European Biophysics Journal 

About: European Biophysics Journal is an academic journal published by Springer Science+Business Media. The journal publishes majorly in the area(s): Membrane & Lipid bilayer. It has an ISSN identifier of 0175-7571. Over the lifetime, 2858 publications have been published receiving 77517 citations. The journal is also known as: European biophysics journal with Biophysics letters & EBJ. European biophysics journal.

Definition and testing of the GROMOS force-field versions 54A7 and 54B7

Abstract: New parameter sets of the GROMOS biomolecular force field, 54A7 and 54B7, are introduced. These parameter sets summarise some previously published force field modifications: The 53A6 helical propensities are corrected through new φ/ψ torsional angle terms and a modification of the N-H, C=O repulsion, a new atom type for a charged -CH(3) in the choline moiety is added, the Na(+) and Cl(-) ions are modified to reproduce the free energy of hydration, and additional improper torsional angle types for free energy calculations involving a chirality change are introduced. The new helical propensity modification is tested using the benchmark proteins hen egg-white lysozyme, fox1 RNA binding domain, chorismate mutase and the GCN4-p1 peptide. The stability of the proteins is improved in comparison with the 53A6 force field, and good agreement with a range of primary experimental data is obtained.

Fluorescence correlation spectroscopy with high count rate and low background: analysis of translational diffusion

Abstract: An epi-illuminated microscope configuration for use in fluorescence correlation spectroscopy in bulk solutions has been analyzed. For determining the effective sample dimensions the spatial distribution of the molecule detection efficiency has been computed and conditions for achieving quasi-cylindrical sample shape have been derived. Model experiments on translational diffusion of rhodamine 6G have been carried out using strong focusing of the laser beam, small pinhole size and an avalanche photodiode in single photon counting mode as the detector. A considerable decrease in background light intensity and measurement time has been observed. The background light is 40 times weaker than the fluorescence signal from one molecule of Rh6G, and the correlation function with signal-to-noise ratio of 150 can be collected in 1 second. The effect of the shape of the sample volume on the autocorrelation function has been discussed.

Elasticity of normal and cancerous human bladder cells studied by scanning force microscopy.

Abstract: Scanning force microscopy was used for the determination of the elastic properties of living cells in their culture conditions. The studies were carried out on human epithelial cells. Two similar lines of normal cells (Hu609 and HCV29) and three cancerous ones (Hu456, T24, BC3726) were measured using the scanning force microscope in order to collect the force versus indentation curves. The BC3726 line originates from the HCV29 cell line which was transformed by the v-ras oncogene. To evaluate their elastic properties, Young's modulus values were determined. The present study has shown that normal cells have a Young's modulus of about one order of magnitude higher than cancerous ones. Such a change might be attributed to a difference in the organisation of cell cytoskeletons and requires further studies.

Allostery without conformational change. A plausible model.

Abstract: A general model is presented whereby lignand-induced changes in protein dynamics could produce allosteric communication between distinct binding sites, even in the absence of a macromolecular conformational change. Theoretical analysis, based on the statistical thermodynamics of ligand binding, shows that cooperative interaction free energies amounting to several kJ · mol-1 may be generated by this means. The effect arises out of the possible changes in frequencies and amplitudes of macromolecular thermal fluctuations in response to ligand attachment, and can involve all forms of dynamic behaviour, ranging from highly correlated, low-frequency normal mode vibrations to random local anharmonic motions of individual atoms or groups. Dynamic allostery of this form is primarily an entropy effect, and we derive approximate expressions which might allow the magnitude of the interaction in real systems to be calculated directly from experimental observations such as changes in normal mode frequencies and mean-square atomic displacements. Long-range influence of kinetic processes at different sites might also be mediated by a similar mechanism. We suggest that proteins and other biological macromolecules may have evolved to take functional advantage not only of mean conformational states but also of the inevitable thermal fluctuations about the mean.

Validation of the 53A6 GROMOS force field.

Abstract: The quality of biomolecular dynamics simulations relies critically on the force field that is used to describe the interactions between particles in the system. Force fields, which are generally parameterized using experimental data on small molecules, can only prove themselves in realistic simulations of relevant biomolecular systems. In this work, we begin the validation of the new 53A6 GROMOS parameter set by examining three test cases. Simulations of the well-studied 129 residue protein hen egg-white lysozyme, of the DNA dodecamer d(CGCGAATTCGCG)(2), and a proteinogenic beta(3)-dodecapeptide were performed and analysed. It was found that the new parameter set performs as well as the previous parameter sets in terms of protein (45A3) and DNA (45A4) stability and that it is better at describing the folding-unfolding balance of the peptide. The latter is a property that is directly associated with the free enthalpy of hydration, to which the 53A6 parameter set was parameterized.