Jonathan Stonehouse

Bio: Jonathan Stonehouse is an academic researcher from University of Cambridge. The author has contributed to research in topics: Magnetization & Multiplet. The author has an hindex of 7, co-authored 8 publications receiving 1143 citations.

Excitation Sculpting in High-Resolution Nuclear Magnetic Resonance Spectroscopy: Application to Selective NOE Experiments

Abstract: Selective pulses are key elements in high-resolution NMR experiments, so great effort has been put into designing pulse shapes with desirable properties'-' In this communication we describe a selective excitation technique which, judged by the usual criteria, outdistances existing methods Our method gives constant phase and amplitude excitation over an easily adjustable bandwidth, can achieve given selectivity in a shorter time than existing methods, has no out-of-band sidelobes, and in exciting a multiplet, refocuses the evolution of scalar coupling The method is tolerant of radio-frequency (fl field inhomogeneity, and altering the net flip angle is easy The use of pulsed field gradients (PFGS)~,~ results in these crucial properties being achieved in a single scan, without difference spectroscopy or phase cycling: magnetization from outside the desired bandwidth is destroyed, thus simplifying the subsequent manipulation of the excited magnetization While PFGs have been used to tailor spectral response using single spin echoes, for example with the WATERGATE sequence,I0 and while selective 180" pulses have been used for selective excitation in conjunction with difference spectroscopy," the approach described here is more general The heart of the method is the double PFG spin echo (DPFGSE) sequence (-GI -S-GI-G~-S-G~-), in which S is any sequence of 13'pulses of any kind and the Gi are PFGs S induces the unitary transformation Us = R-,(/f?) R-y(t9) R,(a) R,(@ R,@) where, eg, R,(y) represents a rotation through an angle y about an axis E , and a, @, and 8 are arbitrary angles It can be shownI2 that applying a DPFGSE to isolated spins transforms a magnetization vector m = (m,,m,,m,) into a vector M with components

Minimisation of sensitivity losses due to the use of gradient pulses in triple-resonance NMR of proteins.

Abstract: The use of pulsed field gradients in multiple-pulse NMR experiments has many advantages, including the possibility of obtaining excellent water suppression without the need for selective presaturation. In such gradient experiments the water magnetization is dephased deliberately; exchange between the saturated protons of the solvent water and the NH protons of a protein transfers this saturation to the protein. As the solvent is in large excess and relaxes relatively slowly, the result is a reduction in the sensitivity of the experiment due to the fact that the NH proton magnetization is only partially recovered. These effects can be avoided by ensuring that the water magnetization remains intact and is returned to the +z-axis at the start of data acquisition. General procedures for achieving this aim in any triple-resonance experiment are outlined and two specific examples are given. Experimental results confirm the sensitivity advantage of the modified sequences.

The use of 2H, 13C, 15N multidimensional NMR to study the structure and dynamics of proteins

Abstract: During the past thirty years, deuterium labeling has been used to improve the resolution and sensitivity of protein NMR spectra used in a wide variety of applications. Most recently, the combination of triple resonance experiments and 2H, 13C, 15N labeled samples has been critical to the solution structure determination of several proteins with molecular weights on the order of 30 kDa. Here we review the developments in isotopic labeling strategies, NMR pulse sequences, and structure-determination protocols that have facilitated this advance and hold promise for future NMR-based structural studies of even larger systems. As well, we detail recent progress in the use of solution 2H NMR methods to probe the dynamics of protein sidechains.

Stability and Lifetime of Quadruply Hydrogen Bonded 2-Ureido-4[1H]-pyrimidinone Dimers

Abstract: 2-Ureido-4[1H]-pyrimidinones are known to dimerize via a strong quadruple hydrogen bond array. A detailed study of the dimerization constant and lifetime of the dimer is presented here. Excimer fluorescence of pyrene-labeled 2-ureido-4[1H]-pyrimidinone 1b was used to determine a dimerization constant Kdim of 6 × 107 M-1 in CHCl3, 1 × 107 M-1 in chloroform saturated with water, and 6 × 108 M-1 in toluene (all at 298 K). Under these conditions, the preexchange lifetime of the similar dimers of both 1d and 1e is 170 ms in CDCl3, 80 ms in wet CDCl3, and 1.7 s in toluene-d8, as determined by dynamic NMR spectroscopy. Association rate constants were calculated from the Kdim values and the preexchange lifetimes. The resulting values are significantly lower than the diffusion-controlled association rate constants calculated using the Stokes−Einstein and the Debeije equations. This difference is ascribed to a tautomeric equilibrium of the monomer between the dimerizing 4[1H]-pyrimidinone and nondimerizing 6[1H]-py...

