Spectroscopy of large molecules in inert gas clusters

Aromatic hydrocarbons provide nucleation centers for the formation of clusters of inert gases in high-flow supersonic beams. Large clusters of Ar, each containing a single tetracene (T) molecule, were prepared by supersonic expansion of the seeded gas at pressures p = 3000–13000 Torr and interrogated by laser-induced fluorescence spectroscopy Evidence is reported for homogeneous line broadening of large TAr_n clusters prepared at p? 8000 Torr.     

Assignments of carbon NMR resonances for microcrystalline ubiquitin

Solid-state NMR 2D spectroscopy was used to correlate carbon backbone and side-chain chemical shifts for uniformly (13)C,(15)N-enriched microcrystalline ubiquitin. High applied field strengths, 800 MHz for protons, moderate proton decoupling fields, 80-100 kHz, and high magic angle sample spinning frequencies, 20 kHz, were used to narrow the most of the carbon line widths to 0.5-0.8 ppm. Homonuclear magnetization transfer was effected by matching the proton RF field to the spinning frequency, the so-called dipolar-assisted rotational resonance (DARR) (Takegoshi, K.; Nakamura, S.; Terao, T. Chem. Phys. Lett. 2001, 344, 631-637), and a mixing time of 20 ms was used to maximize the intensity of one-bond transfers between carbon atoms. This polarization transfer sequence resulted in roughly 14% transfer efficiencies for directly bonded carbon pairs and 4% transfer efficiencies for carbons separated by a third carbon. With this simple procedure, the majority of the one-bond correlations was observed with moderate transfer efficiencies, and many two-bond correlations were also observed with weaker intensities. Spin systems could be identified for more than half of the amino acid side chains, and site-specific assignments were readily possible via comparison with 400 MHz (15)N-(13)C-(13)C correlation spectroscopy (described separately).     

Changes in calmodulin main-chain dynamics upon ligand binding revealed by cross-correlated NMR relaxation measurements

The fast dynamics of protein backbones are often investigated by nuclear magnetic relaxation experiments that report on the degree of spatial restriction of the amide bond vector. By comparing calmodulin in the peptide-bound and peptide-free states with these classical methods, we observe little difference in the dynamics of the polypeptide main chain (average order parameter decrease of 0.01 unit upon binding). However, when using NMR methods that monitor the mobility of the CO-Calpha bond vector, we reveal a significant reduction of dynamics of the protein main chain (average order parameter decrease of 0.048 units). Previous investigations have suggested that the side-chain dynamics is reduced by an average of 0.07 order parameter units upon ligand binding (Lee, A. L.; Kinnear, S. A.; Wand, A. J. Nat. Struct. Biol. 2000, 7, 72-77). The current findings suggest that the change of the CO-Calpha bond vector dynamics is intermediate between the changes in NH and side-chain dynamics and report a previously undetected loss of main-chain entropy. Weak site-to-site correlations between the different motional indicators are also observed.     

Single-molecule nanopore sensing of actin dynamics and drug binding

Actin is a key protein in the dynamic processes within the eukaryotic cell. To date, methods exploring the molecular state of actin are limited to insights gained from structural approaches, providing a snapshot of protein folding, or methods that require chemical modifications compromising actin monomer thermostability. Nanopore sensing permits label-free investigation of native proteins and is ideally suited to study proteins such as actin that require specialised buffers and cofactors. Using nanopores, we determined the state of actin at the macromolecular level (filamentous or globular) and in its monomeric form bound to inhibitors. We revealed urea-dependent and voltage-dependent transitional states and observed the unfolding process within which sub-populations of transient actin oligomers are visible. We detected, in real-time, filament-growth, and drug-binding at the single-molecule level demonstrating the promise of nanopore sensing for in-depth understanding of protein folding landscapes and for drug discovery.

Nanopipettes were used for real-time investigation into actin dynamics and drug binding at single-molecule resolution, showing promise for a better understanding of the mechanism of protein–protein interactions and drug discovery.     

