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Spin Label (spin + label)
Selected AbstractsPDK1 and PKB/Akt: Ideal Targets for Development of New Strategies to Structure-Based Drug DesignIUBMB LIFE, Issue 3 2003Thomas Harris Abstract Growth factor binding events to receptor tyrosine kinases result in activation of phosphatidylinositol 3-kinase (PI3K), and activated PI3K generates the membrane-bound second messengers phosphatidylinositol 3,4-diphosphate [PI(3,4)P2] and PI(3,4,5)P3, which mediate membrane translocation of the phosphoinositide-dependent kinase-1 (PDK1) and protein kinase B (PKB, also known as Akt). In addition to the kinase domain, PDK1 and PKB contain a pleckstrin homology (PH) domain that binds to the second messenger, resulting in the phosphorylation and activation of PKB by PDK1. Recent evidence indicates that constitutive activation of PKB contributes to cancer progression by promoting proliferation and increased cell survival. The indicating of PDK1 and PKB as primary targets for discovery of anticancer drugs, together with the observations that both PDK1 and PKB contain small-molecule regulatory binding sites that may be in proximity to the kinase active site, make PDK1 and PKB ideal targets for the development of new strategies to structure-based drug design. While X-ray structures have been reported for the kinase domains of PDK1 and PKB, no suitable crystals have been obtained for either PDK1 or PKB with their PH domains intact. In this regard, a novel structure-based strategy is proposed, which utilizes segmental isotopic labeling of the PH domain in combination with site-directed spin labeling of the kinase active site. Then, long-range distance restraints between the 15N-labeled backbone amide groups of the PH domain and the unpaired electron of the active site spin label can be determined from magnetic resonance studies of the enhancement effect that the paramagnetic spin label has on the nuclear relaxation rates of the amide protons. The determination of the structure and position of the PH domain with respect to the known X-ray structure of the kinase active site could be useful in the rational design of potent and selective inhibitors of PDK1 and PKB by 'linking' the free energies of binding of substrate (ATP) analogs with analogs of the inositol polar head group of the phospholipid second messenger. The combined use of X-ray crystallography, segmental isotopic and spin labeling, and magnetic resonance studies can be further extended to the study of other dynamic multidomain proteins and targets for structure-based drug design. IUBMB Life, 55: 117-126, 2003 [source] Stability and electronic properties of magnetic peapodsPHYSICA STATUS SOLIDI (B) BASIC SOLID STATE PHYSICS, Issue 10 2008S. Tóth Abstract We report on the temperature stability of N@C60 peapods using electron spin resonance. The atomic nitrogen escapes at higher temperatures in the peapod than in the crystalline form. We also report on the synthesis of novel magnetic fullerene peapod, a fullerene with an attached pyridine-nitroxide spin-label. This molecule can be the ultimate inner spin label for the SWCNTs as it is available in microscopic amounts and is not air sensitive. (© 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Resolution of ligand positions by site-directed tryptophan fluorescence in tear lipocalinPROTEIN SCIENCE, Issue 2 2000Oktay K. Gasymov Abstract The lipocalin superfamily of proteins functions in the binding and transport of a variety of important hydrophobic molecules. Tear lipocalin is a promiscuous lipid binding member of the family and serves as a paradigm to study the molecular determinants of ligand binding. Conserved regions in the lipocalins, such as the G strand and the F-G loop, may play an important role in ligand binding and delivery. We studied structural changes in the G strand of holo- and apo-tear lipocalin using spectroscopic methods including circular dichroism analysis and site-directed tryptophan fluorescence. Apo-tear lipocalin shows the same general structural characteristics as holo-tear lipocalin including alternating periodicity of a ,-strand, orientation of amino acid residues 105, 103, 101, and 99 facing the cavity, and progressive depth in the cavity from residues 105 to 99. For amino acid residues facing the internal aspect of cavity, the presence of a ligand is associated with blue shifted spectra. The collisional rate constants indicate that these residues are not less exposed to solvent in holo-tear lipocalin than in apo-tear lipocalin. Rather the spectral blue shifts may be accounted for by a ligand induced rigidity in holo-TL. Amino acid residues 94 and 95 are consistent with positions in the F-G loop and show greater exposure to solvent in the holo- than the apo-proteins. These findings are consistent with the general hypothesis that the F-G loop in the holo-proteins of the lipocalin family is available for receptor interactions and delivery of ligands to specific targets. Site-directed tryptophan fluorescence was used in combination with a nitroxide spin labeled fatty acid analog to elucidate dynamic ligand interactions with specific amino acid