Skip to main content
SpringerLink
Log in
Book cover

Analysis of Membrane Lipids pp 161–187Cite as

New Family of Fluorescent Probes for Characterizing Depth-Dependent Static and Dynamic Properties of Lipid/Water Interfaces

  • Protocol
  • First Online:

  • 506 Accesses

Part of the book series: Springer Protocols Handbooks ((SPH))

Abstract

The important biological processes that help communicate between intra- and extracellular environments take place at cell membrane/water interface. However, molecular interactions at these interfaces are strongly affected by the depth-dependent hydration and local environmental polarity across the lipid/water interface and also the lipid ordering. A new family of membrane probes based on 4-aminophthalimide (4AP-Cn) have been synthesized, which are of particular interest here because of their extreme sensitivity towards sensing depth-dependent polarity, hydration and energy transfer dynamics at model lipid/water interfaces in sub-nanometre length scale. We envisage that these new probes will be extremely useful for characterizing the static and dynamic properties of naturally occurring membrane/water interfaces as well. This chapter presents the protocol for 4AP-Cn synthesis, as well as detailed experimental and MD simulation methods for measuring depth-dependent polarity, hydration and multi-molecular energy transfer dynamics at lipid/water interfaces of gel and fluid phases of lipid bilayer.

This is a preview of subscription content, log in via an institution.

Protocol
USD   49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   109.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   139.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   249.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

Springer Nature is developing a new tool to find and evaluate Protocols. Learn more

References

  1. Singer SJ, Nicolson GL (1972) The fluid mosaic model of the structure of cell membranes. Science 175:720–731

    Article  CAS  PubMed  Google Scholar 

  2. Van Meer G, Voelker DR, Feigenson GW (2008) Membrane lipids: where they are and how they behave. Nat Rev Mol Cell Biol 9:112–124

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  3. Stillwell W (2013) An introduction to biological membranes. Elsevier, San Diego

    Book  Google Scholar 

  4. Disalvo EA, Lairion F, Martini F, Tymczyszyn E, Frias M, Almaleck H, Gordillo GJ (2008) Structural and functional properties of hydration and confined water in membrane interfaces. Biochim Biophys Acta 1778:2655–2670

    Article  CAS  PubMed  Google Scholar 

  5. Haldar S, Chaudhuri A, Chattopadhyay AJ (2011) Organization and dynamics of membrane probes and proteins utilizing the red edge excitation shift. J Phys Chem B 115:5693–5706

    Article  CAS  PubMed  Google Scholar 

  6. Filipe HAL, Moreno MJ, Loura LMS (2011) Interaction of 7-nitrobenz-2-oxa-1,3-diazol-4-yl-labeled fatty amines with 1-palmitoyl, 2-oleoyl-sn-glycero-3-phosphocholine bilayers: a molecular dynamics study. J Phys Chem B 115:10109–10119

    Article  CAS  PubMed  Google Scholar 

  7. Chakraborty H, Haldar S, Chong SPL-G, Kombrabail M, Krishnamoorthy G, Chattopadhyay A (2015) Depth-dependent organization and dynamics of archaeal and eukaryotic membranes: development of membrane anisotropy gradient with natural evolution. Langmuir 31:11591–11597

    Article  CAS  PubMed  Google Scholar 

  8. Singh MK, Him S, Khan MF, Sen S (2016) New insight into probe-location dependent polarity and hydration at lipid/water interfaces: comparison between gel- and fluid-phases of lipid bilayers. Phys Chem Chem Phys 18:24185–24197

    Article  CAS  PubMed  Google Scholar 

  9. Singh MK, Khan MF, Him S, Sen S (2017) Probe-location dependent resonance energy transfer at lipid/water interfaces: comparison between the gel- and fluid-phase of lipid bilayer. Phys Chem Chem Phys 19:25870–25885

    Article  CAS  PubMed  Google Scholar 

  10. Marsh D (2001) Polarity and permeation profiles in lipid membranes. Proc Natl Acad Sci USA 98:7777–7782

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Marsh D (2002) Membrane water-penetration profiles from spin labels. Eur Biophys J 31:559–562

    Article  CAS  PubMed  Google Scholar 

  12. Martin DR, LeBard DN, Matyushov DV (2013) Coulomb soup of bioenergetics: electron transfer in a bacterial bc 1 complex. J Phys Chem Lett 4:3602–3606

    Article  CAS  Google Scholar 

  13. Kuang G, Liang L, Brown C, Wang Q, Bulone V, Tu Y (2016) Insight into the adsorption profiles of the Saprolegniamonoica chitin synthase MIT domain on POPA and POPC membranes by molecular dynamics simulation studies. Phys Chem Chem Phys 18:5281–5290

    Article  CAS  PubMed  Google Scholar 

  14. Miller AS, Falke JJ (2004) Side chains at the membrane-water interface modulate the signaling state of a transmembrane receptor. Biochemistry 43:1763–1770

