Complex Cooperativity Cooperativity in multisubunit protein complexes is classically understood in terms of either a concerted model, in which all subunits switch conformation simultaneously, or a sequential model, in which a subunit switches conformation whenever a ligand binds. More recently, a “conformational spread” model has suggested that a conformational coupling between subunits and between subunit and ligand is probabilistic. Using high-resolution optical microscopy, Bai et al. (p. 685 ; see the Perspective by Hilser ) observed multistate switching of the bacterial flagellar switch complex that was previously understood in terms of a concerted allosteric model. The conformational spread model gives quantitative agreement with the data.

The combinatorial nature of many important mathematical problems, including nondeterministic-polynomial-time (NP)-complete problems, places a severe limitation on the problem size that can be solved with conventional, sequentially operating electronic computers. There have been significant efforts in conceiving parallel-computation approaches in the past, for example: DNA computation, quantum computation, and microfluidics-based computation. However, these approaches have not proven, so far, to be scalable and practical from a fabrication and operational perspective. Here, we report the foundations of an alternative parallel-computation system in which a given combinatorial problem is encoded into a graphical, modular network that is embedded in a nanofabricated planar device. Exploring the network in a parallel fashion using a large number of independent, molecularmotor-propelled agents then solves the mathematical problem. This approach uses orders of magnitude less energy than conventional computers, thus addressing issues related to power consumption and heat dissipation. We provide a proof-of-concept demonstration of such a device by solving, in a parallel fashion, the small instance {2, 5, 9} of the subset sum problem, which is a benchmark NPcomplete problem. Finally, we discuss the technical advances necessary to make our system scalable with presently available technology.parallel computing | molecular motors | NP complete | biocomputation | nanotechnology M any combinatorial problems of practical importance, such as the design and verification of circuits (1), the folding (2) and design (3) of proteins, and optimal network routing (4), require that a large number of possible candidate solutions are explored in a brute-force manner to discover the actual solution. Because the time required for solving these problems grows exponentially with their size, they are intractable for conventional electronic computers, which operate sequentially, leading to impractical computing times even for medium-sized problems. Solving such problems therefore requires efficient parallel-computation approaches (5). However, the approaches proposed so far suffer from drawbacks that have prevented their implementation. For example, DNA computation, which generates mathematical solutions by recombining DNA strands (6, 7), or DNA static (8) or dynamic (9) nanostructures, is limited by the need for impractically large amounts of DNA (10-13). Quantum computation is limited in scale by decoherence and by the small number of qubits that can be integrated (14). Microfluidics-based parallel computation (15) is difficult to scale up in practice due to rapidly diverging physical size and complexity of the computation devices with the size of the problem, as well as the need for impractically large external pressure.Here, we propose a parallel-computation approach, which is based on encoding combinatorial problems into the geometry of a physical network of lithographically defined channels, followed by exploration of the network in a par...

The dynamic lateral segregation of signaling proteins into microdomains is proposed to facilitate signal transduction, but the constraints on microdomain size, mobility, and diffusion that might realize this function are undefined. Here we interrogate a stochastic spatial model of the plasma membrane to determine how microdomains affect protein dynamics. Taking lipid rafts as representative microdomains, we show that reduced protein mobility in rafts segregates dynamically partitioning proteins, but the equilibrium concentration is largely independent of raft size and mobility. Rafts weakly impede small-scale protein diffusion but more strongly impede long-range protein mobility. The long-range mobility of raft-partitioning and raftexcluded proteins, however, is reduced to a similar extent. Dynamic partitioning into rafts increases specific interprotein collision rates, but to maximize this critical, biologically relevant function, rafts must be small (diameter, 6 to 14 nm) and mobile. Intermolecular collisions can also be favored by the selective capture and exclusion of proteins by rafts, although this mechanism is generally less efficient than simple dynamic partitioning. Generalizing these results, we conclude that microdomains can readily operate as protein concentrators or isolators but there appear to be significant constraints on size and mobility if microdomains are also required to function as reaction chambers that facilitate nanoscale protein-protein interactions. These results may have significant implications for the many signaling cascades that are scaffolded or assembled in plasma membrane microdomains.

