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Duan G, Ji C, Zhang JZH. Developing an effective polarizable bond method for small molecules with application to optimized molecular docking. RSC Adv 2020; 10:15530-15540. [PMID: 35495446 PMCID: PMC9052371 DOI: 10.1039/d0ra01483d] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 03/31/2020] [Indexed: 12/20/2022] Open
Abstract
Electrostatic interaction plays an essential role in protein-ligand binding. Due to the polarization effect, electrostatic interactions are largely impacted by their local environments. However, traditional force fields use fixed point charge-charge interactions to describe electrostatic interactions but is unable to include the polarization effect. The lack of the polarization effect in the force field representation can result in substantial error in biomolecular studies, such as molecular dynamics and molecular docking. Docking programs usually employ traditional force fields to estimate the binding energy between a ligand and a protein for pose selection or scoring. The intermolecular interaction energy mainly consists of van der Waals and electrostatic interaction in the force field representation. In the current study, we developed an Effective Polarizable Bond (EPB) method for small organic molecules and applied this EPB method to optimize protein-ligand docking in computational tests for a variety of protein-ligand systems. We tested the method on a set of 38 cocrystallized structures taken from the Protein Data Bank (PDB) and found that the maximum error was reduced from 7.98 Å to 2.03 Å when using EPB Dock, providing strong evidence that the use of EPB charges is important. We found that our optimized docking approach with EPB charges could improve the docking performance, sometimes dramatically, and the maximum error was reduced from 12.88 Å to 1.57 Å in Optimized Docking (in the case of 1fqx). The average RMSD decreased from 2.83 Å to 1.85 Å. Further investigations showed that the use of the EBP method could enhance intermolecular hydrogen bonding, which is a major contributing factor to improved docking performance. Developed tools for the calculation of the polarized ligand charge from a protein-ligand complex structure with the EPB method are freely available on GitHub (https://github.com/Xundrug/EPB).
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Affiliation(s)
- Guanfu Duan
- Shanghai Engineering Research Center for Molecular Therapeutics and New Drug Development, Shanghai Key Laboratory of Green Chemistry & Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University Shanghai 200062 China
| | - Changge Ji
- Shanghai Engineering Research Center for Molecular Therapeutics and New Drug Development, Shanghai Key Laboratory of Green Chemistry & Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University Shanghai 200062 China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai Shanghai 200062 China
| | - John Z H Zhang
- Shanghai Engineering Research Center for Molecular Therapeutics and New Drug Development, Shanghai Key Laboratory of Green Chemistry & Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University Shanghai 200062 China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai Shanghai 200062 China
- Department of Chemistry, New York University NY NY 10003 USA
- Collaborative Innovation Center of Extreme Optics, Shanxi University Taiyuan Shanxi 030006 China
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Effect of dipole moment on amphiphile solubility and partition into liquid ordered and liquid disordered phases in lipid bilayers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183157. [PMID: 31846646 DOI: 10.1016/j.bbamem.2019.183157] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 12/01/2019] [Accepted: 12/12/2019] [Indexed: 12/20/2022]
Abstract
Association of amphiphiles with biomembranes is important for their availability at specific locations in organisms and cells, being critical for their biological function. A prominent role is usually attributed to the hydrophobic effect, and to electrostatic interactions between charged amphiphiles and lipids. This work explores a closely related and complementary aspect, namely the contribution made by dipole moments to the strength of the interactions established. Two xanthene amphiphiles with opposite relative orientations of their dipole and amphiphilic moments have been selected (Rhodamine-C14 and Carboxyfluorescein-C14). The membranes studied have distinct lipid compositions, representing typical cell membrane pools, ranging from internal membranes to the outer and inner leaflet of the plasma membrane. A comprehensive study is reported, including the affinity of the amphiphiles for the different membranes, the stability of the amphiphiles as monomers and their tendency to form small clusters, as well as their transverse location in the membrane. The orientation of the amphiphile dipole moment, which determines whether its interaction with the membrane dipole potential is repulsive or attractive, is found to exert a large influence on the association of the amphiphile with ordered lipid membranes. These interactions are also responsible for the formation of small clusters or stabilization of amphiphile monomers in the membrane. The results obtained allow understanding the prevalence of protein lipidation at the N-terminal for efficient targeting to the plasma membrane, as well as the tendency of GPI-anchored proteins (usually lipidated at the C-terminal) to form small clusters in the membrane ordered domains.
