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Cited by 71Lipid Membrane Structure and BehaviorReceptor Mechanisms and SignalingProtein Structure and Dynamics

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Lipid membrane-induced optimization for ligand–receptor docking: recent tools and insights for the “membrane catalysis” model

Castanho, Miguel A.R.B., Fernandes, Miguel X.·2006·European Biophysics Journal
DOI 10.1007/s00249-005-0007-9
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Abstract

Cells in living organisms are regulated by chemical and physical stimuli from their environment. Often, ligands interact with membrane receptors to trigger responses and Sargent and Schwyzer conceived a model to describe this process, "membrane catalysis". There is a notion that the physical organization of membranes can control the response of cells by speeding up reactions. We revisit the "membrane catalysis" model in the light of recent technical, methodological and theoretical advances and how they can be exploited to highlight the details of membrane mediated ligand-receptor interactions. We examine the possible effects that ligand concentration causes in the membrane catalysis and focus our attention in techniques used to determine the partition constant. The hypothetical diffusional advantage associated with membrane catalysis is discussed and the applicability of existing models is assessed. The role of in-depth location and orientation of ligands is explored emphasizing the contribution of new analysis methods and spectroscopic techniques. Results suggest that membranes can optimize the interaction between ligands and receptors through several different effects but the relative contribution of each must be carefully investigated. We certainly hope that the conjugation of the methodological and technical advances here reported will revive the interest in the membrane catalysis model.

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Research works printed but not linked: 62

