Molecular Dynamics Simulations of β-turn Forming Tetra- and Hexapeptides

Abstract

It was previously shown that the structural ensemble of model peptides DDKG and GKDG (H. Ishii et al. Biopolymers 24, 2045–2056, 1985), DEKS (A. Otter et al. J. Biomol. Struct. Dyn. 7, 455–476, 1989) NPGQ (F. R. Carbone et al. Int. J. Pept. Protein. Res. 26, 498–508, 1985), SALN (H. Santa et al. J. Biomol. Struct. Dyn. 16, 1033–1041, 1999), SYPFDV and SYPYDV (J. Yao et al. J. Mol. Biol. 243, 736–753, 1994), VP^DAH and VP^DSH (B. Imperiali et al. J. Am. Chem. Soc. 114, 3182–3188, 1992) in solution contains a significant—or in some cases dominant—proportion of β-turn conformation. In this study, a protein database was searched for the above, unprotected sequences which incorporate only L-amino acid residues. Simulated annealing and 25 ns MD simulations of structures were also performed. The DSSP and STRIDE secondary structure-assigning algorithms and clustering were used to analyze trajectories and i, i+3 hydrogen bonds were also sought. The DSSP analysis showed a fluctuation between β-turn and random meander structure, although bend structures were not detected because of the insufficient length of peptide chains. This alternating trend was confirmed when the STRIDE algorithm was used to analyze trajectories, but STRIDE assigned more turn structures. The population of the strongest clusters was above 40% and the middle structures adopted β-turn structure for most sequences. These results are in good agreement with previous experimental results and support the idea of the ultra-marginal stability of turns in the absence of stabilizing long-range interactions of the neighboring segments of a polypeptide chain. However, interactions between the side-chains in tetrapeptides could also contribute to turn stability and result in unusual stability in some cases. Our observations suggest that such interactions are the consequence rather than the driving force of turn formation.     

Molecular dynamics simulations of beta-turn forming tetra- and hexapeptides

It was previously shown that the structural ensemble of model peptides DDKG and GKDG (H. Ishii et al. Biopolymers 24, 2045-2056, 1985), DEKS (A. Otter et al. J. Biomol. Struct. Dyn. 7, 455-476, 1989) NPGQ (F. R. Carbone et al. Int. J. Pept. Protein. Res. 26, 498-508, 1985), SALN (H. Santa et al. J. Biomol. Struct. Dyn. 16, 1033-1041, 1999), SYPFDV and SYPYDV (J. Yao et al. J. Mol. Biol. 243, 736-753, 1994), VP(D)AH and VP(D)SH (B. Imperiali et al. J. Am. Chem. Soc. 114, 3182-3188, 1992) in solution contains a significant - or in some cases dominant - proportion of beta-turn conformation. In this study, a protein database was searched for the above, unprotected sequences which incorporate only L-amino acid residues. Simulated annealing and 25 ns MD simulations of structures were also performed. The DSSP and STRIDE secondary structure-assigning algorithms and clustering were used to analyze trajectories and i, i+3 hydrogen bonds were also sought. The DSSP analysis showed a fluctuation between beta-turn and random meander structure, although bend structures were not detected because of the insufficient length of peptide chains. This alternating trend was confirmed when the STRIDE algorithm was used to analyze trajectories, but STRIDE assigned more turn structures. The population of the strongest clusters was above 40% and the middle structures adopted beta-turn structure for most sequences. These results are in good agreement with previous experimental results and support the idea of the ultra-marginal stability of turns in the absence of stabilizing long-range interactions of the neighboring segments of a polypeptide chain. However, interactions between the side-chains in tetrapeptides could also contribute to turn stability and result in unusual stability in some cases. Our observations suggest that such interactions are the consequence rather than the driving force of turn formation.     

