.P.)
| | - Angela L. Picciano
- Department of Chemistry & Biochemistry, Rowan University, Glassboro, NJ 08028, USA (A.L.P.)
| | - Gregory A. Caputo
- Department of Chemistry & Biochemistry, Rowan University, Glassboro, NJ 08028, USA (A.L.P.)
- Department of Biological & Biomedical Sciences, Rowan University, Glassboro, NJ 08028, USA
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8
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Xu J, Karra V, Large DE, Auguste DT, Hung FR. Understanding the Mechanical Properties of Ultradeformable Liposomes Using Molecular Dynamics Simulations. J Phys Chem B 2023; 127:9496-9512. [PMID: 37879075 PMCID: PMC10641833 DOI: 10.1021/acs.jpcb.3c04386] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 09/19/2023] [Accepted: 10/04/2023] [Indexed: 10/27/2023]
Abstract
Improving drug delivery efficiency to solid tumor sites is a central challenge in anticancer therapeutic research. Our previous experimental study (Guo et al., Nat. Commun. 2018, 9, 130) showed that soft, elastic liposomes had increased uptake and accumulation in cancer cells and tumors in vitro and in vivo respectively, relative to rigid particles. As a first step toward understanding how liposomes' molecular structure and composition modulates their elasticity, we performed all-atom and coarse-grained classical molecular dynamics (MD) simulations of lipid bilayers formed by mixing a long-tailed unsaturated phospholipid with a short-tailed saturated lipid with the same headgroup. The former types of phospholipids considered were 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and 1,2-dipalmitoleoyl-sn-glycero-3-phosphocholine (termed here DPMPC). The shorter saturated lipids examined were 1,2-diheptanoyl-sn-glycero-3-phosphocholine (DHPC), 1,2-didecanoyl-sn-glycero-3-phosphocholine (DDPC), 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC), and 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC). Several lipid concentrations and surface tensions were considered. Our results show that DOPC or DPMPC systems having 25-35 mol % of the shortest lipids DHPC or DDPC are the least rigid, having area compressibility moduli KA that are ∼10% smaller than the values observed in pure DOPC or DPMPC bilayers. These results agree with experimental measurements of the stretching modulus and lysis tension in liposomes with the same compositions. These mixed systems also have lower areas per lipid and form more uneven x-y interfaces with water, the tails of both primary and secondary lipids are more disordered, and the terminal methyl groups in the tails of the long lipid DOPC or DPMPC wriggle more in the vertical direction, compared to pure DOPC or DPMPC bilayers or their mixtures with the longer saturated lipid DLPC or DMPC. These observations confirm our hypothesis that adding increasing concentrations of the short unsaturated lipid DHPC or DDPC to DOPC or DPMPC bilayers alters lipid packing and thus makes the resulting liposomes more elastic and less rigid. No formation of lipid nanodomains was noted in our simulations, and no clear trends were observed in the lateral diffusivities of the lipids as the concentration, type of secondary lipid, and surface tension were varied.
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Affiliation(s)
- Jiaming Xu
- Department
of Chemical Engineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Vyshnavi Karra
- Department
of Chemical Engineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Danielle E. Large
- Department
of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Debra T. Auguste
- Department
of Chemical Engineering, Northeastern University, Boston, Massachusetts 02115, United States
- Department
of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Francisco R. Hung
- Department
of Chemical Engineering, Northeastern University, Boston, Massachusetts 02115, United States
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9
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Konar S, Arif H, Allolio C. Mitochondrial membrane model: Lipids, elastic properties, and the changing curvature of cardiolipin. Biophys J 2023; 122:4274-4287. [PMID: 37798880 PMCID: PMC10645570 DOI: 10.1016/j.bpj.2023.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 06/12/2023] [Accepted: 10/02/2023] [Indexed: 10/07/2023] Open
Abstract
Mammalian and Drosophila melanogaster model mitochondrial membrane compositions are constructed from experimental data. Simplified compositions for inner and outer mitochondrial membranes are provided, including an asymmetric inner mitochondrial membrane. We performed atomistic molecular dynamics simulations of these membranes and computed their material properties. When comparing these properties to those obtained by extrapolation from their constituting lipids, we find good overall agreement. Finally, we analyzed the curvature effect of cardiolipin, considering ion concentration effects, oxidation, and pH. We draw the conclusion that cardiolipin-negative curvature is most likely due to counterion effects, such as cation adsorption, in particular of H3O+. This oft-neglected effect might account for the puzzling behavior of this lipid.
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Affiliation(s)
- Sukanya Konar
- Faculty of Mathematics and Physics, Mathematical Institute, Charles University, Prague, Czech Republic
| | - Hina Arif
- Faculty of Mathematics and Physics, Mathematical Institute, Charles University, Prague, Czech Republic
| | - Christoph Allolio
- Faculty of Mathematics and Physics, Mathematical Institute, Charles University, Prague, Czech Republic.
