A new method for assigning common spot boundaries for multiple gels in two-dimensional gel electrophoresis

The benefits of defining common spot boundaries when several gels from 2-DE are compared and analyzed have lately been stressed by both commercial software producers and users of this software. Though the importance of common spot boundaries is clearly stated, few reports exist that target this issue explicitly. In this study a method for defining common spots boundaries is developed, called the spot density method. The method consists of the following steps: segmentation and spot identification on each individual gel, transferring the spot-center coordinates for all gels onto a single new gel, collecting spot centers clustered together in the new gel and finally assigning pixels and new spot boundaries based on the spots in each cluster. The method is compared to a synthetic gel approach, and validated by visual inspection of three representative areas in the gels. The gel images need to be aligned prior to segmentation and spot identification, but the method can be used regardless of the choice of segmentation procedure. This makes the method an easy extension to existing methods for spot identification and matching. Conclusions based on the visual inspection are that the spot density method identifies partly overlapping spots and low-intensity spots better than the synthetic gel approach.     

Structural flexibility of a helical peptide regulates vibrational energy transport properties

Applying ultrafast vibrational spectroscopy, we find that vibrational energy transport along a helical peptide changes from inefficient but mostly ballistic below approximately 270 K into diffusive and significantly more efficient above. On the basis of molecular dynamics simulations, we attribute this change to the increasing flexibility of the helix above this temperature, similar to the glass transition in proteins. Structural flexibility enhances intramolecular vibrational energy redistribution, thereby refeeding energy into the few vibrational modes that delocalize over large parts of the structure and therefore transport energy efficiently. The paper outlines concepts how one might regulate vibrational energy transport properties in ultrafast photobiological processes, as well as in molecular electronic devices, by engineering the flexibility of their components.     

Curvature coupling dependence of membrane protein diffusion coefficients

We consider the lateral diffusion of a protein interacting with the curvature of the membrane. The interaction energy is minimized if the particle is at a membrane position with a certain curvature that agrees with the spontaneous curvature of the particle. We employ stochastic simulations that take into account both the thermal fluctuations of the membrane and the diffusive behavior of the particle. In this study, we neglect the influence of the particle on the membrane dynamics, thus the membrane dynamics agrees with that of a freely fluctuating membrane. Overall, we find that this curvature coupling substantially enhances the diffusion coefficient. We compare the ratio of the projected or measured diffusion coefficient and the free intramembrane diffusion coefficient, which is a parameter of the simulations, with analytical results that rely on several approximations. We find that the simulations always lead to a somewhat smaller diffusion coefficient than that from our analytical approach. A detailed study of the correlations of the forces acting on the particle indicates that the diffusing inclusion tries to follow favorable positions on the membrane such that forces along the trajectory are on average smaller than they would be for random particle positions.     

Synthesis of multimeric MR contrast agents for cellular imaging

We have prepared a series of molecular multimeric MR contrast agents for cell labeling that are easy to synthesize, relatively low molecular weight, and biocompatible. The relaxivities of the agents range from 17 to 85 mM(-1) s(-1). Cellular uptake is concentration dependent and viability is excellent. MR images of cell pellets reveal a marked increase in observed signal intensity.     

