Electron capture dissociation of singly and multiply phosphorylated peptides

Analysis of phosphotyrosine and phosphoserine containing peptides by nano-electrospray Fourier transform ion cyclotron resonance (FTICR) mass spectrometry established electron capture dissociation (ECD) as a viable method for phosphopeptide sequencing. In general, ECD spectra of synthetic and native phosphopeptides appeared less complex than conventional collision activated dissociation (CAD) mass spectra of these species. ECD of multiply protonated phosphopeptide ions generated mainly c- and z(.)-type peptide fragment ion series. No loss of water, phosphate groups or phosphoric acid from intact phosphopeptide ions nor from the c and z(.) fragment ion products was observed in the ECD spectra. ECD enabled complete or near-complete amino acid sequencing of phosphopeptides for the assignment of up to four phosphorylation sites in peptides in the mass range 1400 to 3500 Da. Nano-scale Fe(III)-affinity chromatography combined with nano-electrospray FTMS/ECD facilitated phosphopeptide analysis and amino acid sequencing from crude proteolytic peptide mixtures.     

Simulation of the rheological properties of liquid media containing solid anisometric particles

Theoretical simulation of the rheological properties of liquid media containing solid anisometric particles is performed. Procedures for the calculation of the degree of ordering in the nematic systems under equilibrium conditions and their rheological characteristics are proposed. Earlier developed notions of the calculation procedures for the properties of systems considered are analyzed and corrections to the theory are substantiated. Based on developed model notions, equilibrium and transport equations are derived and a program for their numerical solution is proposed. Model calculations of the lines of phase transition and the ordering of systems containing isotropic and nematic phases, as well as anisotropic (in orienting field) and effective dynamic viscosities under the conditions of free flow of such systems, are carried out at various concentrations and geometry of anisometric particles. A comparison of calculated and experimental data for the solutions of polymer-salt compositions with induced chain rigidity demonstrates the adequacy of the model proposed.     

On the theory of structuring magnetic suspensions

The results of the three-dimensional computer and analytical simulation are presented for the kinetics of chain-shaped aggregate growth in suspensions of magnetizable non-Brownian particles. The results of the computer experiment show that, when the volume fraction of particles is no larger than 2–3%, chain-shaped aggregates are formed in the suspensions under the action of a field. The dependence of average number <n> of particles in a chain on time t is adequately described by the power law <n> = Ct ^k . The experiment indicates that, in contract to the common power approximations, in which exponent k is considered to be a universal constant parameter, it depends on the concentration of particles and their interactions with walls bounding a suspension. At concentrations noticeably exceeding 2–3%, dense bulk aggregates are formed in suspensions. The kinetics of their growth depends on the sizes of a suspension-containing vessel.     

Amphiphilic gold nanoparticles with V-shaped arms

Here we describe a very efficient method to produce well-defined amphiphilic gold nanoparticles (Au NPs) with an equal number of hydrophobic and hydrophilic arms which are distributed along the surface of a 2-nm gold core in an alternating fashion. The strategy involves direct coupling of V-shaped block copolymer amphiphile 2 with a carboxylic group at its junction point to mercaptophenol-terminated Au NPs. The reaction proceeds under mild esterification conditions and yields the product with a molecular weight of 40 kDa, high grafting density (2.9 chains/nm2), and extremely low polydispersity (1.07). The big advantage of this approach is the opportunity to avoid the use of expensive and often inaccessible polymeric thiols. The method described here is applicable to any carboxyl-terminated molecules and can be used for the preparation of complex, yet well-defined, macromolecular hybrid structures such as 1 (Au(PB-PEG)n). The new product, which was characterized by a combination of SEC, NMR, UV-vis, DLS, and TEM, represents a unique example of gold nanoparticles soluble in any conventional solvent.     

Intercalation of Toluidines into α-Zirconium Hydrogenphosphate

Intercalates of o-, m-, and p-toluidine into α-Zr(HPO₄)₂ · H₂O were prepared and characterized by powder X-ray diffraction, thermogravimetric analysis and infrared spectroscopy. As follows from IR, toludine molecules are protonated in the interlayer space. Toluidine molecules are arranged in a bimolecular way in the intercalates containing more than 1.5 toluidine molecules per Zr atom. On the other hand, a monolayer of the toluidine molecules is supposed in the intercalates with less than one toluidine molecule per Zr atom.     

