Mesoporous tungsten titanate as matrix for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis of biomolecules

In this paper, mesoporous tungsten titanate (WTiO) with different nano-pore structures was utilized as matrix for the analysis of short peptides by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS). Effect of characteristic features of mesoporous matrices on laser desorption/ionization process was investigated. Experiments showed that the ordered two-dimensional and three-dimensional mesoporous matrices were superior in performance to the non-ordered WTiO matrix. The dramatic enhancement of signal sensitivity by the ordered mesoporous matrices can be reasonably attributed to the ordered structure, which facilitated the understanding on structure-function relationship in mesoporous cavity for laser desorption process of adsorbed biomolecules. With the ordered mesoporous matrix, the short peptides are successfully detected. The presence of trace alkali metal salt effectively increased the analyte ion yields and the MALDI-TOFMS using the inorganic mesoporous matrices displayed a high salt tolerance. The developed technique also showed a satisfactory performance in peptide-mapping and amino-acid sequencing analysis.     

Application of FT-ICR-MS for the study of proton-transfer reactions involving biomolecules

Fourier transform ion cyclotron resonance mass spectrometry, combined with modern ionization (fast atom bombardment , electrospray ionization, matrix-assisted laser desorption–ionization), fragmentation (collision-induced dissociation, surface-induced dissociation, one-photon ultraviolet photodissociation, infrared multiphoton dissociation, blackbody infrared radiative dissociation, electron-capture dissociation), and separation (high-performance liquid chromatography, liquid chromatography, capillary electrophoresis) techniques is now becoming one of the most attractive and frequently used instrumental platforms for gas-phase studies of biomolecules such as amino acids, bioamines, peptides, polypeptides, proteins, nucleobases, nucleosides, nucleotides, polynucleotides, nucleic acids, saccharides, polysaccharides, etc. Since it gives the possibilities to trap the ions from a few seconds up to thousands of seconds, it is often applied to study ion/molecule reactions in the gas phase, particularly proton-transfer reactions which provide important information on acid–base properties. These properties determine in part the three-dimensional structure of biomolecules, most of their intramolecular and intermolecular interactions, and consequently their biological activity. They also indicate the form (unionized, zwitterionic, protonated, or deprotonated) which the biomolecule may take in a nonpolar environment. Figure Biomolecules in the gas-phase acidity-basicity scale     

Force spectroscopy of single multidomain biopolymers: A master equation approach

Experiments using atomic force microscopy for unfolding single multidomain biopolymers cover a broad range of time scales from equilibrium to non-equilibrium. A master equation approach allows to identify and treat coherently three dynamical regimes for increasing linear ramp velocity: i) an equilibrium regime, ii) a transient regime where refolding events still occur, and iii) a saw-tooth regime without any refolding events. For each regime, analytical approximations are derived and compared to numerically investigated examples. We analyze in the framework of this model also a periodic experimental protocol instead of a linear ramp. In this case, a major simplification arises if the dynamics can be restricted to an effectively two-dimensional subspace. For transitions with an intermediate meta-stable state, like Immunoglobulin27, a refined model allows to extract previously unknown molecular parameters related to this meta-stable state.     

Log-periodic oscillations for biased diffusion of a polymer chain in a porous medium

A coarse-grained off-lattice bead-spring model is used to reveal the complex dynamics of a polymer chain in a quenched porous medium in the presence of an external field B. The behavior of the mean square displacement (MSD) of the center chain bead and that of the center of mass of the chain as a function of time is studied at different values of the barrier concentration C, the field strength B and the chain length N. In a field, important information on the way in which chains move between obstacles and overcome them is gained from the MSD vs. time analysis in the directions parallel and perpendicular to the flow. Instead of a steady approach to uniform drift-like motion at low C, for sufficiently strong field B we observe logarithmic oscillations in the effective exponents describing the time dependence of the MSD along and perpendicular to field. A common nature of this phenomenon with oscillatory behavior, observed earlier for biased diffusion of tracers on random lattices, is suggested. Received 7 August 1998     

Transverse fluctuation analysis of single extended DNA molecules

We observed fluctuations of elongated DNA molecules by fluorescence microscopy. The molecules are fixed at both ends and undulate. Mode analysis of the thermally excited undulations of the labeled DNA molecules gives access to the spectral density of the amplitude fluctuations. From these measurements we estimate the tension acting on the DNA molecules. We found the forces to be within the entropic elasticity range of a typical DNA molecule (measured on the single-molecule level). Received: 11 November 2002 / Accepted: 12 May 2002 / Published online: 4 June 2003 RID="a" ID="a"Present address: Center for Studies in Physics and Biology, Rockefeller University, 1230 York Avenue, New York, NY 10021, USA. e-mail: zoherg@rockefeller.edu     

