RNA packaging motor: From structure to quantum mechanical modelling and sequential-stochastic mechanism

The bacteriophages of the Cystoviridae family package their single stranded RNA genomic precursors into empty capsid (procapsids) using a hexameric packaging ATPase motor (P4). This molecular motor shares sequence and structural similarity with RecA-like hexameric helicases. A concerted structural, mutational and kinetic analysis helped to define the mechanical reaction coordinate, i.e. the conformational changes associated with RNA translocation. The results also allowed us to propose a possible scheme of coupling between ATP hydrolysis and translocation which requires the cooperative action of three consecutive subunits. Here, we first test this model by preparing hexamers with defined proportions of wild type and mutant subunits and measuring their activity. Then, we develop a stochastic kinetic model which accounts for the catalytic cooperativity of the P4 hexamer. Finally, we use the available structural information to construct a quantum-chemical model of the chemical reaction coordinate and obtain a detailed description of the electron density changes during ATP hydrolysis. The model explains the results of the mutational analyses and yields new insights into the role of several conserved residues within the ATP binding pocket. These hypotheses will guide future experimental work

Force generation in small ensembles of Brownian motors

The motility of certain gram-negative bacteria is mediated by retraction of type IV pili surface filaments, which are essential for infectivity. The retraction is powered by a strong molecular motor protein, PilT, producing very high forces that can exceed 150 pN. The molecular details of the motor mechanism are still largely unknown, while other features have been identified, such as the ring-shaped protein structure of the PilT motor. The surprisingly high forces generated by the PilT system motivate a model investigation of the generation of large forces in molecular motors. We propose a simple model, involving a small ensemble of motor subunits interacting through the deformations on a circular backbone with finite stiffness. The model describes the motor subunits in terms of diffusing particles in an asymmetric, time-dependent binding potential (flashing ratchet potential), roughly corresponding to the ATP hydrolysis cycle. We compute force-velocity relations in a subset of the parameter space and explore how the maximum force (stall force) is determined by stiffness, binding strength, ensemble size, and degree of asymmetry. We identify two qualitatively different regimes of operation depending on the relation between ensemble size and asymmetry. In the transition between these two regimes, the stall force depends nonlinearly on the number of motor subunits. Compared to its constituents without interactions, we find higher efficiency and qualitatively different force-velocity relations. The model captures several of the qualitative features obtained in experiments on pilus retraction forces, such as roughly constant velocity at low applied forces and insensitivity in the stall force to changes in the ATP concentration.Comment: RevTex 9 pages, 4 figures. Revised version, new subsections in Sec. III, removed typo

Spatial and Temporal Variations in the Species Composition of Bycatch Collected During a Striped Mullet (Mugil cephalus) Survey

We examined the variations in species composition of bycatch collected in an annual spawning-season survey of striped mullet, Mugil cephalus, in Tampa Bay and Charlotte Harbor, FL. Bycatch was defined as all species captured with the collection gear other than the target species, M. cephalus. Variations between habitat types, between months, and between years in the species composition of bycatch captured 1993-96 in this ongoing survey were examined using a nonparametric analysis of variance based on Bray-Curtis similarities. Mugil cephalus was the dominant species collected in both study areas, representing 16%-100% of the annual catch. Lagodon rhomboides and Arius felis were the most abundant bycatch species in Tampa Bay, and A. felis and Mugil curema were the most abundant bycatch species in Charlotte Harbor. Archosargus probatocephalus, Sciaenops ocellatus, and Cynoscion nebulosus composed the majority of the remaining bycatch species collected. Bycatch species composition was not significantly different between months, although indices of species richness (Margalef\u27s index, d), species diversity (Shannon index, H\u27 ), and evenness (Pielou\u27s index, J\u27) declined from fall to winter in each year. Species composition differed significantly between riverine and bay habitats and between habitats with and without bottom vegetation (seagrass). Samples from seagrass habitats had more L. rhomboides, A. probatocephalus, and S. ocellatus, and samples from habitats without seagrass had more A. felis. Indices of species richness, diversity, and evenness were lowest in 1996 as a result of increased catches of M. cephalus and decreased occurrence of bycatch in survey samples. The implementation of the Florida net ban in 1995 may have brought about this increased abundance of M. cephalus and concomitant decrease in the percentage of bycatch captured in survey samples in 1996

The Generic, Incommensurate Transition in the two-dimensional Boson Hubbard Model

The generic transition in the boson Hubbard model, occurring at an incommensurate chemical potential, is studied in the link-current representation using the recently developed directed geometrical worm algorithm. We find clear evidence for a multi-peak structure in the energy distribution for finite lattices, usually indicative of a first order phase transition. However, this multi-peak structure is shown to disappear in the thermodynamic limit revealing that the true phase transition is second order. These findings cast doubts over the conclusion drawn in a number of previous works considering the relevance of disorder at this transition.Comment: 13 pages, 10 figure