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10
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Löwe M, Hänsch S, Hachani E, Schmitt L, Weidtkamp-Peters S, Kedrov A. Probing macromolecular crowding at the lipid membrane interface with genetically-encoded sensors. Protein Sci 2023; 32:e4797. [PMID: 37779215 PMCID: PMC10578116 DOI: 10.1002/pro.4797] [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: 05/01/2023] [Revised: 08/25/2023] [Accepted: 09/28/2023] [Indexed: 10/03/2023]
Abstract
Biochemical processes within the living cell occur in a highly crowded environment, where macromolecules, first of all proteins and nucleic acids, occupy up to 30% of the volume. The phenomenon of macromolecular crowding is not an exclusive feature of the cytoplasm and can be observed in the densely protein-packed, nonhomogeneous cellular membranes and at the membrane interfaces. Crowding affects diffusional and conformational dynamics of proteins within the lipid bilayer, alters kinetic and thermodynamic properties of biochemical reactions, and modulates the membrane organization. Despite its importance, the non-invasive quantification of the membrane crowding is not trivial. Here, we developed a genetically-encoded fluorescence-based sensor for probing the macromolecular crowding at the membrane interfaces. Two sensor variants, both composed of fluorescent proteins and a membrane anchor, but differing by flexible linker domains were characterized in vitro, and the procedures for the membrane reconstitution were established. Steric pressure induced by membrane-tethered synthetic and protein crowders altered the sensors' conformation, causing increase in the intramolecular Förster's resonance energy transfer. Notably, the effect of protein crowders only weakly correlated with their molecular weight, suggesting that other factors, such as shape and charge contribute to the crowding via the quinary interactions. Finally, measurements performed in inner membrane vesicles of Escherichia coli validated the crowding-dependent dynamics of the sensors in the physiologically relevant environment. The sensors offer broad opportunities to study interfacial crowding in a complex environment of native membranes, and thus add to the toolbox of methods for studying membrane dynamics and proteostasis.
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Affiliation(s)
- Maryna Löwe
- Synthetic Membrane Systems, Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Sebastian Hänsch
- Center for Advanced imaging, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Eymen Hachani
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Lutz Schmitt
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | | | - Alexej Kedrov
- Synthetic Membrane Systems, Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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11
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Das D, Mattaparthi VSK. Conformational dynamics of A30G α-synuclein that causes familial Parkinson disease. J Biomol Struct Dyn 2023; 41:14702-14714. [PMID: 36961209 DOI: 10.1080/07391102.2023.2193997] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 02/25/2023] [Indexed: 03/25/2023]
Abstract
The first gene shown to be responsible for autosomal-dominant Parkinson's disease (PD) is the SNCA gene, which encodes for alpha synuclein (α-Syn). Recently, a novel heterozygous A30G mutation of the SNCA gene associated with familial PD has been reported. However, little research has been done on how the A30G mutation affects the structure of α-Syn. So, using atomistic molecular dynamics (MD) simulation, we demonstrate here the key structural characteristics of A30G α-Syn in the free monomer form and membrane associated state. From the MD trajectory analysis, the structure of A30G α-Syn was noticed to exhibit rapid conformational change, increase in backbone flexibility near the site of mutation and decrease in α-helical propensity. The typical torsion angles in residues (Val26 and Glu28) near the mutation site were observed to deviate significantly in A30G α-Syn. In the case of membrane bound A30G α-Syn, the regions that were submerged in the lipid bilayer (N-helix (3-37) and turn region (38-44)) found to contain higher helical content than the elevated region above the lipid surface. The bending angle in the helix-N and helix-C regions were noticed to be relatively higher in the free form of A30G α-Syn (38.50) than in the membrane bound form (370). The A30G mutation in α-Syn was predicted to have an impact on the stability and function of the protein based on ΔΔG values obtained from the online servers. Our results demonstrate that the A30G mutation in α-Syn altered the protein's α-helical structure and slightly altered the membrane binding.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Dorothy Das
- Molecular Modelling and Simulation Laboratory, Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, India
| | - Venkata Satish Kumar Mattaparthi
- Molecular Modelling and Simulation Laboratory, Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, India
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12
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Won T, Mohid SA, Choi J, Kim M, Krishnamoorthy J, Biswas I, Bhunia A, Lee D. The role of hydrophobic patches of de novo designed MSI-78 and VG16KRKP antimicrobial peptides on fragmenting model bilayer membranes. Biophys Chem 2023; 296:106981. [PMID: 36871366 DOI: 10.1016/j.bpc.2023.106981] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/06/2023] [Accepted: 02/21/2023] [Indexed: 02/26/2023]
Abstract
Antimicrobial peptides (AMPs) with cell membrane lysing capability are considered potential candidates for the development of the next generation of antibiotics. Designing novel AMPs requires an in-depth understanding of the mechanism of action of the peptides. In this work, we used various biophysical techniques including 31P solid-state NMR to examine the interaction of model membranes with amphipathic de novo-designed peptides. Two such peptides, MSI-78 and VG16KRKP, were designed with different hydrophobicity and positive charges. The model lipid membranes were constituted by mixing lipids of varying degrees of 'area per lipid' (APL), which directly affected the packing properties of the membrane. The observed emergence of the isotropic peak in 31P NMR spectra as a function of time is a consequence of the fragmentation of the membrane mediated by the peptide interaction. The factors such as the charges, overall hydrophilicity of the AMPs, as well as lipid membrane packing, contributed to the kinetics of membrane fragmentation. Furthermore, we anticipate the designed AMPs follow the carpet and toroidal pore mechanisms when lysing the cell membrane. This study highlights the significance of the effect of the overall charges and the hydrophobicity of the novel AMPs designed for antimicrobial activity.
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Affiliation(s)
- TaeJun Won
- Department of Fine Chemistry, Seoul National University of Science and Technology, Seoul 01811, Republic of Korea
| | - Sk Abdul Mohid
- Department of Biophysics, Bose Institute, Unified Academic Campus, Bidhan Nagar EN 80, Kolkata 700 091, India
| | - JiHye Choi
- Department of Fine Chemistry, Seoul National University of Science and Technology, Seoul 01811, Republic of Korea
| | - MinSoo Kim
- Department of Fine Chemistry, Seoul National University of Science and Technology, Seoul 01811, Republic of Korea
| | | | - Indranil Biswas
- Department of Microbiology, Molecular Genetics, and Immunology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Anirban Bhunia
- Department of Biophysics, Bose Institute, Unified Academic Campus, Bidhan Nagar EN 80, Kolkata 700 091, India.
| | - DongKuk Lee
- Department of Fine Chemistry, Seoul National University of Science and Technology, Seoul 01811, Republic of Korea.
