Biomedical subjects

Jonathan A Jones

Publications and source records attributed to Jonathan A Jones.

7 recordsLinked to original sources

PubMed2006

Contrasting photochemical and thermal reactivity of Ru(CO)2(PPh3)(dppe) towards hydrogen rationalised by parahydrogen NMR and DFT studies.

The synthesis, characterisation and thermal and photochemical reactivity of Ru(CO)2(PPh3)(dppe) 1 towards hydrogen are described. Compound proved to exist in both fac (major) and mer forms in solution. Under thermal conditions, PPh3 is lost from 1 in the major reaction pathway and the known complex Ru(CO)2(dppe)(H)2 2 is formed. Photochemically, CO loss is the dominant process, leading to the alternative dihydride Ru(CO)(PPh3)(dppe)(H)2 3. The major isomer of 3, viz. 3a, contains hydride ligands that are trans to CO and trans to one of the phosphorus atoms of the dppe ligand but a second isomer, 3b, where both hydride ligands are trans to distinct phosphines, is also formed. On the NMR timescale, no interconversion of 3a and 3b was observed, although hydride site interchange is evident with activation parameters of DeltaH(double dagger) = 95 +/- 6 kJ mol(-1) and DeltaS(double dagger) = 26 +/- 17 J K(-1) mol(-1). Density functional theory confirms that the observed species are the most stable isomeric forms, and suggests that hydride exchange occurs via a transition state featuring an eta2-coordinated H2 unit.

Journal Article↗

PubMed2004

A combined parahydrogen and theoretical study of H2 activation by 16-electron d8 ruthenium(0) complexes and their subsequent catalytic behaviour.

The photochemical reaction of Ru(CO)(3)(L)(2), where L = PPh(3), PMe(3), PCy(3) and P(p-tolyl)(3) with parahydrogen (p-H(2)) has been studied by in-situ NMR spectroscopy and shown to result in two competing processes. The first of these involves loss of CO and results in the formation of the cis-cis-trans-L isomer of Ru(CO)(2)(L)(2)(H)(2), while in the second, a single photon induces loss of both CO and L and leads to the formation of cis-cis-cis Ru(CO)(2)(L)(2)(H)(2) and Ru(CO)(2)(L)(solvent)(H)(2) where solvent = toluene, THF and pyridine (py). In the case of L = PPh(3), cis-cis-trans-L Ru(CO)(2)(L)(2)(H)(2) is shown to be an effective hydrogenation catalyst with rate limiting phosphine dissociation proceeding at a rate of 2.2 s(-1) in pyridine at 355 K. Theoretical calculations and experimental observations show that H(2) addition to the Ru(CO)(2)(L)(2) proceeds to form cis-cis-trans-L Ru(CO)(2)(L)(2)(H)(2) as the major product via addition over the pi-accepting OC-Ru-CO axis.

Journal Article↗

PubMed2003

Rapid sample-mixing technique for transient NMR and photo-CIDNP spectroscopy: applications to real-time protein folding.

We describe the development and application of a novel rapid sample-mixing technique for real-time NMR (nuclear magnetic resonance) spectroscopy. The apparatus consists of an insert inside a conventional NMR tube coupled to a rapid injection syringe outside the NMR magnet. Efficient and homogeneous mixing of solutions in the NMR tube is achieved with a dead time of tens of milliseconds, without modification of the NMR probe or additional hardware inside the magnet. Provision is made for the inclusion of an optical fiber to allow in situ laser irradiation of samples, for example to generate photo-CIDNP (chemically induced dynamic nuclear polarization). An NMR water suppression method has been implemented to allow experiments in H(2)O as well as in deuterated solvents. The performance of the device has been tested and optimized by a variety of methods, including sensitive detection of residual pH gradients and the use of NMR imaging to monitor the extent of mixing in real time. The potential utility of this device, in conjunction with the sensitivity and selectivity of photo-CIDNP, is demonstrated by experiments on the protein hen lysozyme. These measurements involve the direct detection of spectra during real-time refolding, and the use of CIDNP pulse labeling to study a partially unfolded state of the protein under equilibrium conditions. Magnetization transfer from this disordered state to the well-characterized native state provides evidence for the remarkable persistence of nativelike elements of structure under conditions in which the protein is partially denatured and aggregation prone.

