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Cordeiro MM, Filipe HAL, dos Santos P, Samelo J, Ramalho JPP, Loura LMS, Moreno MJ. Interaction of Hoechst 33342 with POPC Membranes at Different pH Values. Molecules 2023; 28:5640. [PMID: 37570608 PMCID: PMC10420284 DOI: 10.3390/molecules28155640] [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: 06/30/2023] [Revised: 07/18/2023] [Accepted: 07/21/2023] [Indexed: 08/13/2023] Open
Abstract
Hoechst 33342 (H33342) is a fluorescent probe that is commonly used to stain the DNA of living cells. To do so, it needs to interact with and permeate through cell membranes, despite its high overall charge at physiological pH values. In this work, we address the effect of pH in the association of H33342 with lipid bilayers using a combined experimental and computational approach. The partition of H33342 to 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid membranes was experimentally quantified using fluorescence spectroscopy and isothermal titration calorimetry (ITC) measurements. Quantum chemical calculations were performed to select the most stable isomer of H33342 for the overall charges 0, +1, and +2, expected to predominate across the 5 < pH < 10 range. The interaction of these isomers with POPC bilayers was then studied by both unrestrained and umbrella sampling molecular dynamics (MD) simulations. Both experimental results and computational free energy profiles indicate that the partition coefficient of H33342 displays a small variation over a wide pH range, not exceeding one order of magnitude. The enthalpy variation upon partition to the membrane suggests efficient hydrogen bonding between the probe and the lipid, namely, for the protonated +2 form, which was confirmed in the MD simulation studies. The relatively high lipophilicity obtained for the charged species contrasts with the decrease in their general hydrophobicity as estimated from octanol/water partition. This highlights the distinction between lipophilicity and hydrophobicity, as well as the importance of considering the association with lipid bilayers when predicting the affinity for biomembranes.
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Affiliation(s)
- Margarida M. Cordeiro
- Coimbra Chemistry Center, Institute of Molecular Sciences (CQC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal; (M.M.C.); (H.A.L.F.); (J.S.)
- Department of Chemistry, Faculty of Sciences and Technology, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Hugo A. L. Filipe
- Coimbra Chemistry Center, Institute of Molecular Sciences (CQC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal; (M.M.C.); (H.A.L.F.); (J.S.)
- Polytechnic of Guarda, CPIRN-IPG—Center of Potential and Innovation of Natural Resources, 6300-559 Guarda, Portugal
| | - Patrícia dos Santos
- Coimbra Chemistry Center, Institute of Molecular Sciences (CQC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal; (M.M.C.); (H.A.L.F.); (J.S.)
- Department of Chemistry, Faculty of Sciences and Technology, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Jaime Samelo
- Coimbra Chemistry Center, Institute of Molecular Sciences (CQC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal; (M.M.C.); (H.A.L.F.); (J.S.)
- Department of Chemistry, Faculty of Sciences and Technology, University of Coimbra, 3004-535 Coimbra, Portugal
| | - João P. Prates Ramalho
- LAQV, REQUIMTE, Hercules Laboratory, Department of Chemistry, School of Science and Technology, University of Évora, 7000-671 Évora, Portugal;
| | - Luís M. S. Loura
- Coimbra Chemistry Center, Institute of Molecular Sciences (CQC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal; (M.M.C.); (H.A.L.F.); (J.S.)
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-535 Coimbra, Portugal
- Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Maria J. Moreno
- Coimbra Chemistry Center, Institute of Molecular Sciences (CQC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal; (M.M.C.); (H.A.L.F.); (J.S.)
- Department of Chemistry, Faculty of Sciences and Technology, University of Coimbra, 3004-535 Coimbra, Portugal
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-535 Coimbra, Portugal
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Fluorescent Probes cis- and trans-Parinaric Acids in Fluid and Gel Lipid Bilayers: A Molecular Dynamics Study. Molecules 2023; 28:molecules28052241. [PMID: 36903487 PMCID: PMC10005308 DOI: 10.3390/molecules28052241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/20/2023] [Accepted: 02/23/2023] [Indexed: 03/04/2023] Open
Abstract
Fluorescence probes are indispensable tools in biochemical and biophysical membrane studies. Most of them possess extrinsic fluorophores, which often constitute a source of uncertainty and potential perturbation to the host system. In this regard, the few available intrinsically fluorescent membrane probes acquire increased importance. Among them, cis- and trans-parinaric acids (c-PnA and t-PnA, respectively) stand out as probes of membrane order and dynamics. These two compounds are long-chained fatty acids, differing solely in the configurations of two double bonds of their conjugated tetraene fluorophore. In this work, we employed all-atom and coarse-grained molecular dynamics simulations to study the behavior of c-PnA and t-PnA in lipid bilayers of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), representative of the liquid disordered and solid ordered lipid phases, respectively. All-atom simulations indicate that the two probes show similar location and orientation in the simulated systems, with the carboxylate facing the water/lipid interface and the tail spanning the membrane leaflet. The two probes establish interactions with the solvent and lipids to a similar degree in POPC. However, the almost linear t-PnA molecules have tighter lipid packing around them, especially in DPPC, where they also interact more with positively charged lipid choline groups. Probably for these reasons, while both probes show similar partition (assessed from computed free energy profiles across bilayers) to POPC, t-PnA clearly partitions more extensively than c-PnA to the gel phase. t-PnA also displays more hindered fluorophore rotation, especially in DPPC. Our results agree very well with experimental fluorescence data from the literature and allow deeper understanding of the behavior of these two reporters of membrane organization.
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Magalhães N, Simões GM, Ramos C, Samelo J, Oliveira AC, Filipe HAL, Ramalho JPP, Moreno MJ, Loura LMS. Interactions between Rhodamine Dyes and Model Membrane Systems—Insights from Molecular Dynamics Simulations. Molecules 2022; 27:molecules27041420. [PMID: 35209208 PMCID: PMC8876248 DOI: 10.3390/molecules27041420] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/15/2022] [Accepted: 02/16/2022] [Indexed: 02/04/2023] Open
Abstract
Background: rhodamines are dyes widely used as fluorescent tags in cell imaging, probing of mitochondrial membrane potential, and as P-glycoprotein model substrates. In all these applications, detailed understanding of the interaction between rhodamines and biomembranes is fundamental. Methods: we combined atomistic molecular dynamics (MD) simulations and fluorescence spectroscopy to characterize the interaction between rhodamines 123 and B (Rh123 and RhB, respectively) and POPC bilayers. Results: while the xanthene moiety orients roughly parallel to the membrane plane in unrestrained MD simulations, variations on the relative position of the benzoic ring (below the xanthene for Rh123, above it for RhB) were observed, and related to the structure of the two dyes and their interactions with water and lipids. Subtle distinctions were found among different ionization forms of the probes. Experimentally, RhB displayed a lipid/water partition coefficient more than two orders of magnitude higher than Rh123, in agreement with free energy profiles obtained from umbrella sampling MD. Conclusions: this work provided detailed insights on the similarities and differences in the behavior of bilayer-inserted Rh123 and RhB, related to the structure of the probes. The much higher affinity of RhB for the membranes increases the local concentration and explains its higher apparent affinity for P-glycoprotein reconstituted in model membranes.
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Affiliation(s)
- Nisa Magalhães
- Coimbra Chemistry Center—Institute of Molecular Sciences (CQC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal; (N.M.); (G.M.S.); (C.R.); (J.S.); (A.C.O.); (H.A.L.F.); (M.J.M.)
- Department of Chemistry, Faculty of Sciences and Technology, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Guilherme M. Simões
- Coimbra Chemistry Center—Institute of Molecular Sciences (CQC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal; (N.M.); (G.M.S.); (C.R.); (J.S.); (A.C.O.); (H.A.L.F.); (M.J.M.)
- Department of Chemistry, Faculty of Sciences and Technology, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Cristiana Ramos
- Coimbra Chemistry Center—Institute of Molecular Sciences (CQC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal; (N.M.); (G.M.S.); (C.R.); (J.S.); (A.C.O.); (H.A.L.F.); (M.J.M.)
- Department of Chemistry, Faculty of Sciences and Technology, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Jaime Samelo
- Coimbra Chemistry Center—Institute of Molecular Sciences (CQC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal; (N.M.); (G.M.S.); (C.R.); (J.S.); (A.C.O.); (H.A.L.F.); (M.J.M.)