High-resolution e-beam patterning exposure of the surface of poly[(tert-butyl-methacrylate)-co-(methyl methacrylate)]-a common e-beam and deep-UV resist used in semiconductor microlithography-induced sharp changes in the surface hydrophobicity. These differences in hydrophobicity resulted in the selective attachment of heavy meromyosin to hydrophobic, unexposed surfaces. The movement of the actin filaments on myosin-rich and myosin-poor surfaces was statistically characterized in terms of velocity, acceleration, and angle of movement. The actin filaments have a smooth motion on myosin-rich surfaces and an uneven motion on myosin-poor surfaces. Interestingly, an excess of myosin sites has a slowing, albeit mild effect on the motion of the actin filaments. It was also found that the myosin-rich/myosin-poor boundary has an alignment-enforcement effect, especially for the filaments approaching the border from the myosin-rich side. Based on these results, we discuss the feasibility of building purposefully designed molecular motor arrays and the testing of the hypotheses regarding the functioning of the molecular motors.

No abstract

A stochastic random walk model of protein molecule diffusion on a cell membrane was used to investigate the fundamental causes of anomalous diffusion in two-dimensional biological media. Three different interactions were considered: collisions with fixed obstacles, picket fence posts, and capture by, or exclusion from, lipid rafts. If motion is impeded by randomly placed, fixed obstacles, we find that diffusion can be highly anomalous, in agreement with previous studies. In contrast, collision with picket fence posts has a negligible effect on the anomalous exponent at realistic picket fence parameters. The effects of lipid rafts are more complex. If proteins partition into lipid rafts there is a small to moderate effect on the anomalous exponent, whereas if proteins are excluded from rafts there is a large effect on the anomalous exponent. In combination, these mechanisms can explain the level of anomaly in experimentally observed membrane diffusion, suggesting that anomalous diffusion is caused by multiple mechanisms whose effects are approximately additive. Finally, we show that the long-range diffusion rate, D(macro), estimated from fluorescence recovery after photobleaching studies, can be much smaller than D(micro), the small-scale diffusion rate, and is highly sensitive to obstacle densities and other impeding structures.

Four strains of marine, aerobic, agar-decomposing bacteria with one polar flagellum and with DNA G+C contents of 3809402 mol% were isolated from the Far-Eastern mussels Crenomytilus grayanus and Patinopecten yessoensis. These four strains were identified as Pseudoalteromonas; however, they were phenotypically different from species described previously according to carbon compound utilization tests and the BIOLOG identification system. High agardecomposing activity was found in two strains, in one of which agarase, agalactosidase, pustulanase and laminarinase had been detected. The level of DNA homology of three of the strains was 70-100°/~. The fourth isolate was genetically less related to the others (67 O/ O DNA relatedness) and phenotypically was more distant from other members of this group; however, all four strains were assigned to a single species genotypically. DNA from the strains isolated from mussels showed 4 0 4 5 YO genetic relatedness with the DNA of Alteromonas atlantica, 8-36 YO with DNA of Pseudoalteromonas haloplanktis subsp. haloplanktis, Pseudoalteromon as haloplanktis subsp. tetraodonis, Pseudoalteromon as undina, Pseudoalteromon as nigrifaciens andPseudoalteromon as carrageenovora, 53 YO with Pseudoalteromon as elyakovii, 3 2 4 8 % with marine P. nigrifaciens from mussels and 14-16% with Alteromonas macleodii. The DNA-DNA hybridization data revealed that the levels of relatedness between the strains isolated and the type strains of Pseudoalteromonas citrea and Pseudoalteromonas fuliginea described recently were significant (95-85 YO). These results were confirmed by serological data employing polyclonal antibodies to cell surface antigens. The strains isolated from mussels were identified as P. citrea. The hybridization data showed that the name P. fuliginea Romanenko e t a / . 1994 should be recognized as a junior subjective synonym of P. citrea Gauthier 1977. A notable phenotypic diversity of P. citrea which might be a reflection of their ecological habitats is discussed. Keywords : marine bacteria, Pseudoalteromonas citrea INTRODUCTIONIntensive investigations stricted to a single species, Alteromonas macleodii, while a new genus, Pseudoalteromonas, was created for 13 other Alteromonas species. The latter are common of the genus Alteromonas during the last few years have led to revision and inhabitants of the aquatic environment, and were specification of its taxonomic structure on the one isolated mainly from sea water (8,14). Pseudohand (1, 2,14,15, 38), and broadening of the list of alteromonas strains, typically associated with marine species on the other (1 1, 12,24,33). The resulting data animals (16,29), might be of particular interest as a from small-subunit rDNA sequence analysis (1 5) promising source for new species with distinct features. revealed that the genus Alteromonas should be reOne such feature is a high hydrolytic activity, par- (v/v) distilled water at pH 7.5-743 as described elsewhere (19). Strains were maintained on the same semi-solid B medium in tubes und...

No abstract