| 1. |
- Graslund, A., et al.
(författare)
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DYNAMICS OF BENZO A PYRENE DIOL EPOXIDE ADDUCTS IN POLY(DG-DC) . (DG-DC) STUDIED BY SYNCHROTRON EXCITED FLUORESCENCE POLARIZATION ANISOTROPY DECAY
- 1992
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Ingår i: Biophysical Chemistry. - : Elsevier BV. - 1873-4200 .- 0301-4622. ; 44:1, s. 21-28
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Tidskriftsartikel (refereegranskat)abstract
- Time-resolved fluorescence studies have been performed on (+)-anti-7,8-dihydrodiol-9,10-epoxy-benzo[a]pyrene adducts in double-stranded poly(dG-dC) . (dG-dC). Part of the adduct population gives rise to excimer fluorescence. The heterogeneous fluorescence emission decay curves at 22-degrees-C could be resolved into three components with lifetimes: 0.4 ns, 3 ns and 24 ns for the total fluorescence (monomer and excimer emission), and 0.5 ns, 5 ns and 24 ns, respectively, for excimer emission alone. The relative amplitudes for the longer lifetimes were larger for the pure excimer population than for the mixed population. The fluorescence polarization anisotropy decay curves were resolved into two components of rotational correlation times: 0.4 ns and 25 ns for the total fluorescence and 0.3 ns and 33 ns for the excimer fluorescence. We interpret the two rotational correlation times to correspond to local motion of the adduct and segmental motion of the polynucleotide, respectively.
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| 2. |
- Mörgelin, Matthias, et al.
(författare)
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The cartilage proteoglycan aggregate: assembly through combined protein-carbohydrate and protein-protein interactions
- 1994
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Ingår i: Biophysical Chemistry. - : Elsevier BV. - 1873-4200 .- 0301-4622. ; 50:1-2, s. 113-128
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Tidskriftsartikel (refereegranskat)abstract
- In vitro reassembled aggregates of cartilage proteoglycan (aggrecan) were studied by glycerol spraying/rotary shadowing electron microscopy and compared to the corresponding native (i.e. never dissociated) structures. In both cases a tightly packed central filament structure was observed consisting of the hyaluronate binding region (HABR) of the proteoglycan, link protein (LP) and hyaluronate (HA). This differs from earlier results where a discontinuous central filament structure was seen after spreading proteoglycan aggregates at a water/air interphase. Binding of isolated HABR to HA is random but upon addition of link protein a clustering of the HA-binding proteins is observed, indicating a cooperativity. In a fully saturated aggregate the HA is covered by a continuous protein shell consisting of HABR and LP. When added in amounts below saturation HABR and LP bind to the HA in clusters which are interrupted by free strands of HA. The proteoglycan aggregate is thus an example for a structure where a polysaccharide forms a template for a supramolecular assembly largely stabilized by protein-protein interactions.
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| 3. |
- Nordén, Bengt, 1945, et al.
(författare)
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High-sensitivity linear dichroism as a tool for equilibrium analysis in biochemistry- stability constant of DNA-ethidiumbromide complex
- 1976
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Ingår i: Biophysical Chemistry. - : Elsevier BV. - 1873-4200 .- 0301-4622. ; 4:2, s. 191-198
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Tidskriftsartikel (refereegranskat)abstract
- A stoichiometrical application of a sensitive method for linear dichroism (LD) detection is suggested for biochemical purposes. The complex formation between a binding site on a polynucleotide and a ligand may be studied with high precision if the following conditions are fulfilled: (1) The polymer can be given a fixed degree of orientation. (2) The site has a specific orientation with respect to the orientation axis of the polymer (e.g., intercalation). (3) The ligand has an anisotropic optical absorption property.The method was applied to studying the complex between DNA and ethidiumbromide, which was detected by LD with precision of ± 0.5 × 10−7 M in a 4 × 10−4 M DNA solution, i.e., 0.1% occupation of the total site concentration can be detected. The complsxation could be explained by a single type of site (n = 0.14 ± 0.01 sites per nucleotide residue) and a stability constant K1 = (2.5 ± 1) × 105 M−1 at 0.2 M ionic strength.From the specific LD an average angle 60° was concluded between the helix axis and the long axis of the ethidiumbromide molecule.This value formally contradicts the Watson-Crick model or the intercalation model but may be explained by extension and deformation effects on the xhain by the flow.
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| 4. |
- Nordén, Bengt, 1945, et al.
