Dual bloom of green algae and purple bacteria in an extremely shallow soda pan

Extremophiles - In April 2014, dual bloom of green algae and purple bacteria occurred in a shallow, alkaline soda pan (Kiskunság National Park, Hungary). The water was only 5 cm deep,...     

Numerical calculations of the pH of maximal protein stability. The effect of the sequence composition and three-dimensional structure.

A large number of proteins, found experimentally to have different optimum pH of maximal stability, were studied to reveal the basic principles of their preference for a particular pH. The pH-dependent free energy of folding was modeled numerically as a function of pH as well as the net charge of the protein. The optimum pH was determined in the numerical calculations as the pH of the minimum free energy of folding. The experimental data for the pH of maximal stability (experimental optimum pH) was reproducible (rmsd = 0.73). It was shown that the optimum pH results from two factors - amino acid composition and the organization of the titratable groups with the 3D structure. It was demonstrated that the optimum pH and isoelectric point could be quite different. In many cases, the optimum pH was found at a pH corresponding to a large net charge of the protein. At the same time, there was a tendency for proteins having acidic optimum pHs to have a base/acid ratio smaller than one and vice versa. The correlation between the optimum pH and base/acid ratio is significant if only buried groups are taken into account. It was shown that a protein that provides a favorable electrostatic environment for acids and disfavors the bases tends to have high optimum pH and vice versa.     

Cleavage of peptidic inhibitors by target protease is caused by peptide conformational transition

Some peptide sequences can behave as either substrates or inhibitors of serine proteases. Working with a cyclic peptidic inhibitor of the serine protease urokinase-type plasminogen activator (uPA), we have now demonstrated a new mechanism for an inhibitor-to-substrate switch. The peptide, CSWRGLENHAAC (upain-2), is a competitive inhibitor of human uPA, but is also slowly converted to a substrate in which the bond between Arg⁴ and Gly⁵ (the P1-P1′ bond) is cleaved. Substituting the P2 residue Trp³ to an Ala or substituting the P1 Arg⁴ residue with 4-guanidino-phenylalanine strongly increased the substrate cleavage rate. We studied the structural basis for the inhibitor-to-substrate switch by determining the crystal structures of the various peptide variants in complex with the catalytic domain of uPA. While the slowly cleaved peptides bound clearly in inhibitory mode, with the oxyanion hole blocked by the side chain of the P3′ residue Glu⁷, peptides behaving essentially as substrates with a much accelerated rate of cleavage was observed to be bound to the enzyme in substrate mode. Our analysis reveals that the inhibitor-to-substrate switch was associated with a 7?Å translocation of the P2 residue, and we conclude that the inhibitor-to-substrate switch of upain-2 is a result of a major conformational change in the enzyme-bound state of the peptide. This conclusion is in contrast to findings with so-called standard mechanism inhibitors in which the inhibitor-to-substrate switch is linked to minor conformational changes in the backbone of the inhibitory peptide stretch.     

Interplay of folded domains and the disordered low-complexity domain in mediating hnRNPA1 phase separation

Liquid–liquid phase separation underlies the membrane-less compartmentalization of cells. Intrinsically disordered low-complexity domains (LCDs) often mediate phase separation, but how their phase behavior is modulated by folded domains is incompletely understood. Here, we interrogate the interplay between folded and disordered domains of the RNA-binding protein hnRNPA1. The LCD of hnRNPA1 is sufficient for mediating phase separation in vitro. However, we show that the folded RRM domains and a folded solubility-tag modify the phase behavior, even in the absence of RNA. Notably, the presence of the folded domains reverses the salt dependence of the driving force for phase separation relative to the LCD alone. Small-angle X-ray scattering experiments and coarse-grained MD simulations show that the LCD interacts transiently with the RRMs and/or the solubility-tag in a salt-sensitive manner, providing a mechanistic explanation for the observed salt-dependent phase separation. These data point to two effects from the folded domains: (i) electrostatically-mediated interactions that compact hnRNPA1 and contribute to phase separation and (ii) increased solubility at higher ionic strengths mediated by the folded domains. The interplay between disordered and folded domains can modify the dependence of phase behavior on solution conditions and can obscure signatures of physicochemical interactions underlying phase separation.     