Slow nucleic acid unzipping kinetics from sequence-defined barriers

Recent experiments on unzipping of RNA helix-loop structures by force have shown that ≈40-base molecules can undergo kinetic transitions between two well-defined “open” and “closed” states, on a timescale ≈1 sec [Liphardt et al., Science 297, 733-737 (2001)]. Using a simple dynamical model, we show that these phenomena result from the slow kinetics of crossing large free energy barriers which separate the open and closed conformations. The dependence of barriers on sequence along the helix, and on the size of the loop(s) is analyzed. Some DNA and RNA sequences that could show dynamics on different time scales, or three(or more)-state unzipping, are proposed. Our dynamical model is also applied to the unzipping of long (kilo-basepair) DNA molecules at constant force. Received 29 July 2002 / Received in final form 5 February 2003 Published online: 16 April 2003 RID="a" ID="a"e-mail: cocco@ldfc.u-strasbg.fr RID="b" ID="b"e-mail: jmarko@uic.edu RID="c" ID="c"e-mail: monasson@lpt.ens.fr     

Two-dimensional functional molecular nanoarchitectures – Complementary investigations with scanning tunneling microscopy and X-ray spectroscopy

Functional molecular nanoarchitectures (FMNs) are highly relevant for the development of future nanotechnology devices. Profound knowledge about the atomically controlled construction of such nanoscale assemblies is an indispensable requirement to render the implementation of such components into a real product successful. For exploiting their full potential the architectures’ functionalities have to be characterized in detail including the ways to tailor them. In recent years a plethora of sophisticated constructs were fabricated touching a wide range of research topics.     

Chemiluminescence from singlet oxygen that was detected at two wavelengths and effects of biomolecules on it

We developed the detection apparatus that equipped with the two-photomultiplier tubes for chemiluminescence from singlet oxygen. Singlet oxygen was generated with reaction between sodium hypochlorite and hydrogen peroxide. The chemiluminescence from singlet oxygen, the dimol light emission (ca. 634 nm) and the monomol light emission (ca. 1270 nm), was observed simultaneously for the same reaction cell. The effects of sodium azide as an antioxidant, human serum albumin, and α-amino acids on the chemiluminescence based on the both emissions were examined; the observed chemiluminescence could provide direct information with regard to the reaction between singlet oxygen and antioxidant/biomolecules. The apparent rate constants for quenching singlet oxygen in the presence of human serum albumin were calculated to be ca. 3.3 × 10⁹ and ca. 8.8 × 10⁸ M⁻¹ s⁻¹ for the dimol and monomol light emissions, respectively, under the present conditions. The chemiluminescence intensities of the dimol emission decreased in the presence of His, Asp, Phe, Ser, and Tyr, and that of the monomol decreased in the presence of Cys and Trp. The chemiluminescence observed in the presence of biomolcules was discussed together with the reactivities of sodium hypochlorite and hydrogen peroxide to biomolecules.     

Fibril stability in solutions of twisted -sheet peptides: a new kind of micellization in chiral systems

The problem of fibril (fibre) formation in chiral systems is explored theoretically being supported by experiments on synthetic de novo 11-mer peptide forming self-assembled -sheet tapes. Experimental data unambiguously indicate that the tapes form fibrils of nearly monodisperse thickness ca . 8-10 nm. Fibril formation and stabilisation are attributed to inter-tape face-to-face attraction and their intrinsic twist, correspondingly. The proposed theory is capable of predicting the fibril aggregation number and its equilibrium twist in terms of molecular parameters of the primary tapes. The suggested novel mechanism of twist stabilisation of finite aggregates (fibrils) is different to the well-known stabilisation of micelles in amphiphilic systems, and it is likely to explain the formation and stability of fibrils in a wide variety of systems including proteinaceous amyloid fibres, sickle-cell hemoglobin fibres responsible for HbS anemia, corkscrew threads found in chromonics in the presence of chiral additives and native cellulose microfibrillar crystallites. The theory also makes it possible to extract the basic molecular parameters of primary tapes (inter-tape attraction energy, helical twist step, elastic moduli) from the experimental data. Received 7 May 1999 and Received in final form 15 February 2000