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3
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Pokorny A, Khatib TO, Stevenson H. A Quantitative Model of Daptomycin Binding to Lipid Bilayers. J Phys Chem B 2018; 122:9137-9146. [DOI: 10.1021/acs.jpcb.8b07503] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Antje Pokorny
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina 28403, United States
| | - Tala O. Khatib
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina 28403, United States
| | - Heather Stevenson
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina 28403, United States
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4
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Coreta-Gomes FM, Vaz WLC, Moreno MJ. Effect of Acyl Chain Length on the Rate of Phospholipid Flip-Flop and Intermembrane Transfer. J Membr Biol 2017; 251:431-442. [PMID: 29264685 DOI: 10.1007/s00232-017-0009-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 12/13/2017] [Indexed: 11/25/2022]
Abstract
The rate at which phospholipids equilibrate between different membranes and between the non-polar environments in biological fluids is of high importance in the understanding of biomembrane diversity, as well as in the development of liposomes for drug delivery. In this work, we characterize the rate of insertion into and desorption from POPC bilayers for a homologous series of amphiphiles with the fluorescent NBD group attached to phosphoethanolamines of different acyl chain lengths, NBD-diC n -PE with n = 6, 8, 10, and 12. The rate of translocation between bilayer leaflets was also characterized, providing all the relevant parameters for their interaction with lipid bilayers. The results are complemented with data for NBD-diC14-PE obtained from literature (Abreu et al. Biophys J 87:353-365, 2004; Moreno et al. Biophys J 91:873-881, 2006). The rate of translocation between the POPC leaflets is not dependent on the length of the acyl chains, while this affects strongly the rate of desorption from the bilayer. Insertion in the POPC bilayer is not diffusion controlled showing a significant dependence on the acyl chain length and on temperature. The results obtained are compared with those previously reported for NBD-LysoC14-PE (Sampaio et al. Biophys J 88:4064-4071, 2005), and with the homologous series of single chain amphiphiles NBD-C n (Cardoso et al. J Phys Chem B 114:16337-16346, 2010; J Phys Chem B 115:10098-10108, 2011). This allows the establishment of important relations between the rate constants for interaction with the lipid bilayers and the structural properties of the amphiphiles, namely the total surface and the cross-section of their non-polar region.
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Affiliation(s)
- Filipe M Coreta-Gomes
- CQC-Biological Chemistry Group, Chemistry Department FCTUC, Largo D. Dinis, Rua Larga, 3004-535, Coimbra, Portugal
- QOPNA, Chemistry Department, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Winchil L C Vaz
- CEDOC, NOVA Medical School, Faculdadede Ciências Médicas, Universidade NOVA de Lisboa, 1169-056, Lisbon, Portugal
| | - Maria J Moreno
- CQC-Biological Chemistry Group, Chemistry Department FCTUC, Largo D. Dinis, Rua Larga, 3004-535, Coimbra, Portugal.
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5
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Ben-Shalom IY, Pfeiffer-Marek S, Baringhaus KH, Gohlke H. Efficient Approximation of Ligand Rotational and Translational Entropy Changes upon Binding for Use in MM-PBSA Calculations. J Chem Inf Model 2017; 57:170-189. [DOI: 10.1021/acs.jcim.6b00373] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Ido Y. Ben-Shalom
- Institute
for Pharmaceutical and Medicinal Chemistry, Department of Mathematics
and Natural Sciences, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Stefania Pfeiffer-Marek
- LGCR/Pharmaceutical
Sciences Operations, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - Karl-Heinz Baringhaus
- R&D Resources/Site Direction, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - Holger Gohlke
- Institute
for Pharmaceutical and Medicinal Chemistry, Department of Mathematics
and Natural Sciences, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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6
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Metal ion binding to phospholipid bilayers evaluated by microaffinity chromatography. J Chromatogr A 2016; 1451:75-82. [DOI: 10.1016/j.chroma.2016.05.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 05/02/2016] [Accepted: 05/04/2016] [Indexed: 02/01/2023]
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7
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Kageyama Y, Ikegami T, Hiramatsu N, Takeda S, Sugawara T. Structure and growth behavior of centimeter-sized helical oleate assemblies formed with assistance of medium-length carboxylic acids. SOFT MATTER 2015; 11:3550-3558. [PMID: 25781720 DOI: 10.1039/c5sm00370a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The nonequilibrium organization of self-assemblies from small building-block molecules offers an attractive and essential means to develop advanced functional materials and to understand the intrinsic nature of life systems. Fatty acids are well-known amphiphiles that form self-assemblies of several shapes. Here, we found that the lengths of helical structures of oleic acid formed in a buffered aqueous solution are dramatically different by the presence or absence of certain amphiphilic carboxylic acids. For example, under the coexistence of a small amount of N-decanoyl-l-alanine, we observed the formation of over 1 centimeter-long helical assemblies of oleate with a regular pitch and radius, whereas mainly less than 100 μm-long helices formed without this additive. Such long helical assemblies are unique in terms of their highly dimensional helical structure and growth dynamics. Results from the real-time observation of self-assembly formation, site-selective small-angle X-ray scattering, high-performance liquid chromatography analysis, and pH titration experiments suggested that the coexisting carboxylates assist in elongation by supplying oleate molecules to a scaffold for oleate helical assembly.
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Affiliation(s)
- Yoshiyuki Kageyama
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan.
