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Biomedical subjects

P J Hore

Publications and source records attributed to P J Hore.

At least 19 recordsLinked to original sources
PubMed2007

Oligomerization of the human prion protein proceeds via a molten globule intermediate.

The conformational transition of the human prion protein from an alpha-helical to a beta-sheet-rich structure is believed to be the critical event in prion pathogenesis. The molecular mechanism of misfolding and the role of intermediate states during this transition remain poorly understood. To overcome the obstacle of insolubility of amyloid fibrils, we have studied a beta-sheet-rich misfolded isoform of the prion protein, the beta-oligomer, which shares some structural properties with amyloid, including partial proteinase resistance. We demonstrate here that the beta-oligomer can be studied by solution-state NMR spectroscopy and obtain insights into the misfolding mechanism via its transient monomeric precursor. It is often assumed that misfolding into beta-sheet-rich isoforms proceeds via a compatible precursor with a beta-sheet subunit structure. We show here, on the contrary, evidence for an almost natively alpha-helix-rich monomeric precursor state with molten globule characteristics, converting in vitro into the beta-oligomer. We propose a possible mechanism for the formation of the beta-oligomer, triggered by intermolecular contacts between constantly rearranging structures. It is concluded that the beta-oligomer is not preceded by precursors with beta-sheet structure but by a partially unfolded clearly distinguishable alpha-helical state.

Amyloid↗
PubMed2006

Bloch-Redfield-Wangsness theory engine implementation using symbolic processing software.

We describe a general method for the automated symbolic processing of Bloch-Redfield-Wangsness relaxation theory equations for liquid-phase spin dynamics in the algebraically challenging case of rotationally modulated interactions. The processing typically takes no more than a few seconds (on a contemporary single-processor workstation) and yields relaxation rate expressions that are completely general with respect to the spectral density functions, relative orientations, and magnitudes of the interaction tensors, with all cross-correlations accounted for. The algorithm easily deals with fully rhombic interaction tensors, and is able, with little if any modification, to treat a large variety of the relaxation mechanisms encountered in NMR, EPR, and spin dynamics in general.

Algorithms↗
PubMed2006

19F NMR studies of the native and denatured states of green fluorescent protein.

Biosynthetic preparation and (19)F NMR experiments on uniformly 3-fluorotyrosine-labeled green fluorescent protein (GFP) are described. The (19)F NMR signals of all 10 fluorotyrosines are resolved in the protein spectrum with signals spread over 10 ppm. Each tyrosine in GFP was mutated in turn to phenylalanine. The spectra of the Tyr --> Phe mutants, in conjunction with relaxation data and results from (19)F photo-CIDNP (chemically induced dynamic nuclear polarization) experiments, yielded a full (19)F NMR assignment. Two (19)F-Tyr residues (Y92 and Y143) were found to yield pairs of signals originating from ring-flip conformers; these two residues must therefore be immobilized in the native structure and have (19)F nuclei in two magnetically distinct positions depending on the orientation of the aromatic ring. Photo-CIDNP experiments were undertaken to probe further the structure of the native and denatured states. The observed NMR signal enhancements were found to be consistent with calculations of the HOMO (highest occupied molecular orbital) accessibilities of the tyrosine residues. The photo-CIDNP spectrum of native GFP shows four peaks corresponding to the four tyrosine residues that have solvent-exposed HOMOs. In contrast, the photo-CIDNP spectra of various denatured states of GFP show only two peaks corresponding to the (19)F-labeled tyrosine side chains and the (19)F-labeled Y66 of the chromophore. These data suggest that the pH-denatured and GdnDCl-denatured states are similar in terms of the chemical environments of the tyrosine residues. Further analysis of the sign and amplitude of the photo-CIDNP effect, however, provided strong evidence that the denatured state at pH 2.9 has significantly different properties and appears to be heterogeneous, containing subensembles with significantly different rotational correlation times.

Green Fluorescent Proteins↗
PubMed2006

Analysis of the spin-polarized electron spin echo of the [P700+ A1-] radical pair of photosystem I indicates that both reaction center subunits are competent in electron transfer in cyanobacteria, green algae, and higher plants.

