DOCSLIB.ORG

Baral Udel 0060D 143

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Baral Udel 0060D 143 QUANTITATIVE PREDICTION OF SPECTRAL PROPERTIES OF POLARITY SENSITIVE DYES USING A MD/QM APPROACH by Swapnil Baral A dissertation submitted to the Faculty of the University of Delaware in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Physics Summer 2020 © 2020 Swapnil Baral All Rights Reserved QUANTITATIVE PREDICTION OF SPECTRAL PROPERTIES OF POLARITY SENSITIVE DYES USING A MD/QM APPROACH by Swapnil Baral Approved: Edmund Nowak, Ph.D. Chair of the Department of Physics and Astronomy Approved: John Pelesko, Ph.D. Dean of the College of Arts and Sciences Approved: Douglas J. Doren, Ph.D. Interim Vice Provost for Graduate and Professional Education and Dean of the Graduate College I certify that I have read this dissertation and that in my opinion it meets the academic and professional standard required by the University as a dis- sertation for the degree of Doctor of Philosophy. Signed: Edward Lyman, Ph.D. Professor in charge of dissertation I certify that I have read this dissertation and that in my opinion it meets the academic and professional standard required by the University as a dis- sertation for the degree of Doctor of Philosophy. Signed: Björn Baumeier, Ph.D. Professor in charge of dissertation I certify that I have read this dissertation and that in my opinion it meets the academic and professional standard required by the University as a dis- sertation for the degree of Doctor of Philosophy. Signed: Sandeep Patel, Ph.D. Member of dissertation committee I certify that I have read this dissertation and that in my opinion it meets the academic and professional standard required by the University as a dis- sertation for the degree of Doctor of Philosophy. Signed: Lars Gundlach, Ph.D. Member of dissertation committee I certify that I have read this dissertation and that in my opinion it meets the academic and professional standard required by the University as a dis- sertation for the degree of Doctor of Philosophy. Signed: James MacDonald, Ph.D. Member of dissertation committee ACKNOWLEDGEMENTS I want to acknowledge the advice and support of many people and organiza- tions. This dissertation would not have been possible without my direct supervisor Dr. Edward R. Lyman, whose guidance and limitless patience have helped me de- velop professionally and become a critically thinking scientist. A huge thank you for mentoring and guiding me to complete this work. You have always encouraged me to focus on research and supported me to present my work at several conferences. I also want to thank all the group members (undergraduates, graduate students, and postdoctoral researchers) of our group (Lyman Group) from 2014 to 2020 for the engaging physics discussion on countless occasions. I want to thank Dr. Björn Baumeier (Eindhoven University of Technology (TU/e)), who taught me a lot about quantum mechanical calculations, especially the GW -BSE and its implementation in VOTCA-XTP. This work would not have been possible without the collaboration of Baumeier Research Group. I also thank you for generously covering a significant portion of my visit to TU/e. I want to express my gratitude towards Dr. Sandeep Patel for generously pro- viding about year-long financial support to me. You have also helped me understand the importance of Laurdan research and taught me how to get started with quantum calculations in Gaussian, especially during my early days in graduate school. I want to thank Dr. Lars Gundlach for raising profound discussions about my research and motivating me every time we met. Your group (Gundlach Group), v thorough our collaboration, has played a crucial role in testing the results of my calculations. I want to thank