The Experts below are selected from a list of 469710 Experts worldwide ranked by ideXlab platform

Nongjian Tao - One of the best experts on this subject based on the ideXlab platform.

  • probing single molecule Binding and free energy profile with plasmonic imaging of nanoparticles
    Journal of the American Chemical Society, 2019
    Co-Authors: Hui Wang, Nongjian Tao, Zhuodong Tang, Yan Wang
    Abstract:

    Measuring Binding between molecules is critical for understanding basic biochemical processes, developing Molecular diagnosis, and screening drugs. Here we study Molecular Binding at the single molecule level by attaching nanoparticles to the Molecular Binding pairs. We track the thermal fluctuations of the individual nanoparticles with sub-nanometer precision using a plasmonic scattering imaging technique and show that the fluctuations are controlled by the Molecular Binding pairs rather than by the nanoparticles. Analysis of the thermal fluctuations provides unique information on Molecular Binding, including Binding energy profile, effective spring constant, and switching between single and multiple Molecular Binding events. The method provides new insights into Molecular Binding and also allows one to differentiate nonspecific Binding from specific Binding, which has been a difficult task in biosensors.

  • Label-Free Quantification of Small-Molecule Binding to Membrane Proteins on Single Cells by Tracking Nanometer-Scale Cellular Membrane Deformation
    ACS Nano, 2018
    Co-Authors: Fenni Zhang, Wenwen Jing, Ashley Hunt, Yunze Yang, Shaopeng Wang, Hong Yuan Chen, Nongjian Tao
    Abstract:

    Measuring Molecular Binding to membrane proteins is critical for understanding cellular functions, validating biomarkers, and screening drugs. Despite the importance, developing such a capability has been a difficult challenge, especially for small-molecule Binding to membrane proteins in their native cellular environment. Here we show that the Binding of both large and small molecules to membrane proteins can be quantified on single cells by trapping single cells with a microfluidic device and detecting Binding-induced cellular membrane deformation on the nanometer scale with label-free optical imaging. We develop a thermodynamic model to describe the Binding-induced membrane deformation, validate the model by examining the dependence of membrane deformation on cell stiffness, membrane protein expression level, and Binding affinity, and study four major types of membrane proteins, including glycoproteins, ion channels, G-protein coupled receptors, and tyrosine kinase receptors. The single-cell detection ...

  • Surface impedance imaging technique.
    Analytical chemistry, 2008
    Co-Authors: Kyle J. Foley, Xiaonan Shan, Nongjian Tao
    Abstract:

    We demonstrate here a surface impedance imaging technique based on sensitive dependence of surface plasmon resonance (SPR) on local surface charge density. By applying a potential modulation to a sensor surface, we are able to simultaneously obtain three images: the dc component and the amplitude and phase of the ac component. The dc image measures local Molecular Binding activity on the surface, as found in the conventional SPR imaging technique, and the ac images are directly related to the local impedance of the surface. Our experimental data can be analyzed quantitatively in terms of the simple free electron gas model for the sensor surface and the Randles equivalent circuit model for interfacial impedance.

Jurgen Gauss - One of the best experts on this subject based on the ideXlab platform.

  • w3 theory robust computational thermochemistry in the kj mol accuracy range
    Journal of Chemical Physics, 2004
    Co-Authors: Daniel A Boese, Mikhal Oren, Onur Atasoylu, Jan M L Martin, Mihaly Kallay, Jurgen Gauss
    Abstract:

    We are proposing a new computational thermochemistry protocol denoted W3 theory, as a successor to W1 and W2 theory proposed earlier [Martin and De Oliveira, J. Chem. Phys. 111, 1843 (1999)]. The new method is both more accurate overall (error statistics for total atomization energies approximately cut in half) and more robust (particularly towards systems exhibiting significant nondynamical correlation) than W2 theory. The cardinal improvement rests in an approximate account for post-CCSD(T) correlation effects. Iterative T3 (connected triple excitations) effects exhibit a basis set convergence behavior similar to the T3 contribution overall. They almost universally decrease Molecular Binding energies. Their inclusion in isolation yields less accurate results than CCSD(T) nearly across the board: It is only when T4 (connected quadruple excitations) effects are included that superior performance is achieved. T4 effects systematically increase Molecular Binding energies. Their basis set convergence is quit...