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13
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Somberg NH, Wu WW, Medeiros-Silva J, Dregni AJ, Jo H, DeGrado WF, Hong M. SARS-CoV-2 Envelope Protein Forms Clustered Pentamers in Lipid Bilayers. Biochemistry 2022; 61:2280-2294. [PMID: 36219675 PMCID: PMC9583936 DOI: 10.1021/acs.biochem.2c00464] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/26/2022] [Indexed: 11/30/2022]
Abstract
The SARS-CoV-2 envelope (E) protein is a viroporin associated with the acute respiratory symptoms of COVID-19. E forms cation-selective ion channels that assemble in the lipid membrane of the endoplasmic reticulum Golgi intermediate compartment. The channel activity of E is linked to the inflammatory response of the host cell to the virus. Like many viroporins, E is thought to oligomerize with a well-defined stoichiometry. However, attempts to determine the E stoichiometry have led to inconclusive results and suggested mixtures of oligomers whose exact nature might vary with the detergent used. Here, we employ 19F solid-state nuclear magnetic resonance and the centerband-only detection of exchange (CODEX) technique to determine the oligomeric number of E's transmembrane domain (ETM) in lipid bilayers. The CODEX equilibrium value, which corresponds to the inverse of the oligomeric number, indicates that ETM assembles into pentamers in lipid bilayers, without any detectable fraction of low-molecular-weight oligomers. Unexpectedly, at high peptide concentrations and in the presence of the lipid phosphatidylinositol, the CODEX data indicate that more than five 19F spins are within a detectable distance of about 2 nm, suggesting that the ETM pentamers cluster in the lipid bilayer. Monte Carlo simulations that take into account peptide-peptide and peptide-lipid interactions yielded pentamer clusters that reproduced the CODEX data. This supramolecular organization is likely important for E-mediated virus assembly and budding and for the channel function of the protein.
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Affiliation(s)
- Noah H. Somberg
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139
| | - Westley W. Wu
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139
| | - João Medeiros-Silva
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139
| | - Aurelio J. Dregni
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139
| | - Hyunil Jo
- Department of Pharmaceutical Chemistry, 555 Mission Bay Blvd. South, University of California, San Francisco, San Francisco, CA 94158
| | - William F. DeGrado
- Department of Pharmaceutical Chemistry, 555 Mission Bay Blvd. South, University of California, San Francisco, San Francisco, CA 94158
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139
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14
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Naz Z, Shrestha R, Moin ST, Monticelli L. Interaction of Phthalates with Lipid Bilayer Membranes. J Phys Chem B 2022; 126:4679-4688. [PMID: 35708295 DOI: 10.1021/acs.jpcb.2c02007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Phthalates are esters of phthalic acid, widely used as additives in the manufacture of plastics. They are not covalently linked to polymer chains and can easily leach out, disperse in the environment, and get into contact with living organisms. Several short chain phthalates are classified as endocrine disruptors or hormonal active agents, and have also been reported to promote various kinds of cancer. However, the biological effects of longer chain analogues are less well known. Moreover, little is known on the permeation of phthalates and their metabolites through biological membranes and on their effects on the physical properties of membranes. Here we explore the interaction of a group of phthalates and their main metabolites with model biological membranes. We focus on three industrially relevant phthalates, with acyl chains of different sizes, and their monoester metabolites. We use molecular dynamics simulations to predict the distribution in model membranes, as well as permeabilities and effects on the structural, dynamic, and elastic properties of the membranes. We find that alterations of membrane properties are significant and only weakly affected by the size of acyl chains, suggesting that modifications of molecular size may not be sufficient to reduce the impact of this class of molecules on the environment and health.
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Affiliation(s)
- Zobia Naz
- Third World Center for Science and Technology, H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Roshan Shrestha
- Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS & University of Lyon, Lyon 69007, France
| | - Syed Tarique Moin
- Third World Center for Science and Technology, H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Luca Monticelli
- Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS & University of Lyon, Lyon 69007, France
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15
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Jin R, Cao R, Baumgart T. Curvature dependence of BAR protein membrane association and dissociation kinetics. Sci Rep 2022; 12:7676. [PMID: 35538113 PMCID: PMC9091223 DOI: 10.1038/s41598-022-11221-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 04/18/2022] [Indexed: 11/09/2022] Open
Abstract
BAR (Bin/Amphiphysin/Rvs) domain containing proteins function as lipid bilayer benders and curvature sensors, and they contribute to membrane shaping involved in cell signaling and metabolism. The mechanism for their membrane shape sensing has been investigated by both equilibrium binding and kinetic studies. In prior research, stopped-flow spectroscopy has been used to deduce a positive dependence on membrane curvature for the binding rate constant, kon, of a BAR protein called endophilin. However, the impact of bulk diffusion of endophilin, on the kinetic binding parameters has not been thoroughly considered. Employing similar methods, and using lipid vesicles of multiple sizes, we obtained a linear dependence of kon on vesicle curvature. However, we found that the observed relation can be explained without considering the local curvature sensing ability of endophilin in the membrane association process. In contrast, the diffusion-independent unbinding rate constant (koff) obtained from stopped-flow measurements shows a negative dependence on membrane curvature, which is controlled/mediated by endophilin-membrane interactions. This latter dependency, in addition to protein-protein interactions on the membrane, explains the selective binding of BAR proteins to highly curved membranes in equilibrium binding experiments.
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Affiliation(s)
- Rui Jin
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
| | - Rui Cao
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA.,Division of Biostatistics, University of Minnesota, Minneapolis, MN, USA
| | - Tobias Baumgart
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA.