- Department of Chemistry, Faculty of Sciences and Technology, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Alexandre C. Oliveira
- Coimbra Chemistry Center—Institute of Molecular Sciences (CQC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal; (N.M.); (G.M.S.); (C.R.); (J.S.); (A.C.O.); (H.A.L.F.); (M.J.M.)
- Department of Chemistry, Faculty of Sciences and Technology, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Hugo A. L. Filipe
- Coimbra Chemistry Center—Institute of Molecular Sciences (CQC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal; (N.M.); (G.M.S.); (C.R.); (J.S.); (A.C.O.); (H.A.L.F.); (M.J.M.)
- CPIRN-IPG—Center of Potential and Innovation of Natural Resources, Polytechnic Institute of Guarda, 6300-559 Guarda, Portugal
| | - João P. Prates Ramalho
- Hercules Laboratory, LAQV, REQUIMTE, Department of Chemistry, School of Science and Technology, University of Évora, 7000-671 Evora, Portugal;
| | - Maria João Moreno
- Coimbra Chemistry Center—Institute of Molecular Sciences (CQC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal; (N.M.); (G.M.S.); (C.R.); (J.S.); (A.C.O.); (H.A.L.F.); (M.J.M.)
- Department of Chemistry, Faculty of Sciences and Technology, University of Coimbra, 3004-535 Coimbra, Portugal
- CNC—Center for Neuroscience and Cell Biology, 3004-504 Coimbra, Portugal
| | - Luís M. S. Loura
- Coimbra Chemistry Center—Institute of Molecular Sciences (CQC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal; (N.M.); (G.M.S.); (C.R.); (J.S.); (A.C.O.); (H.A.L.F.); (M.J.M.)
- CNC—Center for Neuroscience and Cell Biology, 3004-504 Coimbra, Portugal
- Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal
- Correspondence:
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Filipe HAL, Moreno MJ, Loura LMS. The Secret Lives of Fluorescent Membrane Probes as Revealed by Molecular Dynamics Simulations. Molecules 2020; 25:E3424. [PMID: 32731549 PMCID: PMC7435664 DOI: 10.3390/molecules25153424] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 07/23/2020] [Accepted: 07/25/2020] [Indexed: 12/15/2022] Open
Abstract
Fluorescent probes have been employed for more than half a century to study the structure and dynamics of model and biological membranes, using spectroscopic and/or microscopic experimental approaches. While their utilization has led to tremendous progress in our knowledge of membrane biophysics and physiology, in some respects the behavior of bilayer-inserted membrane probes has long remained inscrutable. The location, orientation and interaction of fluorophores with lipid and/or water molecules are often not well known, and they are crucial for understanding what the probe is actually reporting. Moreover, because the probe is an extraneous inclusion, it may perturb the properties of the host membrane system, altering the very properties it is supposed to measure. For these reasons, the need for independent methodologies to assess the behavior of bilayer-inserted fluorescence probes has been recognized for a long time. Because of recent improvements in computational tools, molecular dynamics (MD) simulations have become a popular means of obtaining this important information. The present review addresses MD studies of all major classes of fluorescent membrane probes, focusing in the period between 2011 and 2020, during which such work has undergone a dramatic surge in both the number of studies and the variety of probes and properties accessed.
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Affiliation(s)
- Hugo A. L. Filipe
- Chemistry Department, Coimbra Chemistry Center, Faculty of Sciences and Technology, University of Coimbra, 3004-535 Coimbra, Portugal;
| | - Maria João Moreno
- Coimbra Chemistry Center and CNC—Center for Neuroscience and Cell Biology, Chemistry Department, Faculty of Sciences and Technology, University of Coimbra, 3004-535 Coimbra, Portugal;
| | - Luís M. S. Loura
- Coimbra Chemistry Center and CNC—Center for Neuroscience and Cell Biology, Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal
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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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Maleki R, Afrouzi HH, Hosseini M, Toghraie D, Rostami S. Molecular dynamics simulation of Doxorubicin loading with N-isopropyl acrylamide carbon nanotube in a drug delivery system. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2020; 184:105303. [PMID: 31901633 DOI: 10.1016/j.cmpb.2019.105303] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 12/22/2019] [Accepted: 12/25/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND AND OBJECTIVE Doxorubicin is one of the common drugs used for cancer therapy. Molecular dynamics were applied to investigate the loading of Doxorubicin with thermosensitive N-isopropyl acrylamide Carbon nanotube carrier. METHODS The results showed that the smaller polymer chain length has more decrease of gyration radius. A decrease of gyration radius resulted in more concentrated aggregation with stronger bonds. Therefore, the shorter the polymer chain lengths, the more stable polymer interaction and better Doxorubicin delivery. Smaller polymers also form more hydrogen bonds with the drug leading to stronger and more stable carriers. RESULTS A lower amount of wall shear stress was found near the inner wall of the artery, distal to the plaque region (stenosis), and in both percentages of stenosis the maximum wall shear stress will accrue in the middle of the stenosis; however it is much more in the higher rate of stenosis. CONCLUSIONS The results indicated that N-isopropyl acrylamide - Carbon nanotube is suitable for the delivery of Doxorubicin, and five mer N-isopropyl acrylamide is the optimum carrier for Doxorubicin loading.
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Affiliation(s)
- Reza Maleki
- Department of Chemical Engineering, Shiraz University, Shiraz, Iran
| | | | - Mirollah Hosseini
- Department of Mechanical Engineering, Qaemshahr Branch, Islamic Azad University, Qaemshahr, Mazandaran, Iran
| | - Davood Toghraie
- Department of Mechanical Engineering, Khomeinishahr Branch, Islamic Azad University, Khomeinishahr, Iran
| | - Sara Rostami
- Laboratory of Magnetism and Magnetic Materials, Advanced Institute of Materials Science, Ton Duc Thang University, Ho Chi Minh City, Vietnam; Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam.
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Temperature Dependence of the Structure and Dynamics of a Dye-Labeled Lipid in a Planar Phospholipid Bilayer: A Computational Study. J Membr Biol 2019; 252:227-240. [PMID: 31332471 DOI: 10.1007/s00232-019-00081-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 07/11/2019] [Indexed: 10/26/2022]
Abstract
Fluorescent probes are widely employed to label lipids for the investigation of structural and dynamic properties of model and cell membranes through optical microscopy techniques. Although the effect of tagging a lipid with an organic dye is generally assumed to be negligible, optically modified lipids can nonetheless affect the local lipid structure and, in turn, the lipid lateral mobility. To better assess this potential issue, all-atom (MD) molecular dynamics simulations have been performed to study structural and dynamic effects in a model DOPC membrane in the presence of a standard Rhodamine B-labeled DOPE lipid (RHB) as a function of temperature, i.e., 293 K, 303 K, and 320 K. As the temperature is increased, we observe similar changes in the structural properties of both pure DOPC and RHB-DOPC lipid bilayers: an increase of the area per lipid, a reduction of the membrane thickness and a decrease of lipid order parameters. The partial density profile of the RHB headgroups and their orientation within the lipid bilayer confirm the amphiphilic nature of the RHB fluorescent moiety, which mainly partitions in the DOPC glycerol backbone region at each temperature. Moreover, at all temperatures, our results on lipid lateral diffusion support a non-neutral role of the dye with respect to the unlabeled lipid mobility, thus suggesting important implications for optical microscopy studies of lipid membranes.
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8
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Houang EM, Sham YY, Bates FS, Metzger JM. Muscle membrane integrity in Duchenne muscular dystrophy: recent advances in copolymer-based muscle membrane stabilizers. Skelet Muscle 2018; 8:31. [PMID: 30305165 PMCID: PMC6180502 DOI: 10.1186/s13395-018-0177-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 09/13/2018] [Indexed: 02/07/2023] Open
Abstract
The scientific premise, design, and structure-function analysis of chemical-based muscle membrane stabilizing block copolymers are reviewed here for applications in striated muscle membrane injury. Synthetic block copolymers have a rich history and wide array of applications from industry to biology. Potential for discovery is enabled by a large chemical space for block copolymers, including modifications in block copolymer mass, composition, and molecular architecture. Collectively, this presents an impressive chemical landscape to leverage distinct structure-function outcomes. Of particular relevance to biology and medicine, stabilization of damaged phospholipid membranes using amphiphilic block copolymers, classified as poloxamers or pluronics, has been the subject of increasing scientific inquiry. This review focuses on implementing block copolymers to protect fragile muscle membranes against mechanical stress. The review highlights interventions in Duchenne muscular dystrophy, a fatal disease of progressive muscle deterioration owing to marked instability of the striated muscle membrane. Biophysical and chemical engineering advances are presented that delineate and expand upon current understanding of copolymer-lipid membrane interactions and the mechanism of stabilization. The studies presented here serve to underscore the utility of copolymer discovery leading toward the therapeutic application of block copolymers in Duchenne muscular dystrophy and potentially other biomedical applications in which membrane integrity is compromised.