Dr. James MacDonald for supporting me throughout my stay at UD and agreeing to serve on my committee. You have been extremely helpful even before I joined UD during the application process. I want to thank Dr. Jeffrey R. Comer (Kansas State University) for helping me compute the Adaptive Biasing Force calculation and Dr. Alex MacKerell and Dr. Fang-Yu Lin (University of Maryland, Baltimore) for teaching me protocols of CHARMM Force Field parametrization. This work was supported by a National Institutes of Health grant NIH R01GM116961. Computations were performed on the Stampede supercomputer at the Texas Advanced Computing Center of the University of Texas at Austin (sup- ported through the XSEDE program of the NSF (TG-MCB170146)) which is sup- ported by National Science Foundation grant number ACI-1548562. I want to express my gratitude towards all the faculty, staff, and members in the Department of Physics and Astronomy (DPA) at the University of Delaware for continuously supporting me in times of need. Thanks to Physics and Astronomy Graduate Student Association for allowing me to serve as a vice-president (2015-2016), Graduate Student Government for al- lowing me to serve as a senator representing DPA (2016-2017), and Nepalese Student Association for allowing me to serve as the president (2017-2018). I want to thank all my teachers and mentors, from my first schools, River Valley and Pushpa Sadan Boarding High School, to the current school, the University of Delaware. I also want to remember the physics department at the National School of Sciences (Lainchaur, Kathmandu), the University of Texas at Arlington, and the Georgia Institute of Technology. vi I want to express my love to my mother, Dr. Sushma Banskota Baral, who was the first person to support me when I decided to study Physics in the United States. I want to thank my father, Dr. Krishnahari Baral, the hero of my life, for helping me pursue a career in Physics. I want to dedicate this work to both of you. I want to remember my siblings (Smriti Baral and Swikriti Baral), relatives, and friends who always stand by my side and continuously support me. I express my love to my wife, Aastha Dahal, for supporting me on my journey. Without your colorful smile, everything I achieve becomes colorless. vii TABLE OF CONTENTS LIST OF TABLES ::::::::::::::::::::::::::::::: xiii LIST OF FIGURES :::::::::::::::::::::::::::::: xv ABSTRACT :::::::::::::::::::::::::::::::::: xxii Chapter 1 BILAYERS AND CELL MEMBRANES: COMPOSITION, PHASES, AND PACKING ::::::::::::::::::::::: 1 1.1 Introduction ::::::::::::::::::::::::::::::: 1 1.2 Basic lipid chemistry :::::::::::::::::::::::::: 3 1.2.1 Membrane heterogeneity and lipid phases :::::::::: 6 2 INTRODUCTION TO FLUORESCENCE :::::::::::::: 9 2.1 Introduction ::::::::::::::::::::::::::::::: 9 2.2 Jablonski Diagram ::::::::::::::::::::::::::: 9 2.3 Stokes Shift ::::::::::::::::::::::::::::::: 12 2.4 Quantum Yield and Lifetime :::::::::::::::::::::: 12 2.5 Solvent effects and Polarity Sensitive Dyes :::::::::::::: 13 2.5.1 Solvent relaxation ::::::::::::::::::::::: 13 3 SPECTRAL PROPERTIES OF PRODAN AND LAURDAN :: 16 3.1 Introduction ::::::::::::::::::::::::::::::: 16 3.2 Prodan Structure :::::::::::::::::::::::::::: 16 viii 3.3 Nature of Prodan Emitting State ::::::::::::::::::: 17 3.4 Prodan Dipole Moment :::::::::::::::::::::::: 20 3.5 Prodan Absorption and Emission Spectra in Bulk Solvents ::::: 26 4 THEORETICAL BACKGROUND :::::::::::::::::: 28 4.1 Introduction ::::::::::::::::::::::::::::::: 28 4.2 Many-electron quantum mechanics :::::::::::::::::: 29 4.3 Wave-function :::::::::::::::::::::::::::::: 30 4.4 Born-Oppenheimer approximation ::::::::::::::::::: 32 4.5 Classical molecular dynamics simulation ::::::::::::::: 34 4.5.1 Force-Fields and