The lifetimes of Pharaonis phoborhodopsin signaling states depend on the rates of proton transfers--effects of hydrostatic pressure and stopped flow experiments

Pharaonis phoborhodopsin (ppR), a negative phototaxis receptor of Natronomonas pharaonis, undergoes photocycle similar to the light-driven proton pump bacteriorhodopsin (BR), but the turnover rate is much slower due to much longer lifetimes of the M and O intermediates. The M decay was shown to become as fast as it is in BR in the L40T/F86D mutant. We examined the effects of hydrostatic pressure on the decay of these intermediates. For BR, pressure decelerated M decay but slightly affected O decay. In contrast, with ppR and with its L40T/F86D mutant, pressure slightly affected M decay but accelerated O decay. Clearly, the pressure-dependent factors for M and O decay are different in BR and ppR. In order to examine the deprotonation of Asp75 in unphotolyzed ppR we performed stopped flow experiments. The pH jump-induced deprotonation of Asp75 occurred with 60 ms, which is at least 20 times slower than deprotonation of the equivalent Asp85 in BR and about 10-fold faster than the O decay of ppR. These data suggest that proton transfer is slowed not only in the cytoplasmic channel but also in the extracellular channel of ppR and that the light-induced structural changes in the O intermediate of ppR additionally decrease this rate.     

Correlations between distribution coefficients of various biomolecules in different polymer/polymer aqueous two-phase systems

Distribution coefficients for a variety of proteins and certain other biomolecules (peptides, amino acids, and carbohydrates) (overall 27 different solutes) were measured in aqueous two-phase systems (ATPSs) dextran (Dex)–polyethylene glycol (PEG) and Dex–Ucon 50-HB-5100 (Ucon—a random copolymer of ethylene glycol and propylene glycol) both containing 0.15 M NaCl in 0.01 M phosphate buffer, pH 7.4, at 23 °C. Distribution coefficients of some selected solutes were also measured in the above two-phase systems at three different polymer concentrations for each system. It was established that the distribution coefficients for all the proteins examined in the ATPSs are correlated according to the so-called Collander linear equation.     

Associativity in multiary quasigroups: the way of biased expansions

A multiary (polyadic, n-ary) quasigroup is an n-ary operation which is invertible with respect to each of its variables. A biased expansion of a graph is a kind of branched covering graph with an additional structure similar to the combinatorial homotopy of circles. A biased expansion of a circle with chords encodes a multiary quasigroup, the chords corresponding to factorizations, i.e., associative structure. Some but not all biased expansions are constructed from groups (group expansions); these include all biased expansions of complete graphs (with at least four nodes), which correspond to Dowling’s lattices of a group and encode an iterated group operation. We show that any biased expansion of a 3-connected graph (with at least four nodes) is a group expansion, and that all 2-connected biased expansions are constructed by the identification of edges from group expansions and irreducible multiary quasigroups. If a 2-connected biased expansion covers every base edge at most three times, or if every four-node minor that contains a fixed edge is a group expansion, then the whole biased expansion is a group expansion. We deduce that if a multiary quasigroup has a factorization graph that is 3-connected, or if every ternary principal retract is an iterated group isotope, it is isotopic to an iterated group. We mention applications of generalizing Dowling geometries and of transversal designs of high strength.     

Passive tracer dynamics in 4 point-vortex flow

The advection of passive tracers in a system of 4 identical point vortices is studied when the motion of the vortices is chaotic. The phenomenon of vortex-pairing has been observed and statistics of the pairing time is computed. The distribution exhibits a power-law tail with exponent ∼ 3.6 implying finite average pairing time. This exponents is in agreement with its computed analytical estimate of 3.5. Tracer motion is studied for a chosen initial condition of the vortex system. Accessible phase space is investigated. The size of the cores around the vortices is well approximated by the minimum inter-vortex distance and stickiness to these cores is observed. We investigate the origin of stickiness which we link to the phenomenon of vortex pairing and jumps of tracers between cores. Motion within the core is considered and fluctuations are shown to scale with tracer-vortex distance r as r ⁶. No outward or inward diffusion of tracers are observed. This investigation allows the separation of the accessible phase space in four distinct regions, each with its own specific properties: the region within the cores, the reunion of the periphery of all cores, the region where vortex motion is restricted and finally the far-field region. We speculate that the stickiness to the cores induced by vortex-pairings influences the long-time behavior of tracers and their anomalous diffusion. Received 28 September 2000 and Received in final form 9 February 2001