Distinct Binding States Research Articles

Understanding Molecular Motor Walking along a Microtubule: A Themosensitive Asymmetric Brownian Motor Driven by Bubble Formation

The "asymmetric Brownian ratchet model", a variation of Feynman's ratchet and pawl system, is invoked to understand the kinesin walking behavior along a microtubule. The model system, consisting of a motor and a rail, can exhibit two distinct binding states, namely, the random Brownian state and the asymmetric potential state. When the system is transformed back and forth between the two states, the motor can be driven to "walk" in one direction. Previously, we suggested a fundamental mechanism, that is, bubble formation in a nanosized channel surrounded by hydrophobic atoms, to explain the transition between the two states. In this study, we propose a more realistic and viable switching method in our computer simulation of molecular motor walking. Specifically, we propose a thermosensitive polymer model with which the transition between the two states can be controlled by temperature pulses. Based on this new motor system, the stepping size and stepping time of the motor can be recorded. Remarkably, the "walking" behavior observed in the newly proposed model resembles that of the realistic motor protein. The bubble formation based motor not only can be highly efficient but also offers new insights into the physical mechanism of realistic biomolecule motors.

Interaction of Sc and O on W

The surface chemistry on top of scandate cathodes plays a fundamental role in the performance and reliability of the cathodes. The surface chemical reaction is a complex dynamical process that involves Sc, Ba, O, W and noble metals at elevated temperatures. An initial approach is to investigate the interaction among the elements in subsets separately. In this study we investigate the interaction of Sc and O on W substrates, combining temperature-programmed desorption (TPD) and Auger electron spectroscopy (AES).There are three distinct states of Sc adsorption on W that originate from the first-layer, second-layer and multiple-layer states in a decreasing order of binding energy. The first layer grows to about 2/3 completion when the second layer begins to form, but the second layer is unstable. Agglomeration into multiple layers occurs when the second layer exceeds 1/3 layer. Sc bonds to W more strongly than Ba to W. The desorption maximum of the first-layer Sc occurs at 1575±22K, in comparison with the desorption maximum of Ba from W at 1250±4K. The addition of O strengthens the Sc-to-W bonds. There are also three distinct binding states that emerge simultaneously during the growth of oxidized Sc. The weakest binding state has a desorption maximum at 1732±29K, which is about 300K higher than the desorption maximum of the oxygen-enhanced Ba adsorption on W.Evaporation rates as a function of temperature are determined from TPD spectra of thick films. The results suggest that during activation of a scandate cathode the loss of metallic Sc can be substantial while the loss of oxidized Sc is minimal. It implies also that thermal evaporation from oxidized Sc may not be an effective method to replenish the Sc, the loss of which could occur from ion sputtering during operation in a vacuum electron device.

Adsorption of acenes on flat and vicinal Cu(111) surfaces: Step induced formation of lateral order

The adsorption of benzene, naphthalene, and anthracene on Cu(111) and its vicinal Cu(221) and Cu(443) surfaces has been studied by means of thermal desorption spectra (TDS) and low energy electron diffraction. For each of the studied acenes (C4n+2H2n+4, n=1,2,3) two distinct binding states were observed in the TDS corresponding to adsorption on terraces and at step edges. The binding energies of both states are found to increase linearly with the number of aromatic rings n. In contrast to the Cu(111) surface where these acenes form disordered adlayers only, ordered films of naphthalene and anthracene with an alignment of the molecular axis along the steps could be prepared on the vicinal surfaces.

Probing quantum coherence in a biological system by means of DNA amplification

As a result of rapid decoherence, quantum effects in biological systems are usually confined to single electron or hydrogen delocalizations. In principle, molecular interactions at high temperatures can be guided by quantum coherence if embedded in a dynamics preventing decoherence. This was experimentally investigated by analyzing the thermodynamics, kinetics, and quantum mechanics of the primer/template duplex formation during DNA amplification by polymerase chain reaction. The structures of the two oligonucleotide primers used for amplification of a cDNA template were derived either from a repetitive motif or a fractal distribution of nucleotide residues. Contrary to the computer-based calculation of the primer melting temperatures ( T m) that predicted a higher T m for the non-fractal primer due to nearest-neighbor effects, it was found that the T m of the non-fractal primer was actually 2°C lower than that of its fractal counterpart. A thermodynamic analysis of the amplification reaction indicated that the primer annealing process followed Bose–Einstein instead of Boltzmann statistics, with an additional binding potential of μ=500 J/mol or 10 −21 J/molecule due to a superposition of binding states within the primer/template duplex. The temporal evolution of the Bose–Einstein state was determined by enzyme kinetic analysis of the association of the primer/template duplex to Taq polymerase. Assuming that collision with the enzyme interrupted the superposition, it was found that the Bose–Einstein state lasted for t dec=0.7×10 −12 s, corresponding to the energy dispersion (Δ E) of quantum coherent states ( μ=ΔE≥ h/ t dec). A quantum mechanical analysis revealed that the coherent state was stabilized by almost vanishing separation energies between distinct binding states during a temperature-driven shifting of the two DNA strands in the primer/template duplex. The additional binding potential is suggested to arise from a short-lived electron tunneling as the result of overlapping orbitals along the axis of the primer/template duplex. This effect was unique to the fractal primer due to the number of binding states that remained almost constant, irrespective of the size of shifting. It is suggested that fractal structures found in proteins or other macromolecules may facilitate a short-lived quantum coherent superposition of binding states. This may stabilize molecular complexes for rapid sorting of correct-from-false binding, e.g. during folding or association of macromolecules. The experimental model described in this paper provides a low-cost tool for simulating and probing quantum coherence in a biological system.

