| 1. |
- Reymer, Anna, 1983, et al.
(författare)
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ATP Hydrolysis in the RecA-DNA Filament Promotes Structural Changes at the Protein-DNA Interface
- 2015
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Ingår i: Biochemistry. - : American Chemical Society (ACS). - 0006-2960 .- 1520-4995. ; 54, s. 4579-4582
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Tidskriftsartikel (refereegranskat)abstract
- To address the mechanistic roles of ATP hydrolysis in RecA-promoted strand exchange reaction in homologous recombination, quantum mechanical calculations are performed on key parts of the RecA-DNA complex. We find that ATP hydrolysis may induce changes at the protein-DNA interface, resulting in the rearrangement of the hydrogen bond network connecting the ATP and the DNA binding sites.
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| 2. |
- James, PL, et al.
(författare)
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Effects of a hairpin polyamide on DNA melting: comparison with distamycin and Hoechst 33258
- 2004
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Ingår i: Biophysical Chemistry. - : Elsevier BV. - 1873-4200 .- 0301-4622. ; 111:3, s. 205-212
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Tidskriftsartikel (refereegranskat)abstract
- We have used DNase I footprinting and fluorescence melting studies to study the interaction of the hairpin polyamide Im-Py-Py-Py-(R)(H2N)gamma-Im`-PY-PY-PY-beta-Dp with its preferred binding sites (5'-WGWWCW; W=A or T) and other sequences. DNase I footprinting confirmed that the ligand binds to the sequence AGAACA at nanomolar concentrations and that changing the terminal A to G causes a dramatic decrease in affinity, while there was no. interaction with the reverse sequence WCWWGW Fluorescence melting studies with I I mer duplexes showed that the polyamide had very different effects on the forward (TGWWCT) and reverse (TCTAGT) sequences. At low concentrations, the polyamide produced biphasic melting curves with TGATCT, TGTACT and TGAACT, suggesting a strong interaction. In contrast, the melting profiles with TCTAGT were always monophasic and showed much smaller concentration dependent changes in T-m. The polyamide also showed weak binding to the sequence TGATCT when one of the central AT pairs was replaced with an AC mismatch. These melting profiles were compared with those produced by the AT-selective minor groove binding agents distamycin and Hoechst 33258 at the same site's and at similar sequences containing A(5) and (AT)(3), which are expected to bind distamycin in the 1:1 and 2:1 modes, respectively. These ligands produced simple monophasic melting curves in which the T-m steadily increased as the ligand concentration was raised. (C) 2004 Elsevier B.V. All rights reserved.
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| 3. |
- Hanczyc, Piotr, 1985, et al.
(författare)
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Multiphoton absorption in amyloid protein fibres
- 2013
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Ingår i: Nature Photonics. - : Springer Science and Business Media LLC. - 1749-4885 .- 1749-4893. ; 7:12, s. 969-972
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Tidskriftsartikel (refereegranskat)abstract
- Fibrillization of peptides leads to the formation of amyloid fibres, which, when in large aggregates, are responsible for diseases such as Alzheimer's and Parkinson's. Here, we show that amyloids have strong nonlinear optical absorption, which is not present in native non-fibrillized protein. Z-scan and pump-probe experiments indicate that insulin and lysozyme β-amyloids, as well as α-synuclein fibres, exhibit either two-photon, three-photon or higher multiphoton absorption processes, depending on the wavelength of light. We propose that the enhanced multiphoton absorption is due to a cooperative mechanism involving through-space dipolar coupling between excited states of aromatic amino acids densely packed in the fibrous structures. This finding will provide the opportunity to develop nonlinear optical techniques to detect and study amyloid structures and also suggests that new protein-based materials with sizable multiphoton absorption could be designed for specific applications in nanotechnology, photonics and optoelectronics.
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| 4. |
- Börjesson, Karl, 1982, et al.
(författare)
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Membrane-Anchored DNA Assembly for Energy and Electron Transfer
- 2009
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 1520-5126 .- 0002-7863. ; 131:8, s. 2831-2839
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Tidskriftsartikel (refereegranskat)abstract
- In this work we examine the trapping and conversion of visible light energy into chemical energy using a supramolecular assembly. The assembly consists of a light-absorbing antenna and a porphyrin redox center, which are covalently attached to two complementary 14-mer DNA strands, hybridized to form a double helix and anchored to a lipid membrane. The excitation energy Is finally trapped In the lipid phase of the membrane as a benzoquinone radical anion that could potentially be used In subsequent chemical reactions. In addition, In this model complex, the hydrophobic porphyrin moiety acts as an anchor into the liposome positioning the DNA construct on the lipid membrane surface. The results show the suitability of our system as a prototype for DNA-based light-harvesting devices, In which energy transfer from the aqueous phase to the interior of the lipid membrane Is followed by charge separation. © 2009 American Chemical Society.
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| 5. |
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| 6. |
- Lundberg, Erik, 1981, et al.
(författare)
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Nanofabrication Yields. Hybridization and Click-Fixation of Polycyclic DNA Nanoassemblies
- 2011
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Ingår i: ACS Nano. - : American Chemical Society (ACS). - 1936-086X .- 1936-0851. ; 5:9, s. 7565-7575
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Tidskriftsartikel (refereegranskat)abstract
- We demonstrate the stepwise assembly of a fully addressable polycyclic DNA hexagon nanonetwork for the preparation of a lour-ring system, one of the biggest networks yet constructed from tripodal building blocks. We find that the yield exhibits a distinct upper level
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| 7. |
- Olesiak-Banska, J., et al.
