Structural Analysis of a Helical Peptide Unfolding Pathway

The analysis of the folding mechanism in peptides adopting well‐defined secondary structure is fundamental to understand protein folding. Herein, we describe the thermal unfolding of a 15‐mer vascular endothelial growth factor mimicking α‐helical peptide (QK_L10A) through the combination of spectroscopic and computational analyses. In particular, on the basis of the temperature dependencies of QK_L10A H_α chemical shifts we show that the first phase of the thermal helix unfolding, ending at around 320 K, involves mainly the terminal regions. A second phase of the transition, ending at around 333 K, comprises the central helical region of the peptide. The determination of high‐resolution QK_L10A conformational preferences in water at 313 K allowed us to identify, at atomic resolution, one intermediate of the folding–unfolding pathway. Molecular dynamics simulations corroborate experimental observations detecting a stable central helical turn, which represents the most probable site for the helix nucleation in the folding direction. The data presented herein allows us to draw a folding–unfolding picture for the small peptide QK_L10A compatible with the nucleation–propagation model. This study, besides contributing to the basic field of peptide helix folding, is useful to gain an insight into the design of stable helical peptides, which could find applications as molecular scaffolds to target protein–protein interactions.     

Application of displacement chromatography for the proteome analysis of a human plasma protein fraction

It was the aim of this study to compare the performance of displacement chromatography with gradient elution chromatography both applied as the cation-exchange separation step for a proteome analysis in a bottom-up approach using multidimensional chromatography for the separation of tryptic peptides prior to their mass spectrometric analysis. The tryptic digest of the human Cohn fraction IV-4 served as a sample. For both chromatography modes commonly used operating parameters were chosen thus ensuring optimal separation results of equal sample amounts for each mode. All resulting fractions were analyzed with an HPLC-chip–LC–MS system. The eluate of the HPLC-chip column was ionized by electrospray ionization (ESI) and analyzed with an ion-trap mass spectrometer. For guaranteeing high confidence concerning the identity of the peptides, the mass spectrometric data were processed by different bioinformatic tools applying stringent criteria. By the displacement approach the total amount of identified proteins (78) was significantly higher than in the gradient mode (58). The results showed that displacement chromatography is a well suited alternative in comparison to gradient elution separation for analysis of proteomes via the bottom-up approach applying multidimensional chromatography, especially in those cases when larger quantities of proteins are available.     

Coaxial fiber-optic chemical-sensing excitation-emission matrix fluorometer

Great reductions in the overall size and complexity of high throughput multichannel UV-visible fluorometers were achieved by coupling a compact optical fiber array to compact dispersive transmission optics. The coaxial configuration centers on the insertion of a silica/silica optical fiber into the hollow region of a UV-fused silica capillary waveguide. The outer core delivers the maximum power of the narrow wavelength region of the excitation spectrum created by coupling a xenon arc discharge lamp to a compact spectrometer. The molecular fluorescence resulting from the interaction of light emitted at the distal end of the hollow waveguide and the sample matrix is received and transmitted to a CCD via a compact dispersive grating-prism (grism) optical assembly. A linear array of the coaxial optical fibers permits a full excitation-emission matrix spectrum of the analyte matrix to be projected onto the face of the CCD. The in situ identification and monitoring of polycyclic aromatic hydrocarbons was carried out for the initial application testing for this prototype.     

Localization of compact invariant sets and global stability in analysis of one tumor growth model

In this paper, we study some features of global behavior of the four‐dimensional superficial bladder cancer model with Bacillus Calmette‐Guérin (BCG) immunotherapy described by Bunimovich‐Mendrazitsky et al. in 2007 with the help of localization analysis of its compact invariant sets. Its dynamics is defined by the BCG treatment and by densities of three cells populations: effector cells, tumor infected cells by BCG, and tumor uninfected cells. We find upper bounds for ultimate dynamics of the whole state vector in the positive orthant and also under condition that there are no uninfected tumor cells. Further, we prove the existence of the bounded positively invariant domain in both of these two situations. Finally, by using these assertions, we derive our main result: sufficient conditions of global asymptotic stability of the tumor‐free equilibrium point in the positive orthant. Copyright © 2013 John Wiley & Sons, Ltd.     

Protein analysis of laser capture micro-dissected tissues revealed cell-type specific biological functions in developing barley grains

Both the nucellar projection (NP) and endosperm transfer cells (ETC) of the developing barley grain (harvested 8 days after flowering) were isolated by laser capture micro-dissection combined with pressure catapulting. Protein extracts were analyzed by nanoUPLC separation combined with ESI-Q-TOF mass spectrometry. The majority of the ～160 proteins identified were involved in translation, protein synthesis, or protein destination. The NP proteome was enriched for stress defense molecules, while proteins involved in assimilate transport and the mobilization of nutrients were common to both the NP and the ETC. The combined qualitative and quantitative protein profiling allowed for the identification of several proteins showing tissue specificity in their expression, which underlines the distinct biological functions of these two tissues within the developing barley grain.     

Frame expansions in separable Banach spaces

Banach frames are defined by straightforward generalization of (Hilbert space) frames. We characterize Banach frames (and Xd-frames) in separable Banach spaces, and relate them to series expansions in Banach spaces. In particular, our results show that we can not expect Banach frames to share all the nice properties of frames in Hilbert spaces.     

Bounded rational expectations and the stability of interest rate policy

The New Keynesian model has recently been subject to two serious criticisms: the model cannot produce plausible inflation and output dynamics following a monetary shock, and the stability of its dynamics suffers from indeterminacy. The procedures that have been proposed to eliminate these two shortcomings fall into two categories: the introduction of some sort of backward price indexation into the standard model and/or other forms of stickiness (like sticky information); and the adoption of some form of policy rule that completely offsets the effects of forward looking dynamics in the optimization process. In this paper we do not eradicate forward looking behavior from the dynamics of the New Keynesian model, neither do we impose some form of backward price indexation. We assume that private economic agents have forward looking behavior and that they do try to optimize with all available information; the only novelty is that they are allowed to make small mistakes near the rational expectations equilibrium, in a fully deterministic setup. These “near rational” or “bounded rational” expectations show that the dynamics of the model with active interest rate rules is much richer than the simple problem of local indeterminacy as is usually found in the literature.