Dominant species, functional assemblages and frequency of equilibrium phases in late summer phytoplankton assemblages in Hungarian small shallow lakes

Late summer phytoplankton associations were studied qualitatively and quantitatively in 80 Hungarian lakes altogether (mostly shallow salt lakes, reservoirs, oxbows, gravel pit lakes). Equilibrium phases sensu Sommer et al. (1993) were found only in 17 lakes. Most of them were under some kind (high salt content or very low level of nutrients) of stress factor. It is concluded that environmental stress forces phytoplankton communities towards equilibrium. No relationship between occurrence of equilibria and trophic state was found. Species number of non-equilibrated lakes was almost three times as high as those in equilibrium. Of the 31 recently described (Reynolds et al., 2002) phytoplankton assemblages most of those were recognized that are likely to occur in shallow lakes. Separation of a functional group W _S from W2 for Synura dominated lakes is suggested. It seemed also necessary to raise a group (Y _Ph) for lakes dominated by Phacotus. Sorting of Dinophyta species into different already described functional groups is desirable.     

Littoral macrophyte–periphyton complexes in two Hungarian shallow waters

Periphyton developing on the surfaces of emergent and submerged aquatic plants has a significant influence on water quality. The periphyton types that form on various plant species can be characterized by their mass values, the proportion of the present organic and inorganic fractions, as well as their chlorophyll-a contents. Studies on periphyton complexes constituting integrated biomonitoring systems are useful to gain essential long-term information about the performance of shallow water bodies. The filtering and settling effect of Phragmites and other aquatic plants, as well as their periphyton was examined and clearly observable in the water areas and non-flooded aquatic habitats belonging to the second phase of Kis-Balaton Protection System, as it was indicated by the mass values and ash contents. The periphyton forming on the aquatic vegetation that annually develops in Kisköre Reservoir and yields a considerable biomass has a critical part in influencing water quality. The only difference (p<0.05) was found in the ash content of the periphyton, being lower in Kis-Balaton (48.64 ± 2.29 S.E., %) and higher in Kisköre Reservoir (57.42 ± 2.54 S.E., %). This paper presents the dry mass of the periphyton, as well as its ash and chlorophyll-a content, and the results obtained on the composition of the alga species of the periphyton.

     

Synthesis,receptor binding studies,optical spectroscopic and in silico structural characterization of morphiceptin analogs with cis‐4‐amino‐L‐proline residues

Three novel morphiceptin analogs, in which Pro in position 2 and/or 4 was replaced by cis‐4‐aminoproline connected with the preceding amino acid through the primary amino group, were synthesized. The opioid receptor affinities, functional assay results, enzymatic degradation studies and experimental and in silico structural analysis of such analogs are presented. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.     

Resisting annihilation: relationships between functional trait dissimilarity,assemblage competitive power and allelopathy

Allelopathic species can alter biodiversity. Using simulated assemblages that are characterised by neutrality, lumpy coexistence and intransitivity, we explore relationships between within‐assemblage competitive dissimilarities and resistance to allelopathic species. An emergent behaviour from our models is that assemblages are more resistant to allelopathy when members strongly compete exploitatively (high competitive power). We found that neutral assemblages were the most vulnerable to allelopathic species, followed by lumpy and then by intransitive assemblages. We find support for our modeling in real‐world time‐series data from eight lakes of varied morphometry and trophic state. Our analysis of this data shows that a lake's history of allelopathic phytoplankton species biovolume density and dominance is related to the number of species clusters occurring in the plankton assemblages of those lakes, an emergent trend similar to that of our modeling. We suggest that an assemblage's competitive power determines its allelopathy resistance.     

Functional groups of phytoplankton shaping diversity of shallow lake ecosystems

Phytoplankton of eutrophic shallow lakes are frequently dominated by one species or species of the same functional group, resulting in species-pure algal assemblages. Knowledge of the structure of these assemblages is essential to understand their functioning; therefore, species and functional diversity were investigated in five sub-types of eutrophic shallow lake. Among the sub-types, astatic saline lakes and hypertrophic ponds had type-specific assemblages dominated by S_N and W0, W1 codons. The diversity of the phytoplankton in the sub-types was quite similar, except for the astatic saline lakes, which were characterised by lower values of both functional and species diversity. We found that both functional and species diversity were low when bloom-forming cyanobacteria (H1, S_N functional groups) became dominant. Dominance of other groups (J, Y, L_O and W1) did not coincide with decrease in species diversity. Analysis of the biovolume versus diversity relationships revealed that decrease in diversity might be expected at biovolume >20 mm³ l⁻¹ for shallow lakes.     

