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PubMedDate not supplied

Ensemble docking into flexible active sites. Critical evaluation of FlexE against JNK-3 and beta-secretase.

One of the main complicating factors in structure-based drug design is the conformational rearrangement of the receptor upon ligand binding implicating protein flexibility as a crucial component in virtual screening. The FlexE approach allows flexibility through discrete alternative conformations of varying parts of the protein taken from structures having similar backbone traces. Here the performance of FlexE was tested against that of FlexX and FlexX-Pharm, by carrying out virtual screening experiments on two sets of structurally distinct complexes, for the enzymes beta-secretase (BACE), and c-jun N-terminal kinase 3 (JNK-3). A large number of incompatible instances occurred between structural elements of the proteins thus loop movements could not be studied in JNK-3 as well as in BACE. The investigation of the side-chain flexibility revealed that at the most FlexE could achieve the enrichment yielded by FlexX in JNK-3 but not in BACE. Although limited side-chain variations (e.g. different protonation states) can be treated by FlexE, docking into protein ensembles remains a practical tool that decreases the average run time for a ligand.

Amyloid Precursor Protein Secretases↗

PubMed2001

Hydrogen-bond-mediated photoinduced electron-transfer: novel dimethylaniline-anthracene ensembles formed via Watson-Crick base-pairing.

The synthesis of a new, noncovalent anthracene-dimethylaniline dyad (ensemble I) held together via guanosine-cytidine Watson-Crick base-pairing interactions is reported. Upon excitation at 420 nm, photoinduced electron-transfer from the dimethylaniline donor to the singlet excited state of the anthracene acceptor occurs, as inferred from a combination of time-resolved fluorescence quenching and transient absorption measurements. In toluene at room temperature, the rate constants for photoinduced intraensemble electron-transfer and subsequent back-electron-transfer (charge recombination) are k(CS) = (3.5 +/- 0.03) x 10(10) s(-1) and k(CR) = (1.42 +/- 0.03) x 10(9) s(-1), respectively.

Aniline Compounds↗

PubMed2002

Rigid dendritic donor-acceptor ensembles: control over energy and electron transduction.

Several generations of phenylenevinylene dendrons, covalently attached to a C(60) core, have been developed as synthetic model systems with hierarchical, fine-tuned architectures. End-capping of these dendritic spacers with dibutylaniline or dodecyloxynaphthalene, as antennas/electron donors, yielded new donor-bridge-acceptor ensembles in which one, two, or four donors are allocated at the peripheral positions of the well-defined dendrons, while the electron accepting fullerene is placed at the focal point of the dendron. On the basis of our cyclic voltammetry experiments, which disclose a single anodic oxidation and several cathodic reduction processes, we rule out significant, long-range couplings between the fullerene core and the end-standing donors in their ground-state configuration. Photophysical investigations, on the other hand, show that upon photoexcitation an efficient and rapid transfer of singlet excited-state energy (6 x 10(10) to 2.5 x 10(12) s(-1)) controls the reactivity of the initially excited antenna portion. Spectroscopic and kinetic evidence suggests that yet a second contribution, that is, an intramolecular electron-transfer, exists, affording C(60)(.-) -dendron(.+) with quantum yields (Phi) as high as 0.76 and lifetimes (tau) that are on the order of hundreds of nanoseconds (220-725 ns). Variation of the energy gap modulates the interplay of these two pathways (i.e., competition or sequence between energy and electron transfer).

Journal Article↗

PubMed2005

Probing intramolecular Förster resonance energy transfer in a naphthaleneimide-peryleneimide-terrylenediimide-based dendrimer by ensemble and single-molecule fluorescence spectroscopy.

