Cationic amphipathic histidine-rich peptides for gene delivery

Besides being a useful tool in research, gene transfer has a high potential as treatment for a variety of genetic and acquired diseases. However, in order to enable a gene to become a pharmaceutical, efficient and safe methods of delivery have to be developed. We recently found that cationic amphipathic histidine-rich peptide antibiotics can efficiently deliver DNA into mammalian cells. Our lead compound, LAH4 (KKALLALALHHLAHLALHLALALKKA), demonstrated in vitro transfection efficiencies comparable to those of commercially available reagents. Synthesis and evaluation of LAH mutants provided evidence that the transfection efficiency depends on the number and positioning of histidine residues in the peptide as well as on the pH at which the in-plane to transmembrane transition takes place. Moreover, recent results suggest that binding of the DNA complexes to the plasma membrane is mediated by heparan sulfate proteoglycans and that anionic phospholipids may be involved in the endosomal destabilization process. Finally, we also describe in this review the rationale that led to the development of LAH4 as a DNA carrier as well as the biophysical methods that have allowed us to propose a model which could explain the way this peptide destabilizes the endosomal bilayer.     

Spontaneous deadlock breaking on amoeba-based neurocomputer

Any artificial concurrent computing system involves a potential risk of “deadlock” that its multiple processes sharing common computational resources are stuck in starved conditions, if simultaneous accesses of the processes to the resources were unconditionally permitted. To avoid the deadlock, it is necessary to set up some form of central control protocol capable of appropriately regulating the resource allocation. On the other hand, many decentralized biological systems also perform concurrent computing based on interactions of components sharing limited amounts of available resources. Despite the absence of a central control unit, they appear to be free from the deadlock implying their death, as long as they are alive. Should we consider that biological computing paradigms are essentially different from artificial ones? Here we employ a photosensitive amoeboid cell known as a model organism for studying cellular information processing and construct an experimental system to explore how the amoeba copes with deadlock-like situations induced by optical feedback control. The feedback control is implemented by a recurrent neural network algorithm for leading the amoeba to solve a particular constraint satisfaction problem. We show that the amoeba is capable of breaking through the deadlock-like situations because its oscillating cellular membrane spontaneously produces a wide variety of spatiotemporal patterns. The result implies that our system can be developed to a neurocomputer that works as logical circuit, associative memory device, combinatorial optimization problem solver, and chaotic computer capable of spontaneous transition among multiple solutions.     

Linear remodeling of helical virus by movement protein binding

Previously we have shown that encapsidated potato virus X (PVX) RNA was nontranslatable in vitro, but could be converted into a translatable form by binding of the PVX-coded movement protein (termed TGBp1) to one end of a polar helical PVX virion. We reported that binding of TGBp1 to coat protein (CP) subunits located at one extremity of the helical particles induced a linear destabilization of the CP helix, which was transmitted along the whole particle. Two model structures were used: (i) native PVX and (ii) artificial polar helical PVX-like particles lacking intact RNA (PVX(RNA-DEG)). Binding of TGBp1 to the end of either of these particles led to their destabilization, but no disassembly of the CP helix occurred. Influence of additional factors was required to trigger rapid disassembly of TGBp1-PVX and TGBp1-PVX(RNA-DEG) complexes. Thus: (i) no disassembly was observed unless TGBp1-PVX complex was translated. A novel phenomenon of TGBp1-dependent, ribosome-triggered disassembly of PVX was described: initiation of translation and few translocation steps were needed to trigger rapid (and presumably cooperative) disassembly of TGBp1-PVX into protein subunits and RNA. Importantly, the whole of the RNA molecule (including its 3'-terminal region) was released. The TGBp1-induced linear destabilization of CP helix was reversible, suggesting that PVX in TGBp1-PVX complex was metastable; (ii) entire disassembly of the TGBp1-PVX(RNA-DEG) complex (but not of the TGBp1-free PVX(RNA-DEG) particles) into 2.8S subunits was triggered under influence of a centrifugal field. To our knowledge, transmission of the linear destabilization along the polar helical protein array induced by a foreign protein binding to the end of the helix represents a novel phenomenon. It is tempting to suggest that binding of TGBp1 to the end of the PVX CP helix induced conformational changes in terminal CP subunits that can be linearly transferred along the whole helical particle, i.e. that intersubunit conformational changes may be transferred along the CP helix.     

Vyazniki biotic assemblage of the terminal Permian

A new unique and diverse biotic assemblage of the terminal Permian has recently been discovered in the town of Vyazniki (Central Russia). The Vyazniki terrestrial community is transitional between Permian and Triassic ones and represents the last, so far unknown stage of the global ecological crisis of the continental biota at the Permian-Triassic boundary. The successive development of land biotic crisis in the Late Permian, which was followed by mass extinction at the Permian-Triassic boundary, and long, successive postcrisis development and specialization of new Triassic groups as well as rearrangement and diversification of the biotic assemblage composition and community structure suggest predominance of intrinsic, biotic causes of this crisis, realized in destabilization, alteration, and new stabilization of continental communities and ecosystems.     

