Determination of chemical shift anisotropy tensors of carbonyl nuclei in proteins through cross-correlated relaxation in NMR.

The principal components and orientations of the chemical shift anisotropy (CSA) tensors of nearly all 13C carbonyl nuclei in a small protein have been determined in isotropic solution by a combination of three complementary cross-correlation measurements.     

Chemical shift anisotropy tensors of carbonyl, nitrogen, and amide proton nuclei in proteins through cross-correlated relaxation in NMR spectroscopy

The principal components and orientations of the chemical shift anisotropy (CSA) tensors of the carbonyl (C'), nitrogen (N), and amide proton (H(N)) nuclei of 64 distinct amide bonds in human ubiquitin have been determined in isotropic solution by a set of 14 complementary auto- and cross-correlated relaxation rates involving the CSA interactions of the nuclei of interest and several dipole-dipole (DD) interactions. The CSA parameters thus obtained depend to some degree on the models used for local motions. Three cases have been considered: restricted isotropic diffusion, three-dimensional Gaussian axial fluctuations (3D-GAF), and independent out-of-plane motions of the NH(N) vectors with respect to the peptide planes.     

Measurement and ab initio calculation of CSA/dipole-dipole cross-correlated relaxation provide insight into the mechanism of a H2-forming dehydrogenase

Using transferred cross-correlated relaxation and DFT calculations, the conformation of the relevant conformation of N5,N10-methylenetetrahydromethanopterin, a reaction intermediate bound to the 80 kD H2-forming N5,N10-methylenetetrahydromethanopterin dehydrogenase is determined. The conformation of the intermediate differs from the free form in solution and makes the reaction mechanism plausible.     

Mismatched Hartmann-Hahn conditions cause proton-mediated intermolecular magnetization transfer between dilute low-spin nuclei in NMR of static solids

Mismatched Hartmann-Hahn conditions between the protons and dilute spins (such as 15N) are found to cause intermolecular magnetization transfer between the low-gamma nuclei over long distances. This transfer is purely proton mediated and occurs even in the absence of direct 15N-15N couplings. This has been demonstrated experimentally using a static single crystal of n-acetyl Leucine with intermolecular distances between the 15N nuclei exceeding 6.5 A. A quantum-mechanical explanation of this phenomenon is given based on the average-Hamiltonian theory which was confirmed by detailed numerical many-spin simulations. The theory and experiment presented in the present paper may help in the development of solid-state NMR methods for studying interhelical contacts in membrane proteins, as well as for their spectral assignment.     

Coexistence of magnetization relaxation and dielectric relaxation in a single-chain magnet

A novel single-chain magnet, [MnIII3O(Meppz)3(EtOH)4(OAc)] (1), has been successfully synthesized from a secondary building block [MnIII3O(Meppz)3(EtOH)5Cl] (2) with an S = 1 ground state. SCM 1 exhibits both magnetization relaxation and dielectric relaxation properties.     

Excited state proton transfer and solvent relaxation of a 3-hydroxyflavone probe in lipid bilayers

The photophysics of a ratiometric fluorescent probe, N-[[4'- N, N-diethylamino-3-hydroxy-6-flavonyl]methyl]- N-methyl- N-(3-sulfopropyl)-1-dodecanaminium, inner salt (F2N12S), incorporated into phospholipid unilamellar vesicles is presented. The reconstructed time-resolved emission spectra (TRES) unravels a unique feature in the photophysics of this probe. TRES exhibit signatures of both an excited-state intramolecular proton transfer (ESIPT) and a dynamic Stokes shift associated with solvent relaxation in the lipid bilayer. The ESIPT is fast, being characterized by a risetime of approximately 30-40 ps that provides an equilibrium to be established between the excited normal (N*) and the ESIPT tautomer (T*) on a time scale of 100 ps. On the other hand, the solvent relaxation displays a bimodal decay kinetics with an average relaxation time of approximately 1 ns. The observed slow solvent relaxation dynamics likely embodies a response of nonspecific dipolar solvation coupled with formation of probe-water H-bonds as well as the relocation of the fluorophore in the lipid bilayer. Taking into account that ESIPT and solvent relaxation are governed by different physicochemical properties of the probe microenvironment, the present study provides a physical background for the multiparametric sensing of lipid bilayers using ESIPT based probes.     