Noncovalent triblock copolymers based on a coiled-coil peptide motif

The formation of a noncovalent triblock copolymer based on a coiled-coil peptide motif is demonstrated in solution. A specific peptide pair (E and K) able to assemble into heterocoiled coils was chosen as the middle block of the polymer and conjugated to poly(ethylene glycol) (PEG) and polystyrene (PS) as the outer blocks. Mixing equimolar amounts of the polymer-peptide block copolymers PS-E and K-PEG resulted in the formation of coiled-coil complexes between the peptides and subsequently in the formation of the amphiphilic triblock copolymer PS-E/K-PEG. Aqueous self-assembly of the separate peptides (E and K), the block copolymers (PS-E and K-PEG), and equimolar mixtures thereof was studied by circular dichroism, dynamic light scattering, and cryogenic transmission electron microscopy. It was found that the noncovalent PS-E/K-PEG copolymer assembled into rodlike micelles, while in all other cases, spherical micelles were observed. Temperature-dependent studies revealed the reversible nature of the coiled-coil complex and the influence of this on the morphology of the aggregate. A possible mechanism for these transitions based on the interfacial free energy and the free energy of the hydrophobic blocks is discussed. The self-assembly of the polymer-peptide conjugates is compared to that of polystyrene-b-poly(ethylene glycol), emphasizing the importance of the coiled-coil peptide block in determining micellar structure and dynamic behavior.     

Optical constants, dielectric constants, molar absorption coefficients, molar polarizability, vibrational assignment and transition moments of liquid iodobenzene between 4000 and 400 cm(-1) at 25 degrees C

This paper reports the complex refractive index, molar absorption coefficient and imaginary molar polarizability spectra of liquid iodobenzene at 25 degrees C. The imaginary molar polarizability spectrum was fitted with 184 classical damped harmonic bands to determine the integrated intensity of the individual transitions. The standard deviation of the fitted spectrum from the experimental spectrum is 0.024 cm(3) mol(-1), and the R(2) value of the fit is 0.9968 indicating that the fitted spectrum is an accurate representation of the experimental spectrum. The dipole moment derivatives with respect to the normal coordinates and transition moments were determined for 26 of the 30 fundamentals. The total intensities of the in-plane and out-of-plane fundamentals were compared to benzene and other monosubstituted benzene derivatives using the F-sum rule. It was found that the total intensity of the out-of-plane fundamentals is essentially the same for the different compounds while the total intensities for the in-plane fundamentals varies according to the electronegativities of the substituents.     

n + n]-Heterometallomacrocyclic complexes (n > or = 2) prepared from platinum(II)-centred ditopic 2,2':6',2'-terpyridine ligands: dimensional cataloguing by pulsed-field gradient spin-echo NMR spectroscopy

The reaction of 4'-(2-propyn-1-oxy)-2,2':6',2'-terpyridine (HC[triple bond]CCH2Oterpy) with trans-[PtI2(PR3)2] (R = Et, (n)Bu, Ph) results in the regioselective formation of the metalloditopic ligands trans-[Pt(C[triple bond]CCH2Oterpy)2(PR3)2], crystallographic data for which are presented. Each ditopic ligand reacts with FeCl(2).4H(2)O to give heterometallomacrocycles, the smallest of which is a [2 + 2] macrocycle, confirmed structurally for R = Et. The NMR spectroscopic data confirm the formation of symmetrical species, i.e. macrocyclic and not polymeric species. The distribution of products has been investigated using pulsed-field gradient spin-echo (PGSE) diffusion NMR spectroscopy, and indicates that the kinetic products from the reactions of 1, 2 or 3(L) with iron(II) are [Fe(n)L(n)](2n+) with n = 2, 3 or 4. For L = 1 and 2, these mixtures of products convert in solution to the thermodynamically favoured [Fe(2)L(2)](4+).     

Ultrafast electron-induced desorption of water from nanometer amorphous solid water films

Laser-induced desorption of water molecules from nanometer amorphous solid water films supported on a single-crystal platinum substrate is reported. A femtosecond laser pulse creates hot substrate electrons, which are injected into the water layer, resulting in significant desorption at the water-vacuum interface. The dependence of the desorption yield on film thickness and results for isotopic spacer and capping layers reveal that the desorbing water originates from relatively deep down into the water layer, i.e., from several nanometers below the surface. This is proposed to be the result of cooperative electronic effects resulting from the high electron densities in the thin water film, which cause a transient destabilization of the water H-bonded network. Motion of excited water molecules through the layer is enabled by mixing within the layer on ultrafast timescales during the desorption process.