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8
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Dye-release assay for investigation of antimicrobial peptide activity in a competitive lipid environment. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2014; 43:445-50. [PMID: 24906225 DOI: 10.1007/s00249-014-0970-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 05/13/2014] [Accepted: 05/20/2014] [Indexed: 10/25/2022]
Abstract
A dye-release method for investigating the effect of a competitive lipid environment on the activity of two membrane-disrupting antimicrobial peptides (AMP), maculatin 1.1 and aurein 1.2, is presented. The results support the general conclusion that AMP have greater affinity for negatively charged membranes, for example bacterial membranes, than for the neutral membrane surface found in eukaryotic cells, but only within a competitive lipid environment. Indeed, in a single-model membrane environment, both peptides were more potent against neutral vesicles than against charged vesicles. The approach was also used to investigate the effect of pre-incubating the peptides in a neutral lipid environment then introducing charged lipid vesicles. Maculatin was shown to migrate from the neutral lipid bilayers, where pores had already formed, to the charged membrane bilayers. This result was also observed for charged-to-charged bilayers but, interestingly, not for neutral-to-neutral lipid interfaces. Aurein was able to migrate from either lipid environment, indicating weaker binding to lipid membranes, and a different molecular mechanism for lysis of lipid bilayers. Competitive lipid environments could be used to assess other critical conditions that modulate the activity of membrane peptides or proteins.
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9
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Filipe HAL, Moreno MJ, Róg T, Vattulainen I, Loura LMS. How to tackle the issues in free energy simulations of long amphiphiles interacting with lipid membranes: convergence and local membrane deformations. J Phys Chem B 2014; 118:3572-81. [PMID: 24635540 DOI: 10.1021/jp501622d] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
One of the great challenges in membrane biophysics is to find a means to foster the transport of drugs across complex membrane structures. In this spirit, we elucidate methodological challenges associated with free energy computations of complex chainlike molecules across lipid membranes. As an appropriate standard molecule to this end, we consider 7-nitrobenz-2-oxa-1,3-diazol-4-yl-labeled fatty amine, NBD-Cn, which is here dealt with as a homologous series with varying chain lengths. We found the membrane-water interface region to be highly sensitive to details in free energy computations. Despite considerable simulation times, we observed substantial hysteresis, the cause being the small frequency of insertion/desorption events of the amphiphile's alkyl chain in the membrane interface. The hysteresis was most pronounced when the amphiphile was pulled from water to the membrane and compromised the data that were not in line with experiments. The subtleties in umbrella sampling for computing distance along the transition path were also observed to be potential causes of artifacts. With the PGD (pull geometry distance) scheme, in which the distance from the molecule was computed to a reference plane determined by an average over all lipids in the membrane, we found marked deformations in membrane structure when the amphiphile was close to the membrane. The deformations were weaker with the PGC (pull geometry cylinder) method, where the reference plane is chosen based on lipids that are within a cylinder of radius 1.7 nm from the amphiphile. Importantly, the free energy results given by PGC were found to be qualitatively consistent with experimental data, while the PGD results were not. We conclude that with long amphiphiles there is reason for concern with regard to computations of their free energy profiles. The membrane-water interface is the region where the greatest care is warranted.
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Affiliation(s)
- Hugo A L Filipe
- Centro de Química de Coimbra, Largo D. Dinis, Rua Larga, 3004-535 Coimbra, Portugal
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10
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Cardoso RMS, Martins PAT, Gomes F, Doktorovova S, Vaz WLC, Moreno MJ. Chain-length dependence of insertion, desorption, and translocation of a homologous series of 7-nitrobenz-2-oxa-1,3-diazol-4-yl-labeled aliphatic amines in membranes. J Phys Chem B 2011; 115:10098-108. [PMID: 21749127 DOI: 10.1021/jp203429s] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a complete characterization of the kinetics of interaction between the homologous series of fluorescent fatty amines with the fluorescent moiety 7-nitrobenz-2-oxa-1,3-diazol-4-yl covalently bound to the amine group, NBD-C(n) (n = 8-16), and a lipid bilayer in the liquid disordered phase. The insertion into and the desorption from the lipid bilayer, as well as the rate of translocation across the two bilayer leaflets, has been measured at different temperatures, allowing an estimation of the thermodynamic parameters in the formation of the transition state. This is the first report on the complete characterization of the kinetics of the interaction of a large series of structurally homologous amphiphiles. In a recent paper from this research group, the equilibrium interaction of NBD-C(n) (n = 4-10) with POPC bilayers and serum albumin was reported. This information allows the calculation of the equilibrium distribution of the amphiphiles among the aqueous phase, serum proteins, and biomembranes. The data presented in this manuscript complement its characterization with information on the kinetics of the interactions, making possible the quantitative evaluation of their pharmacokinetics. The rate of translocation is shown to decrease with increasing alkyl chain length up to n = 12, becoming relatively insensitive to further increases in n. The Gibbs free energy variation associated with the rate of desorption from the lipid bilayer increased linearly with n, with ΔΔG(‡o) = 3.4 ± 0.5 kJ mol(-1) per methylene group. It was also found that the process of insertion in the lipid bilayer is not diffusion-limited, although it is close to this limit for the smaller amphiphiles in the homologous series at high temperatures.
