Protein dynamics from solution NMR

Solution nuclear magnetic resonance (NMR) spectroscopy is unique in its ability to elucidate the details of atomic-level structural and dynamical properties of biological macromolecules under native-like conditions. Recent advances in NMR techniques and protein sample preparation now allow comprehensive investigation of protein dynamics over timescales ranging 14 orders of magnitude at nearly every atomic site. Thus, solution NMR is poised to reveal aspects of the physico-chemical properties that govern the ensemble distribution of protein conformers and the dynamics of their interconversion. We review these advances as well as their recent application to the study of proteins.     

The effect of ambient redox potential on the transient electron spin echo signals observed in chloroplasts and photosynthetic algae

Time-resolved electron spin echo (ESE) studies were carried out at room temperature on chloroplast preparations and whole cells of photosynthetic algae. The signals observed exhibit the unexpected special ESE signal which we have proposed to be the result of transient interactions between P⁺-700 and an early electron acceptor of Photosystem I (Thurnauer, M.C. and Norris, J.R. (1980) Chem. Phys. Lett. 76, 557–561). The intensity of the special ESE signal decreases with the chemical reduction of the Center A-Center B complex. The results suggest that in the untreated photosynthetic systems we are initially observing P⁺-700 as it interacts with the reduced acceptor which precedes the Center A-Center B complex. Then the decay of the special ESE signal (approx. 170 ns) gives the lifetime of this reduced acceptor as it participates in forward electron transport.     

Electron spin resonance--spin stabilization in enzymatic systems: detection of semiquinones produced during peroxidatic oxidation of catechols and catecholamines

The electron spin resonance-spin stabilization technique has been applied in an enzymatic system. This technique, which generates radicals in high steady-state concentration under static conditions, involves the use of limited quantities of enzyme and substrate while allowing facile spectral interpretation. In this work $\text{o}$-semiquinone intermediates produced during peroxidase-catalyzed oxidation of catechols and catecholamines have been detected as their metal complexes with Zn²⁺. No significant effect on the peroxidase activity was found for the concentrations of Zn²⁺ ions employed.     

Enzymatic copolymerization of nitroxide labelled uridine derivatives with nucleoside diphosphates

Nucleic acids with nitroxide radicals covalently bound to a limited number of bases in the lattice are valuable for monitoring the interaction of nucleic acids in complex biological systems. An enzymatic approach is described for obtaining spin labelled polyribonucleotides where the position of the nitroxide radical(s) with respect to the base is well defined. The synthesis and properties of (RUGT.U)_n, (RUGT. C)_n, (RUGT. A)_n), and the biradical system (lRUGT, U)_n are reported.     

Identification of irradiated lentils

In the recent years, increasing attention has been given to irradiation as a method of food preservation. Since the treatment of foods with radiation has to include dose limits, this requires the development of appropriate and reliable method for determining whether a particular food has been irradiated or not and, if possible, at what dose. Various methods are possible depending on the nature of the food. Only electron spin resonance (ESR) and thermoluminescence (TL) detection will be considered here. Studies were carried out on green lentils and encouraging results were obtained.     

Cytochrome c/H2O2-mediated one electron oxidation of carcinogenic N-fluorenylacetohydroxamic acids to nitroxyl free radicals