  1. Adam G, Delbrück M (1968) Reduction of dimensionality in biological diffusion processes. In: Rich A, Davidson N (eds) Structural Chemistry and Molecular Biology. W.H. Freeman & Co., San Francisco, pp 198–215
  2. Almeida RFM, Loura LMS, Prieto M (2005) Application of fluorescence to understand the interaction of peptides with binary lipid membranes. In: Geddes C, Lakowicz JR (eds) Reviews in Fluorescence 2005. Springer, Berlin Heidelberg New York, pp 271–323 · DOI
  3. Arkin IT, MacKenzie KR, Brijnger AT (1997) Site-Directed Dichroism As a Method for Obtaining Rotational and Orientational Constraints for Oriented Polymers. J Am Chem Soc 119:8973–8980 · DOI
  4. Axelrod D, Wang MD (1994) Reduction-of-dimensionality kinetics at reaction-limited cell surface receptors. Biophys J 66:588–600 · DOI
  5. Axelsen PH, Citra MJ (1996) Orientational order determination by internal reflection infrared spectroscopy. Prog Biophys Molec Biol 66:227–253 · DOI
  6. Baldo M, Grassi A, Raudino A (1991) Diffusion-controlled reactions among ligands and receptor clusters. Effects of competition for ligands. J Chem Phys 95:6734–6740 · DOI
  7. Bechinger B, Ruysschaert J-M, Goormaghtigh E (1999) Membrane helix orientation from linear dichroism of infrared attenuated total reflection spectra. Biophys J 76:552–563 · DOI
  8. Bechinger B, Aisenbrey C, Bertani P (2004) The alignment, structure and dynamics of membrane-associated polypeptides by solid-state NMR spectroscopy. Biochim Biophys Acta Biomemb 1666:190–204 · DOI
  9. Benninger RKP, Önfelt B, Davis DM, Neil M, French PMW (2005) Fluorescence imaging of two-photon linear dichroism: cholesterol depletion disrupts molecular orientation in cell membranes. Biophys J 88:609–622 · DOI
  10. Bombelli C, Borocci S, Lupi F, Mancini G, Mannina L, Segre AL, Viel S (2004) Chiral Recognition of Dipeptides in a Biomembrane Model. J Am Chem Soc 126:13354–13362 · DOI
  11. Brattwall CEB, Lincoln P, Norden B (2003) Orientation and Conformation of Cell-Penetrating Peptide Penetratin in Phospholipid Vesicle Membranes Determined by Polarized-Light Spectroscopy. J Am Chem Soc 125:14214–14215 · DOI
  12. Carrion-Vazquez M, Oberhauser AF, Fowler SB, Marszalek PE, Broedel SE, Clarke J, Fernandez JM (1999) Mechanical and chemical unfolding of a single protein: A comparison. Proc Nat Acad Sci USA 96:3694–3699 · DOI
  13. Castanho M, Prieto M (1992) Fluorescence study of the macrolide pentaene antibiotic filipin in aqueous solution and in a model system of membranes. Eur J Biochem 207:125–134 · DOI
  14. Castanho MARB, Lopes S, Fernandes M (2003) Using UV–Vis linear dichroism to study the orientation of molecular probes and biomolecules in lipid membranes. Spectroscopy Int J 17:377–398 · DOI
  15. Chan DC, Kim PS (1998) HIV entry and its inhibition. Cell 93:681–684 · DOI
  16. 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 · DOI
  17. Cukier RI (1983) The effect of surface diffusion on surface reaction rates. J Chem Phys 79:2430–2435 · DOI
  18. Dafforn TMR, Rodger A (2005) Linear dichroism of biomolecules: which way is up?. Curr Opin Struc Biol 14:541–546 · DOI
  19. DeLisi C (1980) The biophysics of ligand–receptor interactions. Q Rev Biophys 13:201–230 · DOI
  20. Dhanasekaran M, Palian MM, Alves I, Yeomans L, Keyari CM, Davis P, Bilsky EJ, Egleton RD, Yamamura HI, Jacobsen NE, Tollin G, Hruby VJ, Porreca F, Polt R (2005) Glycopeptides Related to -Endorphin Adopt Helical Amphipathic Conformations in the Presence of Lipid Bilayers. J Am Chem Soc 127:5435–5448 · DOI
  21. Erickson J, Goldstein B, Holowka D, Baird B (1987) The effect of receptor density on the forward rate constant for binding of ligands to cell surface receptors. Biophys J 52:657–663 · DOI
  22. Fernandes MX, García de la Torre J, Castanho MARB (2002) Joint determination by Brownian dynamics and fluorescence quenching of the in-depth location profile of biomolecules in membranes. Analytical Biochemistry 307:1–12 · DOI
  23. Fung BM (2003) New angles for NMR studies of biological molecules. Biophys J 85:3429–3430 · DOI
  24. Gershon ND, Porter KR, Trus BL (1985) The cytoplasmic matrix: its volume and surface area and the diffusion of molecules through it. Proc Natl Acad Sci 82:5030–5034 · DOI
  25. Goormaghtigh E, Raussens V, Ruysschaert J-M (1999) Attenuated total reflection infrared spectroscopy of proteins and lipids in biological membranes. Biochim Biophys Acta 1422:105–185 · DOI
  26. Haugh JM, Lauffenburger DA (1997) Physical modulation of intracellular signalling processes by locational regulation. Biophys J 72:2014–2031 · DOI
  27. Henriques S, Castanho M (2004) Consequences of Nonlytic Membrane Perturbation to the Translocation of the Cell Penetrating Peptide Pep-1 in Lipidic Vesicles. Biochemistry 43:9716–9724 · DOI
  28. Henriques S, Castanho M (2005) Environmental factors that enhance the action of the cell penetrating peptide pep-1. A spectroscopic study using lipidic vesicles. Biochim Biophys Acta Biomemb 1669:75–86 · DOI
  29. Heyse S, Stora T, Schmid E, Lakey JH, Vogel H (1998) Emerging techniques for investigating molecular interactions at lipid membranes. Biochim Biophys Acta 85507:319–338 · DOI
  30. Høyrup P, Davidsen J, Jørgensen K (2001) Lipid membrane partitioning of lysolipids and fatty acids: effects of membrane phase structure and detergent chain length. J Phys Chem B 105:2649– 2657 · DOI
  31. Johansson LB-Å (1985) Order parameters of fluorophores in ground and excited states. Probe molecules in a lyotropic liquid crystal. Chem Phys Lett 118:516–521 · DOI