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Affiliation(s)
- Renato M S Cardoso
- Departamento de Química, Faculdade de Ciencias e Tecnologia da Universidade de Coimbra (FCTUC), Largo D. Dinis, Rua Larga, 3004-535 Coimbra, Portugal
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11
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Lipid membrane interactions of indacaterol and salmeterol: Do they influence their pharmacological properties? Eur J Pharm Sci 2009; 38:533-47. [DOI: 10.1016/j.ejps.2009.10.001] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2009] [Revised: 09/28/2009] [Accepted: 10/01/2009] [Indexed: 01/24/2023]
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12
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Ishikawa FN, Stauffer B, Caron DA, Zhou C. Rapid and label-free cell detection by metal-cluster-decorated carbon nanotube biosensors. Biosens Bioelectron 2009; 24:2967-72. [PMID: 19342216 DOI: 10.1016/j.bios.2009.03.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2008] [Revised: 02/15/2009] [Accepted: 03/02/2009] [Indexed: 11/30/2022]
Abstract
In this paper, the use of carbon nanotube biosensors toward alga cell detection was examined. The biosensor devices were fabricated on complete 4 in. wafers by first growing carbon nanotubes (CNTs) and then depositing metal electrodes using a shadow mask. In addition, we decorated the biosensors with metal-clusters resulted in enhancing the sensitivity by 2000-folds and has enabled the detection of streptavidin down to 10 pM concentration. This sensitivity enhancement was attributed to activation of CNT channels due to formation of Schottky junctions between CNTs and metal-clusters. Real-time cell detection has been successfully carried out using the CNT biosensors for two kinds of alga related to brown tides: Aureococcus anophagefferens and BT3. Functionalization of the CNT biosensors with the monoclonal antibody for A. anophagefferens has led to detection at a concentration of 10(4) cells/ml, with sensitivity lower than 10(4) cells/ml projected based on the signal-to-noise ratio of the sensors. Further functionalization with tween 20 led to suppression of non-specific binding of BT3 and enabled label-free and selective detection of A. anophagefferens. These nanobiosensors may find potential applications for environmental monitoring and disease diagnosis.
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Affiliation(s)
- Fumiaki N Ishikawa
- Department of Electrical Engineering, University of Southern California, Los Angeles, CA 90089, USA
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13
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Affiliation(s)
- Stefan Balaz
- Department of Pharmaceutical Sciences, College of Pharmacy, North Dakota State University, Fargo, North Dakota 58105, USA.
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14
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Rossetti G, Magistrato A, Pastore A, Persichetti F, Carloni P. Structural Properties of Polyglutamine Aggregates Investigated via Molecular Dynamics Simulations. J Phys Chem B 2008; 112:16843-50. [DOI: 10.1021/jp806548p] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Giulia Rossetti
- International School for Advanced Studies, via Beirut 2-4, Trieste, Italy, CNR-INFM-Democritos National Simulation Center, Beirut 2-4, Trieste, Italy, Italian Institute of Technology - SISSA Unit, via Beirut 2-4, Trieste, Italy, and National Institute for Medical Research, The Ridgeway London, NW71AA, U.K
| | - Alessandra Magistrato
- International School for Advanced Studies, via Beirut 2-4, Trieste, Italy, CNR-INFM-Democritos National Simulation Center, Beirut 2-4, Trieste, Italy, Italian Institute of Technology - SISSA Unit, via Beirut 2-4, Trieste, Italy, and National Institute for Medical Research, The Ridgeway London, NW71AA, U.K
| | - Annalisa Pastore
- International School for Advanced Studies, via Beirut 2-4, Trieste, Italy, CNR-INFM-Democritos National Simulation Center, Beirut 2-4, Trieste, Italy, Italian Institute of Technology - SISSA Unit, via Beirut 2-4, Trieste, Italy, and National Institute for Medical Research, The Ridgeway London, NW71AA, U.K
| | - Francesca Persichetti
- International School for Advanced Studies, via Beirut 2-4, Trieste, Italy, CNR-INFM-Democritos National Simulation Center, Beirut 2-4, Trieste, Italy, Italian Institute of Technology - SISSA Unit, via Beirut 2-4, Trieste, Italy, and National Institute for Medical Research, The Ridgeway London, NW71AA, U.K
| | - Paolo Carloni
- International School for Advanced Studies, via Beirut 2-4, Trieste, Italy, CNR-INFM-Democritos National Simulation Center, Beirut 2-4, Trieste, Italy, Italian Institute of Technology - SISSA Unit, via Beirut 2-4, Trieste, Italy, and National Institute for Medical Research, The Ridgeway London, NW71AA, U.K
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Yang LMC, Diaz JE, McIntire TM, Weiss GA, Penner RM. Direct electrical transduction of antibody binding to a covalent virus layer using electrochemical impedance. Anal Chem 2008; 80:5695-705. [PMID: 18590279 DOI: 10.1021/ac8008109] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Electrochemical impedance spectroscopy is used to detect the binding of a 148.2 kDa antibody to a "covalent virus layer" (CVL) immobilized on a gold electrode. The CVL consisted of M13 phage particles covalently anchored to a 3 mm diameter gold disk electrode. The ability of the CVL to distinguish this antibody ("p-Ab") from a second, nonbinding antibody ("n-Ab") was evaluated as a function of the frequency and phase of the measured current relative to the applied voltage. The binding of p-Ab to the CVL was correlated with a change in the resistance, reducing it at low frequency (1-40 Hz) while increasing it at high frequency (2-140 kHz). The capacitance of the CVL was virtually uncorrelated with p-Ab binding. At both low and high frequency, the electrode resistance was linearly dependent on the p-Ab concentration from 20 to 266 nM but noise compromised the reproducibility of the p-Ab measurement at frequencies below 40 Hz. A "signal-to-noise" ratio for antibody detection was computed based upon the ratio between the measured resistance change upon p-Ab binding and the standard deviation of this change obtained from multiple measurements. In spite of the fact that the impedance change upon p-Ab binding in the low frequency domain was more than 100 times larger than that measured at high frequency, the S/N ratio at high frequency was higher and virtually independent of frequency from 4 to 140 kHz. Attempts to release p-Ab from the CVL using 0.05 M HCl, as previously described for mass-based detection, caused a loss of sensitivity that may be associated with a transition of these phage particles within the CVL from a linear to a coiled conformation at low pH.