GTSF‐1 is required for formation of a functional RNA‐dependent RNA Polymerase complex in Caenorhabditis elegans

Argonaute proteins and their associated small RNAs (sRNAs) are evolutionarily conserved regulators of gene expression. Gametocyte‐specific factor 1 (Gtsf1) proteins, characterized by two tandem CHHC zinc fingers and an unstructured C‐terminal tail, are conserved in animals and have been shown to interact with Piwi clade Argonautes, thereby assisting their activity. We identified the Caenorhabditis elegans Gtsf1 homolog, named it gtsf‐1 and characterized it in the context of the sRNA pathways of C. elegans. We report that GTSF‐1 is not required for Piwi‐mediated gene silencing. Instead, gtsf‐1 mutants show a striking depletion of 26G‐RNAs, a class of endogenous sRNAs, fully phenocopying rrf‐3 mutants. We show, both in vivo and in vitro, that GTSF‐1 interacts with RRF‐3 via its CHHC zinc fingers. Furthermore, we demonstrate that GTSF‐1 is required for the assembly of a larger RRF‐3 and DCR‐1‐containing complex (ERIC), thereby allowing for 26G‐RNA generation. We propose that GTSF‐1 homologs may act to drive the assembly of larger complexes that act in sRNA production and/or in imposing sRNA‐mediated silencing activities.     

Über das führende Zentrum im Herzen von Testudo graeca L.

Zusammenfassung Die einzelnen Anteile des venösen Vorherzens sind bei der Schildkröte untereinander nicht ganz gleichwertig. Als Schrittmacher des Herzens funktioniert in der Norm die Einmündungsstelle der rechten oberen Hohlvene in den Sinus. Von dort aus empfangen die Hohlvenen ihre Antriebe zur Tätigkeit. Da die rechte obere Hohlvene dieser Stelle näher gelegen ist als die linke, so erklärt sich, daß beim Schildkrötenherzen die rechte obere Hohlvene in ihrer Tätigkeit der linken für gewöhnlich vorangeht.Die automatischen Eigenschaften des venösen Vorherzens sind bei der Schildkröte im Gegensatz zu den Amphibien nicht an allen Stellen gleichmäßig entwickelt. Mit höchster Automatie ist der Sinus an der Einmündungsstelle der rechten oberen Hohlvene ausgerüstet. Es folgen dann die Hohlvenen in der Reihenfolge: rechte obere, linke obere und untere Hohlvene.Durch Erwärmung der verschiedenen Anteile des venösen Vorherzens, besonders der oberen und unteren Hohlvene ist man imstande eine Frequenzzunahme des ganzen Herzens zu bewirken. Doch tritt diese niemals so rasch ein und ist auch niemals in so hohem Maße ausgeprägt, wie wenn man jene ventral gelegenen Partien des Sinus erwärmt, die der rechten oberen Hohlvene benachbart sind. Man kann also schon beim Schildkrötenherzen von einer gewissen Differenzierung in der Anlage der führenden Stelle sprechen. Doch geht diese noch nicht so weit, daß nicht etwa auch andere Stellen die Führung des Herzens übernehmen könnten, falls das Hauptzentrum versagt. Man beobachtet vielmehr in völliger Übereinstimmung mit den Ergebnissen örtlich ungleicher Erwärmung der einzelnen Anteile des venösen Vorherzens, daß beim Versagen des Hauptzentrums sofort ein anderer Teil einzutreten vermag. Dies äußert sich einfach darin, daß ein Wechsel in der Schlagfolge von rechter und linker oberer Hohlvene eintritt. Es geht dann nicht mehr die rechte obere in der Tätigkeit der linken voran, sondern es arbeiten entweder beide Venen gleichzeitig öder aber es arbeitet die linke obere Hohlvene vor der rechten.Herrn Prof. Dr. Adolf Loewy, dem Leiter des Schweizerischen Forschungsinstituts, sage ich auch an dieser Stelle meinen ergebensten Dank für seine freundliche Aufnahme und tatkräftige Unterstützung.