We report on the ensemble and single-molecule (SM) dynamics of Förster resonance energy transfer (FRET) in a multichromophoric rigid polyphenylenic dendrimer (triad) with spectrally different rylene chromophores featuring distinct absorption and emission spectra which cover the whole visible spectral range: a terrylenediimide (TDI) core, four perylenemonoimides (PMIs) attached at the scaffold, and eight naphthalenemonoimides (NMIs) at the rim. For FRET from PMI to TDI taking place with an efficiency of 99.5%, single triad molecules optically excited at 490 nm show fluorescence exclusively from the TDI side in the beginning of their emission. On 360-nm excitation, NMI chromophores transfer their excitation energy either directly or in a stepwise fashion to the core TDI, the latter case involving scaffold-substituted PMIs as intermediate acceptors. Indeed, SM experiments on 360-nm excitation evidence highly efficient FRET from NMI chromophores to the TDI core since individual triad molecules show fluorescence exclusively either from TDI or from an intermediate (oxidized) species but never from PMI. Because PMI and TDI are chromophores with high fluorescence quantum yields and high resistance to photobleaching compared to NMI, 360-nm excitation of a single triad molecule leads to bleaching of NMI chromophores with no chance for PMI to be observed. The spatial positioning and the spectral properties of the chosen rylene chromophores make this multichromophoric system an efficient light collector, able to capture light over the whole visible spectral range and to transfer it finally to the core TDI, the latter releasing it as red fluorescence.

Journal Article↗

PubMed2005

Mapping long-range interactions in alpha-synuclein using spin-label NMR and ensemble molecular dynamics simulations.

The intrinsically disordered protein alpha-synuclein plays a key role in the pathogenesis of Parkinson's disease (PD). We show here that the native state of alpha-synuclein consists of a broad distribution of conformers with an ensemble-averaged hydrodynamic radius significantly smaller than that expected for a random coil structure. This partial condensation is driven by interactions between the highly charged C-terminus and a large hydrophobic central region of the protein sequence. We suggest that this structure could inhibit the formation of alpha-synuclein aggregates, which are thought to be the cytotoxic species responsible for neurodegeneration in PD.

Computer Simulation↗

PubMed2005

Catalysts for hydrogen evolution from the [NiFe] hydrogenase to the Ni2P(001) surface: the importance of ensemble effect.

Density functional theory (DFT) was employed to investigate the behavior of a series of catalysts used in the hydrogen evolution reaction (HER, 2H(+) + 2e(-) --> H(2)). The kinetics of the HER was studied on the [NiFe] hydrogenase, the [Ni(PS3*)(CO)](1)(-) and [Ni(PNP)(2)](2+) complexes, and surfaces such as Ni(111), Pt(111), or Ni(2)P(001). Our results show that the [NiFe] hydrogenase exhibits the highest activity toward the HER, followed by [Ni(PNP)(2)](2+) > Ni(2)P > [Ni(PS3*)(CO)](1)(-) > Pt > Ni in a decreasing sequence. The slow kinetics of the HER on the surfaces is due to the fact that the metal hollow sites bond hydrogen too strongly to allow the facile removal of H(2). In fact, the strong H-Ni interaction on Ni(2)P(001) can lead to poisoning of the highly active sites of the surface, which enhances the rate of the HER and makes it comparable to that of the [NiFe] hydrogenase. In contrast, the promotional effect of H-poisoning on the HER on Pt and Ni surfaces is relatively small. Our calculations suggest that among all of the systems investigated, Ni(2)P should be the best practical catalyst for the HER, combining the high thermostability of the surfaces and high catalytic activity of the [NiFe] hydrogenase. The good behavior of Ni(2)P(001) toward the HER is found to be associated with an ensemble effect, where the number of active Ni sites is decreased due to presence of P, which leads to moderate bonding of the intermediates and products with the surface. In addition, the P sites are not simple spectators and directly participate in the HER.

Catalysis↗

PubMed2003

Probing charge separation in structurally different C60/exTTF ensembles.

The scope of the present work is to highlight the effects stemming from different C60/exTTF linkages (exTTF = 9,10-bis(1,3-dithiol-2-ylidene)-9,10-dihydroanthracene)-either via an anthracene unit or a dithiole ring. Particular emphasis is placed on photoinduced electron-transfer features. Therefore, we devised a new series of C60-exTTF ensembles, synthesized via 1,3-dipolar cycloaddition and Diels-Alder cycloaddition reactions, in which exTTF units are separated from C60 by two single bonds (3a-c, 4), one vinylene unit (5a), or two vinylene units (5b). The cyclic voltammetry reveals an amphoteric redox behavior with remarkably strong electron-donor ability of the trimethyl-substituted exTTF moiety in 4 and 5a,b. Steady-state and time-resolved photolytic techniques show that the fullerene singlet excited state in (3a-c, 4, and 5a,b) is subject to a rapid electron-transfer quenching. The resulting charge-separated states, that is C60*(-)-exTTF*+, were identified by transient absorption spectroscopy. We determined radical pair lifetimes of the order of 200 ns in benzonitrile. This suggests (i) that the positive charge of the exTTF*+ is delocalized over the entire donor rather than localized on one of the 1,3-dithiole rings and (ii) that linking exTTF via the anthracene or 1,3-dithiole ring has no appreciable influence. Increasing the donor-acceptor separation via implementing one or two vinylene units as spacers led to improved radical pair lifetimes (5a: tau = 725 ns; 5b: tau = 1465 ns).