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Affiliation(s)
- Evelyne M Houang
- Department of Integrative Biology and Physiology, University of Minnesota Medical School, 6-125 Jackson Hall, 321 Church Street SE, Minneapolis, MN, 55455, USA
| | - Yuk Y Sham
- Department of Integrative Biology and Physiology, University of Minnesota Medical School, 6-125 Jackson Hall, 321 Church Street SE, Minneapolis, MN, 55455, USA.,University of Minnesota Informatics Institute, MN, USA.,Bioinformatics and Computational Biology Program, University of Minnesota, MN, USA
| | - Frank S Bates
- Department of Chemical Engineering and Materials Science, University of Minnesota, MN, USA
| | - Joseph M Metzger
- Department of Integrative Biology and Physiology, University of Minnesota Medical School, 6-125 Jackson Hall, 321 Church Street SE, Minneapolis, MN, 55455, USA.
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Location of fluorescent probes (2′-hydroxy derivatives of 2,5-diaryl-1,3-oxazole) in lipid membrane studied by fluorescence spectroscopy and molecular dynamics simulation. Biophys Chem 2018; 235:9-18. [DOI: 10.1016/j.bpc.2018.01.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 01/26/2018] [Accepted: 01/28/2018] [Indexed: 11/20/2022]
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10
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Flynn KR, Sutti A, Martin LL, Leigh Ackland M, Torriero AAJ. Critical effects of polar fluorescent probes on the interaction of DHA with POPC supported lipid bilayers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:1135-1142. [PMID: 29338975 DOI: 10.1016/j.bbamem.2018.01.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Revised: 12/22/2017] [Accepted: 01/11/2018] [Indexed: 01/16/2023]
Abstract
The understanding of lipid bilayer structure and function has been advanced by the application of molecular fluorophores. However, the effects of these probe molecules on the physicochemical properties of membranes being studied are poorly understood. A quartz crystal microbalance with dissipation monitoring instrument was used in this work to investigate the impact of two commonly used fluorescent probes, 1‑palmitoyl‑2‑{12‑[(7‑nitro‑2‑1,3‑benzoxadiazol‑4‑yl)amino]dodecanoyl}‑sn‑glycero‑3‑phosphocholine (NBD-PC) and 1,2‑dipalmitoyl‑sn‑glycero‑3‑phosphoethanolamine‑n‑(lissamine rhodamine‑B‑sulfonyl) (Lis-Rhod PE), on the formation and physicochemical properties of a 1‑palmitoyl‑2‑oleoyl‑sn‑glycero‑3‑phosphocholine supported lipid bilayer (POPC-SLB). The interaction of the POPC-SLB and fluorophore-modified POPC-SLB with docosahexaenoic acid, DHA, was evaluated. The incorporation of DHA into the POPC-SLB was observed to significantly decrease in the presence of the Lis-Rhod PE probe compared with the POPC-SLB. In addition, it was observed that the small concentration of DHA incorporated into the POPC:NBD-PC SLB can produce rearrangement processes followed by the lost not only of DHA but also of POPC or NBD-PC molecules or both during the washing step. This work has significant implications for the interpretation of data employing fluorescent reporter molecules within SLBs.
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Affiliation(s)
- Kiera R Flynn
- Centre for Cellular and Molecular Biology, School of Life and Environmental Sciences, Deakin University, Burwood, Victoria 3125, Australia
| | - Alessandra Sutti
- Institute for Frontier Materials, Deakin University, Geelong, Australia
| | | | - M Leigh Ackland
- Centre for Cellular and Molecular Biology, School of Life and Environmental Sciences, Deakin University, Burwood, Victoria 3125, Australia
| | - Angel A J Torriero
- School of Life and Environmental Sciences, Deakin University, Burwood, Victoria 3125, Australia.
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11
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Lee BL, Kuczera K. Simulating the free energy of passive membrane permeation for small molecules. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2017.1407029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Brent L. Lee
- Department of Chemistry, The University of Kansas , Lawrence, KS, USA
| | - Krzysztof Kuczera
- Department of Chemistry, The University of Kansas , Lawrence, KS, USA
- Department of Molecular Biosciences, The University of Kansas , Lawrence, KS, USA
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12
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Houang EM, Bates FS, Sham YY, Metzger JM. All-Atom Molecular Dynamics-Based Analysis of Membrane-Stabilizing Copolymer Interactions with Lipid Bilayers Probed under Constant Surface Tensions. J Phys Chem B 2017; 121:10657-10664. [PMID: 29049887 DOI: 10.1021/acs.jpcb.7b08938] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
An all-atom phospholipid bilayer and triblock copolymer model was developed for molecular dynamics (MD) studies. These were performed to investigate the mechanism of interaction between membrane-stabilizing triblock copolymer P188 and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (POPC) lipid bilayers under applied lateral surface tension (γ) to model membrane mechanical stress. Results showed that P188 insertion is driven by the hydrophobic poly(propylene oxide) (PPO) core and dependent on bilayer area per lipid. Moreover, insertion of P188 increased the bilayer's resistance to mechanical rupture, as observed by a significant increase in the absolute lateral pressure required to disrupt the bilayer. To further investigate the specific chemical features of P188 underlying membrane stabilizer function, a series of MD simulations with triblock copolymers of the same class as P188 but of varying chemical composition and sizes were performed. Results showed that triblock copolymer insertion into the lipid bilayer is dependent on overall copolymer hydrophobicity, with higher copolymer hydrophobicity requiring a reduced bilayer area per lipid ratio for insertion. Further analysis revealed that the effect of copolymer insertion on membrane mechanical integrity was also dependent on hydrophobicity. Here, P188 insertion significantly increased the absolute apparent lateral pressure required to rupture the POPC bilayer, thereby protecting the membrane against mechanical stress. In marked contrast, highly hydrophobic copolymers decreased the lateral pressure necessary for membrane rupture and thus rendering the membrane significantly more susceptible to mechanical stress. These new in silico findings align with recent experimental findings using synthetic lipid bilayers and in muscle cells in vitro and mouse models in vivo. Collectively, these data underscore the importance of PEO-PPO-PEO copolymer chemical composition in copolymer-based muscle membrane stabilization in vitro and in vivo. All-atom modeling with MD simulations holds promise for investigating novel copolymers with enhanced membrane interacting properties.
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Affiliation(s)
- Evelyne M Houang
- Integrative Biology and Physiology, University of Minnesota Medical School , Minneapolis, Minnesota 55455, United States
| | - Frank S Bates
- Department of Chemical Engineering and Materials Science, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Yuk Y Sham
- Integrative Biology and Physiology, University of Minnesota Medical School , Minneapolis, Minnesota 55455, United States.,University of Minnesota Informatics Institute , Minneapolis, Minnesota 55455, United States.,Bioinformatics and Computational Biology Program, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Joseph M Metzger
- Integrative Biology and Physiology, University of Minnesota Medical School , Minneapolis, Minnesota 55455, United States
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13
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Mantil E, Crippin T, Ianoul A, Avis TJ. Experimental Parameters Leading to Optimal Bilayers for Total Internal Reflection Fluorescence Microscopy Visualization. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2017; 23:97-112. [PMID: 28228172 DOI: 10.1017/s1431927617000083] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Supported lipid bilayer systems were evaluated following various experimental procedures in an effort to determine their appropriateness for visualization using total internal reflection fluorescence (TIRF) microscopy. The incorporation and distribution of Texas Red® 1,2-dihexadecanoyl-sn-glycero-3-phosphoethanolamine (TR-DHPE) was studied when incorporated into bilayers of variable lipid composition using different forms of mechanical shearing. Results showed that 0.8 mol% TR-DHPE provides the most optimum TIRF images. At this concentration, a sufficient level of photostability can be achieved without an undesirable increase in TR-DHPE aggregates caused by excess probe molecules. Solutions composed of a 3:1 molar ratio of DOPC:DPPC with 0.8 mol% TR-DHPE produce bilayers that consistently display clear, distinct, rounded domains, whereas other lipid compositions did not. This optimum phase separation appears to be influenced by an increase in mechanical shearing during the vesicle formation process, when the lipid solutions were exposed to sonication and extrusion processes. The combination of a sonication and extrusion process also helped with eliminating the presence of TR-DHPE aggregates within the model membranes. It was also shown that bilayers formed on conditioned glass, placed on a slide, produced more highly detailed bilayers in which distinct lipid phase separation could be optimally visualized using TIRF microscopy.
