Divalent metal ion-peptide interactions probed by electron capture dissociation of trications

Electron capture dissociation (ECD) of the peptide Substance P (SubP) complexed with divalent metals has been investigated. ECD of [SubP + H + M]3+ (M2+ = Mg2+ -Ba2+ and Mn2+ -Zn2+) allowed observation of a larger number of product ions than previous investigations of doubly charged metal-containing peptides. ECD of Mg-Ba, Mn, Fe, and Zn-containing complexes resulted in product ions with and without the metal from cleavage of backbone amine bonds (c' and z* -type ions). By contrast, ECD of Co and Ni-containing complexes yielded major bond cleavages within the C-terminal methionine residue (likely to be the metal ion binding site). Cu-containing complexes displayed yet another behavior: amide bond cleavage (b and y'-type ions). We believe some results can be rationalized both within the hot hydrogen atom mechanism and mechanisms involving electron capture into excited states, such as the recently proposed amide superbase mechanism. However, some behavior, including formation of (cn 'M - H)+ ions for Ca-Ba, is best explained within the latter mechanisms with initial electron capture at the metal. In addition, the ECD behavior appears to correlate with the metal second ionization energy (IE2). Co and Ni (displaying sequestered fragmentation) have IE2s of 17.1 and 18.2 eV, respectively, whereas IE2s for Mg-Ba, Mn, and Fe (yielding random cleavage) are 10.0 to 16.2 eV. This behavior is difficult to explain within the hot hydrogen atom mechanism because hydrogen transfer should not be influenced by IE2s. However, the drastically different fragmentation patterns for Co, Ni, and Cu compared to the other metals can also be explained by their higher propensity for nitrogen (as opposed to oxygen) binding. Nevertheless, these results imply that directed fragmentation can be accomplished via careful selection of the cationizing agent.     

Solute-solvent interactions probed by intermolecular NOEs

Nuclear Overhauser effects arising from the interactions of spins of solvent molecules with spins of a solute should reveal the "exposure" of solute spins to collisions with solvent. Such intermolecular NOEs could, therefore, provide information regarding conformation or structure of the solute. Determinations of solute-solvent NOEs of 1,3-di-tert-butylbenzene in solvents composed of perfluoro-tert-butyl alcohol, tetramethylsilane, and carbon tetrachloride have been carried out. A crude, but apparently reliable, method for prediction of intermolecular solvent-solute NOEs based on hard (noninteracting) spheres was developed. Comparison of experimental to predicted NOEs indicates that tetramethylsilane interacts with the solute according to the model. By contrast, intermolecular NOE data indicate attractive interactions between the solute and perfluoro-tert-butyl alcohol. All NOE results and the corresponding predictions confirm that proton H2 of the solute is protected by the flanking tert-butyl groups from interactions with solvent molecules.     

Mucin-electrolyte interactions at the solid-liquid interface probed by QCM-D

The interaction between mucin and ions has been investigated by employing the quartz crystal microbalance technique with measurement of energy dissipation. The study was partially aimed at understanding the adsorption of mucin on surfaces with different chemistry, and for this purpose, surfaces exposing COOH, OH, and CH(3) groups were prepared. Mucin adsorbed to all three types of functionalized gold surfaces. Adsorption to the hydrophobic surface and to the charged hydrophilic surface (COOH) occured with high affinity despite the fact that in the latter case both mucin and the surface were negatively charged. On the uncharged hydrophilic surface exposing OH groups, the adsorption of mucin was very low. Another aim was to elucidate conformational changes induced by electrolytes on mucin layers adsorbed on hydrophobic surfaces from 30 mM NaNO(3). To this end, we investigated the effect of three electrolytes with increasing cation valance: NaCl, CaCl(2) and LaCl(3). At low NaCl concentrations, the preadsorbed layer expands, whereas at higher concentrations of NaCl the layer becomes more compact. This swelling/compacting of the mucin layer is fully reversible for NaCl. When the mucin layer instead is exposed to CaCl(2) or LaCl(3), compaction is observed at 1 mM. For CaCl(2), this process is only partially reversible, and for LaCl(3), the changes are irreversible within the time frame of the experiment. Finally, mucin interaction with the DTAB cationic surfactant in an aqueous solution of different electrolytes was evaluated with turbidimetry measurements. It is concluded that the electrolytes used in this work screen the association between mucin and DTAB and that the effect increases with increasing cation valency.     