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Affiliation(s)
- Li-Mei C Yang
- Department of Chemistry, University of California, Irvine, California 92697-2025, USA
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Pokorny A, Yandek LE, Elegbede AI, Hinderliter A, Almeida PFF. Temperature and composition dependence of the interaction of delta-lysin with ternary mixtures of sphingomyelin/cholesterol/POPC. Biophys J 2006; 91:2184-97. [PMID: 16798807 PMCID: PMC1557559 DOI: 10.1529/biophysj.106.085027] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The kinetics of carboxyfluorescein efflux induced by the amphipathic peptide delta-lysin from vesicles of porcine brain sphingomyelin (BSM), 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC), and cholesterol (Chol) were investigated as a function of temperature and composition. Sphingomyelin (SM)/Chol mixtures form a liquid-ordered (L(o)) phase whereas POPC exists in the liquid-disordered (L(d)) phase at ambient temperature. delta-Lysin binds strongly to L(d) and poorly to L(o) phase. In BSM/Chol/POPC vesicles the rate of carboxyfluorescein efflux induced by delta-lysin increases as the POPC content decreases. This is explained by the increase of delta-lysin concentration in L(d) domains, which enhances membrane perturbation by the peptide. Phase separations in the micrometer scale have been observed by fluorescence microscopy in SM/Chol/POPC mixtures for some SM, though not for BSM. Thus, delta-lysin must detect heterogeneities (domains) in BSM/Chol/POPC on a much smaller scale. Advantage was taken of the inverse variation of the efflux rate with the L(d) content of BSM/Chol/POPC vesicles to estimate the L(d) fraction in those mixtures. These results were combined with differential scanning calorimetry to obtain the BSM/Chol/POPC phase diagram as a function of temperature.
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Affiliation(s)
- Antje Pokorny
- Department of Chemistry and Biochemistry, University of North Carolina-Wilmington, Wilmington, NC, USA
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Silvius JR. Partitioning of membrane molecules between raft and non-raft domains: Insights from model-membrane studies. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2005; 1746:193-202. [PMID: 16271405 DOI: 10.1016/j.bbamcr.2005.09.003] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2005] [Revised: 09/02/2005] [Accepted: 09/07/2005] [Indexed: 11/28/2022]
Abstract
The special physical and functional properties ascribed to lipid rafts in biological membranes reflect their distinctive organization and composition, properties that are hypothesized to rest in part on the differential partitioning of various membrane components between liquid-ordered and liquid-disordered lipid environments. This review describes the principles and findings of recently developed methods to monitor the partitioning of membrane proteins and lipids between liquid-ordered and liquid-disordered domains in model membranes, and how these approaches can aid in elucidating the properties of rafts in biological membranes.
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Affiliation(s)
- John R Silvius
- Department of Biochemistry, McGill University, Montréal, Québec, Canada H3G 1Y6.