Journal Article↗

PubMed2005

Thermodynamic characterization of fluids confined in heterogeneous pores by monte carlo simulations in the grand canonical and the isobaric-isothermal ensembles.

Materials presenting nanoscale porosity are able to condense gases in their structure. This "capillary condensation" phenomenon has been studied for more than one century. Theoretical models help to understand experimental results but fail in explaining all experimental features. Most of the time, the difficulties in making quantitative or even qualitative predictions are due to the geometric complexity of the porous materials, such as large pore size distribution, chemical heterogeneities, or pore interconnections. Numerical calculations (lattice gas models or molecular simulations) are of considerable interest to calculate the adsorption properties of a fluid confined in a porous model with characteristic sizes up to several tens of nanometers. For instance, the grand canonical Monte Carlo method allows one to compute the average amount of fluid adsorbed in the porous model as a function of the temperature and the chemical potential of the fluid. However, the grand potential, necessary for a complete characterization of the system, is not a direct output of the algorithm. It is shown in this paper that the use of the isobaric-isothermal (NPT) ensemble allows one to circumvent this problem; that is, it is possible to get in one single Monte Carlo run the absolute grand potential for any given thermodynamic state of the fluid. A simplified thermodynamic integration scheme is then used to evaluate the grand potential over the whole isotherm branch passing through this initially given point. Since the usual NPT technique is a priori limited to homogeneous pores, it is proposed, for the first time, to generalize this procedure to a pore presenting a chemical heterogeneity along its axis. The new method gives the same results as the previous for homogeneous pores and allows new predictions for chemically heterogeneous pores. Comparison with the full integration scheme shows that the proposed direct calculation is faster since it avoids multiple Monte Carlo runs and more precise because it avoids the possible cumulative errors of the integration procedure.

Journal Article↗

PubMed2005

A coverage-dependent study of pt spontaneously deposited onto Au and Ru surfaces: direct experimental evidence of the ensemble effect for methanol electro-oxidation on Pt.

Direct experimental evidence that can be unambiguously attributed to the need of an ensemble of a minimum number of neighboring Pt atoms for methanol electro-oxidation has been observed for the first time. This was realized by a Pt coverage-dependent investigation of methanol and CO electro-oxidation on Pt sites generated via spontaneous deposition onto both Au and Ru surfaces. CO stripping voltammograms also show clear evidence of a substantially strengthened CO-Pt bonding for submonolayer Pt deposited on the Au substrate over a range of ca. 0.22 to 0.77, which is in qualitative agreement with the theoretical prediction based on the Hammer-Nørskov d-band center model. However, the degree of the bond strengthening depends on the Pt coverage, being stronger for lower coverage. Additionally, evidence of an Ostwald ripening process for Pt islands formation has also been observed.

Journal Article↗

PubMed2006

Spectral identification of specific photophysics of cy5 by means of ensemble and single molecule measurements.

The triplet-state characteristics of the Cy5 molecule related to trans-cis isomerization are investigated by means of ensemble and single molecule measurements. Cy5 has been used frequently in the past 10 years in single molecule spectroscopic applications, e.g., as a probe or fluorescence resonance energy transfer acceptor in large biomolecules. However, the unknown spectral properties of the triplet state and the lack of knowledge on the photoisomerization do not allow us to interpret precisely the unexpected single molecule behaviors. This limits the application of Cy5. The laser photolysis experiments demonstrate that the trans triplet state of Cy5 absorbs about 625 nm, the cis ground state absorbs about 690 nm, and the cis triplet state also absorbs about 690 nm. In other words, the T1-Tn absorptions largely overlap the ground-state absorptions for both trans and cis isomers, respectively. Furthermore, the observation of the cis triplet state indicates an important isomerization pathway from the trans-S1 state to the cis-T1 state upon excitation. The detailed spectra presented in this article let us clearly interpret the exact mechanisms responsible for several important and unexpected photophysical behaviors of single Cy5 molecules such as reverse intersystem crossing (RISC), the observation of dim states with a lower emission intensity and slightly red-shifted fluorescence, and unusual energy transfer from donor molecules to dark Cy5 molecules acting as acceptors in single molecule fluorescence resonance energy transfer (FRET) measurements. Spectral results show that the dim state in the single molecule fluorescence intensity time traces originated from cis-Cy5 because of a lower excitation rate, resulting from the red-shifted ground-state absorption of cis-Cy5 compared to that of the trans-Cy5.