Tertiary contact formation in alpha-synuclein probed by electron transfer

To explore tertiary contact formation in alpha-synuclein, a natively unfolded protein implicated in Parkinson's disease, we have measured the rates of reaction between a powerful electron donor, the tryptophan (W) triplet excited state, and an acceptor, 3-nitro-tyrosine (Y(NO2)) in six different variants, probing loop sizes between 15 and 132 residues. Electron transfer rates decrease with loop size with the fastest contact time of 140 ns for the N-terminal pair and the slowest of 1.2 mus for the N- to C-terminal pair. Diffusion coefficients ranging from approximately 2 x 10-6 to approximately 10-5 cm2 s-1 were extracted from simultaneous fits of the W to Y(NO2) electron (triplet excited state) and energy transfer (singlet excited state) kinetics.     

Intramolecular electron transfer in heterosubstituted benzene derivatives as probed by dissociative electron attachment

The electron transmission and dissociative electron attachment spectra of the 1-chloroalkyl benzene derivatives, C(6)H(5)(CH(2))(3)Cl and C(6)H(5)(CH(2))(4)Cl, and of the sulfur and silicon derivatives, C(6)H(5)SCH(2)Cl, C(6)H(5)Si(CH(3))(2)CH(2)Cl and C(6)H(5)CH(2)Si(CH(3))(2)CH(2)Cl, are presented for the first time. The relative Cl(-) fragment anion currents generated by electron attachment to the benzene pi* LUMO are measured in the series C(6)H(5)(CH(2))(n)Cl, with n = 1-4, and in the heteroatomic compounds. The Cl(-) yield reflects the rate of intramolecular electron transfer between the pi-system and the remote chlorine atom, which in turn depends on the extent of through-bond coupling between the localized pi* and sigma*(Cl-C) orbitals. In compounds C(6)H(5)(CH(2))(n)Cl the Cl(-) current rapidly decreases with increasing length of the saturated chain. This decrease is significantly attenuated when a carbon atom of the alkyl skeleton is replaced with a third-row heteroatom. This greater ability to promote through-bond coupling between the pi* and sigma*(Cl-C) orbitals is attributed to the sizably lower energy of the empty sigma*(S-C) and sigma*(Si-C) orbitals with respect to the sigma*(C-C) orbitals. In the sulfur derivative the increase of the Cl(-) current is larger than in the silicon analogue. In this case, however, other negative fragments are observed, due to dissociation of the S-C bonds.     

Dissociative electron attachment to NO probed by velocity map imaging

An experimental and theoretical investigation of the dissociative electron attachment process in nitric oxide is presented. Measurements using the recently developed ion momentum imaging conclusively show the presence of two resonance features in the O(-) channel. These are found to dissociate to give N atoms in the (2)D and (2)P excited states respectively, thus settling the controversies regarding the possible dissociation limits of this process. Though the angular distribution of O(-) shows the resonances contributing to these dissociations are of Π symmetry and a mixture of Π and Σ or Δ symmetry respectively, our calculations using R-matrix theory show no direct electron attachment channel leading to O(-) through these resonances, as all the allowed resonances below 10 eV decay to either O + N(-) or O(-) + N((4)S) channels. We propose that indirect mechanisms through curve crossings lead to the experimentally observed results.     

Hot electron lifetimes in metals probed by time-resolved two-photon photoemission

This review reports on experimental and theoretical results on the inelastic decay of optically excited volume electrons in different types of metals, including simple metals (Al), noble metals (Au, Ag, Cu), transition metals (Ta, Mo, Rh, Co, Fe, Ni) and rare earth metals (Gd, Tb, Yb, La). The comparison of the different materials and material classes provides particular insight into the relevance of the localization and delocalization of electronic states for inelastic carrier scattering processes. The discussion of the data illustrates furthermore the capabilities and limitations of the time-resolved two-photon photoemission technique as well as current theoretical approaches in analyzing and determining inelastic lifetimes of excited electrons.     