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16
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A Simulation Model for the Non-Electrogenic Uniport Carrier-Assisted Transport of Ions across Lipid Membranes. MEMBRANES 2022; 12:membranes12030292. [PMID: 35323767 PMCID: PMC8955484 DOI: 10.3390/membranes12030292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 02/24/2022] [Accepted: 03/01/2022] [Indexed: 12/10/2022]
Abstract
Impressive work has been completed in recent decades on the transmembrane anion transport capability of small synthetic transporters from many different structural classes. However, very few predicting models have been proposed for the fast screening of compound libraries before spending time and resources on the laboratory bench for their synthesis. In this work, a new approach is presented which aims at describing the transport process by taking all the steps into explicit consideration, and includes all possible experiment-derived parameters. The algorithm is able to simulate the macroscopic experiments performed with lipid vesicles to assess the ion-transport ability of the synthetic transporters following a non-electrogenic uniport mechanism. While keeping calculation time affordable, the final goal is the curve-fitting of real experimental data—so, to obtain both an analysis and a predictive tool. The role and the relative weight of the different parameters is discussed and the agreement with the literature is shown by using the simulations of a virtual benchmark case. The fitting of real experimental curves is also shown for two transporters of different structural type.
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17
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Halder A, Karmakar S. An evidence of pores in phospholipid membrane induced by an antimicrobial peptide NK-2. Biophys Chem 2022; 282:106759. [PMID: 35008010 DOI: 10.1016/j.bpc.2022.106759] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/27/2021] [Accepted: 01/02/2022] [Indexed: 11/19/2022]
Abstract
NK-2, a peptide derived from a cationic core region of NK-lysin, has emerged as a promising candidate for new antibiotics. In contrast to classical antibiotics, antimicrobial peptides target bacterial membranes and disintegrate the membrane by forming the transmembrane pores. However, complete understanding of the precise mechanisms of cellular apoptosis and molecular basis of membrane selectivity is still in dispute. In the present study, we have shown that NK-2 forms trans-membrane pores on negatively charged phospholipid membranes using phase contrast microscopy. As bacteria mimicking membranes, we have chosen large unilamellar vesicles (LUV) and giant unilamellar vesicles (GUV) composed of negatively charged phospholipid, dioleoyl phosphatidyl glycerol (DOPG) and neutral phospholipid, dioleoyl phophatidylcholine (DOPC). Leakage of internal fluid of giant unilamellar vesicles (GUV), leading to decrease in intensity in the halo region of phase contrast micrographs, suggests the formation of transmembrane pores. No such reduction of intensity in the halo region of DOPC was observed, indicating, neutral vesicles does not exhibit pores. Rate constant reckoned from the decaying intensity in the halo region was found to be 0.007 s-1. Further, significant interaction of NK-2 with anionic membranes has been envisaged from zeta potential and dynamic light scattering. Binding free energy and other interaction parameters have been delineated using theoretical ansatz. A proliferation of average Size of anionic LUV on increasing NK-2 concentration indicates membrane-membrane interaction leading to peptide induced large aggregates of vesicles.
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Affiliation(s)
- Animesh Halder
- Soft matter and Biophysics Laboratory, Department of Physics, Jadavpur University, 188, Raja S. C. Mullick Road, Kolkata 700032, India
| | - Sanat Karmakar
- Soft matter and Biophysics Laboratory, Department of Physics, Jadavpur University, 188, Raja S. C. Mullick Road, Kolkata 700032, India.
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18
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Jung Y, Wen L, Altman A, Ley K. CD45 pre-exclusion from the tips of T cell microvilli prior to antigen recognition. Nat Commun 2021; 12:3872. [PMID: 34162836 PMCID: PMC8222282 DOI: 10.1038/s41467-021-23792-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 05/11/2021] [Indexed: 12/18/2022] Open
Abstract
The tyrosine phosphatase CD45 is a major gatekeeper for restraining T cell activation. Its exclusion from the immunological synapse (IS) is crucial for T cell receptor (TCR) signal transduction. Here, we use expansion super-resolution microscopy to reveal that CD45 is mostly pre-excluded from the tips of microvilli (MV) on primary T cells prior to antigen encounter. This pre-exclusion is diminished by depleting cholesterol or by engineering the transmembrane domain of CD45 to increase its membrane integration length, but is independent of the CD45 extracellular domain. We further show that brief MV-mediated contacts can induce Ca2+ influx in mouse antigen-specific T cells engaged by antigen-pulsed antigen presenting cells (APC). We propose that the scarcity of CD45 phosphatase activity at the tips of MV enables or facilitates TCR triggering from brief T cell-APC contacts before formation of a stable IS, and that these MV-mediated contacts represent the earliest step in the initiation of a T cell adaptive immune response.
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Affiliation(s)
- Yunmin Jung
- Center for Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, CA, USA.