(författare)
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Linear dichroism studies of binding site structures in solution: Complexes between DNA and basic arylmethane dyes
- 1978
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Ingår i: Biophysical Chemistry. - : Elsevier BV. - 1873-4200 .- 0301-4622. ; 8:1, s. 1-15
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Tidskriftsartikel (refereegranskat)abstract
- The interaction between B-form DNA and twelve cationic triaryl-methane dyes was studied with respect lo optical properties and stabilities, using linear dichroism (LD) and aqueous two-phase partition techniques. Monovalent dyes derived from crystal violet as a rule form a single strong complex (K1 ca 105 M−1; site density per nucleotide base n1 ca 0.1 at 0.1M ionic strength) in which the plane of the dye is at an angle of less than 50° to the local DNA helix axis. The complex with fuchsin is weaker (104M−1) but can be explained by a similar orientation. For some of the dyes (those with pseudo-C2v symmetry) XXXre angular orientations of two molecule-fixed axes can be obtained. For the divalent methyl green a second complex appears to be formed at low ionic strength. Methyl green (and to some extent 2-thiophene green and malachite green) show exciton splitting in the LD spectrum and circular dichroism assignable to exciton coupling between transition dipoles roughly parallel to the helical strands, indicating a dye-dye interaction. Tne optical data, supported by fitting experiments with space-filling models, suggests a general structure for the binding site. The dye is not intercalated but is bound to exposed hydrophobic regions in the major groove. The ligand is in part (the charged amino groups) in contact with the phosphoribose chain but its main surface lies against the hydrophobic base-pair stack. For a diphenylmethane dye, Michler's hydrol blue, a perpendicular orientation was observed, possibly due to intercaiation.
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| 5. |
- Nordén, Bengt, 1945, et al.
(författare)
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Optical studies on complexes between DNA and pseudoisocyanine
- 1976
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Ingår i: Biophysical Chemistry. - : Elsevier BV. - 1873-4200 .- 0301-4622. ; 6:1, s. 31-45
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Tidskriftsartikel (refereegranskat)abstract
- Linear dichroism (LD) results when pseudoisocyanine = PIC (1, 1-diethyl-2,2'-cyanine iodide) binds to flow-oriented DNA. LD may be used to follow the complexation both stoichiometrically and structurally, since when specified to unit complex concentration LD provides a measure of the average orientation of the absorbing transition dipole.Two different types of complexes can be distinguished: I. One strong, ionic-strength insensitive complex with monomeric PIC with an orientation indicating intercalation. II. Several weaker complexes of electrostatic nature (only observed at I
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| 6. |
- Nordén, Bengt, 1945
(författare)
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Structural evidence on DNA carcinogen interactions: N-acetoxy-N-2acetylaminofluorene binding to DNA
- 1978
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Ingår i: Biophysical Chemistry. - : Elsevier BV. - 1873-4200 .- 0301-4622. ; 8:4, s. 385-391
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Tidskriftsartikel (refereegranskat)abstract
- Linear dichroism (LD) gives useful information on the interaction between DNA and the directly acting carcinogen N-acetoxy-N-2-acetylaminofluorene (AAAF). In 50% methanol solvent with low ionic strength only a weak complex (van der Waals) appears. However, above 40° C strand separation takes place and a covalent aminofluorene complex forms. After renaturation a characteristic positive LD.band is observed at 306 nm. The average angular orientation of the longaxis of the fluorene moiety (47° to the local helix axis) is inconsistent with intercalation- It can be explained for instance by a free rotation around a C(DNA)-N (aminofluorene) bond or by a major groove site. The occupation density was 1–2 aminofluorene residues per 100 bases. With native DNA, AAAF slowly forms a covalent complex which has a negative LD at 307 nm. The orientation (70–90° ) is consistent with steric direction by the strand.
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| 7. |
- Bergstrand, Nill, et al.
(författare)
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Interactions between pH-sensitive liposomes and model membranes
- 2003
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Ingår i: Biophysical Chemistry. - 0301-4622 .- 1873-4200. ; 104:1, s. 361-379
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Tidskriftsartikel (refereegranskat)abstract
- The structure and dynamics of two different pH-sensitive liposome systems were investigated by means of cryo-transmission electron microscopy and different photophysical techniques. Both systems consisted of dioleoylphosphatidylethanolamine (DOPE) and contained either oleic acid (OA) or a novel acid-labile polyethylene glycol-conjugated lipid (DHCho-MPEG5000) as stabiliser. Proton induced leakage, lipid mixing and structural changes were studied in the absence and presence of EPC liposomes, as well as in the presence of liposomes designed to model the endosome membrane. Neither DHCho-MPEG5000- nor OA-stabilised liposomes showed any tendency for fusion with pure EPC liposomes or endosome-like liposomes composed of EPC/DOPE/SM/Cho (40/20/6/34 mol.%). Our investigations showed, however, that incorporation of lipids from the pH-sensitive liposomes into the endosome membrane may lead to increased permeability and formation of non-lamellar structures. Taken together the results suggest that the observed ability of DOPE-containing liposomes to mediate cytoplasmic delivery of hydrophilic molecules cannot be explained by a mechanism based on a direct, and non-leaky, fusion between the liposome and endosome membranes. A mechanism involving destabilisation of the endosome membrane due to incorporation of DOPE, seems more plausible.