The decay of the light-induced spin-correlated radical pair [P700+ A1-] and the associated electron spin echo envelope modulation (ESEEM) have been studied in either thylakoid membranes, cellular membranes, or purified photosystem I prepared from the wild-type strains of Synechocystis sp. PCC 6803, Chlamydomonas reinhardtii, and Spinaceae oleracea. The decay of the spin-correlated radical pair is described in the wild-type membrane by two exponential components with lifetimes of 2-4 and 16-25 micros. The proportions of the two components can be altered by preillumination of the membranes in the presence of reductant at temperatures lower than 220 K, which leads to the complete reduction of the iron-sulfur electron acceptors F(A), F(B), and F(X) and partial photoaccumulation of the reduced quinone electron acceptor A1A-. The "out-of-phase" (OOP) ESEEM attributed to the [P700+ A1-] radical pair has been investigated in the three species as a function of the preillumination treatment. Values of the dipolar (D) and the exchange (J) interactions were extracted by time-domain fitting of the OOP-ESEEM. The results obtained in the wild-type systems are compared with two site-directed mutants of C. reinhardtii [Santabarbara et al. (2005) Biochemistry 44, 2119-2128], in which the spin-polarized signal on either the PsaA- or PsaB-bound electron transfer pathway is suppressed so that the radical pair formed on each electron transfer branch could be monitored selectively. This comparison indicates that when all of the iron-sulfur centers are oxidized, only the echo modulation associated with the A branch [P700+ A1A-] radical pair is observed. The reduction of the iron-sulfur clusters and the quinone A1 by preillumination treatment induces a shift in the ESEEM frequency. In all of the systems investigated this observation can be interpreted in terms of different proportions of the signal associated with the [P700+ A1A-] and [P700+ A1B-] radical pairs, suggesting that bidirectionality of electron transfer in photosystem I is a common feature of all species rather than being confined to green algae.

Animals↗
PubMed2006

Magnetic resonance imaging of the manipulation of a chemical wave using an inhomogeneous magnetic field.

The effects of applied magnetic fields on the traveling wave formed by the reaction of (ethylenediaminetetraacetato)cobalt(II) (Co(II)EDTA2-) and hydrogen peroxide have been studied using magnetic resonance imaging (MRI) . It was found that the wave could be manipulated by applying pulsed magnetic field gradients to a sample contained in a vertical cylindrical tube in the 7.0 T magnetic field of the spectrometer. Transverse field gradients decelerated the propagation of the wave down the high-field side of the tube and accelerated it down the low-field side. This control of the wave propagation eventually promoted the formation of a finger on the low-field side of the tube and allowed the wave to be maneuvered within the sample tube. The origin of these effects is rationalized by considering the Maxwell stress arising from the combined homogeneous and inhomogeneous magnetic fields and the magnetic susceptibility gradient across the wave front.

Journal Article↗
PubMed2005

Intramolecular electron transfer in lysozyme studied by time-resolved chemically induced dynamic nuclear polarization.

The kinetics of the chemically induced dynamic nuclear polarization (CIDNP) produced in reactions of hen lysozyme with photosensitizers have been studied for the native state of the protein at pH 3.8 and for two denatured states. The latter were generated by raising the temperature to 80 degrees C or by combining a temperature rise (to 50 degrees C) with the addition of chemical denaturant (10 M urea). Detailed analysis of the CIDNP time dependence on a microsecond time scale revealed that, in both denatured states, intramolecular electron transfer (IET) from a tyrosine residue to the cation radical of a tryptophan residue (rate constant k(f)) is highly efficient and plays a decisive role in the evolution of the nuclear polarization. To describe the observed CIDNP kinetics with a self-consistent set of parameters, IET in the reverse direction, from a tryptophan residue to a tyrosine residue radical (rate constant k(r)), has also to be taken into account. The IET rate constants determined by analysis of the CIDNP kinetics are, at 80 degrees C: k(f) = 1 x 10(5) s(-1) and k(r) = 1 x 10(4) s(-1); at 50 degrees C in the presence of 10 M urea: k(f) = 7 x 10(4) s(-1), k(r) = 1 x 10(4) s(-1). IET does not appear to influence the CIDNP kinetics of the native state.