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Sampaio JL, Moreno MJ, Vaz WLC. Kinetics and thermodynamics of association of a fluorescent lysophospholipid derivative with lipid bilayers in liquid-ordered and liquid-disordered phases. Biophys J 2005; 88:4064-71. [PMID: 15792982 PMCID: PMC1305637 DOI: 10.1529/biophysj.104.054007] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have measured the rates of insertion into, desorption from, and spontaneous interlayer translocation (flip-flop) of the fluorescent lysophospholipid derivative NBD-lyso-1-myristoylphosphatidylethanolamine in l(d) and l(o) phase lipid bilayer membranes. The lipid bilayers, studied as LUV, were prepared from pure 1-palmitoyl-2-oleoylphosphatidylcholine, in the l(d) phase; and from two Chol-containing binary lipid mixtures, 1-palmitoyl-2-oleoylphosphatidylcholine and Chol (molar ratio of 1:1) and SpM and Chol (molar ratio of 6:4), both in the l(o) phase. Insertion, desorption, and translocation rate constants and equilibrium constants for association of the amphiphile monomer with the lipid bilayers were measured between 15 degrees C and 35 degrees C, and the standard free energies, enthalpies, and entropies, as well as the activation energies for these processes were derived from these data. The equilibrium partition coefficients for partitioning of the amphiphile between the aqueous phase and the different membrane phases were also derived, and an estimation was made of hypothetical partition coefficients and the respective energetic parameters for partitioning between the different lipid phases if these were to coexist in the same membrane. We show that, contrary to general belief, the association of NBD-lysoMPE with lipid bilayers is not a diffusion-controlled process, the rate-limiting step in insertion being the formation of a free area in the membrane surface of an adequate size for insertion to occur.
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Abreu MSC, Moreno MJ, Vaz WLC. Kinetics and thermodynamics of association of a phospholipid derivative with lipid bilayers in liquid-disordered and liquid-ordered phases. Biophys J 2004; 87:353-65. [PMID: 15240470 PMCID: PMC1304356 DOI: 10.1529/biophysj.104.040576] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2004] [Accepted: 03/08/2004] [Indexed: 11/18/2022] Open
Abstract
We have measured the rates of insertion into, desorption from, and spontaneous interlayer translocation (flip-flop) in liquid-disordered and liquid-ordered phase lipid bilayer membranes, of the fluorescent phospholipid derivative NBD-dimyristoylphosphatidyl ethanolamine. This study made use of a recently described method that exploits a detailed knowledge of the binding kinetics of an amphiphile to bovine serum albumin, to recover the insertion and desorption rate constants when the albumin-bound amphiphile is transferred through the aqueous phase to the membrane and vice versa. The lipid bilayers, studied as large unilamellar vesicles, were prepared from pure 1-palmitoyl-2-oleoylphosphatidylcholine in the liquid-disordered phase; and from two cholesterol-containing binary lipid mixtures, 1-palmitoyl-2-oleoylphosphatidylcholine and cholesterol (molar ratio of 1:1), and egg sphingomyelin and cholesterol (molar ratio of 6:4), both in the liquid-ordered phase. Insertion, desorption, and translocation rate constants and equilibrium constants for association of the amphiphile monomer with the lipid bilayers were directly measured between 15 degrees and 35 degrees C, and the standard free energies, enthalpies, and entropies, as well as the activation energies for these processes, were derived from this data. The equilibrium partition coefficients for partitioning of the amphiphile between the aqueous phase and the different membrane phases were also derived, and permitted the estimation of hypothetical partition coefficients and the respective energetic parameters for partitioning between the different lipid phases if these were to coexist in the same membrane.
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Affiliation(s)
- Magda S C Abreu
- Departamento de Quimica, Universidade de Coimbra, Coimbra, Portugal
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Santos NC, Prieto M, Castanho MARB. Quantifying molecular partition into model systems of biomembranes: an emphasis on optical spectroscopic methods. BIOCHIMICA ET BIOPHYSICA ACTA 2003; 1612:123-35. [PMID: 12787930 DOI: 10.1016/s0005-2736(03)00112-3] [Citation(s) in RCA: 208] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Optical spectroscopies have been intensively used to determine partition coefficients by a plethora of methodologies. The present review is intended to give detailed and useful information for the determination of partition coefficients and addresses several relevant aspects, namely: (i) definition and calculation of the partition coefficient between aqueous and lipidic phases; (ii) partition coefficients vs. "binding" formalisms; (iii) advantages of spectroscopic methodologies over separation techniques; (iv) formalisms for various experimental approaches based on UV-Vis absorption or fluorescence parameters (fluorescence intensity, lifetime, anisotropy and quenching); (v) experimental hints, artifacts and model limitations; and (vi) a brief survey of nonoptical techniques.
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Affiliation(s)
- Nuno C Santos
- Instituto de Bioquímica, Faculdade de Medicina de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal
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Abreu MSC, Estronca LMBB, Moreno MJ, Vaz WLC. Binding of a fluorescent lipid amphiphile to albumin and its transfer to lipid bilayer membranes. Biophys J 2003; 84:386-99. [PMID: 12524292 PMCID: PMC1302620 DOI: 10.1016/s0006-3495(03)74859-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Kinetics and thermodynamics of the binding of a fluorescent lipid amphiphile, Rhodamine Green(TM)-tetradecylamide (RG-C(14:0)), to bovine serum albumin were characterized in an equilibrium titration and by stopped-flow fluorimetry. The binding equilibrium of RG-C(14:0) to albumin was then used to reduce its concentration in the aqueous phase to a value below its critical micelle concentration. Under these conditions, the only two species of RG-C(14:0) in the system were the monomer in aqueous solution in equilibrium with the protein-bound species. After previous determination of the kinetic and thermodynamic parameters for association of RG-C(14:0) with albumin, the kinetics of insertion of the amphiphile into and desorption off lipid bilayer membranes in different phases (solid, liquid-ordered, and liquid-disordered phases, presented as large unilamellar vesicles) were studied by stopped-flow fluorimetry at 30 degrees C. Insertion and desorption rate constants for association of the RG-C(14:0) monomer with the lipid bilayers were used to obtain lipid/water equilibrium partition coefficients for this fluorescent amphiphile. The direct measurement of these partition coefficients is shown to provide a new method for the indirect determination of the equilibrium partition coefficient of similar molecules between two defined lipid phases if they coexist in the same membrane.