Animals↗

PubMed2003

Robust quantum information processing with techniques from liquid-state NMR.

While nuclear-magnetic-resonance (NMR) techniques are unlikely to lead to a large-scale quantum computer, they are well suited to investigating basic phenomena and developing new techniques. Indeed, it is likely that many existing NMR techniques will find uses in quantum information processing. Here I describe how the composite-rotation (composite-pulse) method can be used to develop quantum logic gates which are robust against systematic errors.

Journal Article↗

PubMed2003

Oxidative folding intermediates with nonnative disulfide bridges between adjacent cysteine residues.

The oxidative folding of the Amaranthus alpha-amylase inhibitor, a 32-residue cystine-knot protein with three disulfide bridges, was studied in vitro in terms of the disulfide content of the intermediate species. A nonnative vicinal disulfide bridge between cysteine residues 17 and 18 was found in three of five fully oxidized intermediates. One of these, the most abundant folding intermediate (MFI), was further analyzed by (1)H NMR spectroscopy and photochemically induced dynamic nuclear polarization, which revealed that it has a compact structure comprising slowly interconverting conformations in which some of the amino acid side chains are ordered. NMR pulsed-field gradient diffusion experiments confirmed that its hydrodynamic radius is indistinguishable from that of the native protein. Molecular modeling suggested that the eight-membered ring of the vicinal disulfide bridge in MFI may be located in a loop region very similar to those found in experimentally determined 3D structures of other proteins. We suggest that the structural constraints imposed on the folding intermediates by the nonnative disulfides, including the vicinal bridge, may play a role in directing the folding process by creating a compact fold and bringing the cysteine residues into close proximity, thus facilitating reshuffling to native disulfide bridges.

Cysteine↗

PubMed2003

The circularization of amyloid fibrils formed by apolipoprotein C-II.

Amyloid fibrils have historically been characterized by diagnostic dye-binding assays, their fibrillar morphology, and a "cross-beta" x-ray diffraction pattern. Whereas the latter demonstrates that amyloid fibrils have a common beta-sheet core structure, they display a substantial degree of morphological variation. One striking example is the remarkable ability of human apolipoprotein C-II amyloid fibrils to circularize and form closed rings. Here we explore in detail the structure of apoC-II amyloid fibrils using electron microscopy, atomic force microscopy, and x-ray diffraction studies. Our results suggest a model for apoC-II fibrils as ribbons approximately 2.1-nm thick and 13-nm wide with a helical repeat distance of 53 nm +/- 12 nm. We propose that the ribbons are highly flexible with a persistence length of 36 nm. We use these observed biophysical properties to model the apoC-II amyloid fibrils either as wormlike chains or using a random-walk approach, and confirm that the probability of ring formation is critically dependent on the fibril flexibility. More generally, the ability of apoC-II fibrils to form rings also highlights the degree to which the common cross-beta superstructure can, as a function of the protein constituent, give rise to great variation in the physical properties of amyloid fibrils.

Amyloid↗

PubMed2002

Approximate quantum cloning with nuclear magnetic resonance.

Here we describe a nuclear magnetic resonance (NMR) experiment that uses a three qubit NMR device to implement the one-to-two approximate quantum cloning network of Buzek et al. [Phys. Rev. A 56, 3446 (1997)]. As expected the experimental results indicate that the network clones all input states with similar fidelities, but as a result of decoherence and incoherent evolution arising from B(1) inhomogeneity the total fidelity achieved does not exceed the measurement bound.

Journal Article↗