BiPPred: Combined sequence‐ and structure‐based prediction of peptide binding to the Hsp70 chaperone BiP

Substrate binding to Hsp70 chaperones is involved in many biological processes, and the identification of potential substrates is important for a comprehensive understanding of these events. We present a multi‐scale pipeline for an accurate, yet efficient prediction of peptides binding to the Hsp70 chaperone BiP by combining sequence‐based prediction with molecular docking and MMPBSA calculations. First, we measured the binding of 15mer peptides from known substrate proteins of BiP by peptide array (PA) experiments and performed an accuracy assessment of the PA data by fluorescence anisotropy studies. Several sequence‐based prediction models were fitted using this and other peptide binding data. A structure‐based position‐specific scoring matrix (SB‐PSSM) derived solely from structural modeling data forms the core of all models. The matrix elements are based on a combination of binding energy estimations, molecular dynamics simulations, and analysis of the BiP binding site, which led to new insights into the peptide binding specificities of the chaperone. Using this SB‐PSSM, peptide binders could be predicted with high selectivity even without training of the model on experimental data. Additional training further increased the prediction accuracies. Subsequent molecular docking (DynaDock) and MMGBSA/MMPBSA‐based binding affinity estimations for predicted binders allowed the identification of the correct binding mode of the peptides as well as the calculation of nearly quantitative binding affinities. The general concept behind the developed multi‐scale pipeline can readily be applied to other protein‐peptide complexes with linearly bound peptides, for which sufficient experimental binding data for the training of classical sequence‐based prediction models is not available. Proteins 2016; 84:1390–1407. © 2016 Wiley Periodicals, Inc.     

Photopreferendum of migratory and nonmigratory larvae of European river lamprey <Emphasis Type="Italic">Lampetra fluviatilis</Emphasis>

In the light gradient installation, the larvae of European river lamprey Lampetra fluviatilis of 0+ age, migrating downstream (downstream migrants), are distributed predominantly over the zone of dusk illumination (150–1 lx) and less so over the daylight zone (2500–150 lx) and night illumination zone (<1 lx). In 0+ larvae that passed over to the sedentary lifestyle, the photopreferendum changes: they avoid the dusk and daytime illumination and prefer nighttime illumination. Such photopreferendum is retained in later larvae of lamprey (1+ and older).     

Swimming response of goldfish,Carassius auratus,and the tetra,Hemigrammus caudovittatus,larvae to individual food items and patches

Synopsis Swimming speed and swimming path of goldfish and tetra larvae were studied in aquaria containing food patches composed of decapsulated cysts and immobilized nauplii of Artemia salina or sparsely distributed prey. The mean swimming speed of starved larvae in the medium without food was about four times higher than the speed of larvae feeding in a patch. Satiated larvae swam about 1.5 times slower than hungry fish. Consumption of single prey items by starved larvae caused the following sequence of swimming responses: handling pause (cessation of swimming), slow swimming in a restricted area, and fast swimming (approximately twice as fast as hungry larvae before encountering food) accompanied by a widening of the area searched (area increased searching). Mean swimming speed was constant over a broad range (10¹–10³ ind·1^–1 of food density, although at extreme (high or low) values of food density it depended on swimming responses of the predator. Frequency of visits to the different parts of the aquarium strongly depended on encounters of hungry fish with food particles or patches.     

Changes in apolar metabolites during in vitro organogenesis of Pancratium maritimum

Calli, shoot-clumps and regenerated plants were initiated from young fruits of Pancratium maritimum L. Their genetic stability was monitored by flow cytometry before chemical studies. Apolar metabolites (alkaloids extracted at pH > 7, free fatty acids and fatty alcohols, sterols etc.) were qualitatively and quantitatively analyzed by GC–MS. The results clearly demonstrated that alkaloid synthesis in P. maritimum is closely related with tissue differentiation. The highest amounts of alkaloids and presence of homolycorine and tazettine type compounds (end products of the biosynthetic pathway of the Amaryllidaceae alkaloids) were found in highly differentiated tissues. Galanthamine accumulated in the leaves of plantlets. The amount of hordenine, a protoalkaloid, is related with the ability of tissues to synthesize alkaloids. Saturated fatty acids were found in considerably higher levels in undifferentiated callus cultures and partially differentiated shoot-clumps than in regenerated plants. Mono- and dienoic fatty acids were found at higher levels in non-photosynthesizing tissues – calli, and in vitro and intact bulbs, while α-linolenic acid (trienoic acid) was found in higher amounts in the photosynthesizing leaves of shoot-clumps and regenerated plants than in bulbs and calli. Fatty alcohols were found mainly in leaves, while sterols tended to accumulate in photosynthesizing and undifferentiated tissues.     