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Pokorny A, Birkbeck TH, Almeida PFF. Mechanism and kinetics of delta-lysin interaction with phospholipid vesicles. Biochemistry 2002; 41:11044-56. [PMID: 12206677 DOI: 10.1021/bi020244r] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Delta-lysin is a 26 amino acid, hemolytic peptide toxin secreted by Staphylococcus aureus. It has been reported to form an amphipathic helix upon binding to lipid bilayers and is often cited as a typical example of the barrel-stave model for pore formation in lipid bilayer membranes. However, the exact mechanism by which it lyses cells and the physical basis of its target specificity are still unknown. Moreover, the evidence for delta-lysin insertion and pore formation in the membrane stems largely from theoretical modeling of the toxin and lacks experimental confirmation. We investigated binding and insertion of delta-lysin into phospholipid bilayer vesicles. The kinetics of these processes were studied by stopped-flow fluorescence with two types of experiments: (a) carboxyfluorescein release from the vesicles upon peptide-vesicle interaction, with concomitant relief of dye self-quenching; (b) fluorescence energy transfer from the intrinsic tryptophan of the peptide to a membrane-bound lipid probe. We formulated a detailed kinetic mechanism with explicit molecular rate constants for peptide binding, association, and insertion, obtaining a quantitative description of the experimental results. delta-Lysin insertion is strongly dependent on the peptide-to-lipid ratio, suggesting that association of a critical number of monomers on the membrane is required for activity. However, we found no evidence for a stable membrane-inserted pore. Rather, the peptide appears to cross the membrane rapidly and reversibly and cause release of the lipid vesicle contents in this process.
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Affiliation(s)
- Antje Pokorny
- Department of Chemistry, University of North Carolina at Wilmington, Wilmington, North Carolina 28403, USA
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Estronca LMBB, Moreno MJ, Abreu MSC, Melo E, Vaz WLC. Solubility of amphiphiles in membranes: influence of phase properties and amphiphile head group. Biochem Biophys Res Commun 2002; 296:596-603. [PMID: 12176023 DOI: 10.1016/s0006-291x(02)00905-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The solubilities of two fluorescent lipid amphiphiles with comparable apolar structures and different polar head groups, NBD-hexadecylamine and RG-tetradecylamine (or -octadecylamine), were compared in lipid bilayers at a molar ratio of 1/50 at 23 degrees C. Bilayers examined were in the solid, liquid-disordered, or liquid-ordered phases. While NBD-hexadecylamine was soluble in all the examined bilayer membrane phases, RG-tetradecylamine was stably soluble only in the liquid-disordered phase. RG-tetradecylamine insolubility in solid and liquid-ordered phases manifests itself as an aggregation of the amphiphile over a period of several days and the kinetics of aggregation were studied. Solubility of these amphiphiles in the different phases examined seems to be related to the dipole moment of the amphiphile (in particular, of the polar fluorophore) and its orientation relative to the dipolar potential of the membrane. We propose that amphiphilic molecules inserted into membranes (including lipid-attached proteins) partition into different coexisting membrane phases based upon: (1) nature of the apolar structure (chain length, degree of saturation, and chain branching as has been proposed in the literature); (2) magnitude and orientation of the dipole moment of the polar portion of the molecules relative to the membrane dipolar potential; and (3) hydration forces that are a consequence of ordering of water dipoles at the membrane surface.
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Affiliation(s)
- Luís M B B Estronca
- Departamento de Química, Universidade de Coimbra, Coimbra 3004-535, Portugal
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Lu D, Rhodes DG. Binding of phosphorothioate oligonucleotides to zwitterionic liposomes. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1563:45-52. [PMID: 12007624 DOI: 10.1016/s0005-2736(02)00384-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Although double-stranded DNA (dsDNA) has been shown to bind to zwitterionic lipids, it has been reported that this association is stronger for disordered (L(alpha)) phase lipids than for well-ordered (L(beta)) lipids. In this work, the interaction of single-strand phosphorothioate oligonucleotides (ONs) with unilamellar liposomes of saturated and unsaturated zwitterionic phosphocholines (PCs) and phosphoroethylamine (PE) was investigated. It is shown that the association of phosphorothioate ONs to diacyl glycerophosphocholines is strong, but only for L(beta) phase or otherwise ordered bilayers. There is no measurable affinity for PE lipids. The apparent affinity of three different phosphorothioate ONs for L(beta) phase 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) has been measured and the dissociation constants were on the order of 10(-7) M. Purine-rich ON sequences had stronger binding to DPPC liposomes than did pyrimidine-rich sequences, but there were other sequence-dependent factors. This exceptionally high affinity could be an important consideration in ON uptake, delivery, and biodistribution.