Carbocyanines↗

PubMed2006

Study of fluorescence quenching and dialysis process of CdTe quantum dots, using ensemble techniques and fluorescence correlation spectroscopy.

Luminescence properties of quantum dots (QDs) are closely related to their surface structure and chemical properties. In this work some ensemble techniques and fluorescence correlation spectroscopy (FCS) were used to study the fluorescence quenching and dialysis process of CdTe QDs. It is found that when some heavy metal ions, such as silver ions (Ag+), quench QDs, the free Ag+ ions bind with bare Te atoms and form the AgTe structure on the surface. The FCS experimental results show that the quenching process is not the gradual reduction of fluorescence intensity of single QDs, but the decrease in the number of bright QDs with the addition of Ag+ ions. In other words, the bright QDs turn into dark directly in the quenching process. It is observed that some dark QDs converse into the bright QDs in the dialysis experiments and the dialysis process can improve the brightness per QDs. Furthermore, the results of FCS and fluorescence spectroscopy illustrate that the increase of the fluorescence quantum yield (QY) is mainly attributed to the removal of excess unreacted Cd-MPA complex and the possible chemical change of the QDs surface in the dialysis process. These new results can help us to further understand the complex surface structure of water-soluble QDs, improve their surface chemical features, and expand their applications in some fields.

Journal Article↗

PubMed2006

Toward efficient chemical potential calculations by expanded ensemble simulations; to make the free energy pathway fairly level.

A scheme is suggested of how to construct good bias potentials ("balancing factors") to be used in expanded ensemble (EE) calculations of chemical potentials of solutions. A combination of two strategies are used: (i) to use a pathway for particle insertions that avoids large variations in free energy and (ii) to use calculated free energy derivatives to construct a bias potential that makes the pathway fairly level. Only a few very short simulations are needed to accomplish the latter, and then, a full EE simulation is done to obtain the chemical potential. By practical calculations of the chemical potential of benzene, cyclohexane, and benzylamine in water, it is shown that this method is at least equally efficient to the recent adaptive EE (AEE) method by Aberg et al. (J. Chem. Phys. 2004, 120, 3370). Furthermore, the new method provides an alternative strategy that complements existing EE methods.

Journal Article↗

PubMed2006

Equilibrium distributions of dipalmitoyl phosphatidylcholine and dilauroyl phosphatidylcholine in a mixed lipid bilayer: atomistic semigrand canonical ensemble simulations.

Conventional molecular dynamics (MD) simulations are seriously limited by the slow rate of diffusive mixing in their ability to predict lateral distributions of different lipid types within mixed-lipid bilayers using atomistic models. A method to overcome this limitation, using configuration-bias Monte Carlo (MC) "mutation" moves to transform lipids from one type to another in dynamic equilibrium, is demonstrated in binary fluid-phase mixtures of lipids whose tails differ in length by four carbons. The hybrid MC-MD method operates within a semigrand canonical ensemble, so that an equilibrium composition of the mixture is determined by a constant difference in chemical potential (Delta(mu)) chosen for the components. Within several nanoseconds, bilayer structures initiated as pure dipalmitoyl phosphatidylcholine (DPPC) or pure dilauroyl phosphatidylcholine (DLPC) converge to a common composition and structure in independent simulations conducted at the same Delta(mu). Trends in bilayer thickness, area per lipid, density distributions across the bilayer, and order parameters have been investigated at three mixture compositions and compared with results from the pure bilayers at 323 K. The mixtures showed a moderate increase in DPPC acyl tail sites crossing the bilayer midplane relative to pure DPPC. Correlations between lateral positions of the two lipid types within or across the bilayer were found to be weak or absent. While the lateral distribution is consistent with nearly ideal mixing, the dependence of composition on Delta(mu) indicates a positive excess free energy of mixing.