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| 8. |
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| 9. |
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| 10. |
- Huber, M., et al.
(författare)
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Phase memory relaxation times of spin labels in human carbonic anhydrase II : Pulsed EPR to determine spin label location
- 2001
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Ingår i: Biophysical Chemistry. - 0301-4622 .- 1873-4200. ; 94:3, s. 245-256
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Tidskriftsartikel (refereegranskat)abstract
- Phase memory relaxation times (TM or T2) of spin labels in human carbonic anhydrase II (HCA II) are reported. Spin labels (N-(1-oxyl-2,2,5,5-tetramethyl-3-pyrrolidinyl)iodoacetamide, IPSL) were introduced at cysteines, by site-directed mutagenesis at seven different positions in the protein. By two pulse electron paramagnetic resonance (EPR), electron spin echo decays at 45 K are measured and fitted by stretched exponentials, resulting in relaxation parameters TM and x. TM values of seven positions are between 1.6 ╡s for the most buried residue (L79C) and 4.7 ╡s for a residue at the protein surface (W245C). In deuteriated buffer, longer TM are found for all but the most buried residues (L79C and W97C), and electron spin echo envelop modulation (ESEEM) of deuterium nuclei is observed. Different deuterium ESEEM patterns for W95C and W16C (surface residue) indicate differences in the local water concentration, or accessibility, of the spin label by deuterium. We propose TM as a parameter to determine the spin label location in proteins. Furthermore, these systems are interesting for studying the pertaining relaxation mechanism. ⌐ 2001 Elsevier Science B.V. All rights reserved.
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| 11. |
- Morozova, Ludmilla, et al.
(författare)
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Stability of equine lysozyme : I. thermal unfolding behaviour
- 1991
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Ingår i: Biophysical Chemistry. - 0301-4622 .- 1873-4200. ; 41:2, s. 185-191
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Tidskriftsartikel (refereegranskat)abstract
- The thermal denaturation of Ca(2+)- and apo-forms of equine lysozyme was followed by using far and near UV circular dichroism and intrinsic fluorescence methods. The difference found between the temperature dependence of the ellipticity at 222 nm and 287 nm, which show two stages in the thermal transition, and those at 228 nm and 294 nm, which indicate only one stage over a wide range of temperatures reflects that different subdivisions of the protein molecule are characterized by a different stability, cooperativity and pathway of denaturation. The first transition, reflected in the increase of the ellipticity at 222 nm and 287 nm, coincides with the transition detected by fluorescence and occurs at 30-50 degrees C for the apo-form and at 50-60 degrees C for the Ca(2+)-form of lysozyme. It seems to correlate with the transfer of some tryptophan residues to a more hydrophobic environment and with a local rearrangement of the tertiary and secondary structures. The unfolding transition detected by the decrease of the ellipticity at all wavelengths occurs nearly in the same temperature region for the apo- and Ca(2+)-forms, i.e. 50-80 degrees C and 55-80 degrees C, respectively. The presence of a Ca(2+)-binding loop in equine lysozyme may be partly responsible for the drastic destabilization of its structure as a whole both in the presence but especially in the absence of Ca2+ in comparison with hen and human lysozymes.
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| 12. |
- Persson, Bengt L., et al.
(författare)
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A circular dichroism study of mitochondrial transhydrogenase from beef heart
- 1991
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Ingår i: Biophysical Chemistry. - 0301-4622 .- 1873-4200. ; 39:3, s. 267-272
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Tidskriftsartikel (refereegranskat)abstract
- This paper describes a circular dichroism (CD) spectroscopy study of purified proton-pumping nicotinamide nucleotide transhydrogenase from beef heart. The CD spectrum obtained was used to estimate the content of secondary structures of the purified enzyme and suggests the presence of 40–45% α-helical structure and long, possibly membrane-spanning α-helices. The spectrum was essentially unaffected by the absence or presence of transhydrogenase substrates, suggesting that the catalytic and proton-translocating activities of the enzyme occur without major rearrangements at the level of secondary structures.
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| 13. |
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| 14. |
- Testorf, Martin, 1972-, et al.
