Biopolym. Cell. 2018; 34(4):251-270.
http://dx.doi.org/10.7124/bc.00097F
Огляди
Флуоресцентні методи у дослідженні вбудовування мембранних білків
1Кириченко О. В., 2Ладохін О. С.
  1. Харківський національний університет ім. В. Н. Каразина
    пл. Свободи, 4, Харків, Україна, 61077
  2. Відділ біохімії і молекулярної біології, Медичний центр, Університет Канзасу
    Канзас Сіті, США, 66160-7421

Abstract

Перехід розчинних білків до ліпідної мембрани та їх подальша перебудова є фундаментальною ланкою у чисельних фізіологічних та біохімічних процесах. У цьому огляді нами наведено підсумки використання флуоресцентної спектроскопії у дослідженні посттрансляційного вбудовування мембранних білків до ліпідних бішарів. Розглянуто різноманітні методи, які використовують спектральні зонди, чутливі до зовнішнього оточення, ферстерівське резонансне перенесення енергії (ФРПЕ), флуоресцентну кореляційну спектроскопію (ФКС) та гасіння флуоресценції у встановленні структурних та кінетичних характеристик білок-ліпідної взаємодії. Наведено приклади застосування стаціонарного та часо-розділенного гасіння флуоресценції ліпідно-зв’язаними гасниками для дослідження занурення мембранних білків до ліпідного бішару. Наприкінці нами показано комбіноване використання різноманітних спектральних підходів для цілісного вивчення структурних, кінетичних та термодинамічних властивостей рН-індукованої послідовності процесів вбудовування\перебудови транслокаційного домену дифтерійного токсину.
Keywords: флуоресцентна спектроскопія, флуоресцентна кореляційна спектроскопія, розподільчий аналіз глибинно-залежного гасіння, анексин, дифтерійний токсин, Bcl-xL
Повний текст: (PDF, англійською)

References

[1] Young JA, Collier RJ. Anthrax toxin: receptor binding, internalization, pore formation, and translocation. Annu Rev Biochem. 2007;76:243-65. Review.
[2] Murphy JR. Mechanism of diphtheria toxin catalytic domain delivery to the eukaryotic cell cytosol and the cellular factors that directly participate in the process. Toxins (Basel). 2011;3(3):294-308.
[3] Skehel JJ, Wiley DC. Receptor binding and membrane fusion in virus entry: the influenza hemagglutinin. Annu Rev Biochem. 2000;69:531-69.
[4] Shamas-Din A, Kale J, Leber B, Andrews DW. Mechanisms of action of Bcl-2 family proteins. Cold Spring Harb Perspect Biol. 2013;5(4):a008714.
[5] Bogner C, Leber B, Andrews DW. Apoptosis: embedded in membranes. Curr Opin Cell Biol. 2010;22(6):845-51.
[6] Vargas-Uribe M, Rodnin MV, Ladokhin AS. Comparison of membrane insertion pathways of the apoptotic regulator Bcl-xL and the diphtheria toxin translocation domain. Biochemistry. 2013;52(45):7901-9.
[7] Moldoveanu T, Follis AV, Kriwacki RW, Green DR. Many players in BCL-2 family affairs. Trends Biochem Sci. 2014;39(3):101-11.
[8] Luna-Vargas MP, Chipuk JE. The deadly landscape of pro-apoptotic BCL-2 proteins in the outer mitochondrial membrane. FEBS J. 2016;283(14):2676-89.
[9] Ladokhin AS. pH-triggered conformational switching along the membrane insertion pathway of the diphtheria toxin T-domain. Toxins (Basel). 2013;5(8):1362-80.
[10] Youle RJ, Strasser A. The BCL-2 protein family: opposing activities that mediate cell death. Nat Rev Mol Cell Biol. 2008;9(1):47-59.
[11] Ladokhin AS. Fluorescence spectroscopy in thermodynamic and kinetic analysis of pH-dependent membrane protein insertion. Methods Enzymol. 2009;466:19-42.
[12] Ladokhin AS. Measuring membrane penetration with depth-dependent fluorescence quenching: distribution analysis is coming of age. Biochim Biophys Acta. 2014;1838(9):2289-95.
[13] Ladokhin AS, Legmann R, Collier RJ, White SH. Reversible refolding of the diphtheria toxin T-domain on lipid membranes. Biochemistry. 2004;43(23):7451-8.
[14] Palchevskyy SS, Posokhov YO, Olivier B, Popot JL, Pucci B, Ladokhin AS. Chaperoning of insertion of membrane proteins into lipid bilayers by hemifluorinated surfactants: application to diphtheria toxin. Biochemistry. 2006;45(8):2629-35.
