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Fluorescence studies of complex systems: organisation of biomolecules
Umeå University, Faculty of Science and Technology, Department of Chemistry.
2007 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The homo and hetero dimerisation of two spectroscopically different chromophores were studied, namely: 4,4-difluoro-4-bora-3a,4a-diazas-indacene (g-BODIPY) and its 5-styryl-derivative (r-BODIPY). Various spectroscopic properties of the r-BODIPY in different common solvents were determined. It was shown that g- and r-BODIPY in the ground state can form homo- as well as hetero dimers.

We demonstrate that the ganglioside GM1 in lipid bilayers of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) exhibits a non-uniform lateral distribution, which is an argument in favour of self-aggregation of GM1 being an intrinsic property of the GM1. This was concluded from energy transfer/migration studies of BODIPY-labelled gangliosides.

An algorithm is presented that quantitatively accounts for donor–donor energy migration (DDEM) among fluorophore-labelled proteins forming regular non-covalent polymers. The DDEM algorithm is based on Monte Carlo (MC) and Brownian dynamics (BD) simulations and applies to the calculation of fluorescence depolarisation data, such as the fluorescence anisotropy. Thereby local orientations, as well as reorienting motions of the fluorescent groups are considered in the absence and presence of DDEM among them.

A new method, in which a genetic algorithm (GA) was combined with BD and MC simulations, was developed to analyse fluorescence depolarisation data collected by the time-correlated single photon counting technique. It was applied to study g-BODIPY-labelled filamentous actin (F-actin). The technique registered the local order and reorienting motions of the fluorophores, which were covalently coupled to cysteine 374 (C374) in actin and interacted by means of electronic energy migration within the polymer. Analyses of F-actin samples composed of different fractions of labelled actin molecules revealed the known helical organiszation of F-actin, and demonstrated the usefulness of this technique for structure determination of complex protein polymers. The distance from the filament axis to the fluorophore was found to be considerably less than expected from the proposed position of C374 at a high filament radius. In addition, polymerisation experiments with BODIPY-actin suggest a 25-fold more efficient signal for filament formation than pyrene-actin.

Place, publisher, year, edition, pages
Umeå: Kemi , 2007. , 44 p.
Keyword [en]
Fluorescence anisotropy, BODIPY, homo and hetero dimerisation, protein aggregates, protein polymer structures, actin polymerisation, FRET, donor–acceptor energy transfer DAET, donor-donor energy migration DDEM, homotransfer, Monte Carlo simulation, MC, Brownian dynamics, BD, Genetic Algorithm, GA., Ganglioside GM1
National Category
Physical Chemistry
Identifiers
URN: urn:nbn:se:umu:diva-979ISBN: 978-91-7264-260-7 (print)OAI: oai:DiVA.org:umu-979DiVA: diva2:145267
Public defence
2007-02-16, KB3A9, KBC, SE-901 87, Umeå, 13:15 (English)
Opponent
Supervisors
Available from: 2007-01-25 Created: 2007-01-25 Last updated: 2011-03-09Bibliographically approved
List of papers
1. Pyrromethene dyes (BODIPY) can form ground state homo and hetero dimers: photophysics and spectral properties.
Open this publication in new window or tab >>Pyrromethene dyes (BODIPY) can form ground state homo and hetero dimers: photophysics and spectral properties.
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2006 (English)In: Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, ISSN 1386-1425, Vol. 65, no 1, 113-22 p.Article in journal (Refereed) Published
Abstract [en]

Homo and hetero dimerisation of two spectroscopically different BODIPY chromophores was studied, namely, 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene and its 5-styryl-derivative. These exhibit very similar absorption and fluorescence spectral shape, but are mutually shifted by ca. 70 nm. For this reason the former and the latter are referred to as the green and red BODIPY, which here are denoted gB and rB, respectively. Various spectroscopic properties of the rB in different common solvents were determined. The calculated and experimental fluorescence quantum yield is found to be close to 100%, the fluorescence relaxation has a single exponential decay with a lifetime of about 4.5 ns, and the Forster radius for donor-donor energy migration is 67+/-1A. The dimerisation in different solvents was examined by using custom synthesised; mono and bis BODIPY-labelled forms of 1,2-cis-diaminocyclohexane. It is shown that gB and rB can form ground state homo- as well as hetero dimers. The dimers are non-fluorescent, compatible with H-dimers and may act as excitation traps or as acceptors to the corresponding excited monomers.