1,2-Dipalmitoylphosphatidylcholine↗

PubMed2005

Facile preparation of nanoelectrode ensembles using amphiphilic block copolymer film.

Taking advantage of both the self-organizing characteristics and the amphiphilic property of poly(styrene-block-ethyleneoxide) (P(S-b-EO)), we have realized one-step fabrication of nanoelectrode ensembles (NEEs). By choosing the electrolyte solution elaborately, only the poly(ethylene oxide) (PEO) segment in the P(S-b-EO) film was swollen to serve as nanoscale tunnels for solvated ions, whereas the polystyrene segment remained robust to be the electrode mask. An electrochemical analysis indicated that a transition between linear diffusion and nonlinear diffusion could be observed due to the small diffusion coefficient of ferrocene in PEO nanodomains.

Journal Article↗

PubMed2001

Principal components analysis of protein structure ensembles calculated using NMR data.

One important problem when calculating structures of biomolecules from NMR data is distinguishing converged structures from outlier structures. This paper describes how Principal Components Analysis (PCA) has the potential to classify calculated structures automatically, according to correlated structural variation across the population. PCA analysis has the additional advantage that it highlights regions of proteins which are varying across the population. To apply PCA, protein structures have to be reduced in complexity and this paper describes two different representations of protein structures which achieve this. The calculated structures of a 28 amino acid peptide are used to demonstrate the methods. The two different representations of protein structure are shown to give equivalent results, and correct results are obtained even though the ensemble of structures used as an example contains two different protein conformations. The PCA analysis also correctly identifies the structural differences between the two conformations.

Macromolecular Substances↗

PubMed2002

Reweighted atomic densities to represent ensembles of NMR structures.

A reweighted atomic probability density is introduced as a means of representing ensembles of NMR structures in a simple, concise and informative manner. This density is shown to give a better visual representation of molecular structure information than an unweighted density, and should provide a useful interactive graphics tool during the course of iterative NMR structure refinement. The approach is illustrated using several examples.

Animals↗

PubMedDate not supplied

Computation by ensemble synchronization in recurrent networks with synaptic depression.

While computation by ensemble synchronization is considered to be a robust and efficient way for information processing in the cortex (C. Von der Malsburg and W. Schneider (1986) Biol. Cybern. 54: 29-40; W. Singer (1994) Inter. Rev. Neuro. 37: 153-183; J.J. Hopfield (1995) Nature 376: 33-36; E. Vaadia et al. (1995) Nature 373: 515-518), the neuronal mechanisms that might be used to achieve it are yet to be uncovered. Here we analyze a neural network model in which the computations are performed by near coincident firing of neurons in response to external inputs. This near coincident firing is enabled by activity dependent depression of inter-neuron connections. We analyze the network behavior by using a mean-field approximation, which allows predicting the network response to various inputs. We demonstrate that the network is very sensitive to temporal aspects of the inputs. In particular, periodically applied inputs of increasing frequency result in different response profiles. Moreover, applying combinations of different stimuli lead to a complex response, which cannot be easily predicted from responses to individual components. These results demonstrate that networks with synaptic depression can perform complex computations on time-dependent inputs utilizing the ability to generate temporally synchronous firing of single neurons.

Action Potentials↗

PubMed2000

Real-time prediction of hand trajectory by ensembles of cortical neurons in primates.

Signals derived from the rat motor cortex can be used for controlling one-dimensional movements of a robot arm. It remains unknown, however, whether real-time processing of cortical signals can be employed to reproduce, in a robotic device, the kind of complex arm movements used by primates to reach objects in space. Here we recorded the simultaneous activity of large populations of neurons, distributed in the premotor, primary motor and posterior parietal cortical areas, as non-human primates performed two distinct motor tasks. Accurate real-time predictions of one- and three-dimensional arm movement trajectories were obtained by applying both linear and nonlinear algorithms to cortical neuronal ensemble activity recorded from each animal. In addition, cortically derived signals were successfully used for real-time control of robotic devices, both locally and through the Internet. These results suggest that long-term control of complex prosthetic robot arm movements can be achieved by simple real-time transformations of neuronal population signals derived from multiple cortical areas in primates.

Animals↗