Animals↗
PubMed2005

Photo-CIDNP experiments with an optimized presaturation pulse train, gated continuous illumination, and a background-nulling pulse grid.

Methods to record chemically induced dynamic nuclear polarization (CIDNP) spectra that are virtually free from background magnetization and avoid the sensitivity loss and subtraction artifacts of difference spectroscopy have been developed. Presaturation by a string of composite pi/2 pulses, each followed by a defocussing field gradient, is analyzed, and guidelines for the optimization of pulse phases and gradient strengths are derived. Subsequent gated illumination during a grid of pi pulses with a prescribed timing causes the background magnetization to vanish at those moments of a pulse sequence when CIDNP magnetization is to be sampled or transferred. By shifting the illumination intervals within such a grid, the sign of the polarizations can be inverted without influencing the development of the background magnetization, allowing a further strong suppression of residual background by a phase cycle. Experimental examples for the application of these methods to more complex CIDNP experiments (1D-CIDNP-COSY, 1D-CIDNP-TOCSY, CIDNP-induced heteronuclear Overhauser effects, water suppression in protein CIDNP) are given.

Animals↗
PubMed2005

Low-field optically detected EPR spectroscopy of transient photoinduced radical pairs.

The effects of simultaneously applied weak static and weak radio frequency magnetic fields on the recombination of transient (<100 ns) radical pairs have been investigated using a low-field optically detected electron paramagnetic resonance technique. Measurements on the photoinduced electron-transfer reaction of perdeuterated pyrene with 1,3-dicyanobenzene using a approximately 0.3 mT radio frequency field at three separate frequencies (5, 20, and 65 MHz) in the presence of 0-4 mT static fields yield spectra that are strikingly sensitive to the frequency of the time-dependent field, to the strength of the static field, and to the relative orientation of the two fields. The spectra are simulated using a modified form of the gamma-COMPUTE algorithm originally devised for calculating magic angle spinning NMR spectra of polycrystalline samples. The essential features of the spectra are consistent with the radical pair mechanism and were satisfactorily simulated using parameters whose values are either known independently or for which estimates are readily available. The calculations included hyperfine couplings to four deuterons in the pyrene cation radical and three protons in the 1,3-dicyanobenzene anion radical. Spin-selective recombination was modeled using an exponential distribution of radical encounter times. The results are discussed in the context of the proposal that radical pair chemistry forms the basis of the magnetoreceptor that allows birds to sense the Earth's magnetic field as a source of compass information during migration.

Journal Article↗
PubMed2005

Multiple subsets of side-chain packing in partially folded states of alpha-lactalbumins.

Photochemically induced dynamic nuclear polarization NMR pulse-labeling techniques have been used to obtain detailed information about side-chain surface accessibilities in the partially folded (molten globule) states of bovine and human alpha-lactalbumin prepared under a variety of well defined conditions. Pulse labeling involves generating nuclear polarization in the partially folded state, rapidly refolding the protein within the NMR sample tube, then detecting the polarization in the well dispersed native-state spectrum. Differences in the solvent accessibility of specific side chains in the various molten globule states indicate that the hydrophobic clusters involved in stabilizing the alpha-lactalbumin fold can be formed from interactions between a variety of different hydrophobic residues in both native and non-native environments. The multiple subsets of hydrophobic clusters are likely to result from the existence of distinct but closely related local minima on the free-energy landscape of the protein and show that the fold and topology of a given protein may be formed from degenerate groups of side chains.

Amino Acid Sequence↗
PubMed2005

Time-resolved CIDNP study of non-native states of bovine and human alpha-lactalbumins.