Keyword
Boron Compounds/*chemistry, Dimerization, Fluorescent Dyes/*chemistry, Molecular Conformation, Molecular Structure, Spectrometry; Fluorescence
Identifiers
urn:nbn:se:umu:diva-11786 (URN)doi:10.1016/j.saa.2005.09.035 (DOI)16455298 (PubMedID)
Available from: 2007-06-26 Created: 2007-06-26 Last updated: 2011-01-11Bibliographically approved
2. Self-aggregation: an intrinsic property of GM1 in lipid bilayers
Open this publication in new window or tab >>Self-aggregation: an intrinsic property of GM1 in lipid bilayers
2007 (English)In: Molecular membrane biology, ISSN 0968-7688, E-ISSN 1464-5203, Vol. 24, no 2, 102-112 p.Article in journal (Refereed) Published
Abstract [en]

We demonstrate that the ganglioside GM1 in lipid bilayers of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) exhibits a non-uniform lateral distribution, i.e., enriched regions of GM1 molecules are formed, which is an argument in favour of self-aggregation of GM1 being an intrinsic property of GM1 ganglioside. This was concluded from energy transfer/migration studies of BODIPY-labelled gangliosides by means of time-resolved fluorescence lifetime and depolarization experiments. Three fluorophore-labelled gangliosides were synthesized to include either of two spectroscopically different BODIPY groups. These were specifically localized either in the polar headgroup region or in the non-polar region of the lipid bilayer. An eventual ganglioside-ganglioside affinity/aggregation induced by the BODIPY groups was experimentally excluded, which suggests their use in examining the influence of GM1 in more complex systems.

Place, publisher, year, edition, pages
London: Taylor & Francis, 2007
Keyword
Ganglioside GM1, lipid rafts, aggregation, DDEM, DAET, FRET
Identifiers
urn:nbn:se:umu:diva-15005 (URN)doi:10.1080/09687860600995235 (DOI)
Available from: 2007-06-26 Created: 2007-06-26 Last updated: 2017-12-14Bibliographically approved
3. On the quantitative treatment of donor-donor energy migration in regularly aggregated proteins
Open this publication in new window or tab >>On the quantitative treatment of donor-donor energy migration in regularly aggregated proteins
2005 (English)In: Journal of Fluorescence, ISSN 1053-0509, E-ISSN 1573-4994, Vol. 15, no 5, 797-803 p.Article in journal (Refereed) Published
Abstract [en]

An algorithm is presented that quantitatively accounts for donor–donor energy migration (DDEM) among fluorophore-labeled proteins forming regular aggregates. The DDEM algorithm is based on Monte Carlo and Brownian dynamics simulations and applies to calculation of fluorescence depolarisation data, such as the fluorescence anisotropy. Thereby local orientations, as well as reorienting motions of the fluorescent group are considered in the absence and presence of DDEM and among, in principle, infinitely many proteins as they form regular aggregates. Here we apply the algorithm for calculating and illustrating the DDEM and the time-resolved fluorescence anisotropy under static as well as dynamic conditions within helical, linear and circular aggregate structures. A principal approach of the DDEM algorithm for analysing protein aggregates is also outlined.

Place, publisher, year, edition, pages
New York: Plenum Press, 2005
Keyword
Protein aggregates, protein polymers, fluorescence anisotropy, donor-donor energy migration, homo transfer, amyloid diseases, Monte Carlo simulation, Brownian dynamics
Identifiers
urn:nbn:se:umu:diva-5671 (URN)10.1007/s10895-005-2989-1 (DOI)
Available from: 2007-01-25 Created: 2007-01-25 Last updated: 2017-12-14Bibliographically approved
4. Fluorescence depolarisation studies of filamentous actin analysed with a genetic algorithm
Open this publication in new window or tab >>Fluorescence depolarisation studies of filamentous actin analysed with a genetic algorithm
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In: PNASArticle in journal (Refereed) Submitted
Identifiers
urn:nbn:se:umu:diva-5672 (URN)
Available from: 2007-01-25 Created: 2007-01-25Bibliographically approved

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