Determination of the anomeric configuration in carbohydrates by longitudinal cross-correlated relaxation studies: application to mono- and disaccharides

The role of cross-correlated relaxation between the anomeric proton chemical shift anisotropy (CSA) and its dipolar relaxation with nearby proton on the longitudinal relaxation in mono- and disaccharides at two magnetic field strengths has been investigated and shown to directly report the identity of their anomeric configuration.     

Water/polymer interactions in poly(amidoamine) hydrogels by 1H nuclear magnetic resonance relaxation and magnetization transfer

Hydrated cross-linked polymers belonging to the family of poly(amidoamine)s were investigated by high and low resolution (1)H nuclear magnetic resonance techniques in order to obtain information on water/polymer interactions in the swollen state. (1)H spin-spin and spin-lattice relaxation time analysis, as well as magnetization transfer experiments, indicated that water and polymer proton pools are essentially uncoupled, with water molecules diffusing fast within the hydrogel structure and exchanging between "bound" and free sites. For the polymer characterized by the highest cross-linking degree, there is strong evidence of a beadlike structure resulting in higher network rigidity and hydrogel micrometric heterogeneity.     

Distinguishing between relaxation pathways by combining dissociative ionization pump probe spectroscopy and ab initio calculations: a case study of cytosine

We present a general method for tracking molecular relaxation along different pathways from an excited state down to the ground state. We follow the excited state dynamics of cytosine pumped near the S(0)-S(1) resonance using ultrafast laser pulses in the deep ultraviolet and probed with strong field near infrared pulses which ionize and dissociate the molecules. The fragment ions are detected via time of flight mass spectroscopy as a function of pump probe delay and probe pulse intensity. Our measurements reveal that different molecular fragments show different timescales, indicating that there are multiple relaxation pathways down to the ground state. We interpret our measurements with the help of ab initio electronic structure calculations of both the neutral molecule and the molecular cation for different conformations en route to relaxation back down to the ground state. Our measurements and calculations show passage through two seams of conical intersections between ground and excited states and demonstrate the ability of dissociative ionization pump probe measurements in conjunction with ab initio electronic structure calculations to track molecular relaxation through multiple pathways.     

Intramolecular energy transfer between chromophores separated by a rigid steroid bridge: II. Energy transfer as a probe to determine the ratio of two epimers

The singlet-singlet intramolecular energy transfer between naphthalene moiety and dansy! group held apart by a rigid steroid bridge was investigated for two molecules: β-(1-naphthyl) acetoxy-17α-dansyl-Δ⁵androstene (3a) and 3β-(1-naphthyl)acetoxy-17 β-dansyl-Δ⁵androstene (3b). The rates of energy transfer for 3a and 3b in cyclohexane are 6.9 × 10⁶ and 1.1 × 10⁸ s^?1 respectively. The difference in energy transfer rate between 3a and 3b is attributed to the different donor-acceptor separation and orientation. The ratio of the two epimers in the synthesized product mixture was obtained from the fluorescence decay measurements.     

Electrospray-assisted modification of proteins: a radical probe of protein structure

A new approach is described to probe the structure of proteins through their reactivity with oxygen-containing radicals. Radical-induced oxidative modification of proteins is achieved within an electrospray ion source using oxygen as a reactive nebulizer gas at high needle voltages. This method facilitates the rapid oxidation of proteins as the molecules emerge from the electrospray needle tip. Electrospray mass spectra of both ubiquitin and lysozyme reveal that over 50% of the protein can be modified under these conditions. The radical-induced oxidative modification of amino acid side chains is correlated with their solvent accessibility to obtain information on a protein's higher-order structure. The oxidation sites in hen lysozyme have been identified by proteolysis of the condensed protein solution and tandem mass spectrometry (MS/MS). Oxidation of tryptophan at positions 62 and 123 occurs exclusively over all other tryptophan residues, consistent with the relative solvent accessibilities of the residue side chains based on the NMR structure of the protein. Radical-induced oxidative modification of cysteine (Cys), methionine (Met), tryptophan (Trp), phenylalanine (Phe), tyrosine (Tyr), proline (Pro), histidine (His), and leucine (Leu) residues is also reported, providing sufficient reactive markers to span a protein sequence. This facile oxidation process could be applied to investigate the molecular mechanism by which reactive oxygen species interact with a particular protein domain as a means to investigate the onset of certain diseases.     