The reaction mechanism and details of the formation of CIDNP (chemically induced dynamic nuclear polarization) in the photoreactions of the aromatic dye 2,2'-dipyridyl with non-native states of bovine and human alpha-lactalbumins (BLA and HLA) in aqueous solution have been studied using the time-resolved CIDNP technique. Non-native states have been obtained at pH 2 in the presence of 0, 8, and 10 M urea-d(4) and at pH 6.7 in the presence of 10 M urea-d(4). The dependence of the geminate CIDNP spectra of the two proteins on the denaturant concentration is shown to be determined by the intrinsic reactivity of the amino acid residues toward the triplet excited dye rather than by structural changes in the proteins. Values of the proton paramagnetic relaxation times (T(1)) have been obtained from an analysis of the CIDNP kinetics. For tryptophan and tyrosine residues, the T(1) values change in opposite directions when the proteins are progressively denatured, reflecting the different internal mobilities of the two types of residues. It has been found that for both BLA and HLA the CIDNP kinetics of the non-native states formed at pH 6.7 in the presence of 10 M urea are almost identical to those at pH 2 with no urea, suggesting that the polarizable amino acid side chains have closely similar solvent accessibilities and motional properties in the two non-native states.

Amino Acids↗
PubMed2005

Influence of dipolar interactions on radical pair recombination reactions subject to weak magnetic fields.

Monte Carlo simulations of the effects of weak magnetic fields on the recombination of interacting radical pairs undergoing free diffusion in solution have been performed, with the aim of determining the influence on the low field effect of the magnetic dipolar coupling between the radicals. The suppression of singlet-triplet interconversion in the radical pair by the dipolar interaction is found to be pronounced at magnetic field strengths comparable to the hyperfine interactions in the radicals, to the extent that the low field effect is completely abolished. The averaging of the dipolar coupling by the translational diffusion of the radicals around one another is relatively efficient in the presence of strong magnetic fields but becomes ineffective in weak applied fields where the strength of the dipolar interaction is independent of the orientation of the inter-radical vector. Low field effects are only likely to be observed if the motion of the radical pair is restricted in some way so as to increase the likelihood that, having separated to the large distance required for the dipolar interaction to have a negligible effect, the radicals subsequently encounter and have the opportunity to recombine.

Free Radicals↗
PubMed2005

Photo-CIDNP NMR spectroscopy of a heme-containing protein.

There are relatively few examples of the application of photo-CIDNP NMR spectroscopy to chromophore-containing proteins. The most likely reason for this is that simultaneous absorption of light by the photosensitiser molecule and the protein chromophore reduces the effectiveness of the photochemical reaction that produces the observed nuclear polarisation. We present details of experiments performed on the air-oxidised form of a small cytochrome, from the thermophilic bacterium Hydrogenobacter thermophilus, using both the wild-type protein and apo and holo forms of a double alanine b-type mutant. We show that, along with the apo state, it is possible to generate CIDNP in the air-oxidised form of the b-type mutant, but not in the corresponding c-type cytochrome. This finding is supported by control experiments using horse-heart cytochrome c.

Animals↗
PubMed2005

Increasing the sensitivity of time-resolved photo-CIDNP experiments by multiple laser flashes and temporary storage in the rotating frame.

Pulse sequences have been developed that add up time-resolved photo-CIDNP signals from n successive laser flashes not in the acquisition computer of the NMR spectrometer but in the experiment itself, resulting in a greatly improved signal-to-noise ratio. For this accumulation, CIDNP is first stored in the transverse plane and then on the z axis, and finally superimposed on CIDNP produced by the next flash. These storage cycles also result in a very efficient background suppression. Because only one free induction decay is acquired for n flashes, the noise is digitized only once. The signal gain is demonstrated experimentally and analyzed theoretically. Losses are mostly due to nuclear spin relaxation, and to a small extent to instrument imperfections. With 10 laser flashes, a signal increase by a factor of about 7.5 was realized. As their main advantage compared to signal averaging in the usual way, these sequences yield the same signal-to-noise ratio with fewer laser flashes; the theoretical improvement is by a factor of n.

Journal Article↗
PubMed2004

Radio frequency magnetic field effects on a radical recombination reaction: a diagnostic test for the radical pair mechanism.

