Electron spin resonance melting of chemically spin-labeled nucleic acids

NMR approaches for structural analysis of multidomain proteins and complexes in solution

NMR spectroscopy is a key method for studying the structure and dynamics of (large) multidomain proteins and complexes in solution. It plays a unique role in integrated structural biology approaches as especially information about conformational dynamics can be readily obtained at residue resolution. Here, we review NMR techniques for such studies focusing on state-of-the-art tools and practical aspects. An efficient approach for determining the quaternary structure of multidomain complexes starts from the structures of individual domains or subunits. The arrangement of the domains/subunits within the complex is then defined based on NMR measurements that provide information about the domain interfaces combined with (long-range) distance and orientational restraints. Aspects discussed include sample preparation, specific isotope labeling and spin labeling; determination of binding interfaces and domain/subunit arrangements from chemical shift perturbations (CSP), nuclear Overhauser effects (NOEs), isotope editing/filtering, cross-saturation, and differential line broadening; and based on paramagnetic relaxation enhancements (PRE) using covalent and soluble spin labels. Finally, the utility of complementary methods such as small-angle X-ray or neutron scattering (SAXS, SANS), electron paramagnetic resonance (EPR) or fluorescence spectroscopy techniques is discussed. The applications of NMR techniques are illustrated with studies of challenging (high molecular weight) protein complexes.

Complex Formation of E. coli RNA Polymerase with Bacteriophage T2 DNA: Long-Range Effects in DNA

Conformation behavior of phase T2 DNA in the process of its interaction with it E. coli RNA polymerase was studied using spin labeling technique. T2 DNA was modified by the spin-labeled imidazole at OH-groups of glucosylated cytidine residues. It was shown that the binding of RNA polymerase under the conditions favoring the formation of open promoter complexes induces specific conformational changes in the spin-labeled DNA. The observed conformational changes encompass not only the promoter regions of DNA which are involved in direct contacts with RNA polymerase molecules but extend over remote DNA sites (long-range effect). In relation to this effect, current theoretical models of DNA dynamics are discussed.

Spin-labelled nucleic acids

The spin label method developed by McConnell 15 years ago is now widely used in studies of the structure and dynamic properties of a variety of the biological systems such as proteins and protein complexes, lipids and membranes, nucleic acids, nucleoproteins, etc.

The ESR spectrum of the nitroxide radcal – the spin label – is very sensitive to its microenvironment and permits easy registration of even subtle alterations in it. If spin labels are attached to different sites of a macromolecule the information can be gained about conformational properties of all these local regions and, as a result, about the dynamic behaviour of the object as a whole.