  32. Kooyman RPH, Levine YK (1981) Measurement of second and fourth rank order parameters by fluorescence polarization experiments in a lipid membrane system. Chem Phys 60:317–326 · DOI
  33. Ladokhin AS (1997) Distribution analysis of depth-dependent fluorescence quenching in membranes. Methods Enzymol 278:462–473 · DOI
  34. Lopes S, Castanho MARB (2002) Revealing the Orientation of Nystatin and Amphotericin B in Lipidic Multilayers by UV–Vis Linear Dichroism. J Phys Chem B 106:7278–7282 · DOI
  35. Lopes S, Castanho MARB (2004) Does Aliphatic Chain Length Influence Carbocyanines’ Orientation in Supported Lipid Multilayers?. Journal of Fluorescence 14:281–287 · DOI
  36. Lopes SCDN, Castanho MARB (2005) Overview of Common Spectroscopic Methods to Determine the Orientation/Alignment of Membrane Probes and Drugs in Lipidic Bilayers. Curr Org Chemistry 9:889–898 · DOI
  37. Lopes S, Fernandes MX, Prieto M, Castanho MARB (2001) Orientational Order of the Polyene Fatty Acid Membrane Probe trans-Parinaric Acid in Langmuir-Blodgett Multilayer Films. J Phys Chem B 105:562–568 · DOI
  38. Lopes S, Fedorov A, Castanho M (2004) Cholesterol modulates maculosin’s orientation in model systems of biological membranes. Relevance towards putative molecular recognition. Steroids 69:825–830 · DOI
  39. Lopes SCDN, Goormaghtigh E, Costa Cabral BJ, Castanho MARB (2004) Filipin Orientation Revealed by Linear Dichroism. Implication for a Model of Action. J Am Chem Soc 126:5396–5402 · DOI
  40. Lopes SCDN, Fedorov A, Castanho MARB (2005) Lipidic Membranes Are Potential “Catalysts” in the Ligand Activity of the Multifunctional Pentapeptide Neokyotorphin. Chem Bio Chem 6:697–702 · DOI
  41. Martins J, Melo E, Naqvi KR (2004) Reappraisal of four different approaches for finding the mean reaction time in the multi-trap variant of the Adam-Delbrück problem. J Chem Phys 120:9390–9393 · DOI
  42. Mitchell DC, Litman BJ (1998) Molecular order and dynamics in bilayers consisting of highly polyunsaturated phospholipids. Biophys J 74:879–891 · DOI
  43. Murray D, Arbuzova A, Honig B, McLaughlin S (2002) The role of electrostatic and nonpolar interactions in the association of peripheral proteins with membranes. In: Simon SA, McIntosh TJ (eds) Peptide-lipid interactions. Academic Press, San Diego, pp 277–307 · DOI
  44. Reddy CVG, Malinowska K, Menhart N, Wang R (2004) Identification of TrkA on living PC12 cells by atomic force microscopy. Biochim Biophys Acta Biomemb 1667:15–25 · DOI
  45. Roberts GG (1990) Langmuir Blodgett films. Plenum Press, New York · DOI
  46. Santos N, Prieto M, Castanho M (2003) Quantifying molecular partition into model systems of biomembranes: an emphasis on optical spectroscopic methods. Biochim Biophys Acta Biomemb 1612:123– 135 · DOI
  47. Sarai N, Matile S (2003) Anion-mediated transfer of polyarginine across liquid and bilayer membranes. J Am Chem Soc 125:14348–14356 · DOI
  48. Sargent DF, Schwyzer R (1986) Membrane lipid phase as catalyst for peptide-receptor interactions. Proc Natl Acad Sci USA 83:5774–5778 · DOI · Paper page
  49. Schwartz DK (1997) Langmuir-Blodgett film structure. Surf Sci Rep 27:245–334 · DOI
  50. Schwyzer R (1991) New principles in QSAR: membrane requirements. J Recept Res 11:45–47 · DOI
  51. Schwyzer R (1992) How do peptides interact with lipid membranes and how does this affect their biological affinity?. Braz J Med Biol Res 25:1077–1089
  52. Schwyzer R (1995a) 100 years lock-and-key concept: are peptides keys shaped and guided to their receptors by the target cell membrane?. Biopolymers 37:5–16 · DOI
  53. Schwyzer R (1995b) In search of the ‘bio-active conformation’–is it induced by the target cell membrane?. J Mol Recognit 8:3–8 · DOI
  54. Tatulian SA (2003) Attenuated total reflection Fourier transform infrared spectroscopy: a method of choice for studying membrane proteins and lipids. Biochemistry 42:11898–11907 · DOI
  55. Van der Meer W, Pottel H, Herrennan W, Ameloot M, Hendrickx M, Schröder H (1984) Effect of orientational order on the decay of the fluorescence anisotropy in membrane suspensions. A new approximate solution of the rotational diffusion equation. Biophys J 46:515–523 · DOI
  56. Veiga S, Henriques S, Santos N, Castanho M (2004a) Putative role of membranes in the HIV fusion inhibitor enfuvirtide mode of action at the molecular level. Biochem J 377:107–110 · DOI
  57. Veiga S, Santos N, Loura L, Fedorov A, Castanho M (2004b) HIV Fusion Inhibitor Peptide T-1249 Is Able To Insert or Adsorb to Lipidic Bilayers. Putative Correlation with Improved Efficiency. J Am Chem Soc 126:14758–14763 · DOI
  58. Vigano C, Manciu L, Buyse F, Goormaghtigh E, Ruysschaert J-M (2000) Attenuated total reflection IR spectroscopy as a tool to investigate the structure, orientation and tertiary structure changes in peptides and membrane proteins. Biopolymers 55:373–380 · DOI
  59. Wasniewski CM, Parkanzky PD, Bodner ML, Weliky DP (2004) Solid-state nuclear magnetic resonance studies of HIV and influenza fusion peptide orientations in membrane bilayers using stacked glass plate samples. Chem Phys Lipids 132:89–100 · DOI
  60. Wieprecht T, Seelig J (2002) Isothermal titration calorimetry for studying interactions between peptides and lipid membranes. In: Simon SA, McIntosh TJ (eds) Peptide-lipid interactions. Academic Press, San Diego, pp 31–56 · DOI
  61. Zandomeneghi G, Tomaselli M, van Beek JD, Meier BH (2001) Manipulation of the Director in Bicellar Mesophases by Sample Spinning: A New Tool for NMR Spectroscopy. J Am Chem Soc 123:910–913 · DOI
  62. Zannoni C, Arcioni A, Cavatorta P (1983) Fluorescence depolarization in liquid crystals and membrane bilayers. Chem Phys Lipids 32:179–250 · DOI