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Affiliation(s)
- Elisabeth Mantil
- 1Department of Chemistry,Carleton University,1125 Colonel By Drive,Ottawa,ON K1S 5B6,Canada
| | - Trinda Crippin
- 2Department of Biology,Carleton University,1125 Colonel By Drive,Ottawa,ON K1S 5B6,Canada
| | - Anatoli Ianoul
- 1Department of Chemistry,Carleton University,1125 Colonel By Drive,Ottawa,ON K1S 5B6,Canada
| | - Tyler J Avis
- 1Department of Chemistry,Carleton University,1125 Colonel By Drive,Ottawa,ON K1S 5B6,Canada
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14
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Basso LGM, Vicente EF, Crusca E, Cilli EM, Costa-Filho AJ. SARS-CoV fusion peptides induce membrane surface ordering and curvature. Sci Rep 2016; 6:37131. [PMID: 27892522 PMCID: PMC5125003 DOI: 10.1038/srep37131] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Accepted: 10/24/2016] [Indexed: 12/23/2022] Open
Abstract
Viral membrane fusion is an orchestrated process triggered by membrane-anchored viral fusion glycoproteins. The S2 subunit of the spike glycoprotein from severe acute respiratory syndrome (SARS) coronavirus (CoV) contains internal domains called fusion peptides (FP) that play essential roles in virus entry. Although membrane fusion has been broadly studied, there are still major gaps in the molecular details of lipid rearrangements in the bilayer during fusion peptide-membrane interactions. Here we employed differential scanning calorimetry (DSC) and electron spin resonance (ESR) to gather information on the membrane fusion mechanism promoted by two putative SARS FPs. DSC data showed the peptides strongly perturb the structural integrity of anionic vesicles and support the hypothesis that the peptides generate opposing curvature stresses on phosphatidylethanolamine membranes. ESR showed that both FPs increase lipid packing and head group ordering as well as reduce the intramembrane water content for anionic membranes. Therefore, bending moment in the bilayer could be generated, promoting negative curvature. The significance of the ordering effect, membrane dehydration, changes in the curvature properties and the possible role of negatively charged phospholipids in helping to overcome the high kinetic barrier involved in the different stages of the SARS-CoV-mediated membrane fusion are discussed.
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Affiliation(s)
- Luis G M Basso
- Grupo de Biofísica Molecular Sérgio Mascarenhas, Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador São-carlense, 400, Centro, São Carlos, SP, Brazil.,Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo. Av. Bandeirantes, 3900, 14040-901, Ribeirão Preto, SP, Brazil
| | - Eduardo F Vicente
- Faculdade de Ciências e Engenharia, UNESP - Univ Estadual Paulista, Campus de Tupã. Rua Domingos da Costa Lopes, 780, 17602-496, Tupã, SP, Brazil
| | - Edson Crusca
- Departamento de Bioquímica e Tecnologia Química, Instituto de Química, UNESP - Univ Estadual Paulista. Rua Prof. Franscisco Degni, 55, 14800-900, Araraquara, SP, Brazil
| | - Eduardo M Cilli
- Departamento de Bioquímica e Tecnologia Química, Instituto de Química, UNESP - Univ Estadual Paulista. Rua Prof. Franscisco Degni, 55, 14800-900, Araraquara, SP, Brazil
| | - Antonio J Costa-Filho
- Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo. Av. Bandeirantes, 3900, 14040-901, Ribeirão Preto, SP, Brazil
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15
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Xu W, Zeng Z, Jiang JH, Chang YT, Yuan L. Wahrnehmung der chemischen Prozesse in einzelnen Organellen mit niedermolekularen Fluoreszenzsonden. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201510721] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Wang Xu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 Volksrepublik China
- Department of Chemistry and Medicinal Chemistry Programme; National University of Singapore; Singapore 117543 Singapur
- Laboratory of Bioimaging Probe Development, A*STAR; Singapur
- Department of Chemistry; Stanford University; USA
| | - Zebing Zeng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 Volksrepublik China
| | - Jian-Hui Jiang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 Volksrepublik China
| | - Young-Tae Chang
- Department of Chemistry and Medicinal Chemistry Programme; National University of Singapore; Singapore 117543 Singapur
- Laboratory of Bioimaging Probe Development, A*STAR; Singapur
| | - Lin Yuan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 Volksrepublik China
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16
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Xu W, Zeng Z, Jiang JH, Chang YT, Yuan L. Discerning the Chemistry in Individual Organelles with Small-Molecule Fluorescent Probes. Angew Chem Int Ed Engl 2016; 55:13658-13699. [DOI: 10.1002/anie.201510721] [Citation(s) in RCA: 526] [Impact Index Per Article: 65.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Indexed: 12/22/2022]
Affiliation(s)
- Wang Xu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 P.R. China
- Department of Chemistry and Medicinal Chemistry Programme; National University of Singapore; Singapore 117543 Singapore
- Laboratory of Bioimaging Probe Development, A*STAR; Singapore
- Department of Chemistry; Stanford University; USA
| | - Zebing Zeng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 P.R. China
| | - Jian-Hui Jiang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 P.R. China
| | - Young-Tae Chang
- Department of Chemistry and Medicinal Chemistry Programme; National University of Singapore; Singapore 117543 Singapore
- Laboratory of Bioimaging Probe Development, A*STAR; Singapore
| | - Lin Yuan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 P.R. China
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17
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do Canto AMTM, Robalo JR, Santos PD, Carvalho AJP, Ramalho JPP, Loura LMS. Diphenylhexatriene membrane probes DPH and TMA-DPH: A comparative molecular dynamics simulation study. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2647-2661. [PMID: 27475296 DOI: 10.1016/j.bbamem.2016.07.013] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 07/05/2016] [Accepted: 07/25/2016] [Indexed: 10/21/2022]
Abstract
Fluorescence spectroscopy and microscopy have been utilized as tools in membrane biophysics for decades now. Because phospholipids are non-fluorescent, the use of extrinsic membrane probes in this context is commonplace. Among the latter, 1,6-diphenylhexatriene (DPH) and its trimethylammonium derivative (TMA-DPH) have been extensively used. It is widely believed that, owing to its additional charged group, TMA-DPH is anchored at the lipid/water interface and reports on a bilayer region that is distinct from that of the hydrophobic DPH. In this study, we employ atomistic MD simulations to characterize the behavior of DPH and TMA-DPH in 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and POPC/cholesterol (4:1) bilayers. We show that although the dynamics of TMA-DPH in these membranes is noticeably more hindered than that of DPH, the location of the average fluorophore of TMA-DPH is only ~3-4Å more shallow than that of DPH. The hindrance observed in the translational and rotational motions of TMA-DPH compared to DPH is mainly not due to significant differences in depth, but to the favorable electrostatic interactions of the former with electronegative lipid atoms instead. By revealing detailed insights on the behavior of these two probes, our results are useful both in the interpretation of past work and in the planning of future experiments using them as membrane reporters.
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Affiliation(s)
- António M T M do Canto
- Centro de Química de Évora e Departamento de Química, Escola de Ciências e Tecnologia, Colégio Luís Verney, Rua Romão Ramalho 59, P-7002-554 Évora, Portugal
| | - João R Robalo
- Centro de Química de Évora e Departamento de Química, Escola de Ciências e Tecnologia, Colégio Luís Verney, Rua Romão Ramalho 59, P-7002-554 Évora, Portugal; Theory and Bio-Systems Department, Max Planck Institute of Colloids and Interfaces, Wissenschaftspark Golm, D-14424 Potsdam, Germany
| | - Patrícia D Santos
- Centro de Química de Évora e Departamento de Química, Escola de Ciências e Tecnologia, Colégio Luís Verney, Rua Romão Ramalho 59, P-7002-554 Évora, Portugal
| | - Alfredo J Palace Carvalho
- Centro de Química de Évora e Departamento de Química, Escola de Ciências e Tecnologia, Colégio Luís Verney, Rua Romão Ramalho 59, P-7002-554 Évora, Portugal
| | - J P Prates Ramalho
- Centro de Química de Évora e Departamento de Química, Escola de Ciências e Tecnologia, Colégio Luís Verney, Rua Romão Ramalho 59, P-7002-554 Évora, Portugal
| | - Luís M S Loura
- Faculdade de Farmácia, Universidade de Coimbra, Pólo das Ciências da Saúde, Azinhaga de Santa Comba, P-3000-548 Coimbra, Portugal; Centro de Química de Coimbra, Largo D. Dinis, Rua Larga, P-3004-535 Coimbra, Portugal.