| | - Lai Wen
- Center for Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Amnon Altman
- Center for Cancer Immunotherapy, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Klaus Ley
- Center for Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
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19
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Koulgi S, Jani V, Nair V, Saini JS, Phukan S, Sonavane U, Joshi R, Kamboj R, Palle V. Molecular dynamics of hERG channel: insights into understanding the binding of small molecules for detuning cardiotoxicity. J Biomol Struct Dyn 2021; 40:5996-6012. [PMID: 33494645 DOI: 10.1080/07391102.2021.1875883] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Evaluation of cardiotoxicity potential of new chemical entities (NCEs) has lately become one of the stringent filters in the drug discovery and development process. Cardiotoxicity is caused mainly by the inhibition of human ether-a-go-go related gene (hERG) channel protein. Inhibition of the hERG channel leads to a life-threatening condition known as cardiac arrhythmia. Knowledge of the structural behaviour of the hERG would aid greatly in the design of new drug molecules that do not interact with the protein and add to the safety index. In this study, a computational model for the active-state of hERG was developed. This model was equilibrated by performing the molecular dynamics simulations for 100 ns followed by clustering and selection of a representative structure based on the largest populated cluster. To study the changes in the protein structure on inhibition, three inhibitory ligands, namely, dofetilide, cisapride and terfenadine were docked, followed by molecular dynamics simulations of 200 ns for the apo and each ligand-bound structure. It was observed that docking and simulation studies of the hERG model exhibited noticeable conformational changes in the protein upon ligand-binding. A significant change in the kink of the S6-transmembrane helix was observed. Inter-chain distances between the crucial residues Y652 and F656 (present below the ion-selectivity filter), their side-chain orientation and hydrogen bonding indicated a probable collapse of the pore. These changes may infer the initiation in transition of hERG from an open to an inactive state. Hence, these findings would help in designing compounds devoid of hERG inhibition with reduced cardiotoxicity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shruti Koulgi
- High Performance Computing - Medical and Bioinformatics Applications Group, Centre for Development of Advanced Computing, Panchawati, Pashan, Pune
| | - Vinod Jani
- High Performance Computing - Medical and Bioinformatics Applications Group, Centre for Development of Advanced Computing, Panchawati, Pashan, Pune
| | | | - Jagmohan S Saini
- Novel Drug Discovery and Development, Lupin Research Park, Pune, India
| | - Samiron Phukan
- Novel Drug Discovery and Development, Lupin Research Park, Pune, India
| | - Uddhavesh Sonavane
- High Performance Computing - Medical and Bioinformatics Applications Group, Centre for Development of Advanced Computing, Panchawati, Pashan, Pune
| | - Rajendra Joshi
- High Performance Computing - Medical and Bioinformatics Applications Group, Centre for Development of Advanced Computing, Panchawati, Pashan, Pune
| | - Raj Kamboj
- Novel Drug Discovery and Development, Lupin Research Park, Pune, India
| | - Venkata Palle
- Novel Drug Discovery and Development, Lupin Research Park, Pune, India
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20
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Ausili A, Gómez-Murcia V, Candel AM, Beltrán A, Torrecillas A, He L, Jiang Y, Zhang S, Teruel JA, Gómez-Fernández JC. A comparison of the location in membranes of curcumin and curcumin-derived bivalent compounds with potential neuroprotective capacity for Alzheimer's disease. Colloids Surf B Biointerfaces 2020; 199:111525. [PMID: 33373844 DOI: 10.1016/j.colsurfb.2020.111525] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 10/14/2020] [Accepted: 12/07/2020] [Indexed: 11/30/2022]
Abstract
Curcumin and two bivalent compounds, namely 17MD and 21MO, both obtained by conjugation of curcumin with a steroid molecule that acts as a membrane anchor, were comparatively studied. When incorporated into 1,2-dipalmitoyl-sn-glycero-3-phosphocholine the compounds showed a very limited solubility in the model membranes. Curcumin and the two bivalent compounds were also incorporated in membranes of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine and quenching the fluorescence of pure curcumin or of the curcumin moiety in the bivalent compounds by acrylamide it was seen that curcumin was accessible to this water soluble quencher but the molecule was somehow located in a hydrophobic environment. This was confirmed by quenching with doxyl-phosphatidylcholines, indicating that the curcumin moieties of 17MD and 21MO were in a more polar environment than pure curcumin itself. 1H NOESY MAS-NMR analysis supports this notion by showing that the orientation of curcumin was parallel to the plane of the membrane surface close to C2 and C3 of the fatty acyl chains, while the curcumin moiety of 17MD and 21MO positioned close to the polar part of the membrane with the steroid moiety in the centre of the membrane. Molecular dynamics studies were in close agreement with the experimental results with respect to the likely proximity of the protons studied by NMR and show that 17MD and 21MO have a clear tendency to aggregate in a fluid membrane. The anchorage of the bivalent compounds to the membrane leaving the curcumin moiety near the polar part may be very important to facilitate the bioactivity of the curcumin moiety when used as anti-Alzheimer drugs.
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Affiliation(s)
- Alessio Ausili
- Departamento De Bioquímica y Biología Molecular "A", Facultad de Veterinaria, Regional Campus of International Excellence "Campus Mare Nostrum", Universidad de Murcia, Apartado de Correos 4021, Murcia, E-30080, Spain
| | - Victoria Gómez-Murcia
- Departamento de Farmacología, Facultad de Medicina, IMIB, Regional Campus of International Excellence "Campus Mare Nostrum", Universidad de Murcia, Apartado de Correos 4021, Murcia, E-30080, Spain
| | - Adela M Candel
- Departamento De Bioquímica y Biología Molecular "A", Facultad de Veterinaria, Regional Campus of International Excellence "Campus Mare Nostrum", Universidad de Murcia, Apartado de Correos 4021, Murcia, E-30080, Spain
| | - Andrea Beltrán
- Departamento De Bioquímica y Biología Molecular "A", Facultad de Veterinaria, Regional Campus of International Excellence "Campus Mare Nostrum", Universidad de Murcia, Apartado de Correos 4021, Murcia, E-30080, Spain
| | - Alejandro Torrecillas
- Departamento De Bioquímica y Biología Molecular "A", Facultad de Veterinaria, Regional Campus of International Excellence "Campus Mare Nostrum", Universidad de Murcia, Apartado de Correos 4021, Murcia, E-30080, Spain
| | - Liu He
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia, 23298, United States
| | - Yuqi Jiang
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia, 23298, United States
| | - Shijun Zhang
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia, 23298, United States
| | - José A Teruel
- Departamento De Bioquímica y Biología Molecular "A", Facultad de Veterinaria, Regional Campus of International Excellence "Campus Mare Nostrum", Universidad de Murcia, Apartado de Correos 4021, Murcia, E-30080, Spain
| | - Juan C Gómez-Fernández
- Departamento De Bioquímica y Biología Molecular "A", Facultad de Veterinaria, Regional Campus of International Excellence "Campus Mare Nostrum", Universidad de Murcia, Apartado de Correos 4021, Murcia, E-30080, Spain.