Electron exchange between alpha-Keggin tungstoaluminates and a well-defined cluster-anion probe for studies in electron transfer

Fully oxidized alpha-AlIIIW12O40(5-) (1ox), and one-electron-reduced alpha-AlIIIW12O40(6-) (1red), are well-behaved (stable and free of ion pairing) over a wide range of pH and ionic-strength values at room temperature in water. Having established this, 27Al NMR spectroscopy is used to measure rates of electron exchange between 1ox (27Al NMR: 72.2 ppm relative to Al(H2O)63+; nu(1/2) = 0.77 Hz) and 1red (74.1 ppm; nu(1/2) = 0.76 Hz). Bimolecular rate constants, k, are obtained from line broadening in 27Al NMR signals as ionic strength, mu, is increased by addition of NaCl at the slow-exchange limit of the NMR time scale. The dependence of k on is plotted using the extended Debye-Hückel equation: log k = log k0 + 2alphaz1z2mu(1/2)/(1 + betarnu(1/2)), where z1 and z2 are the charges of 1ox and 1red, alpha and beta are constants, and r, the distance of closest contact, is fixed at 1.12 nm, the crystallographic diameter of a Keggin anion. Although not derived for highly charged ions, this equation gives a straight line (R2 = 0.996), whose slope gives a charge product, z1z2, of 29 +/- 2, statistically identical to the theoretical value of 30. Extrapolation to mu = 0 gives a rate constant k11 of (6.5 +/- 1.5) x 10(-3) M(-1) s(-1), more than 7 orders of magnitude smaller than the rate constant [(1.1 +/- 0.2) x 10(5) M(-1) s(-1)] determined by 31P NMR for self-exchange between P(V)W12O40(3-) and its one-electron-reduced form, P(V)W12O40(4-). Sutin's semiclassical model reveals that this dramatic difference arises from the large negative charges of 1ox and 1red. These results, including independent verification of k11, recommend 1red as a well-behaved electron donor for investigating outer-sphere electron transfer to molecules or nanostructures in water, while addressing a larger issue, the prediction of collision rates between uniformly charged nanospheres, for which 1ox and 1red provide a working model.     

New probes of ligand flexibility in drug design: transferred (13)C CSA-dipolar cross-correlated relaxation at natural abundance

Understanding the impact of molecular flexibility remains an important outstanding problem in rational drug design. Toward this end, we present new NMR relaxation methods that describe ligand flexibility at the atomic level. Specifically, we measure natural abundance (13)C cross-correlated relaxation parameters for ligands in rapid exchange between the free and receptor-bound states. The rapid exchange transfers the bound state relaxation parameters to the free state, such that a comparison of relaxation rates in the absence and presence of protein receptor yields site-specific information concerning the bound ligand flexibility. We perform these measurements for aromatic carbons, which are highly prevalent in drug-like molecules and demonstrate significant cross-correlated relaxation between the (13)C-(1)H dipole-dipole (DD) and (13)C chemical shift anisotropy (CSA) relaxation mechanisms. Our use of natural abundance measurements addresses the practical difficulties of obtaining isotope-labeled ligands in pharmaceutical research settings. We demonstrate our methods on a small ligand of the 42 kDa kinase domain of the p38 MAP kinase. We show that exchange-transferred cross-correlated relaxation measurements are not only sensitive probes of bound ligand flexibility but also offer complementary advantages over standard R(1) = 1/T(1) and R(2) = 1/T(2) measurements. The ligand flexibility profiles obtained from the relaxation data can help assess the influence of dynamics on ligand potency or pharmacokinetic properties or both, and thereby include inherent molecular flexibility in drug design.     

Long-range electron transfer in porphyrin-containing [2]-rotaxanes: tuning the rate by metal cation coordination