DNA polymerase template interactions probed by degenerate isosteric nucleobase analogs

The development of novel artificial nucleobases and detailed X-ray crystal structures for primer/template/DNA polymerase complexes provide opportunities to assess DNA-protein interactions that dictate specificity. Recent results have shown that base pair shape recognition in the context of DNA polymerase must be considered a significant component. The isosteric azole carboxamide nucleobases (compounds 1-5; ) differ only in the number and placement of nitrogen atoms within a common shape and therefore present unique electronic distributions that are shown to dictate the selectivity of template-directed nucleotide incorporation by DNA polymerases. The results demonstrate how nucleoside triphosphate substrate selection by DNA polymerase is a complex phenomenon involving electrostatic interactions in addition to hydrogen bonding and shape recognition. These azole nucleobase analogs offer unique molecular tools for probing nonbonded interactions dictating substrate selection and fidelity of DNA polymerases.     

Electron-acceptor properties of phospha-alkynes as probed by electron transmission and dissociative electron attachment spectroscopies

Electron transmission spectroscopy is applied for the first time to a phospha-alkyne derivative, (CH₃)₃CCP. Electron attachment to the π^* LUMO in the gas-phase occurs at 0.63 eV. Formation of the temporary π^* anion state is also observed in measurements of the total anion current, as a function of the incident electron energy. Comparison with the ethyne analogue shows that replacement of a CH group with a P atom causes a very strong increase (2.3 eV) of the vertical electron affinity. Simple Koopmans’ theorem calculations reproduce the experimental data.     

Disorder and intermolecular interactions in a family of tetranuclear Ni(II) complexes probed by high-frequency electron paramagnetic resonance

High-frequency electron paramagnetic resonance (HFEPR) data are presented for four closely related tetranuclear Ni(II) complexes, [Ni(hmp)(MeOH)Cl]4.H2O (1a), [Ni(hmp)(MeOH)Br]4.H2O (1b), [Ni(hmp)(EtOH)Cl]4.H2O (2), and [Ni(hmp)(dmb)Cl]4 (3) (where hmp(-) is the anion of 2-hydroxymethylpyridine and dmb is 3,3'-dimethyl-1-butanol), which exhibit magnetic bistability (hysteresis) and fast magnetization tunneling at low temperatures, properties which suggest they are single-molecule magnets (SMMs). The HFEPR spectra confirm spin S = 4 ground states and dominant uniaxial anisotropy (DSz(2), D < 0) for all four complexes, which are the essential ingredients for a SMM. The individual fine structure peaks (due to zero-field splitting) for complexes 1a, 1b, and 2 are rather broad. They also exhibit further (significant) splitting, which can be explained by the fact that there exists two crystallographically distinct Ni 4 sites in the lattices for these complexes, with associated differences in metal-ligand bond lengths and different zero-field splitting (ZFS) parameters. The broad EPR lines, meanwhile, may be attributed to ligand and solvent disorder, which results in additional distributions of microenvironments. In the case of complex 3, there are no solvate molecules in the structure, and only one distinct Ni 4 molecule in the lattice. Consequently, the HFEPR data for complex 3 are extremely sharp. As the temperature of a crystal of complex 3 is decreased, the HFEPR spectrum splits abruptly at approximately 46 K into two patterns with very slightly different ZFS parameters. Heat capacity data suggest that this is caused by a structural transition at 46.6 K. A single-crystal X-ray structure at 12(2) K indicates large thermal parameters on the terminal methyl groups of the dmb (3,3-dimethyl-1-butanol) ligand. Most likely there exists dynamic disorder of parts of the dmb ligand above 46.6 K; an order-disorder structural phase transition at 46.6 K then removes some of the motion. A further decrease in temperature (<6 K) leads to further fine structure splittings for complex 3. This behavior is thought to be due to the onset of short-range magnetic correlations/coherences between molecules caused by weak intermolecular magnetic exchange interactions.     