Sublethal effects of the toxic alga Heterosigma akashiwo on the southeastern oyster (Crassostrea virginica)

Over the last three years, several blooms of Heterosigma akashiwo (Raphidophyceae) were documented in South Carolina (SC) brackish waters, including areas containing extensive oyster (Crassostrea virginica) beds. This study examined the sublethal effects of H. akashiwo on C. virginica, based on cellular biomarker responses after exposure to laboratory cultures of H. akashiwo isolated from SC waters, and to water collected from two SC H. akashiwo blooms. Exposure to laboratory cultures or blooms of H. akashiwo significantly increased oyster hepatopancreas lysosomal destabilization rates, but had little effect on gill p-glycoprotein (p-gp) expression. Lysosomal destabilization in oysters continued to increase even after a 7-day recovery period in clean seawater, suggesting that H. akashiwo toxin or other cellular byproducts continued to damage the hepatopancreas. These results suggest that even short-term exposures of oysters to high cell densities of H. akashiwo could have long-term adverse physiological effects, and imply that oyster health may be compromised in areas where repetitive H. akashiwo blooms occur.     

Influence of phosphate anions on the stability of immobilized enzymes. Effect of enzyme nature,immobilization protocol and inactivation conditions

A destabilizing effect at pH 7 of sodium phosphate on several lipases immobilized via interfacial activation is shown in this work. This paper investigates if this destabilizing effect is extended to other inactivation conditions, immobilization protocols or even other immobilized enzymes (ficin, trypsin, β-galactosidase, β-glucosidase, laccase, glucose oxidase and catalase). As lipases, those from Candida antarctica (A and B), Candida rugosa and Rhizomucor miehei have been used. Results confirm the very negative effect of 100 mM sodium phosphate at pH 7.0 for the stability of all studied lipases immobilized on octyl agarose, while using glutaraldehyde-support the effect is smaller (still very significant using CALA) and in some cases the effect disappeared (e.g., using CALB). The change of the pH to 5.0 or 9.0, or the addition of 1 M NaCl reduced the negative effect of the phosphate in some instances (e.g., at pH 5.0, this negative effect is only relevant for CALB). Regarding the other enzymes, only the monomeric β-galactosidase from Aspergillus oryzae is strongly destabilized by the phosphate buffer. This way, the immobilization protocol and the inactivation conditions strongly modulate the negative effect of sodium phosphate on the stability of immobilized lipases, and this effect is not extended to other enzymes.     

Interconversion of ATP binding and conformational free energies by tryptophanyl-tRNA synthetase: structures of ATP bound to open and closed,pre-transition-state conformations

Binding ATP to tryptophanyl-tRNA synthetase (TrpRS) in a catalytically competent configuration for amino acid activation destabilizes the enzyme structure prior to forming the transition state. This conclusion follows from monitoring the titration of TrpRS with ATP by small angle solution X-ray scattering, enzyme activity, and crystal structures. ATP induces a significantly smaller radius of gyration at pH=7 with a transition midpoint at approximately 8mM. A non-reciprocal dependence of Trp and ATP dissociation constants on concentrations of the second substrate show that Trp binding enhances affinity for ATP, while the affinity for Trp falls with the square of the [ATP] over the same concentration range ( approximately 5mM) that induces the more compact conformation. Two distinct TrpRS:ATP structures have been solved, a high-affinity complex grown with 1mM ATP and a low-affinity complex grown at 10mM ATP. The former is isomorphous with unliganded TrpRS and the Trp complex from monoclinic crystals. Reacting groups of the two individually-bound substrates are separated by 6.7A. Although it lacks tryptophan, the low-affinity complex has a closed conformation similar to that observed in the presence of both ATP and Trp analogs such as indolmycin, and resembles a complex previously postulated to form in the closely-related TyrRS upon induced-fit active-site assembly, just prior to catalysis. Titration of TrpRS with ATP therefore successively produces structurally distinct high- and low-affinity ATP-bound states. The higher quality X-ray data for the closed ATP complex (2.2A) provide new structural details likely related to catalysis, including an extension of the KMSKS loop that engages the second lysine and serine residues, K195 and S196, with the alpha and gamma-phosphates; interactions of the K111 side-chain with the gamma-phosphate; and a water molecule bridging the consensus sequence residue T15 to the beta-phosphate. Induced-fit therefore strengthens active-site interactions with ATP, substantially intensifying the interaction of the KMSKS loop with the leaving PP(i) group. Formation of this conformation in the absence of a Trp analog implies that ATP is a key allosteric effector for TrpRS. The paradoxical requirement for high [ATP] implies that Gibbs binding free energy is stored in an unfavorable protein conformation and can then be recovered for useful purposes, including catalysis in the case of TrpRS.