Electron capture dissociation proceeds with a low degree of intramolecular migration of peptide amide hydrogens

Hydrogen (1H/2H) exchange combined with mass spectrometry (HX-MS) has become a recognized method for the analysis of protein structural dynamics. Presently, the incorporated deuterons are typically localized by enzymatic cleavage of the labeled proteins and single residue resolution is normally only obtained for a few residues. Determination of site-specific deuterium levels by gas-phase fragmentation in tandem mass spectrometers would greatly increase the applicability of the HX-MS method. The biggest obstacle in achieving this goal is the intramolecular hydrogen migration (i.e., hydrogen scrambling) that occurs during vibrational excitation of gas-phase ions. Unlike traditional collisional ion activation, electron capture dissociation (ECD) is not associated with substantial vibrational excitation. We investigated the extent of intramolecular backbone amide hydrogen (1H/2H) migration upon ECD using peptides with a unique selective deuterium incorporation. Our results show that only limited amide hydrogen migration occurs upon ECD, provided that vibrational excitation prior to the electron capture event is minimized. Peptide ions that are excessively vibrationally excited in the electrospray ion source by, e.g., high declustering potentials or during precursor ion selection (via sideband excitation) in the external linear quadrupole ion trap undergo nearly complete hydrogen (1H/2H) scrambling. Similarly, collision-induced dissociation (CID) in the external linear quadrupole ion trap results in complete or extensive hydrogen (1H/2H) scrambling. This precludes the use of CID as a method to obtain site-specific information from proteins that are labeled in solution-phase 1H/2H exchange experiments. In contrast, the deuteration levels of the c- and z-fragment ions generated from ECD closely mimic the known solution deuteration pattern of the selectively labeled peptides. This excellent correlation between the results obtained from gas phase and solution suggests that ECD holds great promise as a general method to obtain single residue resolution in proteins from solution 1H/2H exchange experiments.     

On the theory of phase transitions in magnetic fluids

Particles of magnetic fluids (ferrofluids), as is known from experiments, can condense to bulk dense phases at low temperatures (that are close to room temperature) in response to an external magnetic field. It is also known that a uniform external magnetic field increases the threshold temperature of the observed condensation, thus stimulating the condensation process. Within the framework of early theories, this phenomenon is interpreted as a classical gas-liquid phase transition in a system of individual particles involved in a dipole-dipole interaction. However, subsequent investigations have revealed that, before the onset of a bulk phase transition, particles can combine to form a chain cluster or, possibly, a topologically more complex heterogeneous cluster. In an infinitely strong magnetic field, the formation of chains apparently suppresses the onset of a gas-liquid phase transition and the condensation of magnetic particles most likely proceeds according to the scenario of a gas-solid phase transition with a wide gap between spinodal branches. This paper reports on the results of investigations into the specific features of the condensation of particles in the absence of an external magnetic field. An analysis demonstrates that, despite the formation of chains, the condensation of particles in this case can proceed according to the scenario of a gas-liquid phase transition with a critical point in the continuous binodal. Consequently, a uniform magnetic field not only can stimulate the condensation phase transition in a system of magnetic particles but also can be responsible for a qualitative change in the scenario of the phase transition. This inference raises the problem regarding a threshold magnetic field in which there occurs a change in the scenario of the phase transition.     

Kinetics of internal structures growth in magnetic suspensions

The kinetics of aggregation of non Brownian magnetizable particles in the presence of a magnetic field is studied both theoretically and by means of computer simulations. A theoretical approach is based on a system of Smoluchowski equations for the distribution function of the number of particles in linear chain-like aggregates. Results obtained in the two dimensional (2D) and three dimensional (3D) models are analyzed in relation with the size of the cell, containing the particles, and the particle volume fraction φ$\phi$. The theoretical model reproduces the change of the aggregation kinetics with the size of the cell and with the particle volume fraction as long as the lateral aggregation of chains is negligible.