Optical control of coherent lattice motions probed by femtosecond electron diffraction

We report the study of laser-induced coherent lattice motions using femtosecond electron diffraction. The oscillations of Bragg peak positions associated with a damped lattice vibration along the surface normal were directly observed in real time and with sub-milli-angstrom spatial resolution. In addition, by using a pair of optical excitation pulses and varying their time delay and relative pulse intensities, we demonstrated the successful control of coherent lattice motions.     

Directional dispersion of excitons in anthracene,probed by electron spectroscopy

Anthracene single crystal foils have been investigated by electron energy loss in the range from 3 eV to 25 eV for various directions of the crystal excitation wave vector k. Experimental evidence for axial dispersion is obtained. Calculations in which a dielectric tensor is used in the oriented gas model explain the anisotropy in the energy loss data and allow the assignment of the losses in this whole energy range to ¹A_u and ¹B_u crystal excitations originating from molecular ¹A_1g → ¹B_1u and → ¹B_1u excitations.     

Quality by Design applications in biosimilar pharmaceutical products

A process is well understood when all critical sources of variability are identified and explained, variability is managed by the process design and monitoring, and product quality attributes are accurately and reliably predicted over the design space. Quality by Design (QbD) is a systematic approach to product development and process control that begins with predefined objectives, emphasizes product and process understanding, and sets up process control based on sound science and quality risk management. The Food and Drug Administration (FDA) and the International Conference on Harmonization of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH) have recently started promoting QbD in an attempt to curb rising development costs and regulatory barriers to innovation and creativity. QbD is partially based on the application of multivariate statistical methods and a statistical Design of Experiments strategy to the development of both analytical methods and pharmaceutical formulations. In this paper, we review the basics of QbD and their impact on the innovative, generic, and biosimilar pharmaceutical industry. In particular, we consider the challenge of mapping the control space in biotechnological processes and how advances in statistical methods can contribute to QbD.     

Charge transfer interactions in liquid crystalline polymers probed by fluorescence spectroscopy

Rigid-rod aromatic LC polyester with long alkyl side chains and two thermotropic LC polyesters (PET40/OBA60 and PB-10) were studied by fluorescence spectroscopy to investigate their charge transfer interactions corresponding to LC configuration and changes during phase transition.     

Supramolecular interactions probed by 13C-13C solid-state NMR spectroscopy

We present a robust solid-state NMR approach for the accurate determination of molecular interfaces in insoluble and noncrystalline protein-protein complexes. The method relies on the measurement of intermolecular (13)C-(13)C distances in mixtures of [1-(13)C]glucose- and [2-(13)C]glucose-labeled proteins. We have applied this method to Parkinson's disease-associated α-synuclein fibrils and found that they are stacked in a parallel in-register arrangement. Additionally, intermolecular distance restraints for the structure determination of the fibrils at atomic resolution were measured.     

Intermolecular interactions in electroactive thiol monolayers probed by linear scan voltammetry

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The electronic structure of free water clusters probed by Auger electron spectroscopy

(H2O)(N) clusters generated in a supersonic expansion source with N approximately 1000 were core ionized by synchrotron radiation, giving rise to core-level photoelectron and Auger electron spectra (AES), free from charging effects. The AES is interpreted as being intermediate between the molecular and solid water spectra showing broadened bands as well as a significant shoulder at high kinetic energy. Qualitative considerations as well as ab initio calculations explain this shoulder to be due to delocalized final states in which the two valence holes are mostly located at different water molecules. The ab initio calculations show that valence hole configurations with both valence holes at the core-ionized water molecule are admixed to these final states and give rise to their intensity in the AES. Density-functional investigations of model systems for the doubly ionized final states--the water dimer and a 20-molecule water cluster--were performed to analyze the localization of the two valence holes in the electronic ground states. Whereas these holes are preferentially located at the same water molecule in the dimer, they are delocalized in the cluster showing a preference of the holes for surface molecules. The calculated double-ionization potential of the cluster (22.1 eV) is in reasonable agreement with the low-energy limit of the delocalized hole shoulder in the AES.     