potential energy function :::::::::: 35 4.5.1.1 Bonded terms :::::::::::::::::::: 36 4.5.1.2 Nonbonded terms :::::::::::::::::: 36 4.5.1.2.1 Lennard-Jones :::::::::::::: 36 4.5.1.2.2 Electrostatics :::::::::::::: 37 4.6 Solving electronic Schrödinger equation :::::::::::::::: 38 4.7 Density Functional Theory ::::::::::::::::::::::: 42 4.7.1 Exchange-Correlation Functional ::::::::::::::: 45 4.7.2 Basis sets :::::::::::::::::::::::::::: 46 4.8 Electronic excitations :::::::::::::::::::::::::: 47 4.8.1 General information about excited state calculations :::: 48 4.9 Electronically excited states calculation using Many-body Green’s Function: GW -BSE ::::::::::::::::::::::::::: 51 4.9.1 One particle excitation ::::::::::::::::::::: 51 4.9.2 Two-particle excitations :::::::::::::::::::: 59 4.10 GW -BSE/MM ::::::::::::::::::::::::::::: 65 ix 5 CHARMM GENERAL FORCE FIELD PARTIAL CHARGE PARAMETRIZATION OF PRODAN/LAURDAN :::::::: 67 5.1 Introduction ::::::::::::::::::::::::::::::: 67 5.2 Method ::::::::::::::::::::::::::::::::: 67 5.2.1 Results ::::::::::::::::::::::::::::: 72 6 MOLECULAR DYNAMICS SIMULATION OF LAURDAN IN LIPID MEMBRANES :::::::::::::::::::::::::: 77 6.1 Introduction ::::::::::::::::::::::::::::::: 77 6.2 MD Simulation ::::::::::::::::::::::::::::: 78 6.3 Simulation Results ::::::::::::::::::::::::::: 79 6.4 Discussion :::::::::::::::::::::::::::::::: 84 7 MD/QM CALCULATION OF PRODAN IN BULK SOLVENTS 86 7.1 Background Information :::::::::::::::::::::::: 87 7.2 Theory :::::::::::::::::::::::::::::::::: 89 7.2.1 Quasi-Particle Excitation ::::::::::::::::::: 89 7.2.2 Coupled Electron-Hole Excitations :::::::::::::: 90 7.2.3 Electrostatic embedding :::::::::::::::::::: 92 7.2.4 Transition probability and oscillator strength :::::::: 92 7.3 MD/GW -BSE: Excited state calculation and Iterative solvent relaxation :::::::::::::::::::::::::::::::: 93 7.3.1 Preparing MD trajectory for QM calculation :::::::: 93 7.3.2 MD/GW -BSE iterative protocol ::::::::::::::: 94 7.4 Prodan MD/GW -BSE calculation in bulk solvents :::::::::: 95 7.4.1
Load more

Recommended publications
  • Influence of Cholesterol on Phospholipid Bilayers Phase Domains As Detected by Laurdan Fluorescence
    120 Biophysical Journal Volume 66 January 1994 120-132 Influence of Cholesterol on Phospholipid Bilayers Phase Domains as Detected by Laurdan Fluorescence Tiziana Parasassi,* Massimo Di Stefano,* Marianna Loiero,* Giampietro Ravagnan,* and Enrico Grattont *Istituto di Medicina Sperimentale, Consiglio Nazionale Ricerche, 00137 Rome, Italy, and tLaboratory for Fluorescence Dynamics, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA ABSTRACT Coexisting gel and liquid-crystalline phospholipid phase domains can be observed in synthetic phospholipid vesicles during the transition from one phase to the other and, in vesicles of mixed phospholipids, at intermediate temperatures between the transitions of the different phospholipids. The presence of cholesterol perturbs the dynamic properties of both phases to such an extent as to prevent the detection of coexisting phases. 6-Lauroyl-2-dimethylaminonaphthalene (Laurdan) fluorescence offers the unique advantage of well resolvable spectral parameters in the two phospholipid phases that can be used for the detection and quantitation of coexisting gel and liquid-crystalline domains. From Laurdan fluorescence excitation and emission spectra, the generalized polarization spectra and values were calculated. By the generalized polarization phos- pholipid phase domain coexistence can be detected, and each phase can be quantitated. In the same phospholipid vesicles where without cholesterol domain coexistence can be detected, above 15 mol % and, remarkably, at physiological cholesterol concentrations,
    [Show full text]
