Analytical Approaches for Deriving Friction Coefficients for Selected α‑Helical Peptides Based Entirely on Molecular Dynamics Simulations

In this paper we derive analytically from molecular dynamics (MD) simulations the friction coefficients related to conformational transitions within several model peptides with α-helical structures. We study a series of alanine peptides with various length from ALA5 to ALA21 as well as their two derivatives, the (AAQAA)3 peptide and a 13-residue KR1 peptide that is a derivative of the (AAQAA)2 peptide with the formula GN(AAQAA)2G. We use two kinds of approaches to derive their friction coefficients. In the local approach, friction associated with fluctuations of single hydrogen bonds are studied. In the second approach, friction coefficients associated with a folding transitions within the studied peptides are obtained. In both cases, the respective friction coefficients differentiated very well the subtle structural changes between studied peptides and compared favorably to experimentally available data

Length Dependent Folding Kinetics of Alanine-Based Helical Peptides from Optimal Dimensionality Reduction

We present a computer simulation study of helix folding in alanine homopeptides (ALA)n of length n = 5, 8, 15, and 21 residues. Based on multi-microsecond molecular dynamics simulations at room temperature, we found helix populations and relaxation times increasing from about 6% and ~2 ns for ALA5 to about 60% and ~500 ns for ALA21, and folding free energies decreasing linearly with the increasing number of residues. The helix folding was analyzed with the Optimal Dimensionality Reduction method, yielding coarse-grained kinetic models that provided a detailed representation of the folding process. The shorter peptides, ALA5 and ALA8, tended to convert directly from coil to helix, while ALA15 and ALA21 traveled through several intermediates. Coarse-grained aggregate states representing the helix, coil, and intermediates were heterogeneous, encompassing multiple peptide conformations. The folding involved multiple pathways and interesting intermediate states were present on the folding paths, with partially formed helices, turns, and compact coils. Statistically, helix initiation was favored at both termini, and the helix was most stable in the central region. Importantly, we found the presence of underlying universal local dynamics in helical peptides with correlated transitions for neighboring hydrogen bonds. Overall, the structural and dynamical parameters extracted from the trajectories are in good agreement with experimental observables, providing microscopic insights into the complex helix folding kinetics

Choice of the most useful biological early warning system, based on ahp and rembrandt analysis

In paper, the ability to use of the biological early warning systems, in tap water quality biomonitoring was analyzed, based on multiple-criteria decision analysis. Five groups of organisms (invertebrates, fishes, algae, fungi and bacteria) were analyzed for the sensitivity to disturbance, the area of use, the amount of detected components, the rate of reaction and the data interpretation. Both analyzes revealed, that invertebrates are the most sensitive bioindicators (49% AHP, 29% Rembrandt). The other organisms which are useful in BEWS systems are algae and fishes. More problematic may be systems based on fungi and bacteria.Both analysis Rembrandt, as well as analytic hierarchy process(AHP) have indicated the rate of reaction as the most important factor in BEWS. All of BEWS systems are focused on reduce the time required to obtain the information about pollution presence, because the standard monitoring of tap water quality, based on physical and chemical methods, are usually time consuming

Biological indices applied to benthic macroinvertebrates at reference conditions of mountain streams in two ecoregions (Poland, the Slovak Republic)

The study was carried out from 2007 to 2010 in two ecoregions: the Carpathians and the Central Highlands. The objectives of our survey were to test the existing biological index metric based on benthic macroinvertebrates at reference conditions in the high- and mid-altitude mountain streams of two ecoregions according to the requirements of the EU WFD and to determine which environmental factors influence the distribution of benthic macroinvertebrates. Our results revealed statistically significant differences in the values of the physical and chemical parameters of water as well as the mean values of metrics between the types of streams at the sampling sites. RDA analysis showed that the temperature of the water, pH, conductivity, the stream gradient, values of the HQA index, and altitude were the parameters most associated with the distribution of benthic macroinvertebrate taxa and the values of the metrics. The values of biological indices should be considered according to the stream typology including altitude and geology. At the reference conditions, the suggested border values of biological indices are very harsh. The values of the biological indices of most sampling sites did not correspond to the requirements of the high status in rivers. The streams at altitudes above 1,200 m a.s.l. should be treated as another river type and new reference values should be established

Development of comprehensive river typology based on macrophytes in the mountain-lowland gradient of different Central European ecoregions

The aim of the study was to identify the vegetation pattern in the different types of watercourses basing on survey in reference conditions in a wide geographical gradient, including mountain, upland and lowland rivers. We tested relationship between composition of macrophytes to environmental variables including: altitude, slope, catchment area, geology of valley, land use, hydromorphological sfeatures, water physical and chemical measurements. Analysis based on 109 pristine river sites located throughout major types of rivers in Central Europe. Qualitative and quantitative plant surveys were carried out between 2005 and 2013. Based on TWINSPAN classification and DCA analysis, six macrophyte types were distinguished. The lowland sites were divided into the following three types: humic rivers and two types of siliceous rivers depending on the catchment area, including medium-large and small rivers. The mountain and upland rivers were divided into three geological types: siliceous, calcareous and gravel. We found that the variation of macrophyte communities was determined by several habitat factors (mainly altitude, flow type, riverbed granulometry, conductivity and alkalinity), whereas the spatial factor was rather limited; further, the plant diversity was not reflected accurately by the European ecoregion approach

Macrophyte and macroinvertebrate patterns in unimpacted mountain rivers of two European ecoregions

The aim of the study was to compare the patterns of development of macrophytes and macroinvertebrates in different types of reference mountain rivers. The study is based on reference river sites surveyed throughout the mountains in Poland and Slovakia in two European ecoregions (9—Central Highlands, 10—The Carpathians). A wide range of environmental variables were estimated, including water chemistry, hydromorphology, geology, and the spatial factor. Based on the Jaccard index, macrophyte and macroinvertebrate variation was confirmed between four mountain and upland river types. It was found that the biological diversification is mainly influenced by geological and associated chemical factors. In the case of macroinvertebrates, additionally, the importance of the spatial factor was revealed (difference between ecoregions). Finally, the habitat preferences of various taxa were identified. It was found that extreme mountain conditions can sometimes distort bioindicative response, as was detected in the case of macroinvertebrates in the highest mountain sites. We concluded that consideration of two groups of organisms enables more comprehensive and reliable monitoring than assessment based on a single group, especially when standard bioindicative methods can be distorted by extreme local conditions