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21
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Hosseini ST, Raissi H, Pakdel M. High-performance carbon dioxide capture and storage by multi-functional sphingosine kinase inhibitors through a CO2-philic membrane. NEW J CHEM 2020. [DOI: 10.1039/d0nj01231a] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Carbon dioxide (CO2) capture using environmentally friendly sphingosine-based materials was theoretically studied.
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Affiliation(s)
| | - Heidar Raissi
- Department of Chemistry
- Faculty of Science
- University of Birjand
- Birjand
- Iran
| | - Majid Pakdel
- Department of Chemistry
- Faculty of Science
- University of Birjand
- Birjand
- Iran
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22
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Sampson C, Keens RH, Kattnig DR. On the magnetosensitivity of lipid peroxidation: two- versus three-radical dynamics. Phys Chem Chem Phys 2019; 21:13526-13538. [PMID: 31210238 DOI: 10.1039/c9cp01746a] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
We present a theoretical analysis of the putative magnetosensitivity of lipid peroxidation. We focus on the widely accepted radical pair mechanism (RPM) and a recently suggested idea based on spin dynamics induced in three-radical systems by the mutual electron-electron dipolar coupling (D3M). We show that, contrary to claims in the literature, lipid peroxides, the dominant chain carriers of the autoxidation process, have associated non-zero hyperfine coupling interactions. This suggests that their recombination could, in principle, be magnetosensitive due to the RPM. While the RPM indeed goes a long way to explaining magnetosensitivity in these systems, we show that the simultaneous interaction of three peroxyl radicals via the D3M can achieve larger magnetic field effects (MFE), even if the third radical is remote from the recombining radical pair. For randomly oriented three-radical systems, the D3M induces a low-field effect comparable to that of the RPM. The mechanism furthermore immunizes the spin dynamics to the presence of large exchange coupling interactions in the recombining radical pair, thereby permitting much larger MFE at magnetic field intensities comparable to the geomagnetic field than would be expected for the RPM. Based on these characteristics, we suggest that the D3M could be particularly relevant for MFE at low fields, provided that the local radical concentration is sufficient to allow for three-spin radical correlations. Eventually, our observations suggest that MFEs could intricately depend on radical concentration and larger effects could ensue under conditions of oxidative stress.
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Affiliation(s)
- Chris Sampson
- Living Systems Institute and Department of Physics, University of Exeter, Stocker Road, Exeter, Devon, EX4 4QD, UK.
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23
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Schott-Verdugo S, Gohlke H. PACKMOL-Memgen: A Simple-To-Use, Generalized Workflow for Membrane-Protein-Lipid-Bilayer System Building. J Chem Inf Model 2019; 59:2522-2528. [PMID: 31120747 DOI: 10.1021/acs.jcim.9b00269] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present PACKMOL-Memgen, a simple-to-use, generalized workflow for automated building of membrane-protein-lipid-bilayer systems based on open-source tools including Packmol, memembed, pdbremix, and AmberTools. Compared with web-interface-based related tools, PACKMOL-Memgen allows setup of multiple configurations of a system in a user-friendly and efficient manner within minutes. The generated systems are well-packed and thus well-suited as starting configurations in MD simulations under periodic boundary conditions, requiring only moderate equilibration times. PACKMOL-Memgen is distributed with AmberTools and runs on most computing platforms, and its output can also be used for CHARMM or adapted to other molecular-simulation packages.
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Affiliation(s)
- Stephan Schott-Verdugo
- Institute for Pharmaceutical and Medicinal Chemistry , Heinrich Heine University Düsseldorf , 40225 Düsseldorf , Germany.,Centro de Bioinformática y Simulación Molecular (CBSM), Faculty of Engineering , Universidad de Talca , 1 Poniente 1141 , Casilla 721 , Talca , Chile
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry , Heinrich Heine University Düsseldorf , 40225 Düsseldorf , Germany.,John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC) & Institute for Complex Systems-Structural Biochemistry (ICS 6) , Forschungszentrum Jülich GmbH , 52425 Jülich , Germany
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24
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Marrink SJ, Corradi V, Souza PC, Ingólfsson HI, Tieleman DP, Sansom MS. Computational Modeling of Realistic Cell Membranes. Chem Rev 2019; 119:6184-6226. [PMID: 30623647 PMCID: PMC6509646 DOI: 10.1021/acs.chemrev.8b00460] [Citation(s) in RCA: 422] [Impact Index Per Article: 84.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Indexed: 12/15/2022]
Abstract
Cell membranes contain a large variety of lipid types and are crowded with proteins, endowing them with the plasticity needed to fulfill their key roles in cell functioning. The compositional complexity of cellular membranes gives rise to a heterogeneous lateral organization, which is still poorly understood. Computational models, in particular molecular dynamics simulations and related techniques, have provided important insight into the organizational principles of cell membranes over the past decades. Now, we are witnessing a transition from simulations of simpler membrane models to multicomponent systems, culminating in realistic models of an increasing variety of cell types and organelles. Here, we review the state of the art in the field of realistic membrane simulations and discuss the current limitations and challenges ahead.
