Computational methods and theory for ion channel research

Ion channels are fundamental biological devices that act as gates in order to ensure selective ion transport across cellular membranes; their operation constitutes the molecular mechanism through which basic biological functions, such as nerve signal transmission and muscle contraction, are carried out. Here, we review recent results in the field of computational research on ion channels, covering theoretical advances, state-of-the-art simulation approaches, and frontline modeling techniques. We also report on few selected applications of continuum and atomistic methods to characterize the mechanisms of permeation, selectivity, and gating in biological and model channels.

Characterization of hydration water in supercooled water-trehalose solutions: The role of the hydrogen bonds network

The structural and dynamical properties of hydration water in aqueous solutions of trehalose are studied with molecular dynamics simulation. We simulate the systems in the supercooled region to investigate how the interaction with the trehalose molecules modifies the hydrogen bond network, the structural relaxation, and the diffusion properties of hydration water. The analysis is performed by considering the radial distribution functions, the residence time of water molecules in the hydration shell, the two body excess entropy, and the hydrogen bond water-water and water-trehalose correlations of the hydration water. The study of the two body excess entropy shows the presence of a fragile to strong crossover in supercooled hydration water also found in the relaxation time of the water-water hydrogen bond correlation function, and this is in agreement with predictions of the mode coupling theory and of previous studies of the oxygen-oxygen density correlators [A. Iorio et al., J. Mol. Liq. 282, 617 (2019); Sci. China: Phys., Mech. Astron. 62, 107011 (2019)]. The water-trehalose hydrogen bond correlation function instead evidences a strong to strong crossover in the relaxation time, and this crossover is related to a trehalose dynamical transition. This signals the role that the strong interplay between the soluted molecules and the surrounding solvent has in determining the dynamical transition common to both components of the system that happens upon cooling and that is similar to the well known protein dynamical transition. We connect our results with the cryoprotecting role of trehalose molecules.

An Italian national multicenter study for the definition of reference ranges for normal values of peripheral blood lymphocyte subsets in healthy adults

BACKGROUND AND OBJECTIVE

Reference ranges are necessary in clinical chemistry and hematology to compare an observed value and to provide meaningful information. The aim of this multicenter study was the definition of reference ranges of the relative and absolute numbers of lymphocyte subsets by evaluating a large cohort of healthy adults and by using a standard protocol to reduce the variability in both sample preparation methodology and flow cytometer operation. Other aims of this study were the evaluation of the influence of sex, age, obesity, smoking, sport and some methodological variables on lymphocyte subsets and the comparison of differential white blood cell values obtained by flow cytometry and those obtained by hematology counters.

DESIGN AND METHODS

Blood samples from 1311 healthy adults (blood donors and volunteers chosen according to the Italian law for donor selection) were analyzed to study, by flow cytometry, the immunophenotype of lymphocyte subsets and their distribution in terms of percentages and absolute values. Pre-analytical and analytical phases were performed according to the guidelines of the International Federation of Clinical Chemistry (IFCC) and the Italian Group of Cytometry (GIC). T cells were defined by the expression of CD3; T subpopulations by the coexpression of CD4 or CD8 or HLA-DR; B-lymphocytes were identified by the expression of CD19 while natural killer lymphocytes were identified by positivity of CD16 and/or CD56 without CD3. We calculated, for each laboratory and for all data collected, the frequency distribution percent values and absolute values of each lymphocyte subset. The influence of age, sex, smoking, obesity and sport was calculated by the t-test. The influence of some methodological variables was calculated by the t-test and multiple regression test.

RESULTS

Fifty-three flow cytometry laboratories at different institutions in Italy participated in this study. Data was obtained from 1311 healthy adults aged from 18 to 70; 968 phenotype analyses (74%) were considered eligible for statistical analysis. Significant results were found as regards sex, smoking and some methodological variables (quantity of sample, washing procedures, brand of monoclonal antibodies and kind of instruments used). The comparison between hematology counters and cytometers showed no difference for any of the parameters considered.

INTERPRETATION AND CONCLUSIONS

The large number of cases, the different kinds of laboratories and their distribution throughout the country make our sample representative of the Italian adult population. The standardization criteria of pre-analytical and analytical phases (the most important issues in evaluating reference values for an indicator) assured good reproducibility among laboratories so that the obtained reference ranges may be useful for interlaboratory comparison of results. Instruments and the brand of monoclonal antibodies may represent an inevitable cause of variability.