Rh(II) and Rh(I) two-legged piano-stool complexes: structure,reactivity, and electronic properties

The ligand 1,4-bis[4-(diphenylphosphino)butyl]-2,3,5,6-tetramethylbenzene, 3, was used to synthesize a mononuclear Rh(II) complex [(eta(1):eta(6):eta(1)-1,4-bis[4-(diphenylphosphino)butyl]-2,3,5,6-tetramethylbenzene)Rh][PF(6)](2), 6+, in a two-legged piano-stool geometry. The structural and electronic properties of this novel complex including a single-crystal EPR analysis are reported. The complex can be cleanly interconverted with its Rh(I) form, allowing for a comparison of the structural properties and reactivity of both oxidation states. The Rh(I) form 6 reacts with CO, tert-butyl isocyanide, and acetonitrile to form a series of 15-membered mononuclear cyclophanes [(eta(1):eta(1)-1,4-bis[4-(diphenylphosphino)butyl]-2,3,5,6-tetramethylbenzene)Rh(CO)(3)][PF(6)] (8), [(eta(1):eta(1)-1,4-bis[4-(diphenylphosphino)butyl]-2,3,5,6-tetramethylbenzene)Rh(CNC(CH(3))(3))(2)][PF(6)] (10), and [(eta(1):eta(1)-1,4-bis[4-(diphenylphosphino)butyl]-2,3,5,6-tetramethylbenzene)Rh(CO)(CH(3)CN)][PF(6)] (11). The Rh(II) complex 6+ reacts with the same small molecules, but over shorter periods of time, to form the same Rh(I) products. In addition, a model two-legged piano-stool complex [(eta(1):eta(6):eta(1)-1,4-bis[3-(diphenylphosphino)propoxy]-2,3,5,6-tetramethylbenzene)Rh][B(C(6)F(5))(4)], 5, has been synthesized and characterized for comparison purposes. The solid-state structures of complexes 5, 6, 6+, and 11 are reported. Structure data for 5: triclinic; P(-)1; a = 10.1587(7) A; b = 11.5228(8) A; c = 17.2381(12) A; alpha = 96.4379(13) degrees; beta = 91.1870(12) degrees; gamma = 106.1470(13) degrees; Z = 2. 6: triclinic; P(-)1; a = 11.1934(5) A; b = 12.4807(6) A; c = 16.1771(7) A; alpha = 81.935(7) degrees; beta = 89.943(1) degrees; gamma = 78.292(1) degrees; Z = 2. 6+: monoclinic; P2(1)/n; a = 11.9371(18) A; b = 32.401(5) A; c = 12.782(2) A; beta = 102.890(3) degrees; Z = 4. 11: triclinic; P(-)1; a = 13.5476(7) A; b = 13.8306(7) A; c = 14.9948(8) A; alpha = 74.551(1) degrees; beta = 73.895(1) degrees; gamma = 66.046(1) degrees; Z = 2.     

Laser photoinitiated nitrosylation of 3-electron reduced Nm europaea hydroxylamine oxidoreductase: kinetic and thermodynamic properties of the nitrosylated enzyme

Hydroxylamine-cytochrome c554 oxidoreductase (HAO) catalyzes the 4-e(-) oxidation of NH(2)OH to NO(2)(-) by cytochrome c554. The electrons are transferred from NH(2)OH to a 5-coordinate heme known as P(460), the active site of HAO. From P(460), c-type hemes transport the electrons through the enzyme to a remote solvent-exposed c-heme, where cyt c554 reduction occurs. When 3-60 microM NO* are photogenerated by laser flash photolysis of N,N'-bis-(carboxymethyl)-N,N'-dinitroso-1,4-phenylenediamine, in a solution containing approximately 1 microM HAO prereduced by 3 e(-)/subunit, the HAO c-heme pool is subsequently oxidized by up to 1 e(-)/HAO subunit. The reaction rate for HAO oxidation shows first-order dependence on [HAO], and zero-order dependence on [NO*] (k(obs) = 1250 +/- 150 s(-)(1)). However, the total HAO oxidized shows hyperbolic dependence on [NO*]. We suggest that NO* first binds reversibly to P(460) giving a {Fe(NO)}(6) moiety. Intramolecular electron transfer (IET) from the c-heme pool then reduces P(460) to {Fe(NO)}.(7) The overall binding constant (K) for formation of {Fe(NO)}(7) from free NO* and 3-e(-) reduced HAO was measured at (7.7 +/- 0.6) x10(4) M(-1). This value is larger than that for typical ferriheme proteins ( approximately 10(4) M(-1)), but much smaller than that for the corresponding ferroheme proteins ( approximately 10(11) M(-1)). The final product generated by nitrosylating 3-e(-) reduced HAO is believed to be the same species obtained by adding NH(2)OH to the fully oxidized enzyme. The experiments described herein suggest that when NH(2)OH and HAO first react, only two of the NH(2)OH electrons end up in the c-heme pool. The other two remain at P(460) as part of an {Fe(NO)}(7) moiety. These results are discussed in relation to earlier studies that investigated the effect of putting fully oxidized and fully reduced HAO under 1 atm of NO*.     