    Article  CAS  PubMed  Google Scholar 

  15. Xiang TX, Anderson BD (2006) Liposomal drug transport: a molecular perspective from molecular dynamics simulations in lipid bilayers. Adv Drug Deliv Rev 58:1357–1378

    Article  CAS  PubMed  Google Scholar 

  16. Disalvo EA (2015) Membrane hydration: role of water in structure and function of biological membranes. Springer, Cham

    Book  Google Scholar 

  17. Cipolla D, Shekunov B, Blanchard J, Hickey A (2014) Lipid-based carriers for pulmonary products: preclinical development and case studies in humans. Adv Drug Deliv Rev 75:53–80

    Article  CAS  PubMed  Google Scholar 

  18. Maruyama K (2011) Intracellular targeting delivery of liposomal drugs to solid tumors based on EPR effects. Adv Drug Deliv Rev 63:161–169

    Article  CAS  PubMed  Google Scholar 

  19. Forster V, Signorell RD, Roveri M, Leroux JC (2014) Liposome-supported peritoneal dialysis for detoxification of drugs and endogenous metabolites. Sci Transl Med 6:258

    Article  CAS  Google Scholar 

  20. Damitz R, Chauhan A (2015) Parenteral emulsions and liposomes to treat drug overdose. Adv Drug Deliv Rev 90:12–23

    Article  CAS  PubMed  Google Scholar 

  21. Chattopadhyay A, London E (1987) Parallax method for direct measurement of membrane penetration depth utilizing fluorescence quenching by spin-labeled phospholipids. Biochemistry 26:39–45

    Article  CAS  PubMed  Google Scholar 

  22. Abrams FS, London E (1993) Extension of the parallax analysis of membrane penetration depth to the polar region of model membranes: use of fluorescence quenching by a spin-label attached to the phospholipid polar headgroup. Biochemistry 32:10826–10831

    Article  CAS  PubMed  Google Scholar 

  23. Menger FM, Keiper JS, Caran KL (2002) Depth-profiling with giant vesicle membranes. J Am Chem Soc 124:11842–11843

    Article  CAS  PubMed  Google Scholar 

  24. Kim J, Lu W, Qiu W, Wang L, Caffrey M, Zhong D (2006) Ultrafast hydration dynamics in the lipidic cubic phase: discrete water structures in nanochannels. J Phys Chem B 110:21994–22000

    Article  CAS  PubMed  Google Scholar 

  25. Chattopadhyay A, Mukherjee S (1999) Red edge excitation shift of a deeply embedded membrane probe: implications in water penetration in the bilayer. J Phys Chem B 103:8180–8185

    Article  CAS  Google Scholar 

  26. Klymchenko AS, Mely Y, Demchenko AP, Duportail G (2004) Simultaneous probing of hydration and polarity of lipid bilayers with 3-hydroxyflavone fluorescent dyes. Biochim Biophys Acta 1665:6–19

    Article  CAS  PubMed  Google Scholar 

  27. Parasassi T, De Stasio G, Ravagnan G, Rusch RM, Gratton E (1991) Quantitation of lipid phases in phospholipid vesicles by the generalized polarization of Laurdan fluorescence. Biophys J 60:179–189

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Amaro M, Filipe HAL, Prates Ramalho JP, Hof M, Loura LMS (2016) Fluorescence of nitrobenzoxadiazole (NBD)-labeled lipids in model membranes is connected not to lipid mobility but to probe location. Phys Chem Chem Phys 18:7042–7054

    Article  CAS  PubMed  Google Scholar 

  29. Jurkiewicz P, Olzynska A, Langner M, Hof M (2006) Headgroup hydration and mobility of DOTAP/DOPC bilayers: a fluorescence solvent relaxation study. Langmuir 22:8741–8749

    Article  CAS  PubMed  Google Scholar 

  30. Paul A, Samanta A (2007) Solute rotation and solvation dynamics in an alcohol-functionalized room temperature ionic liquid. J Phys Chem B 111:4724–4731

    Article  CAS  PubMed  Google Scholar 

  31. Ingram JA, Moog RS, Ito N, Biswas R, Maroncelli M (2003) Solute rotation and solvation dynamics in a room-temperature ionic liquid. J Phys Chem B 107:5926–5932

    Article  CAS  Google Scholar 

  32. Reichardt C (1994) Solvatochromicdyes as solvent polarity indicators. Chem Rev 94:2319–2358

    Article  CAS  Google Scholar 

  33. Wolber PK, Hudson BS (1979) An analytic solution to the Förster energy transfer problem in two dimensions. Biophys J 28:197–210

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Lakowicz JR (2006) Principles of fluorescence spectroscopy, 3rd edn. Springer, New York