The photoinduced electron-transfer reaction of chrysene with isomers of dicyanobenzene is used to demonstrate the sensitivity of a radical recombination reaction to the orientation and frequency (5-50 MHz) of a approximately 300 muT radio frequency magnetic field in the presence of a 0-4 mT static magnetic field. The recombination yield is detected via the fluorescence of the exciplex formed exclusively from the electronic singlet state of the radical ion pair Chr*+/DCB*-. Magnetic field effects are simulated using a modified version of the gamma-COMPUTE algorithm, devised for the simulation of magic angle spinning NMR spectra of powdered samples. The response of a chemical or biological system to simultaneously applied radio frequency and static or extremely low-frequency magnetic fields could form the basis for a diagnostic test for the operation of the radical pair mechanism that would not require prior knowledge of the nature and properties of the radical reaction.

Journal Article↗
PubMed2004

Electron self-exchange kinetics determined by MARY spectroscopy: theory and experiment.

The electron self-exchange between a neutral molecule and its charged radical, which is part of a spin-correlated radical ion pair, gives rise to line width effects in the fluorescence-detected MARY (magnetic field effect on reaction yield) spectrum similar to those observed in EPR spectroscopy. An increasing self-exchange rate (i.e., a higher concentration of the neutral molecule) leads to broadening and subsequent narrowing of the spectrum. Along with a series of MARY spectra recorded for several systems (the fluorophores pyrene, pyrene-d(10) and N-methylcarbazole in combination with 1,2- and 1,4-dicyanobenzene) in various solvents, a theoretical model is developed that describes the spin evolution and the diffusive recombination of the radical pair under the influence of the external magnetic field and electron self-exchange, thereby allowing the simulation of MARY spectra of the systems investigated experimentally. The spin evolution of the radicals in the pair is calculated separately using spin correlation tensors, thereby allowing rigorous quantum mechanical calculations for real spin systems. It is shown that the combination of these simulations with high resolution, low noise experimental spectra makes the MARY technique a novel, quantitative method for the determination of self-exchange rate constants. In comparison to a simple analytical formula which estimates the self-exchange rate constant from the slope of the linear part of a line width vs concentration plot, the simulation method yields more reliable and accurate results. The correctness of the results obtained by the MARY method is proved by a comparison with corresponding data from the well-established EPR line broadening technique. With its less stringent restrictions on radical lifetime and stability, the MARY technique provides an alternative to the classical EPR method, in particular for systems involving short-lived and unstable radicals.

Journal Article↗
PubMed2004

Conformational changes in a photosensory LOV domain monitored by time-resolved NMR spectroscopy.

Phototropins are light-activated kinases from plants that utilize light-oxygen-voltage (LOV) domains as blue light photosensors. Illumination of these domains leads to the formation of a covalent linkage between the protein and an internally bound flavin chromophore, destabilizing the surrounding protein and displacing an alpha-helix from its surface. Here we use a combination of spectroscopic tools to monitor the kinetic processes that spontaneously occur in the dark as the protein returns to the noncovalent ground state. Using time-resolved two-dimensional (2D) NMR methods, we measured the rate of this process at over 100 independent sites throughout the protein, establishing that regeneration of the dark state occurs cooperatively within a 1.6-fold range of observed rates. These data agree with other spectroscopic measurements of the kinetics of protein/FMN bond cleavage and global conformational changes, consistent with these processes experiencing a common rate-limiting step. Arrhenius analyses of the temperature dependence of these rates suggest that the transition state visited during this regeneration has higher energy than the denatured form of this protein domain despite the fact that there is no global unfolding of the domain during this process.

Avena↗
PubMed2004

Chemically amplified 19F-1H nuclear Overhauser effects.

Chemically induced dynamic nuclear polarisation (CIDNP) is explored as a source of nuclear hyperpolarisation in heteronuclear Overhauser effect experiments. A photochemical reaction proceeding through a radical pair intermediate is used to enhance (19)F nuclear magnetisation in 3-fluorotyrosine by more than an order of magnitude with a corresponding increase in the amplitudes of (19)F-(1)H cross-relaxation and cross-correlation effects. The reactions employed are cyclic and leave the sample chemically unchanged. The potential for enhancing the sensitivity of heteronuclear NOEs in (19)F-labelled proteins is discussed.

Journal Article↗