| 1. |
- Behzadi, Hadi, et al.
(author)
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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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In: Biophysical Chemistry. - : Elsevier BV. - 0301-4622 .- 1873-4200. ; 137:2-3, s. 76-80
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Journal article (peer-reviewed)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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| 2. |
- Behzadi, Hadi, et al.
(author)
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Role of spin state on the geometry and nuclear quadrupole resonance parameters in hemin complex
- 2008
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In: Biophysical Chemistry. - : Elsevier BV. - 0301-4622 .- 1873-4200. ; 134:3, s. 200-206
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Journal article (peer-reviewed)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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| 3. |
- Björnham, Oscar, 1976-, et al.
(author)
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Dynamic force spectroscopy of the Helicobacter pylori BabA-Lewis b binding
- 2009
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In: Biophysical Chemistry. - Amsterdam : Elsevier. - 0301-4622 .- 1873-4200. ; 143:1-2, s. 102-105
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Journal article (peer-reviewed)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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| 4. |
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| 5. |
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| 6. |
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| 7. |
- Börjesson, Karl, 1982, et al.
(author)
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Nucleic acid structure and sequence probing using fluorescent base analogue tCo
- 2009
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In: Biophysical Chemistry. - : Elsevier BV. - 1873-4200 .- 0301-4622. ; 139:1, s. 24-28
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Journal article (peer-reviewed)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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| 8. |
- Eriksson, Maja, 1975, et al.
(author)
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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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In: Biophysical Chemistry. - : Elsevier BV. - 1873-4200 .- 0301-4622. ; 122:3, s. 195-205
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Journal article (peer-reviewed)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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| 9. |
- Georgieva, Elka R., et al.
(author)
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Secondary structure conversions of Mycobacterium tuberculosis ribonucleotide reductase protein R2 under varying pH and temperature conditions
- 2008
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In: Biophysical Chemistry. - : Elsevier BV. - 0301-4622. ; 137:43-48
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Journal article (peer-reviewed)abstract
- The structural properties of Mycobacterium tuberculosis (Mtb) ribonucleotide reductase R2 protein were studied under varying pH and temperature conditions by circular dichroism (CD) spectroscopy as well as dynamic light scattering (DLS). Under physiological conditions this protein has a high alpha-helical content, similar to the corresponding protein from other species, e.g. mouse. Decreasing the pH induced significant structure conversions. When pH was below 6.5 an aggregated structure was observed and reached a maximum at pH 4. The aggregated state of this protein was verified by DLS and was found to be rich in beta-structure. This amyloid-like structure transformed into a molten globule state with high temperature stability (between 25 and 80 degrees C) at pH below 3. The corresponding mouse protein R2 under similar conditions showed no evidence of an aggregated state around pH 4.
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| 10. |
- Gianni, Stefano, et al.
(author)
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Identification and characterization of protein folding intermediates
- 2007
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In: Biophysical Chemistry. - : Elsevier BV. - 0301-4622 .- 1873-4200. ; 128:2-3, s. 105-113
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Research review (peer-reviewed)abstract
- In order to understand the mechanism by which a polypeptide chain folds into its functionally active native state it is necessary to characterize in detail all the species accumulated along the pathway. The elusive nature of protein folding intermediates poses their identification and characterization as an extremely difficult task in the protein folding field. In the case of small single domain proteins, the direct measurement of the thermodynamics and structural parameters of protein folding intermediates has provided new insights on the nature of the forces involved in the stabilization of nascent protein structures. Here we summarize some of the experimental approaches aimed at the detection and characterization of folding intermediates along with a discussion of some general structural features emerging from these studies.
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