    Book  Google Scholar 

  35. Frisch MJ et al (2009) Gaussian 09, Revision A.02. Gaussian, Wallingford

    Google Scholar 

  36. Cornell WD, Cieplak P, Bayly CI, Kollman PA (1993) Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of salvation. J Am Chem Soc 115:9620–9631

    Article  CAS  Google Scholar 

  37. Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA (2004) Development and testing of a general amber force field. J Comput Chem 34:1157–1174

    Article  CAS  Google Scholar 

  38. Case DA et al (2012) AMBER 12. University of California, San Francisco

    Google Scholar 

  39. Sousa da Silva A, Vranken W (2012) ACPYPE –AnteChamberPYthonparser interfacE. BMC Res Notes 5:367

    Article  PubMed  PubMed Central  Google Scholar 

  40. Spoel DVD, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJC (2005) GROMACS: fast, flexible, and free. J Comput Chem 26:1701–1718

    Article  CAS  Google Scholar 

  41. Jambeck JPM, Lyubartsev AP (2012) An extension and further validation of an all-atomistic force field for biological membranes. J Chem Theory Comput 8:2938–2948

    Article  PubMed  CAS  Google Scholar 

  42. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) J Chem Phys 79:926–935

    Article  CAS  Google Scholar 

  43. Berendsen HJC, Postma JPM, Vangunsteren WF, Dinola A, Haak JR (1984) Molecular dynamics with coupling to an external bath. J Chem Phys 81:3684–3690

    Article  CAS  Google Scholar 

  44. Hoover WG (1985) Canonical dynamics: equilibrium phase-space distributions. Phys Rev A 31:1695–1697

    Article  CAS  Google Scholar 

  45. Nose S (1984) A unified formulation of the constant temperature molecular dynamics methods. J Chem Phys 81:511–519

    Article  CAS  Google Scholar 

  46. Hess B, Bekker H, Berendsen HJC, Fraaije JGEM (1997) LINCS: a linear constraint solver for molecular simulations. J Comput Chem 18:1463–1472

    Article  CAS  Google Scholar 

  47. Darden T, York D, Pedersen L (1993) Particle mesh Ewald: an N·log(N) method for Ewald sums in large systems. J Chem Phys 98:10089–10092

    Article  CAS  Google Scholar 

  48. Parrinello M, Rahman A (1981) Polymorphic transitions in single crystals: a new molecular dynamics method. J Appl Phys 52:7182–7190

    Article  CAS  Google Scholar 

  49. Tristam-Nagle S, Zhang R, Suter RM, Worthinton CR, Sun WJ, Nagle JF (1993) Measurement of chain tilt angle in fully hydrated bilayers of gel phase lecithins. Biophys J 64:1097–1109

    Article  Google Scholar 

  50. Kucerka N, Nagle JF, Sachs JN, Feller SE, Pencer J, Jackson A, Katsaras J (2008) Lipid bilayer structure determined by the simultaneous analysis of neutron and X-ray scattering data. Biophys J 95:2356–2367

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Lafleur M, Bloom M, Eikenberry EF, Gruner SM, Han Y, Cullis PR (1996) Correlation between lipid plane curvature and lipid chain order. Biophys J 70:2747–2757

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. http://www.fos.su.se/~sasha/SLipids/Downloads.html

Download references

Acknowledgements

The works were supported by University Grants Commission (UGC-JNU-UPE-II, project no. 75), Department of Science and Technology (DST-PURSE) and Department of Biotechnology (DBT-BUILDER; project no. BT/PR5006/INF/153/2012). M.K.S. thanks CSIR and DBT-BUILDER, and H.S. thanks UGC for providing fellowships.

Author information

Authors and Affiliations

  1. Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi, India

    Moirangthem Kiran Singh, Him Shweta & Sobhan Sen

Authors
  1. Moirangthem Kiran Singh
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Him Shweta
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Sobhan Sen
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Sobhan Sen .

Editor information

Editors and Affiliations

  1. Amity Institute of Biotechnology and Amity Institute of Integrative Sciences and Health, Amity University Haryana, Gurgaon, Haryana, India

    Rajendra Prasad

  2. Department of Biochemistry, University of Lucknow, Lucknow, Uttar Pradesh, India

    Ashutosh Singh

Rights and permissions

Reprints and permissions

Copyright information

© 2020 Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Singh, M.K., Shweta, H., Sen, S. (2020). New Family of Fluorescent Probes for Characterizing Depth-Dependent Static and Dynamic Properties of Lipid/Water Interfaces. In: Prasad, R., Singh, A. (eds) Analysis of Membrane Lipids. Springer Protocols Handbooks. Springer, New York, NY. https://doi.org/10.1007/978-1-0716-0631-5_10

Download citation

  • DOI: https://doi.org/10.1007/978-1-0716-0631-5_10

  • Published:

  • Publisher Name: Springer, New York, NY

  • Print ISBN: 978-1-0716-0630-8

  • Online ISBN: 978-1-0716-0631-5

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation