Decoding the components of dynamics in three‐domain proteins

In this study, we examine the feasibility and limitations of describing the motional behavior of three‐domain proteins in which the domains are linearly connected. In addition to attempting the determination of the internal and overall reorientational correlation times, we investigate the existence of correlations in the motions between the three domains. Since in linearly arranged three‐domain proteins, there are typically no experimental data that can directly report on motional correlation between the first and the third domain, we address this question by dynamics simulations. Two limiting cases occur: (1) for weak repulsive potentials and (2) when strong repulsive potentials are applied between sequential domains. The motions of the terminal domains become correlated in the case of strong interdomain repulsive potentials when these potentials do not allow the angle between the sequential domains to be smaller than about 60°. Using the model‐free (MF) and extended MF formalisms of Lipari and Szabo, we find that the motional behavior can be separated into two components; the first component represents the concerted overall motion of the three domains, and the second describes the independent component of the motion of each individual domain. We find that this division of the motional behavior of the protein is maintained only when their timescales are distinct and can be made when the angles between sequential domains remain between 60° and 160°. In this work, we identify and quantify interdomain motional correlations. © 2013 Wiley Periodicals, Inc.     

Minimal Hermite-Type Eigenbasis of the Discrete Fourier Transform

There exist many ways to build an orthonormal basis of \(\mathbb {R}^N\), consisting of the eigenvectors of the discrete Fourier transform (DFT). In this paper we show that there is only one such orthonormal eigenbasis of the DFT that is optimal in the sense of an appropriate uncertainty principle. Moreover, we show that these optimal eigenvectors of the DFT are direct analogues of the Hermite functions, that they also satisfy a three-term recurrence relation and that they converge to Hermite functions as N increases to infinity.

     

Parametric polarization pulse shaping demonstrated for optimal control of NaK

We present a routine for calculating and producing customized/parametric femtosecond laser pulses for investigating molecular processes involving the polarization. It is applied on the ionization of NaK molecules by feedback-loop optimization using the recently introduced double-pass "serial setup" that is capable of phase, amplitude, and polarization modulation. The temporal subpulse encoding uses the parameters distance, intensity, zero order spectral phase, and polarization state.     

The RATIO method for time‐resolved Laue crystallography

A RATIO method for analysis of intensity changes in time‐resolved pump–probe Laue diffraction experiments is described. The method eliminates the need for scaling the data with a wavelength curve representing the spectral distribution of the source and removes the effect of possible anisotropic absorption. It does not require relative scaling of series of frames and removes errors due to all but very short term fluctuations in the synchrotron beam.     

Diamino acid derivatives of PpIX as potential photosensitizers for photodynamic therapy of squamous cell carcinoma and prostate cancer: In vitro studies

Photodynamic therapy (PDT) is an alternative treatment modality involving light activated drugs, called photosensitizers (PSs), to treat cancer and non-cancerous conditions. The search for new compounds which might become effective PSs is the major direction for PDT development. In the present work we have studied the dark toxicity, intracellular localization and photodynamic properties of four potential, water soluble, second generation PSs – PP(Arg)₂, PP(Ser)₂Arg₂, PP(Ala)₂Arg₂, PP(Phe)₂Arg₂, all diamino acid derivatives of protoporphyrin IX. Human prostate cancer (DU-145) and squamous carcinoma (A431) cells were used as experimental model.Among investigated compounds PP(Ser)₂Arg₂ exhibited the lowest dark toxicity and the highest PDT effectiveness towards both cell lines. Fluorescence microscopy revealed the time-dependent changes in intracellular localization of the PS which were related to the phototoxicity. The results show that PP(Ser)₂Arg₂ may be a potential PS for PDT.     

Applications of the conformal transformation method in studies of composed superconducting systems

A framework for analytical studies of superconducting systems is presented and illustrated. The formalism, based on the conformal transformation of momentum space, allows one to study the effects of both the dispersion relation and the structure of the pairing interaction in two-dimensional anisotropic high-T _c superconductors. In this method, the number of employed degrees of freedom coincides with the dimension of the momentum space, which is different compared to that in the standard Van Hove scenario with a single degree of freedom. A new function, the kernel of the density of states, is defined and its relation to the standard density of states is explained. The versatility of the method is illustrated by analyzing coexistence and competition between spin-singlet and spin-triplet order parameters in superconducting systems with a tight-binding-type dispersion relation and an anisotropic pairing potential. Phase diagrams of stable superconducting states in the coordinates η (the ratio of hopping parameters) and n (the carrier concentration) are presented and discussed. Moreover, the role of attractive and repulsive on-site interactions for the stability of the s-wave order parameter is explained.     

DOSY NMR as a tool for predicting optimal conditions for hydrogel formation: The case of a hyperbranched polyglycidol cross‐linked with boronic acids

This article demonstrates the utility of DOSY NMR for the determination of the optimal conditions for the efficient covalent, reversible cross‐linking of macromolecules in water for hydrogel formation. The studied model system was hyperbranched polyglycidol (HbPGL) containing numerous diol groups in peripheral regions and two types of boronic acids, that is, B(OH)₄^? and benzene‐1,4‐boronic diacid, as cross‐linking agents. Diffusion coefficient changes of a polymer in solution, under the influence of various concentrations of cross‐linking agent and pH, which influences the equilibrium of the reaction between boronic acids and diols, were recorded. These data are consistent with the rheological properties, namely the G′_max(ω) of hydrogels prepared under analogous conditions, from more concentrated solutions of HbPGL. This approach appears to be promising as it facilitates avoiding the loss of a large amount of polymer that is necessary for the elaboration of appropriate conditions for network formation in aqueous media. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2016 , 54, 2171–2178