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Affiliation(s)
- Dongmei Lu
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, 372 Fairfield Road, Unit 2092, Storrs 06269-2092, USA
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Pokorny A, Almeida PF, Vaz WL. Association of a fluorescent amphiphile with lipid bilayer vesicles in regions of solid-liquid-disordered phase coexistence. Biophys J 2001; 80:1384-94. [PMID: 11222299 PMCID: PMC1301330 DOI: 10.1016/s0006-3495(01)76111-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The effects of solid-fluid phase separations on the kinetics of association of a single-chain fluorescent amphiphile were investigated in two different systems: pure DMPC (dimyristoylphosphatidylcholine) and a 1:1 mixture of DMPC and DSPC (distearoylphosphatidylcholine). In pure DMPC vesicles, solid (s) and fluid (l(d)) phases coexist at the phase transition temperature, T(m), whereas a 1:1 mixture of DMPC and DSPC shows a stable s-l(d) phase separation over a large temperature interval. We found that in single-component bilayers, within the main phase transition, the experimental kinetics of association are clearly not single-exponential, the deviation from that function becoming maximal at the T(m). This observation can be accounted for by a rate of desorption that is slower than desorption from either fluid or solid phases, leaving the rates of insertion unchanged, but a treatment in terms of stable fluid and solid domains may not be adequate for the analysis of the association of an amphiphile with pure DMPC vesicles at the T(m). In DMPC/DSPC mixtures with solid-fluid phase coexistence, association occurs overall faster than expected based on phase composition. The observed kinetics can be described by an increase in the rate of insertion, leaving the desorption rates unchanged. The fast kinetics of insertion of the amphiphile into two-phase bilayers in two-component vesicles is attributed to a more rapid insertion into defect-rich regions, which are most likely phase boundaries between solid and fluid domains. A two-component mixture of lipids that shows a stable phase separation between l(d)-s phases over a large temperature interval thus behaves very differently from a single-component bilayer at the T(m), with respect to insertion of amphiphiles.
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Affiliation(s)
- A Pokorny
- Departamento de Química, Universidade de Coimbra, 3004-535 Coimbra, Portugal.
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Mesquita RM, Melo E, Thompson TE, Vaz WL. Partitioning of amphiphiles between coexisting ordered and disordered phases in two-phase lipid bilayer membranes. Biophys J 2000; 78:3019-25. [PMID: 10827980 PMCID: PMC1300885 DOI: 10.1016/s0006-3495(00)76840-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The partition coefficients (K(P)) of a series of single-chain and double-chain fluorescent amphiphiles, between solid ordered (P(beta') and L(beta)) and liquid disordered (L(alpha) of the type l(d)) lipid phases coexisting in the same lipid bilayer, was studied using steady-state fluorescence emission anisotropy. The single-chain amphiphiles were N-(7-nitrobenzoxa-2, 3-diazol-4-yl)-alkylamines, and the double-chain amphiphiles were N-(7-nitrobenzoxa-2, 3-diazol-4-yl)-phosphatidylethanolamines with chain lengths of 12-18 carbon atoms. Saturated 18-carbon alkyl/acyl chain compounds were also compared with Delta(9)-cis unsaturated chains of the same chain length. The fluorescence anisotropy of the probes was examined in lipid bilayers (multilamellar vesicles) prepared from an equimolar mixture of dilauroylphosphatidylcholine and distearoylphosphatidylcholine and studied as a function of temperature through the entire temperature range of coexistence of ordered gel phases and a disordered fluid phase in this system. The unsaturated chain amphiphiles partitioned exclusively into the fluid phase whenever this phase was present, as did the saturated chain amphiphiles with the shortest chains (C(12:0)), while K(P) ranges between 1 and 2, in favor of the L(beta) solid phase, for the amphiphiles with long saturated (C(18:0)) alkyl/acyl chains, with intermediate behavior for the intermediate chain lengths. All probes appeared to be totally excluded from P(beta') solid (gel) phases. The technique was also used to determine partitioning of some of the probes between coexisting liquid ordered (cholesterol-containing) (l(o)) and liquid disordered (l(d)) L(alpha) phases. In this case the ratio of signal amplitude to noise allowed us to obtain a qualitative, but not quantitative, measure of the phase partitioning of the probes. We conclude that the partitioning behavior of the probes examined between coexisting l(o) and l(d) phases is qualitatively similar to that observed between solid ordered and liquid disordered phases.
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Affiliation(s)
- R M Mesquita
- Instituto de Tecnologia Química e Biológica, P-2780 Oeiras, Portugal
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