(författare)
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A model for switch-like phenomena in biological systems
- 2001
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Ingår i: Biophysical Chemistry. - 0301-4622 .- 1873-4200. ; 94:1-2, s. 1-9
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Tidskriftsartikel (refereegranskat)abstract
- We present a model for the activity of protein clusters based on a simultaneous desorption of an activator (agonist, substrate molecule, etc.) and an inactivator (antagonist, inhibitor, etc.) caused by the collision or interaction between two effector molecules (e.g. receptors, enzymes). This model gives rise to switch-like dose–response curves, which are difficult to explain by ordinary co-operativity. It fits with recent experimental results obtained on single cells. Some other interesting aspects of the model are also pointed out. The model is similar to the model used to explain steep ‘dose–response curves’ in heterogeneous catalysis, caused by the reaction between two different molecules or atoms on the surface of the catalyst.
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| 15. |
- Andersson, Alexandra, et al.
(författare)
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The density of anionic lipids modulates the adsorption of α-Synuclein onto lipid membranes
- 2024
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Ingår i: Biophysical Chemistry. - 0301-4622. ; 305
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Tidskriftsartikel (refereegranskat)abstract
- α-Synuclein is an intrinsically disordered presynaptic protein associated with Parkinson's disease. The physiological role of α-Synuclein is not fully understood, but the protein is known to interact with lipid membranes. We here study how membrane charge affects the adsorption of α-Synuclein to (i) supported lipid bilayers and (ii) small unilamellar vesicles with varying amounts of anionic lipids. The results showed that α-Synuclein adsorbs onto membranes containing ≥5% anionic phosphatidylserine (DOPS) lipids, but not to membranes containing ≤1% DOPS. The density of adsorbed α-Synuclein increased steadily with the DOPS content up to 20% DOPS, after which it leveled off. The vesicles were saturated with α-Synuclein at a 3–5 times higher protein density compared to the supported bilayers, which suggests that a more deformable membrane binds more α-Synuclein. Altogether, the results show that both membrane charge density and flexibility influence the association of α-Synuclein to lipid membranes.
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| 16. |
- Behzadi, Hadi, et al.
(författare)
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A theoretical study of repeating sequence in HRP II : a combination of molecular dynamics simulations and (17)O quadrupole coupling tensors
- 2008
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Ingår i: Biophysical Chemistry. - : Elsevier BV. - 0301-4622 .- 1873-4200. ; 137:2-3, s. 76-80
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Tidskriftsartikel (refereegranskat)abstract
- Histidine rich protein II derived peptide (HRP II 169-182) was investigated by molecular dynamics, MD, simulation and (17)O electric field gradient, EFG, tensor calculations. MD simulation was performed in water at 300 K with alpha-helix initial structure. It was found that peptide loses its initial alpha-helix structure rapidly and is converted to random coil and bent secondary structures. To understand how peptide structure affects EFG tensors, initial structure and final conformations resulting from MD simulations were used to calculate (17)O EFG tensors of backbone carbonyl oxygens. Calculations were performed using B3LYP method and 6-31+G basis set. Calculated (17)O EFG tensors were used to evaluate quadrupole coupling constants, QCC, and asymmetry parameters, eta(Q). Difference between the calculated QCC and eta(Q) values revealed how hydrogen-bonding interactions affect EFG tensors at the sites of each oxygen nucleus.
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| 17. |
- Behzadi, Hadi, et al.
(författare)
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Role of spin state on the geometry and nuclear quadrupole resonance parameters in hemin complex
- 2008
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Ingår i: Biophysical Chemistry. - : Elsevier BV. - 0301-4622 .- 1873-4200. ; 134:3, s. 200-206
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Tidskriftsartikel (refereegranskat)abstract
- Theoretical calculations of structural parameters, 57Fe, 14N and 17 O electric field gradient (EFG) tensors for full size-hemin group have been carried out using density functional theory. These calculations are intended to shed light on the difference between the geometry parameters, nuclear quadrupole coupling constants (QCC), and asymmetry parameters (eta Q) found in three spin states of hemin; doublet, quartet and sextet. The optimization results reveal a significant change for propionic groups and porphyrin plane in different spin states. It is found that all principal components of EFG tensor at the iron site are sensitive to electronic and geometry structures. A relationship between the EFG tensor at the 14N and 17 O sites and the spin state of hemin complex is also detected.
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| 18. |
- Björnham, Oscar, 1976-, et al.