Electrostatic interactions in protein adsorption probed by comparing lysozyme and succinylated lysozyme

In this paper, we present a nanoscale study of the supramolecular structure of the dehydrogenate polymer (ZL-DHP) lignin model compound. The combination of near-field scanning optical microscopy (NSOM or SNOM) and atomic force microscopy (AFM) has been utilized to explore physicochemical properties of the lignin model compound on a scale ranging from individual macromolecules to globular supramolecular assemblies. By utilizing NSOM in transmission mode, the optical inhomogeneity in the lignin supramolecular structure has been observed for the first time. In particular, the transmission-mode NSOM images reveal a combination of hollow and layered supramolecular globular structure in the lignin model compound. Through the paired use of TappingMode and pulsed-mode AFM, we have also confirmed the existence of regions with different rheological properties on the single lignin model compound supramolecular assembly.     

Electron tunneling in lithium-ammonia solutions probed by frequency-dependent electron spin relaxation studies

Electron transfer or quantum tunneling dynamics for excess or solvated electrons in dilute lithium-ammonia solutions have been studied by pulse electron paramagnetic resonance (EPR) spectroscopy at both X- (9.7 GHz) and W-band (94 GHz) frequencies. The electron spin-lattice (T(1)) and spin-spin (T(2)) relaxation data indicate an extremely fast transfer or quantum tunneling rate of the solvated electron in these solutions which serves to modulate the hyperfine (Fermi-contact) interaction with nitrogen nuclei in the solvation shells of ammonia molecules surrounding the localized, solvated electron. The donor and acceptor states of the solvated electron in these solutions are the initial and final electron solvation sites found before, and after, the transfer or tunneling process. To interpret and model our electron spin relaxation data from the two observation EPR frequencies requires a consideration of a multiexponential correlation function. The electron transfer or tunneling process that we monitor through the correlation time of the nitrogen Fermi-contact interaction has a time scale of (1-10) × 10(-12) s over a temperature range 230-290 K in our most dilute solution of lithium in ammonia. Two types of electron-solvent interaction mechanisms are proposed to account for our experimental findings. The dominant electron spin relaxation mechanism results from an electron tunneling process characterized by a variable donor-acceptor distance or range (consistent with such a rapidly fluctuating liquid structure) in which the solvent shell that ultimately accepts the transferring electron is formed from random, thermal fluctuations of the liquid structure in, and around, a natural hole or Bjerrum-like defect vacancy in the liquid. Following transfer and capture of the tunneling electron, further solvent-cage relaxation with a time scale of ～10(-13) s results in a minor contribution to the electron spin relaxation times. This investigation illustrates the great potential of multifrequency EPR measurements to interrogate the microscopic nature and dynamics of ultrafast electron transfer or quantum-tunneling processes in liquids. Our results also impact on the universal issue of the role of a host solvent (or host matrix, e.g. a semiconductor) in mediating long-range electron transfer processes and we discuss the implications of our results with a range of other materials and systems exhibiting the phenomenon of electron transfer.     

Mechanistic aspects of protein/material interactions probed by atomic force microscopy

Physicochemical studies on the mechanisms of protein adsorption onto solid material surfaces have been extensively performed so far, mainly based on the analysis of factors such as the equilibrium adsorbed amount (adsorption isotherms), time-dependent change of adsorbed amount (adsorption kinetics), and conformational change of adsorbed protein. However, direct understanding of the strength of the molecular interaction between protein and the material surface has not been established yet. For this issue, the force measurement techniques of an atomic force microscope (AFM) using a protein-modified probe tip are recently becoming powerful tools to analyze the actual interaction forces between protein and material surfaces. In this mini review, we discuss the characteristics and interpretation of the AFM force-versus-distance curves (f–d curves) obtained with the protein-modified probe tip, and the relationship between the forces measured from the f–d curves and the driving forces in the natural process of protein adsorption. Relative degrees of each of the following contributions which determine the character of protein adsorption are clarified: (1) the intrinsic protein/material forces mediated by solvent, (2) the thermodynamic stability of protein/material adhesion interface, and (3) diffusion force of protein molecules. Within these driving forces, the latter two in particular are confirmed to play essential roles in determining the character of protein adsorption, based on the profiles of f–d curves.