residues. Collisional quenching constants of the nitroxide spin label provide evidence that at least three amino acids of the G strand residues interact with the ligand. Stern-Volmer plots are inconsistent with a ligand that is held in a static position in the calyx, but rather suggest that the ligand is in motion. The combination of site-directed tryptophan fluorescence with quenching by nitroxide labeled species has broad applicability in probing specific interactions in the solution structure of proteins and provides dynamic information that is not attainable by X-ray crystallography. [source] A commonly used spin label: S -(2,2,5,5-tetramethyl-1-oxyl-,3 -pyrrolin-3-ylmethyl) methanethiosulfonateACTA CRYSTALLOGRAPHICA SECTION C, Issue 11 2008Vitali Zielke The title compound, C10H18NO3S2, which finds application as a spin label, has triclinic (P) symmetry at 100,(2),K with two independent molecules in the asymmetric unit. Both molecules are very similar with respect to bond lengths and angles, but molecule 2 shows disordering of its side chain. The pyrroline rings differ slightly with respect to the position of the NO group, which in both cases are sterically shielded by the surrounding methyl groups. The crystal structure of the title compound represents the first example of a 2,2,5,5-tetramethyl-1-oxyl-,3 -pyrroline derivative with a side chain at the double bond which is linked to it through an sp3 -hybridized C atom. In the solid state, the side chain adopts a conformation with the methyl group above/below the pyrroline ring and a H atom directed towards a C atom of the double bond. The disordered side chain of molecule 2 represents a second conformation with low potential energy. Both molecules exhibit planar chirality, but in the solid state both pairs of stereoisomers are present. These four stereoisomers are stacked one behind the other in four different columns, denoted A, A,, B and B,, the angle between the vectors of the N,O bonds in columns A and B being 80.38,(8)°. [source] Accurate long-range distance measurements in a doubly spin-labeled protein by a four-pulse, double electron,electron resonance methodMAGNETIC RESONANCE IN CHEMISTRY, Issue 12 2008Michela G. Finiguerra Abstract Distance determination in disordered systems by a four-pulse double electron,electron resonance method (DEER or PELDOR) is becoming increasingly popular because long distances (several nanometers) and their distributions can be measured. From the distance distributions eventual heterogeneities and dynamics can be deduced. To make full use of the method, typical distance distributions for structurally well-defined systems are needed. Here, the structurally well-characterized protein azurin is investigated by attaching two (1-oxyl-2,2,5,5-tetramethylpyrroline-3-methyl) methanethiosulfonate spin labels (MTSL) by site-directed mutagenesis. Mutations at the surface sites of the protein Q12, K27, and N42 are combined in the double mutants Q12C/K27C and K27C/N42C. A distance of 4.3 nm is found for Q12C/K27C and 4.6 nm for K27C/N42C. For Q12C/K27C the width of the distribution (0.24 nm) is smaller than for the K27C/N42C mutant (0.36 nm). The shapes of the distributions are close to Gaussian. These distance distributions agree well with those derived from a model to determine the maximally accessible conformational space of the spin-label linker. Additionally, the expected distribution for the shorter distance variant Q12C/N42C was modeled. The width is larger than the calculated one for Q12C/K27C by 21%, revealing the effect of the different orientation and shorter distance. The widths and the shapes of the distributions are suited as a reference for two unperturbed MTSL labels at structurally well-defined sites. Copyright © 2008 John Wiley & Sons, Ltd. [source] Mapping ischemic risk region and necrosis in the isolated heart using EPR imagingMAGNETIC RESONANCE IN MEDICINE, Issue 6 2003Murugesan Velayutham Abstract Reperfusion of ischemic tissue is a common event in the treatment of heart attack and stroke. To study disease pathogenesis, methods are required to measure tissue perfusion and area at risk, as well as localized regions of injury. While histology can provide this information, its destructive nature precludes assessment of time course. Thus, there is a critical need for a noninvasive technique to obtain this information. To map myocardial redox state as a possible index of cellular ischemia and viability, electron paramagnetic resonance (EPR) imaging experiments were performed on isolated rat hearts before and after the onset of regional ischemia using nitroxide spin labels. With coronary artery occlusion, the EPR images clearly showed the risk region as a void of lower intensity that reversed upon reperfusion. The extent of risk region in the heart was similar in EPR imaging and histological measurements. The unique information obtained regarding the time course of changes in redox metabolism of the risk region and normal myocardium can provide important insights regarding the mechanisms of myocardial injury during and following ischemia. Magn Reson Med 49:1181,1187, 2003. © 2003 Wiley-Liss, Inc. [source] | ||||||||||