A microchip-based proteolytic digestion system driven by electroosmotic pumping

Microchip-based proteomic analysis requires proteolytic digestion of proteins in microdevices. Enzyme reactors in microdevices, fabricated in glass, silicon, and PDMS substrates, have recently been demonstrated for model protein digestions. The common approach used for these enzyme reactors is employment of a syringe pump(s) to generate hydrodynamic flow, driving the proteins through the reactors. Here we present a novel approach, using electroosmotic flow (EOF) to electrokinetically pump proteins through a proteolytic system. The existence of EOF in the proteolytic system packed with immobilized trypsin gel beads was proven by imaging the movement of a neutral fluorescent marker. Digestions of proteins were subsequently carried out for 12 min, and the tryptic peptides were analyzed independently using capillary electrophoresis (CE) and MALDI-TOF mass spectrometry (MS). The results from CE analysis of the tryptic peptides from the EOF-driven proteolytic system and a conventional water bath digestion were comparable. MALDI-TOF MS was used to identify the parent protein and the tryptic peptides using MS-Fit database searching. The potential utility of the EOF-driven proteolytic system was demonstrated by direct electro-elution of proteins from an acrylamide gel into the proteolytic system, with elution and tryptic digestion achieved in a single step. The EOF-driven proteolytic system, thus, provides a simple way to integrate protein digestion into an electrophoretic micro total analysis system for protein analysis and characterization.     

Perturbations of molecular extravalence excitations by rare-gas fluids

In this paper we report the results of an experimental study of the vacuum ultraviolet absorption spectra of molecular impurity states of methyl iodide in Ar (density range ? = 0–1.4 g cm^?3) and in Kr (? = 0–2.3 g cm^?3), of carbon disulphide in Ar (? = 0–1.4 g cm^?3) and of formaldehyde in Ar (? = 0–1.25 g cm^?3). The experimental results provide new information regarding medium perturbations of intravalenc transitions, of the lowest extravalence transitions and of transitions to mixed valence—Rydberg configurations, which serve as a diagnostic tool to distinguish between different types of electronic excitations. All the lowest extravalence molecular excitations exhibit appreciable blue spectral shifts at moderate and at high fluid densities, intravalence transitions are practically insensitive to medium effects, while excitations to mixed valence—Rydberg configurations are characterized by a moderate blue spectral shift. New information has been obtained concerning the energetics of molecular ionization processes in a dense fluid. The high n = 2–5 Rydberg states of CH₃l exhibit a large red shift at moderate (? = 0–0.5 cm^?3) Ar densities. The ionization potential E_g and the effective Rydberg constant G for CH₃I in Ar was found to decrease from G = 13.6 eV and E_g = 9.55 eV at ? = 0 and E_g = 9.08 eV and constant G for CH₃l in Ar was found to decrease from G = 13.6 eV and E_g = 9.55eV at ? = 0 and E_g = 9.08 eV and G ≈ 7.15 eV at ? = 0.5 g cm^?3. Experimental evidence was obtained for the identification of n = 2 molecular Wannier impurity states of CH₃I and of CH₂O in liquid Ar. These spectroscopic data result in E_g ≈ 8.6 eV for CH₃I in liquid Ar and E_g ≈ 10.2 eV for CH₂O in liquid Ar.     

Positivity notions for coherent sheaves over compact complex spaces

LetX be a reduced compact complex space, X a coherent sheaf, andV=V() its associated linear fiber space. LetV _R be the reduction ofV, letA be the analytic set inX over which is not locally-free, and letV be the closure inV _R ofV _R |(X–A). is (primary) weakly positive if the zerosection ofV (V) is exceptional. is (primary) cohomologically positive if, for any coherent sheaf X, for all 0,k1. Then is (primary) weakly positive if and only if is (primary) cohomologically positive.LetX be a normal irreducible compact complex space. ThenX is Moishezon if and only if it carries a primary weakly positive, and hence primary cohomologically positive, coherent sheaf.Several other positivity notions are also discussed.