  • Disruption of Membrane Cholesterol Organization Impairs the Concerted Activity of PIEZO1 Channel Clusters
    bioRxiv preprint doi: https://doi.org/10.1101/604488; this version posted April 11, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Disruption of membrane cholesterol organization impairs the concerted activity of PIEZO1 channel clusters P. Ridone1,*, E. Pandzic2,*, M. Vassalli3, C. D. Cox1,5, A. Macmillan2, P.A. Gottlieb4 and B. Martinac1,5 1The Victor Chang Cardiac Research Institute, Lowy Packer Building, Darlinghurst, NSW 2010, Australia, 2Biomedical Imaging Facility (BMIF), Mark Wainwright Analytical Centre, Lowy Cancer Research Centre, The University of New South Wales, NSW, 2052, Australia , 3Institute of Biophysics, National Research Council, Genova, Italy , 4Physiology and Biophysics, State University of New York at Buffalo, Buffalo, NY, 14214, USA , 5St Vincent's Clinical School, University of New South Wales, Darlinghurst, NSW 2010, Australia *These authors have equally contributed to this work Corresponding author: Dr. Boris Martinac Victor Chang Cardiac Research Institute Lowy Packer Building Darlinghurst, NSW 2010, Australia E-mail [email protected] Key words: Mechanosensitive channel, Cholesterol, STORM, Patch-Clamp, Fluorescence Microscopy. SUMMARY: The essential mammalian mechanosensitive channel PIEZO1 organizes in the plasma membrane into nanometric clusters which depend on the integrity of cholesterol domains to rapidly detect applied force and especially inactivate syncronously, the most commonly altered feature of PIEZO1 in pathology. 1 bioRxiv preprint doi: https://doi.org/10.1101/604488; this version posted April 11, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved.
    [Show full text]
  • New Insights on the Fluorescent Emission Spectra of Prodan and Laurdan
    J Fluoresc (2015) 25:621–629 DOI 10.1007/s10895-015-1545-x ORIGINAL PAPER New Insights on the Fluorescent Emission Spectra of Prodan and Laurdan Cíntia C. Vequi-Suplicy & Kaline Coutinho & M. Teresa Lamy Received: 12 December 2014 /Accepted: 23 February 2015 /Published online: 10 March 2015 # Springer Science+Business Media New York 2015 Abstract Prodan and Laurdan are fluorescent probes largely Introduction used in biological systems. They were synthetized to be sen- sitive to the environment polarity, and their fluorescent emis- The fluorescent probes Prodan (2-dimethylamino-6- sion spectrum shifts around 120 nm, from cyclohexane to propionylnaphthalene) and Laurdan (2-dimethylamino-6- water. Although accepted that their emission spectrum is com- dodecanoylnaphthalene) have been widely used in biological posed by two emission bands, the origin of these two bands is relevant systems [1–7]. They were synthetized [1]tobesen- still a matter of discussion. Here we analyze the fluorescent sitive to the environment polarity, so their emission spectra spectra of Prodan and Laurdan in solvents of different polar- shifts about 120 nm from cyclohexane to water [1, 8, 9]. ities, both by decomposing the spectrum into two Gaussian Moreover, when inserted into membranes, their emission bands and by computing the Decay Associated Spectra spectra is extremely dependent on the lipid bilayer phase (DAS), the latter with time resolved fluorescence. Our data (gel or fluid), the maximum of the spectrum shifting around show that the intensity of the lower energy emission band of 50 nm from one phase to the other [4, 6, 10]. Prodan and Laurdan (attributed, in the literature, to the decay Although Prodan and Laurdan have been extensively used, of a solvent relaxed state) is higher in cyclohexane than in their structure and electronic distribution, in different solvents, water, showing a decrease as the polarity of the medium in- are still a matter of discussion [11–13].
