The photoreactivation of 6 - 4 photoproducts in chloroplast and nuclear DNA depends on the amount of the Arabidopsis UV repair defective 3 protein.

Background: 6 - 4 photoproducts are the second most common UV-induced DNA lesions after cyclobutane pyrimidine dimers. In plants, they are mainly repaired by photolyases in a process called photoreactivation. While pyrimidine dimers can be deleterious, leading to mutagenesis or even cell death, 6 - 4 photoproducts can activate specific signaling pathways.

Effect of H bond removal and changes in the position of the iron-sulphur head domain on the spin-lattice relaxation properties of the [2Fe-2S](2+) Rieske cluster in cytochrome bc(1).

Here, comparative electron spin-lattice relaxation studies of the 2Fe-2S iron-sulphur (Fe-S) cluster embedded in a large membrane protein complex - cytochrome bc1 - are reported. Structural modifications of the local environment alone (mutations S158A and Y160W removing specific H bonds between Fe-S and amino acid side chains) or in combination with changes in global protein conformation (mutations/inhibitors changing the position of the Fe-S binding domain within the protein complex) resulted in different redox potentials as well as g-, g-strain and the relaxation rates (T1(-1)) for the Fe-S cluster. The relaxation rates for T < 25 K were measured directly by inversion recovery, while for T > 60 K they were deduced from simulation of continuous wave EPR spectra of the cluster using a model that included anisotropy of Lorentzian broadening.

Triplet state of the semiquinone-Rieske cluster as an intermediate of electronic bifurcation catalyzed by cytochrome bc1.

Efficient energy conversion often requires stabilization of one-electron intermediates within catalytic sites of redox enzymes. While quinol oxidoreductases are known to stabilize semiquinones, one of the famous exceptions includes the quinol oxidation site of cytochrome bc1 (Qo), for which detection of any intermediate states is extremely difficult. Here we discover a semiquinone at the Qo site (SQo) that is coupled to the reduced Rieske cluster (FeS) via spin-spin exchange interaction.

Rectangular loop-gap resonator with the light access to the sample.

A modified rectangular loop-gap resonator for X-band electron paramagnetic resonance (EPR) studies of aqueous samples, enabling the light access, is described. Changes introduced into rectangular resonator geometry, previously presented in Piasecki et al. (1998) [1], and redesigned coupling structure lead to the better thermal and mechanical stability.

Magnetic interactions sense changes in distance between heme b(L) and the iron-sulfur cluster in cytochrome bc(1).

During the operation of cytochrome bc(1), a key enzyme of biological energy conversion, the iron-sulfur head domain of one of the subunits of the catalytic core undergoes a large-scale movement from the catalytic quinone oxidation Q(o) site to cytochrome c(1). This changes a distance between the two iron-two sulfur (FeS) cluster and other cofactors of the redox chains. Although the role and the mechanism of this movement have been intensely studied, they both remain poorly understood, partly because the movement itself is not easily traceable experimentally.

Estimation of binding parameters for the protein-protein interaction using a site-directed spin labeling and EPR spectroscopy.

Sensitivity of the electron paramagnetic resonance (CW EPR) to molecular tumbling provides potential means for studying processes of molecular association. It uses spin-labeled macromolecules, whose CW EPR spectra may change upon binding to other macromolecules. When a spin-labeled molecule is mixed with its liganding partner, the EPR spectrum constitutes a linear combination of spectra of the bound and unbound ligand (as seen in our example of spin-labeled cytochrome c(2) interacting with cytochrome bc(1) complex).

Stearic acid spin labels in lipid bilayers: insight through atomistic simulations.

Spin-labeled stearic acid species are commonly used for electron paramagnetic resonance (EPR) studies of cell membranes to investigate phase transitions, fluidity, and other physical properties. In this paper, we use large-scale molecular dynamics simulations to investigate the position and behavior of nitroxide spin labels attached to stearic acid molecules in dipalmitoylphosphatidylcholine (DPPC) bilayers. The results of these studies are potentially very important for the interpretation of EPR spectra, which rely on assumptions about the position of the label in the membrane.

Influence of the disulfide bond configuration on the dynamics of the spin label attached to cytochrome c.

A series of multi-nanosecond molecular dynamics (MD) simulations of wild-type cytochrome c and its spin-labeled variants with the methanethiosulfonate moiety attached at position C102 were performed (1) to elucidate the effect of the spin probe presence on the protein structure and (2) to describe the structure and dynamics of the spin-label moiety. Comparisons with the reference crystal structure of cytochrome c (PDB entry: 1YCC) indicate that the protein secondary structure is well preserved during simulations of the wild-type cytochrome c but slightly changed in simulations of the cytochrome c labeled at position C102. At the time scale covered in our simulations, the spin label exhibits highly dynamical behavior.

Determination of T1-spin-lattice relaxation time in a two-level system by continuous wave multiquantum electron paramagnetic resonance spectroscopy in a presence of tetrachromatic microwave irradiation.

Applicability of continuous wave multiquantum EPR methods to study relaxation times at X-band is examined. Multiquantum transitions excited in a two-level system by tetrachromatic irradiation are used for these studies. The Bloch equation model is applied to simulate lineshapes of the three quantum transitions as a function of frequency difference between exciting fields.