Beta-adrenoceptor density and resolution of high and low affinity state on B- and T-cells in asthmatic and non-asthmatic children.

Beta-adrenoceptor binding in lymphocytes of asthmatic and non-asthmatic children and healthy adult volunteers was investigated with the radioligand 125-iodocyanopindolol (ICYP). Binding studies were performed with 4 to 5 different concentrations of ICYP. Receptor density and affinity were calculated by Scatchard plots. Resolution of beta-adrenoceptors into those of high and low affinity state was obtained from inhibition curves with salbutamol using Hofstee plots. Receptor density in B-cell enriched fractions was two to three-fold higher than in T-cells for all patients and volunteers studied (P less than 0.025). No difference in beta-adrenoceptor density on B and T-cells occurred neither in age-matched asthmatic and non-asthmatic children nor in adult volunteers. The affinity of beta-adrenoceptors did not differ for B and T-cells nor for the patients or volunteers studied. However, when two distinct binding states for beta-adrenoceptor agonists were obtained using salbutamol displacement curves it appeared that beta-adrenoceptors on T-cells were at a higher affinity state compared to those on B-cells in asthmatic and non-asthmatic children, as well as in adults. Since the ability of an agonist to activate adenylate cyclase correlates closely with the amount of high affinity receptor state formed in the presence of the agonist, increased intrinsic activity of the beta-adrenoceptor agonist on T-cells may be postulated. In conclusion, age-related control groups and determination of the B/T ratio are necessary for interpretation of beta-adrenoceptor changes in bronchial asthma.

Density and agonist-promoted high and low affinity states of the beta-adrenoceptor on human B- and T-cells.

beta-Adrenoceptor binding on peripheral blood mononuclear cells (PBMC) of healthy adult volunteers was investigated using the radioligand 125iodo-cyanopindolol (ICYP). Saturation binding studies were performed with nine different concentrations of ICYP. Receptor density and affinity were calculated by Scatchard plots. Resolution of beta-adrenoceptors into those with high and low affinity state of the beta-adrenoceptor was obtained from inhibition curves with salbutamol using Hofstee plots. Receptor density on enriched B-cells ('B-cells') was two-fold higher than on enriched T-cells ('T-cells') (P less than 0.025). Affinity (KD values) of beta-adrenoceptors did not differ for B- and T-cells. However, when two distinct binding states for beta-adrenoceptor agonists were identified using salbutamol displacement curves, beta-adrenoceptors on T-cells presented more receptors in a high affinity state than those on B-cells (P less than 0.01). Since the ability of an agonist to activate adenylate cyclase is closely correlated with the ratio of low to high affinity states formed in the presence of the agonist, increased intrinsic activity for the beta-adrenoceptor agonist on T-cells may be postulated. In conclusion, determination of the B/T ratio is a prerequisite for interpretation of beta-adrenoceptor changes on peripheral lymphocytes in various diseases.

Distinct binding states in adsorption on a homogeneous surface: Te on W(100)

The adsorption of Te on a W(100) surface is studied by thermal desorption spectroscopy (TDS), Auger electron spectroscopy (AES), low energy electron diffraction (LEED) and work function change (Δϕ) measurements. Three distinct binding states are observed in the first monolayer corresponding the coverages from 0 to 1 2 monolayers (ML), 1 2 to 2 3 ML and 2 3 to 1 ML. Within each state a coverage dependence of the desorption parameters is found. The three binding states are discussed in terms of heterogeneity induced by lateral interactions and in terms of inherently different adsorption sites.

Distinct binding states in adsorption on a homogeneous surface: Te on W(100)

Distinct binding states in adsorption on a homogeneous surface: Te on W(100)

Chemisorption on single crystal planes

Chemisorption on well characterized crystal planes, as well as on atomic clusters, can now be routinely observed. Results so far obtained on tungsten are reviewed, with special emphasis on (i) bonding of metal atoms to their own lattice, (ii) the localization of distinct binding states on individual crystal planes, and (iii) atomic and electronic displacements arising from the act of chemisorption.