    [Show full text]
  • Biomimetic Curvature and Tension-Driven Membrane
    1 Biomimetic curvature and tension-driven membrane 2 fusion induced by silica nanoparticles 3 4 Marcos Arribas Perez1 and Paul A. Beales1,2,* 5 6 1 Astbury Centre for Structural Molecular Biology and School of Chemistry, University of Leeds, 7 Leeds, LS2 9JT, UK. 8 2 Bragg Centre for Materials Research, University of Leeds, Leeds, LS2 9JT, UK. 9 10 * Correspondence: [email protected] 11 12 1 13 Abstract 14 Membrane fusion is a key process to develop new technologies in synthetic biology, where 15 artificial cells function as biomimetic chemical microreactors. Fusion events in living cells are 16 intricate phenomena that require the coordinate action of multicomponent protein complexes. 17 However, simpler synthetic tools to control membrane fusion in artificial cells are highly desirable. 18 Native membrane fusion machinery mediates fusion driving a delicate balance of membrane 19 curvature and tension between two closely apposed membranes. Here we show that silica 20 nanoparticles (SiO2 NPs) at a size close to the cross-over between tension-driven and curvature- 21 driven interaction regimes initiate efficient fusion of biomimetic model membranes. Fusion 22 efficiency and mechanisms are studied by Förster Resonance Energy Transfer (FRET) and 23 confocal fluorescence microscopy. SiO2 NPs induce a slight increase in lipid packing likely to 24 increase the lateral tension of the membrane. We observe a connection between membrane 25 tension and fusion efficiency. Finally, real-time confocal fluorescence microscopy reveals three 26 distinct mechanistic pathways for membrane fusion. SiO2 NPs show significant potential for 27 inclusion in the synthetic biology toolkit for membrane remodelling and fusion in artificial cells.
    [Show full text]
  • Laurdan Fluorescence Lifetime Discriminates Cholesterol Content from Changes in Fluidity in Living Cell Membranes
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector 1238 Biophysical Journal Volume 104 March 2013 1238–1247 Laurdan Fluorescence Lifetime Discriminates Cholesterol Content from Changes in Fluidity in Living Cell Membranes Ottavia Golfetto, Elizabeth Hinde, and Enrico Gratton* Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California ABSTRACT Detection of the fluorescent properties of Laurdan has been proven to be an efficient tool to investigate membrane packing and ordered lipid phases in model membranes and living cells. Traditionally the spectral shift of Laurdan’s emission from blue in the ordered lipid phase of the membrane (more rigid) toward green in the disordered lipid phase (more fluid) is quantified by the generalized polarization function. Here, we investigate the fluorescence lifetime of Laurdan at two different emission wavelengths and find that when the dipolar relaxation of Laurdan’s emission is spectrally isolated, analysis of the fluorescence decay can distinguish changes in membrane fluidity from changes in cholesterol content. Using the phasor representation to analyze changes in Laurdan’s fluorescence lifetime we obtain two different phasor trajectories for changes in polarity versus changes in cholesterol content. This gives us the ability to resolve in vivo membranes with different properties such as water content and cholesterol content and thus perform a more comprehensive analysis of cell membrane heterogeneity. We demon- strate this analysis in NIH3T3 cells using Laurdan as a biosensor to monitor changes in the membrane water content during cell migration. INTRODUCTION From the biological perspective, cell membranes influence that provide guidelines for understanding the complexity of many cell functions and are involved in most of the cellular cellular membranes.