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18
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Kepczynski M, Róg T. Functionalized lipids and surfactants for specific applications. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2362-2379. [PMID: 26946243 DOI: 10.1016/j.bbamem.2016.02.038] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 02/23/2016] [Accepted: 02/25/2016] [Indexed: 12/17/2022]
Abstract
Synthetic lipids and surfactants that do not exist in biological systems have been used for the last few decades in both basic and applied science. The most notable applications for synthetic lipids and surfactants are drug delivery, gene transfection, as reporting molecules, and as support for structural lipid biology. In this review, we describe the potential of the synergistic combination of computational and experimental methodologies to study the behavior of synthetic lipids and surfactants embedded in lipid membranes and liposomes. We focused on select cases in which molecular dynamics simulations were used to complement experimental studies aiming to understand the structure and properties of new compounds at the atomistic level. We also describe cases in which molecular dynamics simulations were used to design new synthetic lipids and surfactants, as well as emerging fields for the application of these compounds. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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Affiliation(s)
- Mariusz Kepczynski
- Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Kraków, Poland.
| | - Tomasz Róg
- Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101, Tampere, Finland; Department of Physics, Helsinki University, P.O. Box 64, FI 00014 Helsinki, Finland.
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19
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Faller R. Molecular modeling of lipid probes and their influence on the membrane. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2353-2361. [PMID: 26891817 DOI: 10.1016/j.bbamem.2016.02.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Revised: 02/08/2016] [Accepted: 02/09/2016] [Indexed: 01/03/2023]
Abstract
In this review a number of Molecular Dynamics simulation studies are discussed which focus on the understanding of the behavior of lipid probes in biomembranes. Experiments often use specialized probe moieties or molecules to report on the behavior of a membrane and try to gain information on the membrane as a whole from the probe lipids as these probes are the only things an experiment sees. Probes can be used to make NMR, EPR and fluorescence accessible to the membrane and use fluorescent or spin-active moieties for this purpose. Clearly membranes with and without probes are not identical which makes it worthwhile to elucidate the differences between them with detailed atomistic simulations. In almost all cases these differences are confined to the local neighborhood of the probe molecules which are sparsely used and generally present as single molecules. In general, the behavior of the bulk membrane lipids can be qualitatively understood from the probes but in most cases their properties cannot be directly quantitatively deduced from the probe behavior. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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Affiliation(s)
- Roland Faller
- Department of Chemical Engineering & Materials Science, University of California-Davis, Davis, CA 95616, USA.
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20
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Karilainen T, Vuorela T, Vattulainen I. How Well Does BODIPY-Cholesteryl Ester Mimic Unlabeled Cholesteryl Esters in High Density Lipoprotein Particles? J Phys Chem B 2015; 119:15848-56. [DOI: 10.1021/acs.jpcb.5b10188] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Topi Karilainen
- Department
of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland
| | - Timo Vuorela
- Department
of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland
| | - Ilpo Vattulainen
- Department
of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland
- MEMPHYS-Center
for Biomembrane Physics, University of Southern Denmark, Odense, Denmark
- Department
of Physics, University of Helsinki, P.O. Box 43, FI-00014 Helsinki, Finland
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21
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Singh G, Chamberlin AC, Zhekova HR, Noskov SY, Tieleman DP. Two-Dimensional Potentials of Mean Force of Nile Red in Intact and Damaged Model Bilayers. Application to Calculations of Fluorescence Spectra. J Chem Theory Comput 2015; 12:364-71. [PMID: 26579726 DOI: 10.1021/acs.jctc.5b00520] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Fluorescent dyes revolutionized and expanded our understanding of biological membranes. The interpretation of experimental fluorescence data in terms of membrane structure, however, requires detailed information about the molecular environment of the dyes. Nile red is a fluorescent molecule whose excitation and emission maxima depend on the polarity of the solvent. It is mainly used as a probe to study lipid microenvironments, for example in imaging the progression of damage to the myelin sheath in multiple sclerosis. In this study, we determine the position and orientation of Nile red in lipid bilayers by calculating two-dimensional Potential of Mean Force (2D-PMF) profiles in a defect-free 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayer and in damaged bilayers containing two mixtures of the oxidized lipid 1-palmitoyl-2-(9'-oxo-nonanoyl)-sn-glycero-3-phosphocholine and POPC. From 2D-PMF simulations we obtain positions and orientations of Nile Red corresponding to the minimum on the binding free energy surface in three different membrane environments with increasing amounts of water, mimicking damage in biological tissue. Using representative snapshots from the simulations, we use combined quantum mechanical/molecular mechanical (QM/MM) models to calculate the emission spectrum of Nile red as a function of its local solvation environment. The results of QM and QM/MM computations are in qualitative agreement with the experimentally observed shift in fluorescence for the dye moving from aqueous solution to the more hydrophobic environment of the lipid interiors. The range of the conformation dependent values of the computed absorption-emission spectra and the lack of solvent relaxation effects in the QM/MM calculations made it challenging to delineate specific differences between the intact and damaged bilayers.
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Affiliation(s)
- Gurpreet Singh
- Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary , 2500 University Drive N.W., Calgary, Alberta T2N1N4, Canada
| | - Adam C Chamberlin
- Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary , 2500 University Drive N.W., Calgary, Alberta T2N1N4, Canada
| | - Hristina R Zhekova
- Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary , 2500 University Drive N.W., Calgary, Alberta T2N1N4, Canada
| | - Sergei Y Noskov
- Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary , 2500 University Drive N.W., Calgary, Alberta T2N1N4, Canada
| | - D Peter Tieleman
- Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary , 2500 University Drive N.W., Calgary, Alberta T2N1N4, Canada
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22
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do Canto AM, Santos PD, Martins J, Loura LM. Behavior of pyrene as a polarity probe in palmitoylsphingomyelin and palmitoylsphingomyelin/cholesterol bilayers: A molecular dynamics simulation study. Colloids Surf A Physicochem Eng Asp 2015. [DOI: 10.1016/j.colsurfa.2014.12.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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23
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Fernandes F, Coutinho A, Prieto M, Loura LMS. Electrostatically driven lipid-protein interaction: Answers from FRET. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:1837-48. [PMID: 25769805 DOI: 10.1016/j.bbamem.2015.02.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 02/23/2015] [Indexed: 12/13/2022]
Abstract
Electrostatics govern the association of a large number of proteins with cellular membranes. In some cases, these proteins present specialized lipid-binding modules or membrane targeting domains while in other cases association is achieved through nonspecific interaction of unstructured clusters of basic residues with negatively charged lipids. Given its spatial resolution in the nanometer range, Förster resonance energy transfer (FRET) is a powerful tool to give insight into protein-lipid interactions and provide molecular level information which is difficult to retrieve with other spectroscopic techniques. In this review we present and discuss the basic formalisms of both hetero- and homo-FRET pertinent to the most commonly encountered problems in lipid-protein interaction studies and highlight some examples of implementations of different FRET methodologies to characterize lipid/protein systems in which electrostatic interactions play a crucial role. This article is part of a Special Issue entitled: Lipid-protein interactions.
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Affiliation(s)
- Fábio Fernandes
- Centro de Química-Física Molecular and Institute of Nanoscience and Nanotechnology, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Ana Coutinho
- Centro de Química-Física Molecular and Institute of Nanoscience and Nanotechnology, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal; Dep. Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Manuel Prieto
- Centro de Química-Física Molecular and Institute of Nanoscience and Nanotechnology, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Luís M S Loura
- Faculdade de Farmácia, Universidade de Coimbra, Pólo das Ciências da Saúde, Azinhaga de Santa Comba, 3000-548 Coimbra, Portugal; Centro de Química de Coimbra, Largo D. Dinis, Rua Larga, 3004-535 Coimbra, Portugal.
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24
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Kreder R, Oncul S, Kucherak OA, Pyrshev KA, Real E, Mély Y, Klymchenko AS. Blue fluorogenic probes for cell plasma membranes fill the gap in multicolour imaging. RSC Adv 2015. [DOI: 10.1039/c4ra16225k] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Newly synthesized blue membrane probes, due to high brightness, large Stokes shift and fluorogenic response, overcome the problem of cell auto-fluorescence and enable multicolor cellular imaging with common green and red markers.