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Affiliation(s)
- Siewert J. Marrink
- Groningen
Biomolecular Sciences and Biotechnology Institute & Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Valentina Corradi
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Paulo C.T. Souza
- Groningen
Biomolecular Sciences and Biotechnology Institute & Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Helgi I. Ingólfsson
- Biosciences
and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - D. Peter Tieleman
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Mark S.P. Sansom
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
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25
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Mortezazadeh S, Jamali Y, Naderi-Manesh H, Lyubartsev AP. Implicit solvent systematic coarse-graining of dioleoylphosphatidylethanolamine lipids: From the inverted hexagonal to the bilayer structure. PLoS One 2019; 14:e0214673. [PMID: 30951539 PMCID: PMC6450619 DOI: 10.1371/journal.pone.0214673] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 03/18/2019] [Indexed: 11/21/2022] Open
Abstract
Lamellar and hexagonal lipid structures are of particular importance in the biological processes such as membrane fusion and budding. Atomistic simulations of formation of these phases and transitions between them are computationally prohibitive, hence development of coarse-grained models is an important part of the methodological development in this area. Here we apply systematic bottom-up coarse-graining to model different phase structures formed by 1,2-dioleoylphosphatidylethanolamine (DOPE) lipid molecules. We started from atomistic simulations of DOPE lipids in water carried out at two different water/lipid molar ratio corresponding to the lamellar Lα and inverted hexagonal HII structures at low and high lipid concentrations respectively. The atomistic trajectories were mapped to coarse-grained trajectories, in which each lipid was represented by 14 coarse-grained sites. Then the inverse Monte Carlo method was used to compute the effective coarse-grained potentials which for the coarse-grain model reproduce the same structural properties as the atomistic simulations. The potentials derived from the low concentration atomistic simulation were only able to form a bilayer structure, while both Lα and HII lipid phases were formed in simulations with potentials obtained at high concentration. The typical atomistic configurations of lipids at high concentration combine fragments of both lamellar and non-lamellar structures, that is reflected in the extracted coarse-grained potentials which become transferable and can form a wide range of structures including the inverted hexagonal, bilayer, tubule, vesicle and micellar structures.
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Affiliation(s)
- Saeed Mortezazadeh
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Yousef Jamali
- Department of Mathematics, Tarbiat Modares University, Tehran, Iran
| | - Hossein Naderi-Manesh
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
- School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran
- * E-mail: (HN); (APL)
| | - Alexander P. Lyubartsev
- Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
- * E-mail: (HN); (APL)
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26
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Nademi Y, Tang T, Uludağ H. Steered molecular dynamics simulations reveal a self-protecting configuration of nanoparticles during membrane penetration. NANOSCALE 2018; 10:17671-17682. [PMID: 30206609 DOI: 10.1039/c8nr04287j] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Cell entry of polynucleotide-based therapeutic agents can be facilitated by nanoparticle (NP) mediated delivery. In this work, using steered molecular dynamics simulations, we simulated the membrane penetration process of a NP formed by 2 short interfering RNA (siRNA) and 6 polyethylenimine (PEI) molecules. To the best of our knowledge, this is the first set of simulations that explore the direct penetration of an siRNA/PEI NP through a membrane at an all-atom scale. Three types of PEI molecules were used for NP formation: a native PEI, a PEI modified with caprylic acids and a PEI modified with linoleic acids. We found that hydrogen bond formation between the PEIs and the membrane did not lead to instability of the siRNA/PEI NPs during the internalization process. Instead, our results suggested adoption of a "self-protecting" configuration by the siRNA/PEI NP during membrane penetration, where the siRNA/PEI NP becomes more compact and siRNAs become aligned, leading to more stable configurations while detaching from the membrane. The siRNA/PEI NP modified with linoleic acid showed the smallest structural change due to its strong intra-particle lipid associations and the resulting rigidity, while NP modified with caprylic acid showed the largest structural changes. Our observations provide unique insight into the structural changes of siRNA/PEI NPs when crossing the cell membrane, which can be important for the design of new NP carriers for nucleic acid delivery.
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Affiliation(s)
- Yousef Nademi
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Canada.
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27
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Mendes M, Miranda A, Cova T, Gonçalves L, Almeida AJ, Sousa JJ, do Vale MLC, Marques EF, Pais A, Vitorino C. Modeling of ultra-small lipid nanoparticle surface charge for targeting glioblastoma. Eur J Pharm Sci 2018; 117:255-269. [PMID: 29486328 DOI: 10.1016/j.ejps.2018.02.024] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 01/29/2018] [Accepted: 02/21/2018] [Indexed: 01/31/2023]
Abstract
Surface modification of ultra-small nanostructured lipid carriers (usNLC) via introduction of a positive charge is hypothesized to prompt site-specific drug delivery for glioblastoma multiforme (GBM) treatment. A more effective interaction with negatively charged lipid bilayers, including the blood-brain barrier (BBB), will facilitate the nanoparticle access to the brain. For this purpose, usNLC with a particle size of 43.82 ± 0.03 nm and a polydispersity index of 0.224 were developed following a Quality by Design approach. Monomeric and gemini surfactants, either with conventional headgroups or serine-based ones, were tested for the surface modification, and the respective safety and efficacy to target GBM evaluated. A comprehensive in silico-in vitro approach is also provided based on molecular dynamics simulations and cytotoxicity studies. Overall, monomeric serine-derived surfactants displayed the best performance, considering altogether particle size, zeta potential, cytotoxic profile and cell uptake. Although conventional surfactants were able to produce usNLC with suitable physicochemical properties and cell uptake, their use is discouraged due to their high cytotoxicity. This study suggests that monomeric serine-derived surfactants are promising agents for developing nanosystems aiming at brain drug delivery.