The oxidation of carcinogenic hydroxamic acids, N-hydroxy-N-2-fluorenylacetamide (N-OH-2-FAA) and N-hydroxy-N-3-fluorenylacetamide (N-OH-3-FAA) catalyzed by horseradish peroxidase (HRP) or cytochrome c in the presence of H2O2 was investigated. HRP/H2O2 was a more efficient system in oxidation of both hydroxamic acids and the standard substrate, guaiacol, then cytochrome c/H2O2. Peroxidative activity of cytochrome c was shown after incubation with Triton X-100 and H2O2 for 20 min at room temperature in 0.05 M phosphate buffer (pH 7.5) or in 0.1 M sodium acetate (pH 6.0) without Triton X-100. Both hydroxamic acids were oxidized to nitroxyl free radicals as shown by electron spin resonance (ESR) spectroscopy. These radicals dismutated to equimolar amounts of 2- or 3-nitrosofluorene and acetate esters of the corresponding hydroxamic acids as shown by thin layer chromatography and spectrophotometric analysis of the products. In addition, large amounts of the N-fluorenylamides were generated in the reactions with cytochrome c/H2O2 system. Of the products, only 2- or 3-nitrosofluorene per se or when generated from the oxidation of the hydroxamic acids, interacted with lecithin (1 mg/ml) to yield ESR signals of the immobilized nitroxyl free radicals. In contrast to HRP/H2O2 system, in which the initial velocity of the radical formation was too fast to measure and the maximal concentrations of the nitroxyl free radicals of both hydroxamic acids were similar, in the cytochrome c/H2O2 system the nitroxyl free radical of N-OH-2-FAA formed at a 6-fold faster rate and accumulated at a 2-fold higher concentration than the radical of N-OH-3-FAA. In both enzyme systems, the persistence of the signal and the length of time before it had decreased to one half its maximum were several-fold longer for the nitroxyl free radical of N-OH-3-FAA than for that of N-OH-2-FAA. These data showed that these nitroxyl free radicals differed in their kinetic properties. One electron oxidation of N-OH-3-FAA by HRP/H2O2 system and of both isomeric hydroxamic acids by cytochrome c/H2O2 system are reported for the first time in this work and may be considered an activation reaction in carcinogenesis by these compounds.     

Absence of generation of oxygen-containing free radicals with 4'-deoxydoxorubicin, a non-cardiotoxic anthracycline drug

In vitro ESR studies of doxorubicin and 4'-deoxydoxorubicin have been conducted using the spin traps PBN and DMPO. Solutions prepared in the presence of atmospheric oxygen at pH = 12 exhibited a typical semiquinone signal preceded by a short-lived signal attributed to perhydroxyl radical, HO2. At physiological pH the perhydroxyl signal was observed in the doxorubicin solution but not in 4'-deoxydoxorubicin. In the absence of oxygen, at pH = 7.5, neither drug exhibited a signal. A relationship is proposed between the perhydroxyl radical and the cardiotoxicity observed in doxorubicin but not in 4'-deoxydoxorubicin.     

Studies of the coordination of rare earth and transition metal nucleotide complexes by an electron spin echo method

Titrations of the paramagnetic rate earth ions Ce(III), Nd(III), Er(III), and Yb(III) with ATP, ADP, adenosine, and the hexametaphosphate ligands have been performed in order to establish the conditions required to form saturated complexes. These titrations have been made by recording the decay envelope of electron spin echoes for a range of different concentrations of the species concerned and observing the ‘nuclear modulation effect’ in the echo envelope. This novel method can be used when optical titrations are not feasible. It also yields additional information concerning changes in the number and nature of the coordinating groups, in the distances of these groups from the paramagnetic ion, and in the degree of water coordination in the primary sphere. It was shown that: (a) ATP has a greater affinity than ADP for rate earth ions; (b) Ce(III) has a greater affinity than Nd(III) for ATP; (c) the interaction between rate earth ions and ³¹P nuclei in the added phosphates is greatest for cations with the smallest radii; (d) more phosphate groups are bound in hexametaphosphate complexes of rate earth ions than in the corresponding ATP complexes; (e) some of the coordination sites in rare earth ATP complexes are occupied by water. In othe studies performed with paramagnetic transition metal ions, it was shown that Co(II) can, under certain conditions, bind to the adenine moiety of ATP.     

Challenges in cancer research and multifaceted approaches for cancer biomarker quest

Recent advances in cancer biology have subsequently led to the development of new molecularly targeted anti-cancer agents that can effectively hit cancer-related proteins and pathways. Despite better insight into genomic aberrations and diversity of cancer phenotypes, it is apparent that proteomics too deserves attention in cancer research. Currently, a wide range of proteomic technologies are being used in quest for new cancer biomarkers with effective use. These, together with newer technologies such as multiplex assays could significantly contribute to the discovery and development of selective and specific cancer biomarkers with diagnostic or prognostic values for monitoring the disease state. This review attempts to illustrate recent advances in the field of cancer biomarkers and multifaceted approaches undertaken in combating cancer.