Abstract. By numerical modeling we investigate fluid transport in low-Reynolds-number flow achieved with a special elastic filament or artifical cilium attached to a planar surface. The filament is made of superparamagnetic particles linked together by DNA double strands. An external magnetic field induces dipolar interactions between the beads of the filament which provides a convenient way of actuating the cilium in a well-controlled manner. The filament has recently been used to successfully construct the first artificial micro-swimmer [R. Dreyfus at al., Nature 437, 862 (2005)]. In our numerical study we introduce a measure, which we call pumping performance, to quantify the fluid transport induced by the magnetically actuated cilium and identify an optimum stroke pattern of the filament. It consists of a slow transport stroke and a fast recovery stroke. Our detailed parameter study also reveals that for sufficiently large magnetic fields the artificial cilium is mainly governed by the Mason number that compares frictional to magnetic forces. Initial studies on multi-cilia systems show that the pumping performance is very sensitive to the imposed phase lag between neighboring cilia, i.e., to the details of the initiated metachronal wave.

We discuss the modelling of a microswimmer that operates in a 'squirmer' mode, by means of stochastic rotation dynamics. The squirmer that we model can easily be tuned between a 'pusher' and a 'puller'. We examine the flows produced by the squirmer and find that there is good agreement between both the predicted and simulated velocities of locomotion and the resulting flow field.

Brownian motors are nonequilibrium systems that rectify thermal fluctuations to achieve directed motion, using spatial or temporal asymmetry. We provide a tutorial introduction to this basic concept using the well-known example of a flashing ratchet, discussing the micro- to nanoscopic scale on which such motors can operate. Because of the crucial role of thermal noise, the characterization of the performance of Brownian motors must include their fluctuations, and we review suitable performance measures for motor coherency and efficiency. Specifically, we highlight that it is possible to determine the energy efficiency of Brownian motors by measuring their velocity fluctuations, without detailed knowledge of the motor function and its energy input. Finally, we exemplify these concepts using a model for an artificial single-molecule motor with internal degrees of freedom.

The question of how many chains an elementary cellulose microfibril contains is critical to understanding the molecular mechanism(s) of cellulose biosynthesis and regulation. Given the hexagonal nature of the cellulose synthase rosette, it is assumed that the number of chains must be a multiple of six. We present molecular dynamics simulations on three different models of Ib cellulose microfibrils, 18, 24, and 36 chains, to investigate their structure and dynamics in a hydrated environment. The 36-chain model stays in a conformational space that is very similar to the initial crystalline phase, while the 18-and 24-chain models sample a conformational space different from the crystalline structure yet similar to conformations observed in recent high-temperature molecular dynamics simulations. Major differences in the conformations sampled between the different models result from changes to the tilt of chains in different layers, specifically a second stage of tilt, increased rotation about the O2-C2 dihedral, and a greater sampling of non-TG exocyclic conformations, particularly the GG conformation in center layers and GT conformation in solvent-exposed exocyclic groups. With a reinterpretation of nuclear magnetic resonance data, specifically for contributions made to the C6 peak, data from the simulations suggest that the 18-and 24-chain structures are more viable models for an elementary cellulose microfibril, which also correlates with recent scattering and diffraction experimental data. These data inform biochemical and molecular studies that must explain how a six-particle cellulose synthase complex rosette synthesizes microfibrils likely comprised of either 18 or 24 chains.

Dihydrodipicolinate synthase (DHDPS) catalyzes the rate limiting step in lysine biosynthesis in bacteria and plants. The structure of DHDPS has been determined from several bacterial species and shown in most cases to form a homotetramer or dimer of dimers. However, only one plant DHDPS structure has been determined to date from the wild tobacco species, Nicotiana sylvestris (Blickling et al. (1997) J. Mol. Biol. 274, 608–621). Whilst N. sylvestris DHDPS also forms a homotetramer, the plant enzyme adopts a ‘back-to-back’ dimer of dimers compared to the ‘head-to-head’ architecture observed for bacterial DHDPS tetramers. This raises the question of whether the alternative quaternary architecture observed for N. sylvestris DHDPS is common to all plant DHDPS enzymes. Here, we describe the structure of DHDPS from the grapevine plant, Vitis vinifera, and show using analytical ultracentrifugation, small-angle X-ray scattering and X-ray crystallography that V. vinifera DHDPS forms a ‘back-to-back’ homotetramer, consistent with N. sylvestris DHDPS. This study is the first to demonstrate using both crystal and solution state measurements that DHDPS from the grapevine plant adopts an alternative tetrameric architecture to the bacterial form, which is important for optimizing protein dynamics as suggested by molecular dynamics simulations reported in this study.

No abstract

Electronic structural signatures of the adenine-7H tautomer in its ground state ( X 1 A′) have been identified using dual space analysis. The RHF/TZVP and B3LYP/TZVP calculations employed in the present work have shown that proton transfer from N (9) to N (7) makes the purine rings of adenine-7H geometrically closer to purine rather than adenine-9H, at the cost distortion of the amino group local symmetry. The shifts in ring lengths in [Formula: see text] and [Formula: see text], which are proposed in this work as the summation of the bond lengths in the hex- and pentagon-rings, respectively, are [Formula: see text] and [Formula: see text] for adenine-9H and [Formula: see text] and [Formula: see text] for adenine-7H, respectively, from the corresponding rings in purine. We also demonstrate that energetic properties such as the orbital energies are insensitive to tautomerism. However, the N (9) to N (7) proton transfer significantly changes the dipole moments: a large increase from 2.44D (adenine-9H) to 7.49D (adenine-7H) is observed. Finally, four molecular orbitals, 27a′, 25a′, 24a′ and 23a′ are identified in momentum space as bearing the most important structural signatures of the adenine-7H tautomer.

Equinatoxin II (EqtII) is a soluble, 20 kDa pore-forming protein toxin isolated from the sea anemone Actinia equina. Although pore formation has long been known to occur in distinct stages, including monomeric attachment to phospholipid membranes followed by detachment of the N-terminal helical domain and oligomerization into the final pore assembly, atomistic-level detail of the protein-lipid interactions underlying these events remains elusive. Using high-resolution solution state NMR of uniformly-(15)N-labeled EqtII at the critical micelle concentration of dodecylphosphocholine, we have mapped the lipid-binding site through chemical shift perturbations. Subsequent docking of an EqtII monomer onto a dodecylphosphocholine micelle, followed by 400 ns of all-atom molecular dynamics simulation, saw several high-occupancy lipid-binding pockets stabilized by cation-π, hydrogen bonding, and hydrophobic interactions; and stabilization of the loop housing the conserved arginine-glycine-aspartate motif. Additional simulation of EqtII with an N-acetyl sphingomyelin micelle, for which high-resolution NMR data cannot be obtained due to aggregate formation, revealed that sphingomyelin specificity might occur via hydrogen bonding to the 3-OH and 2-NH groups unique to the ceramide backbone by side chains of D109 and Y113; and main chains of P81 and W112. Furthermore, a binding pocket formed by K30, K77, and P81, proximate to the hinge region of the N-terminal helix, was identified and may be implicated in triggering pore formation.