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Metadata

Authors
Castanho, M. A. R. B., & Fernandes, M. X.
Affiliations
  • University of Lisbon (PT)
  • Centro de Química da Madeira (PT)
Corresponding author
Castanho, Miguel A.R.B.
ORCID
Venue
European Biophysics Journal
Publisher
Springer Science and Business Media LLC
Published
2005-10-11
Volume
35
Issue
2
Pages
92-103
ISSN
  • 0175-7571 (ISSN-L)
  • 1432-1017
DOI
10.1007/s00249-005-0007-9
OpenAlex
W2088137742
Cited by
71
References
0
Citations by year
2025: 3 · 2024: 1 · 2022: 2 · 2021: 3 · 2020: 1 · 2019: 2 · 2018: 3 · 2017: 3 · 2016: 6 · 2015: 3 · 2014: 4 · 2013: 10 · 2012: 3
FWCI
0.24
Type
journal article
Language
en
Open access
closed
Licence
www.springer.com/tdm (tdm)
Locations
  • European Biophysics Journal (publishedVersion)
  • PubMed (publishedVersion)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Lipid Membrane Structure and Behavior
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Receptor Mechanisms and Signaling
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Keywords
membrane catalysis, ligand-receptor docking, cell surface receptors, partition constants, ligand concentration effects, membrane organization, ligand-receptor interactions
MeSH terms
Catalysis, Ligands, Lipid Bilayers, Models, Biological, Receptors, Cell Surface, Biomimetics, Biomimetic Materials

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