    [Show full text]
  • Download Product Insert (PDF)
    PRODUCT INFORMATION Laurdan Item No. 19706 CAS Registry No.: 74515-25-6 Formal Name: 1-[6-(dimethylamino)-2-naphthalenyl]- O 1-dodecanone MF: C24H35NO FW: 353.5 Purity: ≥98% N UV/Vis.: λmax: 230, 250, 259, 284, 362 nm Supplied as: A crystalline solid Storage: -20°C Stability: ≥2 years Information represents the product specifications. Batch specific analytical results are provided on each certificate of analysis. Laboratory Procedures Laurdan is supplied as a crystalline solid. A stock solution may be made by dissolving the laurdan in the solvent of choice, which should be purged with an inert gas. Laurdan is soluble in the organic solvent chloroform at a concentration of approximately 10 mg/ml. Description Laurdan is a membrane-permeable fluorescent probe that displays spectral sensitivity to the phospholipid phase of the cell membrane to which it is bound.1 Quantitation of generalized polarization (GP) of laurdan can be used to identify phospholipid phase. When excited at 340 nm, GP values are 0.6 and -0.2 for gel phase and liquid crystalline phase, respectively. GP does not change with polar head group or pH (in the range 4-10); it changes only with phase state. Reference 1. Parasassi, T., De Stasio, G., Ravagnan, G., et al. Quantitation of lipid phases in phospholipid vesicles by the generalized polarization of Laurdan fluorescence. Biophys. J. 60(1), 179-189 (1991). WARNING CAYMAN CHEMICAL THIS PRODUCT IS FOR RESEARCH ONLY - NOT FOR HUMAN OR VETERINARY DIAGNOSTIC OR THERAPEUTIC USE. 1180 EAST ELLSWORTH RD SAFETY DATA ANN ARBOR, MI 48108 · USA This material should be considered hazardous until further information becomes available.
    [Show full text]
  • Laurdan Identifies Different Lipid Membranes in Eukaryotic Cells
    UC Irvine UC Irvine Previously Published Works Title Laurdan identifies different lipid membranes in eukaryotic cells Permalink https://escholarship.org/uc/item/9m80z238 ISBN 9781482209891 Authors Gratton, E Digman, MA Publication Date 2014 DOI 10.1201/b17634 License https://creativecommons.org/licenses/by/4.0/ 4.0 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Laurdan Identifies 13 Different Lipid Membranes in Eukaryotic Cells Enrico Gratton and Michelle A. Digman CONTENTS 13.1 Introduction ..................................................................................................283 13.1.1 Spectroscopic Properties of Laurdan................................................283 13.2 The Phasor Approach to Spectral and Lifetime Analysis ............................287 13.3 The Lifetime Phasor Transformation and Its Interpretation .........................289 13.4 Results of the Analysis of the Emission of Laurdan Using Spectral and Lifetime Phasors in GUVs Model Systems .................................................. 291 13.5 The Lifetime Phasor for Laurdan in GUVs ..................................................292 13.6 Live Cell Membrane Fluidity .......................................................................295 13.6.1 Spectral Phasors................................................................................295 13.6.2 Lifetime Phasors in Live 3T3 Cells ..................................................297 13.7 Conclusions and Further Considerations ......................................................299
    [Show full text]
  • UC Irvine UC Irvine Previously Published Works
    UC Irvine UC Irvine Previously Published Works Title Water dynamics in glycosphingolipid aggregates studied by LAURDAN fluorescence. Permalink https://escholarship.org/uc/item/2601m9d4 Journal Biophysical journal, 75(1) ISSN 0006-3495 Authors Bagatolli, LA Gratton, E Fidelio, GD Publication Date 1998-07-01 DOI 10.1016/s0006-3495(98)77517-4 License https://creativecommons.org/licenses/by/4.0/ 4.0 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Biophysical Journal Volume 75 July 1998 331–341 331 Water Dynamics in Glycosphingolipid Aggregates Studied by LAURDAN Fluorescence L. A. Bagatolli,*# E. Gratton,# and G. D. Fidelio* *Departamento de Quı´mica Biolo´ gica-CIQUIBIC, Facultad de Ciencias Quı´micas, Universidad Nacional de Co´ rdoba, Argentina and #Laboratory for Fluorescence Dynamics, University of Illinois at Urbana-Champaign, Urbana, Illinois USA ABSTRACT We have characterized the fluorescence properties of 6-dodecanoyl-2-dimethylamine-naphthalene (LAURDAN) in pure interfaces formed by sphingomyelin and 10 chemically related glycosphingolipids (GSLs).1 The GSLs contain neutral and anionic carbohydrate residues in their oligosaccharide chain. These systems were studied at temperatures below, at, or above the main phase transition temperature of the pure lipid aggregates. The extent of solvent dipolar relaxation around the excited fluorescence probe in the GSLs series increases with the magnitude of the glycosphingolipid polar headgroup below the transition temperature. This conclusion is based on LAURDAN’s excitation generalized polarization (GPex) and fluores- cence lifetime values found in the different interfaces. A linear dependence between the LAURDAN GPex and the intermo- lecular spacing among the lipid molecules was found for both neutral and anionic lipids in the GSLs series.