[15] Rodnin MV, Posokhov YO, Contino-Pépin C, Brettmann J, Kyrychenko A, Palchevskyy SS, Pucci B, Ladokhin AS. Interactions of fluorinated surfactants with diphtheria toxin T-domain: testing new media for studies of membrane proteins. Biophys J. 2008;94(11):4348-57.
[16] Kyrychenko A, Posokhov YO, Rodnin MV, Ladokhin AS. Kinetic intermediate reveals staggered pH-dependent transitions along the membrane insertion pathway of the diphtheria toxin T-domain. Biochemistry. 2009;48(32):7584-94.
[17] Rodnin MV, Kyrychenko A, Kienker P, Sharma O, Posokhov YO, Collier RJ, Finkelstein A, Ladokhin AS. Conformational switching of the diphtheria toxin T domain. J Mol Biol. 2010;402(1):1-7.
[18] Rodnin MV, Kyrychenko A, Kienker P, Sharma O, Vargas-Uribe M, Collier RJ, Finkelstein A, Ladokhin AS. Replacement of C-terminal histidines uncouples membrane insertion and translocation in diphtheria toxin T-domain. Biophys J. 2011;101(10):L41-3.
[19] Kyrychenko A, Rodnin MV, Vargas-Uribe M, Sharma SK, Durand G, Pucci B, Popot JL, Ladokhin AS. Folding of diphtheria toxin T-domain in the presence of amphipols and fluorinated surfactants: Toward thermodynamic measurements of membrane protein folding. Biochim Biophys Acta. 2012;1818(4):1006-12.
[20] Kurnikov IV, Kyrychenko A, Flores-Canales JC, Rodnin MV, Simakov N, Vargas-Uribe M, Posokhov YO, Kurnikova M, Ladokhin AS. pH-triggered conformational switching of the diphtheria toxin T-domain: the roles of N-terminal histidines. J Mol Biol. 2013;425(15):2752-64.
[21] Vargas-Uribe M, Rodnin MV, Kienker P, Finkelstein A, Ladokhin AS. Crucial role of H322 in folding of the diphtheria toxin T-domain into the open-channel state. Biochemistry. 2013;52(20):3457-63.
[22] Flores-Canales JC, Vargas-Uribe M, Ladokhin AS, Kurnikova M. Membrane Association of the Diphtheria Toxin Translocation Domain Studied by Coarse-Grained Simulations and Experiment. J Membr Biol. 2015;248(3):529-43.
[23] Ghatak C, Rodnin MV, Vargas-Uribe M, McCluskey AJ, Flores-Canales JC, Kurnikova M, Ladokhin AS. Role of acidic residues in helices TH8-TH9 in membrane interactions of the diphtheria toxin T domain. Toxins (Basel). 2015;7(4):1303-23.
[24] Vargas-Uribe M, Rodnin MV, Öjemalm K, Holgado A, Kyrychenko A, Nilsson I, Posokhov YO, Makhatadze G, von Heijne G, Ladokhin AS. Thermodynamics of Membrane Insertion and Refolding of the Diphtheria Toxin T-Domain. J Membr Biol. 2015;248(3):383-94.
[25] Walla PJ. Optical Properties of Biomolecules. Modern Biophysical Chemistry: Wiley-VCH Verlag GmbH & Co. KGaA; 2014:41-60.
[26] Ladokhin AS, Jayasinghe S, White SH. How to measure and analyze tryptophan fluorescence in membranes properly, and why bother? Anal Biochem. 2000;285(2):235-45.
[27] Demchenko AP, Duportail G, Oncul S, Klymchenko AS, Mély Y. Introduction to fluorescence probing of biological membranes. Methods Mol Biol. 2015;1232:19-43.
[28] Demchenko AP, Mély Y, Duportail G, Klymchenko AS. Monitoring biophysical properties of lipid membranes by environment-sensitive fluorescent probes. Biophys J. 2009;96(9):3461-70. Review.
[29] Ladokhin AS. Fluorescence Spectroscopy in Peptide and Protein Analysis. In^ Encyclopedia of Analytical Chemistry: Applications, Theory and Instrumentation: John Wiley & Sons, Ltd; 2006.
[30] Kyrychenko A. Using fluorescence for studies of biological membranes: a review. Methods Appl Fluoresc. 2015;3(4):042003.
[31] Reshetnyak YK, Segala M, Andreev OA, Engelman DM. A monomeric membrane peptide that lives in three worlds: in solution, attached to, and inserted across lipid bilayers. Biophys J. 2007;93(7):2363-72.