Organometallic Ruthenium(II) Diamine Anticancer Complexes: Arene-Nucleobase Stacking and Stereospecific Hydrogen-Bonding in Guanine Adducts

Abstract: Organometallic ruthenium(II) arene anticancer complexes of the type [(eta(6)-arene)Ru(II)(en)Cl][PF(6)] (en = ethylenediamine) specifically target guanine bases of DNA oligomers and form monofunctional adducts (Morris, R., et al. J. Med. Chem. 2001). We have determined the structures of monofunctional adducts of the "piano-stool" complexes [(eta(6)-Bip)Ru(II)(en)Cl][PF(6)] (1, Bip = biphenyl), [(eta(6)-THA)Ru(II)(en)Cl][PF(6)] (2, THA = 5,8,9,10-tetrahydroanthracene), and [(eta(6)-DHA)Ru(II)(en)Cl][PF(6)] (3, DHA = 9,10-dihydroanthracene) with guanine derivatives, in the solid state by X-ray crystallography, and in solution using 2D [(1)H,(1)H] NOESY and [(1)H,(15)N] HSQC NMR methods. Strong pi-pi arene-nucleobase stacking is present in the crystal structures of [(eta(6)-C(14)H(14))Ru(en)(9EtG-N7)][PF(6)](2).(MeOH) (6) and [(eta(6)-C(14)H(12))Ru(en)(9EtG-N7)][PF(6)](2).2(MeOH) (7) (9EtG = 9-ethylguanine). The anthracene outer ring (C) stacks over the purine base at distances of 3.45 A for 6 and 3.31 A for 7, with dihedral angles of 3.3 degrees and 3.1 degrees, respectively. In the crystal structure of [(eta(6)-biphenyl)Ru(en)(9EtG-N7)][PF(6)](2).(MeOH) (4), there is intermolecular stacking between the pendant phenyl ring and the purine six-membered ring at a distance of 4.0 A (dihedral angle 4.5 degrees). This stacking stabilizes a cyclic tetramer structure in the unit cell. The guanosine (Guo) adduct [(eta(6)-biphenyl)Ru(en)(Guo-N7)][PF(6)](2).3.75(H(2)O) (5) exhibits intramolecular stacking of the pendant phenyl ring with the purine five-membered ring (3.8 A, 23.8 degrees) and intermolecular stacking of the purine six-membered ring with an adjacent pendant phenyl ring (4.2 A, 23.0 degrees). These occur alternately giving a columnar-type structure. A syn orientation of arene and purine is present in the crystal structures 5, 6, and 7, while the orientation is anti for 4. However, in solution, a syn orientation predominates for all the biphenyl adducts 4, 5, and the guanosine 5'-monophosphate (5'-GMP) adduct 8 [(eta(6)-biphenyl)Ru(II)(en)(5'-GMP-N7)], as revealed by NMR NOE studies. The predominance of the syn orientation both in the solid state and in solution can be attributed to hydrophobic interactions between the arene and purine rings. There are significant reorientations and conformational changes of the arene ligands in [(eta(6)-arene)Ru(II)(en)(G-N7)] complexes in the solid state, with respect to those of the parent chloro-complexes [(eta(6)-arene)Ru(II)(en)Cl](+). The arene ligands have flexibility through rotation around the arene-Ru pi-bonds, propeller twisting for Bip, and hinge-bending for THA and DHA. Thus propeller twisting of Bip decreases by ca. 10 degrees so as to maximize intra- or intermolecular stacking with the purine ring, and stacking of THA and DHA with the purine is optimized when their tricyclic ring systems are bent by ca. 30 degrees, which involves increased bending of THA and a flattening of DHA. This flexibility makes simultaneous arene-base stacking and N7-covalent binding compatible. Strong stereospecific intramolecular H-bonding between an en NH proton oriented away from the arene (en NH(d)) and the C6 carbonyl of G (G O6) is present in the crystal structures of 4, 5, 6, and 7 (average N...O distance 2.8 A, N-H...O angle 163 degrees ). NMR studies of the 5'-GMP adduct 8 provided evidence that en NH(d) protons are involved in strong H-bonding with the 5'-phosphate and O6 of 5'-GMP. The strong H-bonding from G O6 to en NH(d) protons partly accounts for the high preference for binding of [(eta(6)-arene)Ru(II)en](2+) to G versus A (adenine). These studies suggest that simultaneous covalent coordination, intercalation, and stereospecific H-bonding can be incorporated into Ru(II) arene complexes to optimize their DNA recognition behavior, and as potential drug design features.