    [Show full text]
  • Naphthalene with Lipid Environments
    Photochemistry and Photobiology, 1999, 70(4): 557-564 A Model for the Interaction of 6-Lauroyl-2-(N,Ak dimethy1amino)naphthalenewith Lipid Environments: Implications for Spectral Properties Luis A. Bagatolliin2*,Tiziana Parasassi3,Gerard0 D. Fidelio2and Enrico Gratton’ ’Laboratory for Fluorescence Dynamics, University of Illinois at Urbana-Champaign, Urbana, IL, USA; *Departamento de Quimica Biol6gica-CIQUIBIC, Facultad de Ciencias Quimicas, Universidad Nacional de C6rdoba, Argentina and 31stituto di Medicina Sperimentale, CNR, Roma, Italy Received 27 January 1999; accepted 24 June 1999 ABSTRACT to proteins and associated with lipids (1-3). This family of probes includes 6-propionyl-2-(N,N-dimethylamino) Although 6-lauroyl-2-(N,N-dimethylamino)naphthalene naphthalene (PRODAN),? 6-lauroyl-2-(N,N-dimethylamino) (LAURDAN) is now widely used a probe for lipid sys- as naphthalene (LAURDAN) and 2’-(N,N-dimethylamino)-6- tems, most studies focus on the effect of the lipid envi- naphthoyl-4-trans-cyclohexanoic acid (DANCA) (Fig. 1). ronment on its emission properties but not on the exci- These probes all possess large excited-state dipoles. In polar tation properties. The present study is intended to inves- solvents, and when the molecular dynamics of solvent di- tigate the excitation properties of LAURDAN in diverse poles occur on the time scale of the probe’s fluorescence lipid environments. To this end, the fluorescence prop- lifetime, a reorientation of solvent dipoles around the probe erties of LAURDAN were studied in synthetic ester and excited-state dipole may occur. The energy required for this ether phosphatidylcholines and sphingomyelin vesicles reorientation results in a red shift of the fluorescence emis- below, at and above the corresponding lipid main phase- sion spectrum.
    [Show full text]
  • Evolutionarily Conserved Long-Chain Acyl- Coa Synthetases Regulate Membrane Composition and Fluidity
    RESEARCH ARTICLE Evolutionarily conserved long-chain Acyl- CoA synthetases regulate membrane composition and fluidity Mario Ruiz1†, Rakesh Bodhicharla1†, Marcus Sta˚ hlman2, Emma Svensk1, Kiran Busayavalasa1, Henrik Palmgren3, Hanna Ruhanen4,5, Jan Boren2, Marc Pilon1* 1Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden; 2Department of Molecular and Clinical Medicine/Wallenberg Laboratory, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden; 3Metabolism BioScience, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden; 4Helsinki University Lipidomics Unit, Helsinki Institute for Life Science, Helsinki, Finland; 5Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland Abstract The human AdipoR1 and AdipoR2 proteins, as well as their C. elegans homolog PAQR- 2, protect against cell membrane rigidification by exogenous saturated fatty acids by regulating phospholipid composition. Here, we show that mutations in the C. elegans gene acs-13 help to suppress the phenotypes of paqr-2 mutant worms, including their characteristic membrane fluidity defects. acs-13 encodes a homolog of the human acyl-CoA synthetase ACSL1, and localizes to the mitochondrial membrane where it likely activates long chains fatty acids for import and *For correspondence: degradation. Using siRNA combined with lipidomics and membrane fluidity assays (FRAP and [email protected] Laurdan dye staining) we further show that the human ACSL1 potentiates lipotoxicity by the †These authors contributed saturated fatty acid palmitate: silencing ACSL1 protects against the membrane rigidifying effects of equally to this work palmitate and acts as a suppressor of AdipoR2 knockdown, thus echoing the C. elegans findings. Competing interest: See We conclude that acs-13 mutations in C.