(författare)
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Nonlinear absorption spectra of ethidium and ethidium homodimer
- 2012
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Ingår i: Chemical Physics. - : Elsevier BV. - 0301-0104. ; 404, s. 33-35
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Tidskriftsartikel (refereegranskat)abstract
- The Z-scan technique was used to determine the spectral dependence of the nonlinear absorption in well-known DNA intercalators: ethidium bromide and its homodimer. It is found that the compounds show essentially the same features of their nonlinear absorption spectra with the magnitudes of the relevant cross sections scaling with molecular weight of chromophore compound.
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| 8. |
- Papp, Dóra, et al.
(författare)
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Structural water stabilizes protein motifs in liquid protein phase: The folding mechanism of short β-sheets coupled to phase transition
- 2021
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Ingår i: International Journal of Molecular Sciences. - : MDPI AG. - 1661-6596 .- 1422-0067. ; 22:16
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Tidskriftsartikel (refereegranskat)abstract
- Macromolecular associates, such as membraneless organelles or lipid-protein assemblies, provide a hydrophobic environment, i.e., a liquid protein phase (LP), where folding preferences can be drastically altered. LP as well as the associated phase change from water (W) is an intriguing phenomenon related to numerous biological processes and also possesses potential in nanotechnological applications. However, the energetic effects of a hydrophobic yet water-containing environment on protein folding are poorly understood. Here, we focus on small β-sheets, the key motifs of proteins, undergoing structural changes in liquid–liquid phase separation (LLPS) and also model the mechanism of energy-coupled unfolding, e.g., in proteases, during W → LP transition. Due to the importance of the accurate description for hydrogen bonding patterns, the employed models were studied by using quantum mechanical calculations. The results demonstrate that unfolding is energetically less favored in LP by ~0.3–0.5 kcal·mol−1 per residue in which the difference further increased by the presence of explicit structural water molecules, where the folded state was preferred by ~1.2–2.3 kcal·mol−1 per residue relative to that in W. Energetics at the LP/W interfaces was also addressed by theoretical isodesmic reactions. While the models predict folded state preference in LP, the unfolding from LP to W renders the process highly favorable since the unfolded end state has >1 kcal·mol−1 per residue excess stabilization.
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| 9. |
- Starikov, E, et al.
(författare)
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Chemical-to-Mechanical Energy Conversion in Biomacromolecular Machines: A Plasmon and Optimum Control Theory for Directional Work. 1. General Considerations
- 2008
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Ingår i: Journal of Physical Chemistry B. - 1520-5207 .- 1520-6106. ; 112:28, s. 8319-8329
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Tidskriftsartikel (refereegranskat)abstract
- To rationalize coherence and mechanochemical aspects of proteins acting as molecular machines, a plasmon concept for dealing with protein nonequilibrium dynamics is introduced and tested with respect to thermodynamic consistency. A stochastic optimum-control theory for protein conformational diffusion is developed and the corresponding stochastic Newton’s second law derived for optimum-controlled conformational diffusion in proteins. The plasmon concept is shown to be consistent with this theory, in that optical plasmons can pump entropy out of (or into) the protein, decreasing (or increasing) its conformational diffusion and, at the same time, help decrease intra- and intermolecular friction, as well as (potentially) break the symmetry of the latter. Instead, acoustic plasmons may break the spatial symmetry of a protein’s “potential of mean force”, thus converting it into an effective Brownian ratchet potential by applying quasistatic deformational corrections to the former. These concepts seem to be of rather general applicability and might also be useful when studying, for example, intercalation of cationic dyes into DNA duplexes, positively charged oligopeptide transduction through cell membranes, or even DNA translocation through nanopores.
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| 10. |
- Tuite, Eimer, 1966, et al.
(författare)
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Structural Heterogeneity in Polynucleotide-Facilitated Assembly of Phenothiazine Dyes
- 2018
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 122:11, s. 2891-2899
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Tidskriftsartikel (refereegranskat)abstract
- The assembly of stacked dyes on DNA is of interest for electron transfer, light harvesting, sensing, and catalysis applications. A combination of UV/vis absorption, linear dichroism (LD), and circular dichroism (CD) was applied to characterize thoroughly the aggregation with DNA of the phenothiazine dyes methylene blue, azure B, and thionine. Aggregates of each dye with [poly(dG-dC)] 2 , [poly(dA-dT)] 2 , and calf thymus DNA were explored at high dye:DNA binding ratios, where excess dye groove-binds after all intercalation sites are filled. The organization of the aggregates (dimers, trimers, and multimers) with polydeoxynucleotides displays a structural diversity that depends on DNA sequence, extent of methylation of dye exocyclic amine groups, and ionic strength. The dyes typically form right-handed H-aggregates having negative LD, consistent with stepped stacking along the minor groove. However, aggregates in some dye:DNA aggregates show left-handed chirality or positive LD, indicating unusual modes of aggregation such as formation of adventitious dimers between intercalated and minor groove bound dye. In terms of sequence-dependence, methylene blue shows more extensive aggregation with [poly(dA-dT)] 2 , while thionine aggregates more with [poly(dG-dC)] 2 . Azure B has distinctive behavior that is unlike either other dyes. Thus, although these phenothiazine dyes possess a common tricyclic framework, the organization of their polynucleotide-facilitated aggregates depends sensitively on the extent of methylation of the exocyclic amines.
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