(författare)
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Dynamic force spectroscopy of the Helicobacter pylori BabA-Lewis b binding
- 2009
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Ingår i: Biophysical Chemistry. - Amsterdam : Elsevier. - 0301-4622 .- 1873-4200. ; 143:1-2, s. 102-105
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Tidskriftsartikel (refereegranskat)abstract
- The binding strength of the Helicobacter pylori adhesin–receptor complex BabA-ABO/Lewis b has been analyzed by means of dynamic force pectroscopy. High-resolution measurements of rupture forces were performed in situ on single bacterial cells, expressing the high-affinity binding BabA adhesin, by the use of force measuring optical tweezers. The resulting force spectra revealed the mechanical properties of a single BabA–Leb bond. It was found that the bond is dominated by one single energy barrier and that it is a slipbond. The bond length and thermal off-rate were assessed to be 0.86±0.07 nm and 0.015±0.006 s−1, respectively.
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| 19. |
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| 20. |
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| 21. |
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| 22. |
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| 23. |
- Börjesson, Karl, 1982, et al.
(författare)
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Nucleic acid structure and sequence probing using fluorescent base analogue tCo
- 2009
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Ingår i: Biophysical Chemistry. - : Elsevier BV. - 1873-4200 .- 0301-4622. ; 139:1, s. 24-28
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Tidskriftsartikel (refereegranskat)abstract
- The fluorescent cytosine analog tC(o) is on average the brightest probe of its kind and, moreover, it introduces minimal perturbations to the normal secondary structure of DNA. Here several ways of how tC(o), with an advantage, can be used as a local fluorescent probe in nucleic acid systems are presented. Most importantly, we show that tCo is an excellent probe for the detection of individual melting processes of complex nucleic acid structures containing a large number of separate secondary structure motifs. Since conventional UV-melting investigations merely monitor the global melting process of the whole nucleic acid structure, e.g. multi-hairpin systems in RNA/DNA, and thus is incapable of estimating individual melting transitions of such systems, tC(o) represents a new method of characterization. Furthermore, we find that tCo may be used to detect bulges and loops in nucleic acids as well as to distinguish a matched base-pair from several of the mismatched.
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| 24. |
- Costas, M, et al.
(författare)
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Thermodynamics of aliphatic and aromatic hydrocarbons in water
- 1998
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Ingår i: Biophysical Chemistry. - 0301-4622 .- 1873-4200. ; 74, s. 83-87
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Tidskriftsartikel (refereegranskat)abstract
- Makhatadze and Privalov have analyzed the thermodynamics of transfer of aliphatic and aromatic hydrocarbons from the gas phase into water. Finding that the hydration free energy of aliphatic and aromatic hydrocarbons trave different signs, they conclude that the mechanism causing hydrophobicity of these solutes is of a different nature. Here, we offer an alternative analysis of the dissolution of these non-polar compounds into water based on a recently published interpretation scheme for thermodynamic transfer functions. Our analysis shows that the hydrophobicity of aromatic and aliphatic hydrocarbons is qualitatively the same, i.e. its causes are the same namely the extremely high cohesive energy of water which overcomes the favorable solute-solute and solute-water interactions. However, both analyses conclude that the experimentally observed quantitative difference between the interactions of water with aliphatic and aromatic hydrocarbons, can be assigned to the formation of aromatic ring-water H-bonds.
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| 25. |
- Eriksson, Maja, 1975, et al.
(författare)
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Comparing mono- and divalent DNA groove binding cyanine dyes--Binding geometries, dissociation rates, and fluorescence properties
- 2006
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Ingår i: Biophysical Chemistry. - : Elsevier BV. - 1873-4200 .- 0301-4622. ; 122:3, s. 195-205
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Tidskriftsartikel (refereegranskat)abstract
- The unsymmetrical cyanine dyes BOXTO-PRO and BOXTO-MEE were derived from the DNA groove binder BOXTO, by adding a positively charged or a non-ionic hydrophilic tail to BOXTO, respectively. The main objective was to obtain more efficient DNA probes, for instance in electrophoresis and microscopy, by slowing down the dissociation of BOXTO from DNA. The interactions with mixed sequence DNA was studied with fluorescence and absorbance spectroscopy, stopped-flow dissociation and gel electrophoresis. Both the derivatives are groove bound as BOXTO, and have similar fluorescence properties when bound to mixed sequence DNA in free solution. BOXTO-PRO exhibits a slower dissociation than BOXTO from DNA, whereas the dissociation rate for BOXTO-MEE is faster and, unexpectedly independent of the ionic strength. During gel electrophoresis both BOXTO-PRO and BOXTO-MEE exhibit a faster dissociation rate than BOXTO. Still, BOXTO-PRO seems to be a good alternative as DNA probe, especially for applications in free solution where the dissociation is slower than for the corresponding intercalator TOPRO-1.
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