Redefinition of Peridinium lomnickii Wołoszynska (Dinophyta) by scanning electronmicroscopical survey

Peridinium lomnickii Wo?oszynska was investigated by scanning electron microscopy with special attention to the importance of development of thecal plate during the life cycle. Different life cycle stages (gymnodinoid-, glenodinoid-, peridinioid) are described on the basis of development of cell wall, presence and development of sutures, appearance of pore and the change of the cell shape. Differences and possible relationships between the three existing varieties of the species are discussed. We suggest that the three varieties of P. lomnickii, P. lomnickii var. lomnickii, P. lomnickii var. wierzejskii and P. lomnickii var. splendida,represent the different life cycle stages of the species. These results and the known ontogenic cycle of dinophyta taxa should be taken into consideration, when a phylogenic tree of the dinophytes is constructed.     

Phenotypic plasticity as a clue for invasion success of the submerged aquatic plant Elodea nuttallii

• Two closely related alien submerged aquatic plants were introduced into Europe. The new invader (Elodea nuttallii) gradually displaced E. canadensis even at sites where the latter was well established. The aim of the study was to evaluate the combined effects of environmental factors on several phenotypic characteristics of the two Elodea species, and to relate these phenotypic characteristics to the invasion success of E. nuttallii over E. canadensis.
• In a factorial design, Elodea plants were grown in aquaria containing five different nitrogen concentrations and incubated at five different light intensities. We used six functional traits (apical shoot RGR), total shoot RGR, relative elongation, root length, lateral spread, branching degree) to measure the environmental response of the species. We calculated plasticity indices to express the phenotypic differences between species.
• Light and nitrogen jointly triggered the development of phenotypic characteristics that make E. nuttallii a more successful invader in eutrophic waters than E. canadensis. The stronger invader showed a wider range of phenotypic plasticity. The apical elongation was the main difference between the two species, with E. nuttallii being more than two times longer than E. canadensis. E. canadensis formed dense side shoots even under high shade and low nitrogen levels, whereas E. nuttallii required higher light and nitrogen levels.
• We found that under more eutrophic conditions, E. nuttallii reach the water surface sooner than E. canadensis and through intensive branching outcompetes all other plants including E. canadensis. Our findings support the theory that more successful invaders have wider phenotypic plasticity.

     

Influence of environmental factors and individual traits on the diet of non-native hybrid bigheaded carp (Hypophthalmichthys molitrix × H. nobilis) in Lake Balaton,Hungary

Planktivorous silver carp and bighead carp (collectively, the bigheaded carps) have been stocked worldwide and their invasion has caused severe impacts on many freshwater ecosystems. Exploiting the chance provided by the specific hybrid bigheaded carp stock in Lake Balaton (Hungary) covering the entire morphological range between the two species (including gill raker morphology), we implemented a comprehensive study (1) to reveal the feeding habits of hybrid bigheaded carps living in a mesotrophic, lacustrine habitat and (2) to assess how biotic and abiotic environmental factors and gill raker morphology affect diet composition. We found that all bigheaded carps utilized primarily zooplankton and neglected the scarce and inefficiently digestible phytoplankton, irrespective of gill raker morphology. Moreover, we observed strikingly high levels of inorganic debris consumption, but the proportion of inorganic matter in the guts was not associated directly with the concentration of suspended inorganic particles. Variance in the diet composition of bigheaded carps was related mostly to environmental factors, including the wind-induced resuspension of inorganic particles and seasonally variable availability of food resources. In conclusion, the effects of abiotic environmental factors and available food resources could overwhelm the effect of gill raker morphology in shaping the feeding habits of bigheaded carps.