[32] Kyrychenko A, Freites JA, He J, Tobias DJ, Wimley WC, Ladokhin AS. Structural plasticity in the topology of the membrane-interacting domain of HIV-1 gp41. Biophys J. 2014;106(3):610-20.
[33] Kyrychenko A, Vasquez-Montes V, Ulmschneider MB, Ladokhin AS. Lipid headgroups modulate membrane insertion of pHLIP peptide. Biophys J. 2015;108(4):791-794.
[34] Kaback HR, Wu J. What to do while awaiting crystals of a membrane transport protein and thereafter. Acc Chem Res. 1999; 32(9):805-13.
[35] Wang J, Rosconi MP, London E. Topography of the hydrophilic helices of membrane-inserted diphtheria toxin T domain: TH1-TH3 as a hydrophilic tether. Biochemistry. 2006;45(26):8124-34.
[36] Rosconi MP, London E. Topography of helices 5-7 in membrane-inserted diphtheria toxin T domain: identification and insertion boundaries of two hydrophobic sequences that do not form a stable transmembrane hairpin. J Biol Chem. 2002;277(19):16517-27.
[37] Kyrychenko A, Posokhov YO, Vargas-Uribe M, Ghatak C, Rodnin MV, Ladokhin AS. Fluorescence Applications for Structural and Thermodynamic Studies of Membrane Protein Insertion. In: Geddes CD, editor. Reviews in Fluorescence 2016. Reviews in Fluorescence. Cham, Switzerland: Springer International Publishing; 2017. p. 243-74.
[38] Montagner C, Perier A, Pichard S, Vernier G, Ménez A, Gillet D, Forge V, Chenal A. Behavior of the N-terminal helices of the diphtheria toxin T domain during the successive steps of membrane interaction. Biochemistry. 2007;46(7):1878-87.
[39] Perier A, Chassaing A, Raffestin S, Pichard S, Masella M, Ménez A, Forge V, Chenal A, Gillet D. Concerted protonation of key histidines triggers membrane interaction of the diphtheria toxin T domain. J Biol Chem. 2007;282(33):24239-45.
[40] May V, Kühn O. Excitation Energy Transfer. In: Charge and Energy Transfer Dynamics in Molecular Systems: Wiley-VCH Verlag GmbH & Co. KGaA; 2011:467-558.
[41] Rusu L, Gambhir A, McLaughlin S, Rädler J. Fluorescence correlation spectroscopy studies of Peptide and protein binding to phospholipid vesicles. Biophys J. 2004;87(2):1044-53.
[42] Rhoades E, Ramlall TF, Webb WW, Eliezer D. Quantification of alpha-synuclein binding to lipid vesicles using fluorescence correlation spectroscopy. Biophys J. 2006;90(12):4692-700.
[43] Posokhov YO, Rodnin MV, Das SK, Pucci B, Ladokhin AS. FCS study of the thermodynamics of membrane protein insertion into the lipid bilayer chaperoned by fluorinated surfactants. Biophys J. 2008;95(8):L54-6.
[44] Posokhov YO, Rodnin MV, Lu L, Ladokhin AS. Membrane insertion pathway of annexin B12: thermodynamic and kinetic characterization by fluorescence correlation spectroscopy and fluorescence quenching. Biochemistry. 2008;47(18):5078-87.
[45] Melo AM, Prieto M, Coutinho A. Quantifying Lipid-Protein Interaction by Fluorescence Correlation Spectroscopy (FCS). In: Engelborghs Y, Visser AJWG, editors. Fluorescence Spectroscopy and Microscopy. Methods in Molecular Biology. 1076: Humana Press; 2014:575-595.
[46] Nguyen TT, Swift JL, Cramb DT. Fluorescence Correlation Spectroscopy: The Measurement of Molecular Binding. In: Ed. Geddes CD. Reviews in Fluorescence 2011: Springer New York; 2011:45-66.
[47] Schwille P, Korlach J, Webb WW. Fluorescence correlation spectroscopy with single-molecule sensitivity on cell and model membranes. Cytometry. 1999;36(3):176-82.
[48] Hink MA. Fluorescence Correlation Spectroscopy. In: Verveer PJ, editor. Advanced Fluorescence Microscopy. Methods in Molecular Biology. 1251: Springer New York; 2015:135-50.
[49] Lee H, Kim H. Membrane topology of transmembrane proteins: determinants and experimental tools. Biochem Biophys Res Commun. 2014;453(2):268-76.
[50] Heuck AP, Tweten RK, Johnson AE. Beta-barrel pore-forming toxins: intriguing dimorphic proteins. Biochemistry. 2001;40(31):9065-73.