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Affiliation(s)
- Rémy Kreder
- Laboratoire de Biophotonique et Pharmacologie UMR 7213 CNRS/Université de Strasbourg
- Illkirch
- France
| | - Sule Oncul
- Laboratoire de Biophotonique et Pharmacologie UMR 7213 CNRS/Université de Strasbourg
- Illkirch
- France
- Istanbul Medeniyet University
- School of Medicine
| | - Oleksandr A. Kucherak
- Laboratoire de Biophotonique et Pharmacologie UMR 7213 CNRS/Université de Strasbourg
- Illkirch
- France
| | - Kyrylo A. Pyrshev
- Laboratoire de Biophotonique et Pharmacologie UMR 7213 CNRS/Université de Strasbourg
- Illkirch
- France
- Laboratory of Nanobiotechnologies
- Department of Molecular immunology
| | - Eleonore Real
- Laboratoire de Biophotonique et Pharmacologie UMR 7213 CNRS/Université de Strasbourg
- Illkirch
- France
| | - Yves Mély
- Laboratoire de Biophotonique et Pharmacologie UMR 7213 CNRS/Université de Strasbourg
- Illkirch
- France
| | - Andrey S. Klymchenko
- Laboratoire de Biophotonique et Pharmacologie UMR 7213 CNRS/Université de Strasbourg
- Illkirch
- France
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25
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Filipe HAL, Santos LS, Prates Ramalho JP, Moreno MJ, Loura LMS. Behaviour of NBD-head group labelled phosphatidylethanolamines in POPC bilayers: a molecular dynamics study. Phys Chem Chem Phys 2015; 17:20066-79. [DOI: 10.1039/c5cp01596k] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An NBD-diC16PE/POPC bilayer with typical fluorophore inverted-snorkelling configurations, and mass density profiles across the membrane. The wide distribution of the NBD fluorophore lies at the origin of its complex emission kinetics.
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Affiliation(s)
- Hugo A. L. Filipe
- Departamento de Química
- Faculty of Science and Technnology
- University of Coimbra
- Rua Larga
- Portugal
| | - Lennon S. Santos
- Departamento de Química
- Faculty of Science and Technnology
- University of Coimbra
- Rua Larga
- Portugal
| | - J. P. Prates Ramalho
- Departamento de Química
- Escola de Ciências e Tecnologia
- Universidade de Évora
- Rua Romão Ramalho
- Portugal
| | - Maria João Moreno
- Departamento de Química
- Faculty of Science and Technnology
- University of Coimbra
- Rua Larga
- Portugal
| | - Luís M. S. Loura
- Centro de Química de Coimbra
- Rua Larga
- Portugal
- Centro de Neurociências e Biologia Celular
- Universidade de Coimbra
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26
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Róg T, Vattulainen I. Cholesterol, sphingolipids, and glycolipids: what do we know about their role in raft-like membranes? Chem Phys Lipids 2014; 184:82-104. [PMID: 25444976 DOI: 10.1016/j.chemphyslip.2014.10.004] [Citation(s) in RCA: 140] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2014] [Revised: 10/24/2014] [Accepted: 10/25/2014] [Indexed: 12/14/2022]
Abstract
Lipids rafts are considered to be functional nanoscale membrane domains enriched in cholesterol and sphingolipids, characteristic in particular of the external leaflet of cell membranes. Lipids, together with membrane-associated proteins, are therefore considered to form nanoscale units with potential specific functions. Although the understanding of the structure of rafts in living cells is quite limited, the possible functions of rafts are widely discussed in the literature, highlighting their importance in cellular functions. In this review, we discuss the understanding of rafts that has emerged based on recent atomistic and coarse-grained molecular dynamics simulation studies on the key lipid raft components, which include cholesterol, sphingolipids, glycolipids, and the proteins interacting with these classes of lipids. The simulation results are compared to experiments when possible.
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Affiliation(s)
- Tomasz Róg
- Department of Physics, Tampere University of Technology, Tampere, Finland
| | - Ilpo Vattulainen
- Department of Physics, Tampere University of Technology, Tampere, Finland; MEMPHYS-Center for Biomembrane Physics, University of Southern Denmark, Odense, Denmark.
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27
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Calibration of Distribution Analysis of the Depth of Membrane Penetration Using Simulations and Depth-Dependent Fluorescence Quenching. J Membr Biol 2014; 248:583-94. [PMID: 25107303 DOI: 10.1007/s00232-014-9709-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 07/15/2014] [Indexed: 10/24/2022]
Abstract
Determination of the depth of membrane penetration provides important information for studies of membrane protein folding and protein-lipid interactions. Here, we use a combination of molecular dynamics (MD) simulations and depth-dependent fluorescence quenching to calibrate the methodology for extracting quantitative information on membrane penetration. In order to investigate the immersion depth of the fluorescent label in lipid bilayer, we studied 7-nitrobenz-2-oxa-1,3-diazole (NBD) attached to the lipid headgroup in NBD-PE incorporated into POPC bilayer. The immersion depth of NBD was estimated by measuring steady-state and time-resolved fluorescence quenching with spin-labeled lipids co-incorporated into lipid vesicles. Six different spin-labeled lipids were utilized: one with headgroup-attached Tempo probe (Tempo-PC) and five with acyl chain-labeled n-Doxyl moieties (n-Doxyl-PC where n is a chain labeling position equal to 5, 7, 10, 12, and 14, respectively). The Stern-Volmer analysis revealed that NBD quenching in membranes occurs by both static and dynamic collisional quenching processes. Using the methodology of Distribution Analysis, the immersion depth and the apparent half-width of the transversal distributions of the NBD moiety were estimated to be 14.7 and 6.7 Å, respectively, from the bilayer center. This position is independently validated by atomistic MD simulations of NBD-PE lipids in a POPC bilayer (14.4 Å). In addition, we demonstrate that MD simulations of the transverse overlap integrals between dye and quencher distributions can be used for proper analysis of the depth-dependent quenching profile. Finally, we illustrate the application of this methodology by determining membrane penetration of site selectively labeled mutants of diphtheria toxin T-domain.
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The challenges of understanding glycolipid functions: An open outlook based on molecular simulations. Biochim Biophys Acta Mol Cell Biol Lipids 2014; 1841:1130-45. [DOI: 10.1016/j.bbalip.2013.12.016] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 12/29/2013] [Accepted: 12/30/2013] [Indexed: 11/20/2022]
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Suárez-Germà C, Hernández-Borrell J, Prieto M, Loura LMS. Modeling FRET to investigate the selectivity of lactose permease ofEscherichia colifor lipids. Mol Membr Biol 2014; 31:120-30. [DOI: 10.3109/09687688.2014.915351] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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30
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Yalcin S, Thomas L, Tian M, Seferoglu N, Ihmels H, Dede Y. Switching Off the Charge Transfer and Closing the S1–T1 ISC Channel in Excited States of Quinolizinium Derivatives: A Theoretical Study. J Org Chem 2014; 79:3799-808. [DOI: 10.1021/jo402756y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Soydan Yalcin
- Department
of Chemistry, Faculty of Science, Gazi University, Teknikokullar, Ankara 06500, Turkey
| | - Laura Thomas
- Organische
Chemie II, Universität Siegen, Adolf-Reichwein-Straße 2, 57068 Siegen, Germany
| | - Maoqun Tian
- Organische
Chemie II, Universität Siegen, Adolf-Reichwein-Straße 2, 57068 Siegen, Germany
| | - Nurgul Seferoglu
- Graduate
School of Natural and Applied Sciences, Advanced Technologies, Gazi University, Ankara 06500, Turkey
| | - Heiko Ihmels
- Organische
Chemie II, Universität Siegen, Adolf-Reichwein-Straße 2, 57068 Siegen, Germany
| | - Yavuz Dede
- Department
of Chemistry, Faculty of Science, Gazi University, Teknikokullar, Ankara 06500, Turkey
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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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Fraňová MD, Repáková J, Holopainen JM, Vattulainen I. How to link pyrene to its host lipid to minimize the extent of membrane perturbations and to optimize pyrene dimer formation. Chem Phys Lipids 2014; 177:19-25. [DOI: 10.1016/j.chemphyslip.2013.10.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Revised: 10/08/2013] [Accepted: 10/11/2013] [Indexed: 11/30/2022]
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33
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Hurjui I, Neamtu A, Dorohoi DO. Computational and spectral studies of 1,6-diphenyl-1,3,5-hexatriene (DPH) multicomponent solutions. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 115:382-387. [PMID: 23867641 DOI: 10.1016/j.saa.2013.06.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Revised: 06/03/2013] [Accepted: 06/05/2013] [Indexed: 06/02/2023]
Abstract
The multicomponent 1,6-diphenyl-1,3,5-hexatriene+tetrahydrofuran+water+ethanol (DPH+THF+W+E) solutions with variable content in water were studied by computational and spectral means. The computational results that indicate micelle formation in multicomponent solutions at high water content were correlated by the independence of the wavenumber in the maximum of the fluorescence on the solvent composition.