    [Show full text]
  • Molecular Dynamics Simulations of Lipid Membranes
    MOLECULAR DYNAMICS SIMULATIONS OF LIPID MEMBRANES: THE EFFECTS OF PROBES, LIPID COMPOSITION AND PEPTIDES A Dissertation Presented to the Faculty of the Graduate School of Cornell University In Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy by David Geoffrey Ackerman August 2015 © 2015 David Geoffrey Ackerman MOLECULAR DYNAMICS SIMULATIONS OF LIPID MEMBRANES: THE EFFECTS OF PROBES, LIPID COMPOSITION AND PEPTIDES David Geoffrey Ackerman, Ph.D. Cornell University 2015 The cell plasma membrane is comprised of hundreds of different lipid species as well as a variety of integral and peripheral proteins. The diversity of molecular constituents leads to the formation of functional lateral heterogeneities within the plane of the membrane, known as lipid rafts, which are distinct from the surrounding membrane. Given the complexity of the plasma membrane, and the importance of rafts in the life of a cell, simplified model mixtures capturing the characteristics of the plasma membrane have been essential for unraveling its underlying behavior. In this work, we use molecular dynamics simulations to study model membranes at resolutions not possible with experimental techniques. We first investigated a fundamental assumption in model membrane experiments: that extrinsic probes added to the membrane do not disrupt membrane behavior. We addressed this issue by simulating single component model membranes that contained commonly used fluorescent lipid analogs. We found that the probes are able to disorder the bilayer and reorient lipid headgroups due to the probes’ large, positively charged headgroups and long, interdigitating acyl chains. Importantly though, these effects die off within a couple of nanometers of the probe.
    [Show full text]
  • Alterations in the Properties of the Cell Membrane Due to Glycosphingolipid
    www.nature.com/scientificreports OPEN Alterations in the properties of the cell membrane due to glycosphingolipid accumulation in a Received: 3 October 2017 Accepted: 11 December 2017 model of Gaucher disease Published: xx xx xxxx Gyula Batta1,2, Lilla Soltész1, Tamás Kovács1, Tamás Bozó3, Zoltán Mészár4, Miklós Kellermayer 3, János Szöllősi1,5 & Peter Nagy 1 Gaucher disease is a lysosomal storage disease characterized by the malfunction of glucocerebrosidase resulting in the accumulation of glucosylceramide and other sphingolipids in certain cells. Although the disease symptoms are usually attributed to the storage of undigested substrate in lysosomes, here we show that glycosphingolipids accumulating in the plasma membrane cause profound changes in the properties of the membrane. The fuidity of the sphingolipid-enriched membrane decreased accompanied by the enlargement of raft-like ordered membrane domains. The mobility of non-raft proteins and lipids was severely restricted, while raft-resident components were only mildly afected. The rate of endocytosis of transferrin receptor, a non-raft protein, was signifcantly retarded in Gaucher cells, while the endocytosis of the raft-associated GM1 ganglioside was unafected. Interferon- γ-induced STAT1 phosphorylation was also signifcantly inhibited in Gaucher cells. Atomic force microscopy revealed that sphingolipid accumulation was associated with a more compliant membrane capable of producing an increased number of nanotubes. The results imply that glycosphingolipid accumulation in the plasma membrane has signifcant efects on membrane properties, which may be important in the pathogenesis of Gaucher disease. Te plasma membrane constitutes an interface between the cell and its surroundings, and it is the site of numer- ous transmembrane signaling and membrane trafcking events.
    [Show full text]