[51] Collier RJ, Young JA. Anthrax toxin. Annu Rev Cell Dev Biol. 2003;19(1):45-70.
[52] Zakharov SD, Cramer WA. Colicin crystal structures: pathways and mechanisms for colicin insertion into membranes. Biochim Biophys Acta. 2002;1565(2):333-46.
[53] Zakharov SD, Cramer WA. On the mechanism and pathway of colicin import across the E. Coli outer membrane. Front Biosci. 2004;9:1311-7. Review.
[54] Isas JM, Cartailler JP, Sokolov Y, Patel DR, Langen R, Luecke H, Hall JE, Haigler HT. Annexins V and XII insert into bilayers at mildly acidic pH and form ion channels. Biochemistry. 2000;39(11):3015-22.
[55] Matsuzaki K, Murase O, Fujii N, Miyajima K. Translocation of a channel-forming antimicrobial peptide, magainin 2, across lipid bilayers by forming a pore. Biochemistry. 1995;34(19):6521-6.
[56] Everett J, Zlotnick A, Tennyson J, Holloway PW. Fluorescence quenching of cytochrome b5 in vesicles with an asymmetric transbilayer distribution of brominated phosphatidylcholine. J Biol Chem. 1986;261(15):6725-9.
[57] Wimley WC, White SH. Determining the membrane topology of peptides by fluorescence quenching. Biochemistry. 2000;39(1):161-70.
[58] Ladokhin AS, White SH. Interfacial folding and membrane insertion of a designed helical peptide. Biochemistry. 2004;43(19):5782-91.
[59] Ladokhin AS, Isas JM, Haigler HT, White SH. Determining the membrane topology of proteins: insertion pathway of a transmembrane helix of annexin 12. Biochemistry. 2002;41(46):13617-26.
[60] Posokhov YO, Ladokhin AS. Lifetime fluorescence method for determining membrane topology of proteins. Anal Biochem. 2006;348(1):87-93.
[61] Ladokhin AS. Distribution analysis of depth-dependent fluorescence quenching in membranes: A practical guide. In: Ludwig Brand MLJ, editor. Methods in enzymology. 278. New York: Academic Press; 1997:462-73.
[62] Ladokhin AS. Analysis of protein and peptide penetration into membranes by depth-dependent fluorescence quenching: theoretical considerations. Biophys J. 1999;76(2):946-55.
[63] London E, Ladokhin AS. Measuring the depth of amino acid residues in membrane-inserted peptides by fluorescence quenching. In: Simon SA, McIntosh TJ, editors. Peptide-Lipid Interactions Current Topics in Membranes. 52. Amsterdam: Elsevier; 2002:89-115.
[64] McIntosh TJ, Holloway PW. Determination of the depth of bromine atoms in bilayers formed from bromolipid probes. Biochemistry. 1987;26(6):1783-8.
[65] Kyrychenko A, Ladokhin AS. Molecular dynamics simulations of depth distribution of spin-labeled phospholipids within lipid bilayer. J Phys Chem B. 2013;117(19):5875-85.
[66] Kyrychenko A, Rodnin MV, Ladokhin AS. Calibration of Distribution Analysis of the Depth of Membrane Penetration Using Simulations and Depth-Dependent Fluorescence Quenching. J Membr Biol. 2015;248(3):583-94.
[67] Kyrychenko A, Ladokhin AS. Refining membrane penetration by a combination of steady-state and time-resolved depth-dependent fluorescence quenching. Anal Biochem. 2014;446:19-21.
[68] Kyrychenko A, Lim NM, Vasquez-Montes V, Rodnin MV, Freites JA, Nguyen LP, Tobias DJ, Mobley DL, Ladokhin AS. Refining Protein Penetration into the Lipid Bilayer Using Fluorescence Quenching and Molecular Dynamics Simulations: The Case of Diphtheria Toxin Translocation Domain. J Membr Biol. 2018;251(3):379-391.
[69] Bennett MJ, Eisenberg D. Refined structure of monomelic diphtheria toxin at 2.3 Å resolution. Protein Science. 1994; 3(9):1464-75.
[70] Flores-Canales JC, Kurnikova M. Microsecond Simulations of the Diphtheria Toxin Translocation Domain in Association with Anionic Lipid Bilayers. J Phys Chem B. 2015;119(36):12074-85.
[71] Ladokhin AS, Vargas-Uribe M, Rodnin MV, Ghatak C, Sharma O. Cellular Entry of the Diphtheria Toxin Does Not Require the Formation of the Open-Channel State by Its Translocation Domain. Toxins (Basel). 2017;9(10). pii: E299.