A series of [2]-rotaxanes has been synthesized in which two Zn(II)-porphyrins (ZnP) electron donors were attached as stoppers on the rod. A macrocycle attached to a Au(III)-porphyrin (AuP+) acceptor was threaded on the rod. By selective excitation of either porphyrin, we could induce an electron transfer from the ZnP to the AuP+ unit that generated the same ZnP*+-AuP* charge-transfer state irrespective of which porphyrin was excited. Although the reactants were linked only by mechanical or coordination bonds, electron-transfer rate constants up to 1.2x10(10) x s(-1) were obtained over a 15-17 A edge-to-edge distance between the porphyrins. The resulting charge-transfer state had a relatively long lifetime of 10-40 ns and was formed in high yield (>80%) in most cases. By a simple variation of the link between the reactants, viz. a coordination of the phenanthroline units on the rotaxane rod and ring by either Ag+ or Cu+, we could enhance the electron-transfer rate from the ZnP to the excited 3AuP+. We interpret our data in terms of an enhanced superexchange mechanism with Ag+ and a change to a stepwise hopping mechanism with Cu+, involving the oxidized Cu(phen)22+ unit as a real intermediate. When the ZnP unit was excited instead, electron transfer from the excited 1ZnP to AuP+ was not affected, or even slowed, by Ag+ or Cu+. We discuss this asymmetry in terms of the different orbitals involved in mediating the reaction in an electron- and a hole-transfer mechanism. Our results show the possibility to tune the rates of electron transfer between noncovalently linked reactants by a convenient modification of the link. The different effect of Ag+ and Cu+ on the rate with ZnP and AuP+ excitation shows an additional possibility to control the electron-transfer reactions by selective excitation. We also found that coordination of the Cu+ introduced an energy-transfer reaction from 1ZnP to Cu(phen)2+ (k = 5.1x10(9) x s(-1)) that proceeded in competition with electron transfer to AuP+ and was followed by a quantitative energy transfer to give the 3ZnP state (k = 1.5x10(9) x s(-1)).     

1H NMR relaxation of water: a probe for surfactant adsorption on kaolin

In this study, (1)H NMR is used to investigate properties of sodium dodecyl sulfate (SDS), tetradecyl trimethyl ammonium bromide (TTAB), and dodecyl trimethyl ammonium bromide (DTAB) adsorbed on kaolin by NMR T(1) and T(2) measurements of the water proton resonance. The results show that adsorbed surfactants form a barrier between sample water and the paramagnetic species present on the clay surface, thus significantly increasing the proton T(1) values of water. This effect is attributed to the amount of adsorbed surfactants and the arrangement of the surfactant aggregates. The total surface area covered by the cationic (DTAB and TTAB) and anionic (SDS) surfactants could be estimated from the water T(1) data and found to correspond to the fractions of negatively and positively charged surface area, respectively. For selected samples, the amount of paramagnetic species on the clay surface was reduced by treatment with hydrofluoric (HF) acid. For these samples, T(1) and T(2) measurements were taken in the temperature range 278-338 K, revealing detailed information on molecular mobility and nuclear exchange for the sample water that is related to surfactant behavior both on the surface and in the aqueous phase.     

Recent advances in studying energy transfer kinetics by using TBP as a chemical probe

The characteristic properties of TBP and the advantage of using TBP as an energy donor or an acceptor have been described. TBP can be used as a probe for detecting the excited states of alkanes, more reliable G values of alkanes have been obtained. The rate constants of the energy transfer for TBP-alkanes binary systems have been determined. The energy transfer process is controlled by diffusive motion of the reactive species. TBP also can be used as a probe for detecting the geminate ion pairs of alkanes.     

High-throughput separation of DNA and proteins by three-dimensional geometry gel electrophoresis: feasibility studies

We report a novel separation method that is applicable to both DNA and protein samples, based on electrophoresis in a three-dimensional (3-D) geometry. In contrast to conventional electrophoresis, samples are applied in a two-dimensional, planar array to one of the surfaces of a 3-D geometry separation medium. Loading onto a plane results in a very high sample capacity. Sample migration and separation occur along the third spatial dimension, which is perpendicular to the loading plane. The key problem of electrophoresis in a 3-D geometry separation setup is that temperature gradients are caused by Joule's heat, affecting the electrical conductivity and viscosity of the separation medium. A means of achieving straight sample migration under these circumstances is to force heat flow through the separation medium parallel to the axis of sample migration. This can be done by dissipating the heat via the electrode sides of the gel and blocking any other heat transfer. The separation of DNA and proteins by this method has been tested using agarose gel electrophoresis, polyacrylamide gel electrophoresis, and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Data were acquired off-line by conventional staining methods as well as on-line by detection of laser-induced fluorescence. We describe how to excise samples from the separation medium for preparative purposes. Possible unique applications of this 3-D geometry electrophoresis separation method are also discussed.