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Affiliation(s)
- Maria Mendes
- Faculty of Pharmacy, University of Coimbra, Pólo das Ciências da Saúde, Azinhaga de Santa Comba, 3000-548 Coimbra, Portugal; Centre for Neurosciences and Cell Biology (CNC), University of Coimbra, Rua Larga, Faculty of Medicine, Pólo I, 1st floor, 3004-504 Coimbra, Portugal
| | - Ana Miranda
- Faculty of Pharmacy, University of Coimbra, Pólo das Ciências da Saúde, Azinhaga de Santa Comba, 3000-548 Coimbra, Portugal; Centre for Neurosciences and Cell Biology (CNC), University of Coimbra, Rua Larga, Faculty of Medicine, Pólo I, 1st floor, 3004-504 Coimbra, Portugal
| | - Tânia Cova
- Coimbra Chemistry Center, Department of Chemistry, University of Coimbra, Rua Larga, 3004-535 Coimbra, Portugal
| | - Lídia Gonçalves
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - António J Almeida
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - João J Sousa
- Faculty of Pharmacy, University of Coimbra, Pólo das Ciências da Saúde, Azinhaga de Santa Comba, 3000-548 Coimbra, Portugal; LAQV - REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Science, University of Porto, 4169-007 Porto, Portugal
| | - Maria L C do Vale
- LAQV - REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Science, University of Porto, 4169-007 Porto, Portugal
| | - Eduardo F Marques
- CIQUP, Department of Chemistry and Biochemistry, Faculty of Science, University of Porto, Porto, 4169-007 Porto, Portugal
| | - Alberto Pais
- Coimbra Chemistry Center, Department of Chemistry, University of Coimbra, Rua Larga, 3004-535 Coimbra, Portugal
| | - Carla Vitorino
- Faculty of Pharmacy, University of Coimbra, Pólo das Ciências da Saúde, Azinhaga de Santa Comba, 3000-548 Coimbra, Portugal; Centre for Neurosciences and Cell Biology (CNC), University of Coimbra, Rua Larga, Faculty of Medicine, Pólo I, 1st floor, 3004-504 Coimbra, Portugal.
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28
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Hills RD. Refining amino acid hydrophobicity for dynamics simulation of membrane proteins. PeerJ 2018; 6:e4230. [PMID: 29340240 PMCID: PMC5767086 DOI: 10.7717/peerj.4230] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 12/14/2017] [Indexed: 11/20/2022] Open
Abstract
Coarse-grained (CG) models have been successful in simulating the chemical properties of lipid bilayers, but accurate treatment of membrane proteins and lipid-protein molecular interactions remains a challenge. The CgProt force field, original developed with the multiscale coarse graining method, is assessed by comparing the potentials of mean force for sidechain insertion in a DOPC bilayer to results reported for atomistic molecular dynamics simulations. Reassignment of select CG sidechain sites from the apolar to polar site type was found to improve the attractive interfacial behavior of tyrosine, phenylalanine and asparagine as well as charged lysine and arginine residues. The solvation energy at membrane depths of 0, 1.3 and 1.7 nm correlates with experimental partition coefficients in aqueous mixtures of cyclohexane, octanol and POPC, respectively, for sidechain analogs and Wimley-White peptides. These experimental values serve as important anchor points in choosing between alternate CG models based on their observed permeation profiles, particularly for Arg, Lys and Gln residues where the all-atom OPLS solvation energy does not agree well with experiment. Available partitioning data was also used to reparameterize the representation of the peptide backbone, which needed to be made less attractive for the bilayer hydrophobic core region. The newly developed force field, CgProt 2.4, correctly predicts the global energy minimum in the potentials of mean force for insertion of the uncharged membrane-associated peptides LS3 and WALP23. CgProt will find application in studies of lipid-protein interactions and the conformational properties of diverse membrane protein systems.
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Affiliation(s)
- Ronald D Hills
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New England, Portland, ME, United States of America
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29
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Li B, Chen Q, Huang S, Liu H. Developing structure and thermodynamic properties-consistent coarse-grained model for random copolymer systems. POLYMER 2017. [DOI: 10.1016/j.polymer.2017.07.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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30
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Fosso-Tande J, Black C, G. Aller S, Lu L, D. Hills Jr R. Simulation of lipid-protein interactions with the CgProt force field. AIMS MOLECULAR SCIENCE 2017. [DOI: 10.3934/molsci.2017.3.352] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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31
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Lopes D, Jakobtorweihen S, Nunes C, Sarmento B, Reis S. Shedding light on the puzzle of drug-membrane interactions: Experimental techniques and molecular dynamics simulations. Prog Lipid Res 2017; 65:24-44. [DOI: 10.1016/j.plipres.2016.12.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 11/30/2016] [Accepted: 12/03/2016] [Indexed: 12/20/2022]
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32
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Kmiecik S, Gront D, Kolinski M, Wieteska L, Dawid AE, Kolinski A. Coarse-Grained Protein Models and Their Applications. Chem Rev 2016; 116:7898-936. [DOI: 10.1021/acs.chemrev.6b00163] [Citation(s) in RCA: 555] [Impact Index Per Article: 69.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Sebastian Kmiecik
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Dominik Gront
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Michal Kolinski
- Bioinformatics
Laboratory, Mossakowski Medical Research Center of the Polish Academy of Sciences, Pawinskiego 5, 02-106 Warsaw, Poland
| | - Lukasz Wieteska
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
- Department
of Medical Biochemistry, Medical University of Lodz, Mazowiecka 6/8, 92-215 Lodz, Poland
| | | | - Andrzej Kolinski
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
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33
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Hills RD, McGlinchey N. Model parameters for simulation of physiological lipids. J Comput Chem 2016; 37:1112-8. [PMID: 26864972 PMCID: PMC5067697 DOI: 10.1002/jcc.24324] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 12/19/2015] [Accepted: 01/17/2016] [Indexed: 12/16/2022]
Abstract
Coarse grain simulation of proteins in their physiological membrane environment can offer insight across timescales, but requires a comprehensive force field. Parameters are explored for multicomponent bilayers composed of unsaturated lipids DOPC and DOPE, mixed-chain saturation POPC and POPE, and anionic lipids found in bacteria: POPG and cardiolipin. A nonbond representation obtained from multiscale force matching is adapted for these lipids and combined with an improved bonding description of cholesterol. Equilibrating the area per lipid yields robust bilayer simulations and properties for common lipid mixtures with the exception of pure DOPE, which has a known tendency to form nonlamellar phase. The models maintain consistency with an existing lipid-protein interaction model, making the force field of general utility for studying membrane proteins in physiologically representative bilayers.
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Affiliation(s)
- Ronald D Hills
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New England, 716 Stevens Ave, Portland, Maine, 04103
| | - Nicholas McGlinchey
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New England, 716 Stevens Ave, Portland, Maine, 04103
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