Fluctuation of free IAA under inductive and non-inductive photoperiods in Chenopodium rubrum

Fluctuation in levels of endogenous free IAA has been followed in the SD plant Chenopodium rubrum under photoperiodic conditions inductive or not inductive of flowering. Endogenous IAA was measured fluorimetrically as -pyrone. The level of IAA shows little fluctuation under continuous illumination. An endogenous rhythm of IAA fluctuation was found in plants transferred from light to continuous darkness, with a natural period of 30 hrs. The troughs of minimum IAA level within the endogenous rhythm coincided with the peaks in the endogenous rhythm of flowering response, which possessed the same period length. The concentration of IAA in the shoot always decreased at the end of cycles of dark period that induce flowering. The results are discussed in relation to the role of IAA in flowering of SD plants.     

Endogenous hormone levels during direct somatic embryogenesis in Medicago falcata

Endogenous indole-3-acetic acid, abscisic acid and cytokinins (zeatin, zeatin riboside, N-isopentenyladenine and N-isopentenyladenosine) were evaluated in initial explants (leaves) of in vitro propagated plants of alfalfa ( Medicago falcata L.) lines varying in embryogenic capacity and during the somatic embryogenesis process. Fast embryo-genic induction was correlated with high IAA and low ABA levels in the initial explants. No significant differences were observed in the cytokinin contents. Our results suggest that a certain hormone balance is necessary to allow the expression of the embryogenic potential. The consistent stages of the direct somatic embryogenesis are also characterized by changes in hormonal levels.     

Rheoreaction type of early juveniles of sockeye salmon Oncorhynchus nerka in the Ozernaya River and Lake Kurilskoe

Rheoreaction of early juveniles of sockeye salmon Oncorhynchus nerka is experimentally investigated, including different spatial groups (denatant migrants, contranatant migrants, specimens living in bays and at closed river banks, juveniles from the coastal zone of the lake). Investigation is made in water of the river flowing from the lake and in water of the stream flowing into the lake. It is shown that the rheoreaction (the type of rheoreaction) is one of behavioral mechanisms performing feeding migration of early juveniles of sockeye salmon. Contranatant migrants that reached the feeding lake retain the positive type of rheoreaction, which favors the exit of juveniles from the zone of discharge exclusion and prevents the drift of juveniles to the river at night at poorer conditions for orientation. Juveniles placed into the water of the inflowing stream manifest a sharply negative rheoreaction type contributing to their rapid lakeward migration for feeding. In water of two steams (taking its beginning in the lake and flowing into it) such type of rheoreaction is observed which ensures migration of sockeye juveniles to their principal feeding water body-Lake Kurilskoe.     

Flavonoids as inhibitors of human neutrophil elastase

Elastase is a proteolytic enzyme belonging to the family of hydrolases produced by human neutrophils, monocytes, macrophages, and endothelial cells. Human neutrophil elastase is known to play multiple roles in the human body, but an increase in its activity may cause a variety of diseases. Elastase inhibitors may prevent the development of psoriasis, chronic kidney disease, respiratory disorders (including COVID-19), immune disorders, and even cancers. Among polyphenolic compounds, some flavonoids and their derivatives, which are mostly found in herbal plants, have been revealed to influence elastase release and its action on human cells. This review focuses on elastase inhibitors that have been discovered from natural sources and are biochemically characterised as flavonoids. The inhibitory activity on elastase is a characteristic of flavonoid aglycones and their glycoside and methylated, acetylated and hydroxylated derivatives. The presented analysis of structure–activity relationship (SAR) enables the determination of the chemical groups responsible for evoking an inhibitory effect on elastase. Further study especially of the in vivo efficacy and safety of the described natural compounds is of interest in order to gain better understanding of their health-promoting potential.     

Regularities of Formation of Diversity of Life Strategy and Genetic Variability of The Kamchatka Rainbow Trout Parasalmo mykiss in a Local Population

Journal of Ichthyology - The diversity of life strategy, population structure, size, age and sex composition, growth and variability of 11 microsatellite loci in mykiss (rainbow trout) Parasalmo...