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Affiliation(s)
- Ion Hurjui
- Biophysical and Medical Physics Dept., Faculty of Medicine, Gr. T. Popa University, 16 University Street, Iasi 700115, Romania
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Robalo JR, Ramalho JPP, Loura LMS. NBD-Labeled Cholesterol Analogues in Phospholipid Bilayers: Insights from Molecular Dynamics. J Phys Chem B 2013; 117:13731-42. [DOI: 10.1021/jp406135a] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- João R. Robalo
- Departamento
de Química, Escola de Ciências e Tecnologia, Universidade de Évora, Rua Romão Ramalho, 59, 7000-671 Évora, Portugal
- Centro
de Química de Évora, Universidade de Évora, Rua
Romão Ramalho, 59, 7000-671 Évora, Portugal
| | - J. P. Prates Ramalho
- Departamento
de Química, Escola de Ciências e Tecnologia, Universidade de Évora, Rua Romão Ramalho, 59, 7000-671 Évora, Portugal
- Centro
de Química de Évora, Universidade de Évora, Rua
Romão Ramalho, 59, 7000-671 Évora, Portugal
| | - Luís M. S. Loura
- Faculdade
de Farmácia, Universidade de Coimbra, Pólo das Ciências da Saúde, Azinhaga de Santa Comba, 3000-548 Coimbra, Portugal
- Centro
de Química de Coimbra, Largo D. Dinis, Rua Larga, 3004-535 Coimbra, Portugal
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35
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Xia Y, Peng L. Photoactivatable Lipid Probes for Studying Biomembranes by Photoaffinity Labeling. Chem Rev 2013; 113:7880-929. [DOI: 10.1021/cr300419p] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Yi Xia
- Aix-Marseille Université, Centre Interdisciplinaire de Nanoscience de Marseille, CNRS UMR 7325, Campus de Luminy, 13288 Marseille, France
| | - Ling Peng
- Aix-Marseille Université, Centre Interdisciplinaire de Nanoscience de Marseille, CNRS UMR 7325, Campus de Luminy, 13288 Marseille, France
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36
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Rabinovich AL, Lyubartsev AP. Computer simulation of lipid membranes: Methodology and achievements. POLYMER SCIENCE SERIES C 2013. [DOI: 10.1134/s1811238213070060] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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37
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Hurjui I, Neamtu A, Dorohoi DO. The interaction of fluorescent DPH probes with unsaturated phospholipid membranes: A molecular dynamics study. J Mol Struct 2013. [DOI: 10.1016/j.molstruc.2012.12.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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38
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Kyrychenko A, Ladokhin AS. Molecular dynamics simulations of depth distribution of spin-labeled phospholipids within lipid bilayer. J Phys Chem B 2013; 117:5875-85. [PMID: 23614631 DOI: 10.1021/jp4026706] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Spin-labeled lipids are commonly used as fluorescence quenchers in studies of membrane penetration of dye-labeled proteins and peptides using depth-dependent quenching. Accurate calculations of depth of the fluorophore rely on the use of several spin labels placed in the membrane at various positions. The depth of the quenchers (spin probes) has to be determined independently; however, experimental determination of transverse distributions of spin probe depths is difficult. In this Article, we use molecular dynamics (MD) simulations to study the membrane behavior and depth distributions of spin-labeled phospholipids in a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayer. To probe different depths within the bilayer, a series containing five Doxyl-labeled lipids (n-Doxyl PC) has been studied, in which a spin moiety was covalently attached to nth carbon atoms (where n = 5, 7, 10, 12, and 14) of the sn-2 stearoyl chain of the host phospholipid. Our results demonstrate that the chain-attached spin labels are broadly distributed across the model membrane and their environment is characterized by a high degree of mobility and structural heterogeneity. Despite the high thermal disorder, the depth distributions of the Doxyl labels were found to correlate well with their attachment positions, indicating that the distribution of the spin label within the model membrane is dictated by the depth of the nth lipid carbon atom and not by intrinsic properties of the label. In contrast, a much broader and heterogeneous distribution was observed for a headgroup-attached Tempo spin label of Tempo-PC lipids. MD simulations reveal that, due to the hydrophobic nature, a Tempo moiety favors partitioning from the headgroup region deeper into the membrane. Depending on the concentration of Tempo-PC lipids, the probable depth of the Tempo moiety could span a range from 14.4 to 18.2 Å from the membrane center. Comparison of the MD-estimated immersion depths of Tempo and n-Doxyl labels with their suggested experimental depth positions allows us to review critically the possible sources of error in depth-dependent fluorescence quenching studies.
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Affiliation(s)
- Alexander Kyrychenko
- Department of Biochemistry and Molecular Biology, Kansas University Medical Center, Kansas City, Kansas 66160-7421, USA.
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Robalo JR, do Canto AMTM, Carvalho AJP, Ramalho JPP, Loura LMS. Behavior of Fluorescent Cholesterol Analogues Dehydroergosterol and Cholestatrienol in Lipid Bilayers: A Molecular Dynamics Study. J Phys Chem B 2013; 117:5806-19. [DOI: 10.1021/jp312026u] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | | | | | - Luís M. S. Loura
- Faculdade de Farmácia, Universidade de Coimbra, Pólo das Ciências
da Saúde, Azinhaga de Santa Comba, 3000-548 Coimbra, Portugal
- Centro de Química de Coimbra, Largo D. Dinis, Rua Larga, 3004-535 Coimbra,
Portugal
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Kyrychenko A, Tobias DJ, Ladokhin AS. Validation of depth-dependent fluorescence quenching in membranes by molecular dynamics simulation of tryptophan octyl ester in POPC bilayer. J Phys Chem B 2013; 117:4770-8. [PMID: 23528135 PMCID: PMC3652981 DOI: 10.1021/jp310638f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Depth-dependent fluorescence quenching is an important tool for studying the penetration of proteins and peptides into lipid bilayers. Extracting quantitative information from quenching data is, however, complicated by (1) a limited number of experimentally available quenchers and (2) thermal disorder resulting in broad distributions of the transverse positions of both quenchers and fluorophores. Here we validate and refine a general approach to determining the location of a fluorescent probe along the bilayer normal from quenching data, based on a molecular dynamics (MD) simulation of a model compound, tryptophan octyl ester (TOE), in a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayer. The TOE ring was found to lie deeply within the bilayer (most probable position of 13.3 Å and center-of-weight of the distribution of 14.8 Å from the bilayer center), and it was very broadly distributed (with 9 Å depth distribution width), which is consistent with previous experimental observations. The depth-dependent quenching profiles were simulated by treating carbon atoms of the lipid acyl chain of POPC as "pseudo-quenchers" and calculating appropriate transverse overlaps and collision rates with indole atoms of TOE. These simulated quenching profiles were well fitted by a Gaussian function of depth, as is routinely done with experimental data subjected to the distribution analysis procedure [Methods Enzymol. 1997, 278, 462-473]. Comparison of the collisional pseudoquenching profiles with the actual profiles of the indole moiety of TOE allows for testing of the validity of the data analysis and identification of the possible sources of error in calculating depths of membrane penetration from quenching data.
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Affiliation(s)
- Alexander Kyrychenko
- Department of Biochemistry and Molecular Biology, Kansas University Medical Center, Kansas City, KS 66160-7421, U.S.A
| | - Douglas J. Tobias
- Department of Chemistry, University of California, Irvine, CA 92697-2025, U.S.A
| | - Alexey S. Ladokhin
- Department of Biochemistry and Molecular Biology, Kansas University Medical Center, Kansas City, KS 66160-7421, U.S.A
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41
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Sensing hydration and behavior of pyrene in POPC and POPC/cholesterol bilayers: A molecular dynamics study. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:1094-101. [DOI: 10.1016/j.bbamem.2012.12.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2012] [Revised: 12/12/2012] [Accepted: 12/18/2012] [Indexed: 01/24/2023]
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42
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FLIM studies of 22- and 25-NBD-cholesterol in living HEK293 cells: Plasma membrane change induced by cholesterol depletion. Chem Phys Lipids 2013; 167-168:62-9. [DOI: 10.1016/j.chemphyslip.2013.02.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 02/15/2013] [Accepted: 02/19/2013] [Indexed: 11/20/2022]
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Abstract
Fluorescence, the absorption and re-emission of photons with longer wavelengths, is one of those amazing phenomena of Nature. Its discovery and utilization had, and still has, a major impact on biological and biomedical research, since it enables researchers not just to visualize normal physiological processes with high temporal and spatial resolution, to detect multiple signals concomitantly, to track single molecules in vivo, to replace radioactive assays when possible, but also to shed light on many pathobiological processes underpinning disease states, which would otherwise not be possible. Compounds that exhibit fluorescence are commonly called fluorochromes or fluorophores and one of these fluorescent molecules in particular has significantly enabled life science research to gain new insights in virtually all its sub-disciplines: Green Fluorescent Protein. Because fluorescent proteins are synthesized in vivo, integration of fluorescent detection methods into the biological system via genetic techniques now became feasible. Currently fluorescent proteins are available that virtually span the whole electromagnetic spectrum. Concomitantly, fluorescence imaging techniques were developed, and often progress in one field fueled innovation in the other. Impressively, the properties of fluorescence were utilized to develop new assays and imaging modalities, ranging from energy transfer to image molecular interactions to imaging beyond the diffraction limit with super-resolution microscopy. Here, an overview is provided of recent developments in both fluorescence imaging and fluorochrome engineering, which together constitute the “fluorescence toolbox” in life science research.
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Simple estimation of Förster Resonance Energy Transfer (FRET) orientation factor distribution in membranes. Int J Mol Sci 2012. [PMID: 23203123 PMCID: PMC3509639 DOI: 10.3390/ijms131115252] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Because of its acute sensitivity to distance in the nanometer scale, Förster resonance energy transfer (FRET) has found a large variety of applications in many fields of chemistry, physics, and biology. One important issue regarding the correct usage of FRET is its dependence on the donor-acceptor relative orientation, expressed as the orientation factor κ2. Different donor/acceptor conformations can lead to κ2 values in the 0 ≤ κ2 ≤ 4 range. Because the characteristic distance for FRET, R0, is proportional to (κ2)1/6, uncertainties in the orientation factor are reflected in the quality of information that can be retrieved from a FRET experiment. In most cases, the average value of κ2 corresponding to the dynamic isotropic limit (<κ2> = 2/3) is used for computation of R0 and hence donor-acceptor distances and acceptor concentrations. However, this can lead to significant error in unfavorable cases. This issue is more critical in membrane systems, because of their intrinsically anisotropic nature and their reduced fluidity in comparison to most common solvents. Here, a simple numerical simulation method for estimation of the probability density function of κ2 for membrane-embedded donor and acceptor fluorophores in the dynamic regime is presented. In the simplest form, the proposed procedure uses as input the most probable orientations of the donor and acceptor transition dipoles, obtained by experimental (including linear dichroism) or theoretical (such as molecular dynamics simulation) techniques. Optionally, information about the widths of the donor and/or acceptor angular distributions may be incorporated. The methodology is illustrated for special limiting cases and common membrane FRET pairs.
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Loura LMS. Lateral distribution of NBD-PC fluorescent lipid analogs in membranes probed by molecular dynamics-assisted analysis of Förster Resonance Energy Transfer (FRET) and fluorescence quenching. Int J Mol Sci 2012; 13:14545-64. [PMID: 23203080 PMCID: PMC3509596 DOI: 10.3390/ijms131114545] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Revised: 10/29/2012] [Accepted: 11/01/2012] [Indexed: 01/19/2023] Open
Abstract
Förster resonance energy transfer (FRET) is a powerful tool used for many problems in membrane biophysics, including characterization of the lateral distribution of lipid components and other species of interest. However, quantitative analysis of FRET data with a topological model requires adequate choices for the values of several input parameters, some of which are difficult to obtain experimentally in an independent manner. For this purpose, atomistic molecular dynamics (MD) simulations can be potentially useful as they provide direct detailed information on transverse probe localization, relative probe orientation, and membrane surface area, all of which are required for analysis of FRET data. This is illustrated here for the FRET pairs involving 1,6-diphenylhexatriene (DPH) as donor and either 1-palmitoyl,2-(6-[N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)amino] hexanoyl)- sn-glycero-3-phosphocholine (C6-NBD-PC) or 1-palmitoyl,2-(12-[N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)amino]dodecanoyl)-sn-glycero-3-phosphocholine (C12-NBD-PC) as acceptors, in fluid vesicles of 1,2-dipalmitoyl-sn-3-glycerophosphocholine (DPPC, 50 °C). Incorporation of results from MD simulations improves the statistical quality of model fitting to the experimental FRET data. Furthermore, the decay of DPH in the presence of moderate amounts of C12-NBD-PC (>0.4 mol%) is consistent with non-random lateral distribution of the latter, at variance with C6-NBD-PC, for which aggregation is ruled out up to 2.5 mol% concentration. These conclusions are supported by analysis of NBD-PC fluorescence self-quenching. Implications regarding the relative utility of these probes in membrane studies are discussed.
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Affiliation(s)
- Luís M S Loura
- Faculty of Pharmacy, University of Coimbra, Health Sciences Campus, Azinhaga de Santa Comba, 3000-548 Coimbra, Portugal.
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46
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Reddy AS, Warshaviak DT, Chachisvilis M. Effect of membrane tension on the physical properties of DOPC lipid bilayer membrane. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1818:2271-81. [PMID: 22588133 DOI: 10.1016/j.bbamem.2012.05.006] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Revised: 05/03/2012] [Accepted: 05/07/2012] [Indexed: 01/15/2023]
Abstract
Molecular dynamics simulations of a dioleoylphosphocholine (DOPC) lipid bilayer were performed to explore its mechanosensitivity. Variations in the bilayer properties, such as area per lipid, volume, thickness, hydration depth (HD), hydration thickness (HT), lateral diffusion coefficient, and changes in lipid structural order were computed in the membrane tension range 0 to 15dyn/cm. We determined that an increase in membrane tension results in a decrease in the bilayer thickness and HD of ~5% and ~5.7% respectively, whereas area per lipid, volume, and HT/HD increased by 6.8%, 2.4%, and 5% respectively. The changes in lipid conformation and orientation were characterized using orientational (S(2)) and deuterium (S(CD)) order parameters. Upon increase of membrane tension both order parameters indicated an increase in lipid disorder by 10-20%, mostly in the tail end region of the hydrophobic chains. The effect of membrane tension on lipid lateral diffusion in the DOPC bilayer was analyzed on three different time scales corresponding to inertial motion, anomalous diffusion and normal diffusion. The results showed that lateral diffusion of lipid molecules is anomalous in nature due to the non-exponential distribution of waiting times. The anomalous and normal diffusion coefficients increased by 20% and 52% when the membrane tension changed from 0 to 15dyn/cm, respectively. In conclusion, our studies showed that membrane tension causes relatively significant changes in the area per lipid, volume, polarity, membrane thickness, and fluidity of the membrane suggesting multiple mechanisms by which mechanical perturbation of the membrane could trigger mechanosensitive response in cells.
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47
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In situ synthesis of fluorescent membrane lipids (ceramides) using click chemistry. J Chem Biol 2012; 5:119-23. [PMID: 23596500 DOI: 10.1007/s12154-012-0075-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Accepted: 04/03/2012] [Indexed: 01/08/2023] Open
Abstract
Ceramide analogues containing azide groups either in the polar head or in the hydrocarbon chains are non-fluorescent. When incorporated into phospholipid bilayers, they can react in situ with a non-fluorescent 1,8-naphthalimide using click chemistry giving rise to fluorescent ceramide derivatives emitting at ≈440 nm. When incorporated into giant unilamellar vesicles, two-photon excitation at 760 nm allows visualization of the ceramide-containing bilayers. This kind of method may be of general applicability in the study of model and cell membranes.
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48
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Loura LMS, Prieto M. Lateral Membrane Heterogeneity Probed by FRET Spectroscopy and Microscopy. SPRINGER SERIES ON FLUORESCENCE 2012. [DOI: 10.1007/4243_2012_59] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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