  • w3 theory robust computational thermochemistry in the kj mol accuracy range
    arXiv: Chemical Physics, 2003
    Co-Authors: Daniel A Boese, Mikhal Oren, Onur Atasoylu, Jan M L Martin, Mihaly Kallay, Jurgen Gauss
    Abstract:

    We are proposing a new computational thermochemistry protocol denoted W3 theory, as a successor to W1 and W2 theory proposed earlier [Martin and De Oliveira, J. Chem. Phys. 111, 1843 (1999)]. The new method is both more accurate overall (error statistics for total atomization energies approximately cut in half) and more robust (particularly towards systems exhibiting significant nondynamical correlation) than W2 theory. The cardinal improvement rests in an approximate account for post-CCSD(T) correlation effects. Iterative T_3 (connected triple excitations) effects exhibit a basis set convergence behavior similar to the T_3 contribution overall. They almost universally decrease Molecular Binding energies. Their inclusion in isolation yields less accurate results than CCSD(T) nearly across the board: it is only when T_4 (connected quadruple excitations) effects are included that superior performance is achieved. $T_4$ effects systematically increase Molecular Binding energies. Their basis set convergence is quite rapid, and even CCSDTQ/cc-pVDZ scaled by an empirical factor of 1.2532 will yield a quite passable quadruples contribution. The effect of still higher-order excitations was gauged for a subset of molecules (notably the eight-valence electron systems): T_5 (connected quintuple excitations) contributions reach 0.3 kcal/mol for the pathologically multireference X ^1\Sigma^+_g state of C_2 but are quite small for other systems. A variety of avenues for achieving accuracy beyond that of W3 theory were explored, to no significant avail. W3 thus appears to represent a good compromise between accuracy and computational cost for those seeking a robust method for computational thermochemistry in the kJ/mol accuracy range on small systems.

Matthias Stein - One of the best experts on this subject based on the ideXlab platform.

  • The Interaction Properties of the Human Rab GTPase Family – A Comparative Analysis Reveals Determinants of Molecular Binding Selectivity
    2013
    Co-Authors: Matthias Stein, Manohar Pilli, Sabine Bernauer, Marino Zerial, Bianca H. Habermann, Rebecca C Wade
    Abstract:

    Background: Rab GTPases constitute the largest subfamily of the Ras protein superfamily. Rab proteins regulate organelle biogenesis and transport, and display distinct Binding preferences for effector and activator proteins, many of which have not been elucidated yet. The underlying Molecular recognition motifs, Binding partner preferences and selectivities are not well understood. Methodology/Principal Findings: Comparative analysis of the amino acid sequences and the three-dimensional electrostatic and hydrophobic Molecular interaction fields of 62 human Rab proteins revealed a wide range of Binding properties with large differences between some Rab proteins. This analysis assists the functional annotation of Rab proteins 12, 14, 26, 37 and 41 and provided an explanation for the shared function of Rab3 and 27. Rab7a and 7b have very different electrostatic potentials, indicating that they may bind to different effector proteins and thus, exert different functions. The subfamily V Rab GTPases which are associated with endosome differ subtly in the interaction properties of their switch regions, and this may explain exchange factor specificity and exchange kinetics. Conclusions/Significance: We have analysed conservation of sequence and of Molecular interaction fields to cluster and annotate the human Rab proteins. The analysis of three dimensional Molecular interaction fields provides detailed insight that is not available from a sequence-based approach alone. Based on our results, we predict novel functions for some Ra

  • the interaction properties of the human rab gtpase family a comparative analysis reveals determinants of Molecular Binding selectivity
    PLOS ONE, 2012
    Co-Authors: Matthias Stein, Manohar Pilli, Sabine Bernauer, Bianca Habermann, Marino Zerial, Rebecca C Wade
    Abstract:

    Background Rab GTPases constitute the largest subfamily of the Ras protein superfamily. Rab proteins regulate organelle biogenesis and transport, and display distinct Binding preferences for effector and activator proteins, many of which have not been elucidated yet. The underlying Molecular recognition motifs, Binding partner preferences and selectivities are not well understood. Methodology/Principal Findings Comparative analysis of the amino acid sequences and the three-dimensional electrostatic and hydrophobic Molecular interaction fields of 62 human Rab proteins revealed a wide range of Binding properties with large differences between some Rab proteins. This analysis assists the functional annotation of Rab proteins 12, 14, 26, 37 and 41 and provided an explanation for the shared function of Rab3 and 27. Rab7a and 7b have very different electrostatic potentials, indicating that they may bind to different effector proteins and thus, exert different functions. The subfamily V Rab GTPases which are associated with endosome differ subtly in the interaction properties of their switch regions, and this may explain exchange factor specificity and exchange kinetics. Conclusions/Significance We have analysed conservation of sequence and of Molecular interaction fields to cluster and annotate the human Rab proteins. The analysis of three dimensional Molecular interaction fields provides detailed insight that is not available from a sequence-based approach alone. Based on our results, we predict novel functions for some Rab proteins and provide insights into their divergent functions and the determinants of their Binding partner selectivity.

  • The Interaction Properties of the Human Rab GTPase Family – A Comparative Analysis Reveals Determinants of Molecular Binding Selectivity
    2012
    Co-Authors: Matthias Stein, Manohar Pilli, Sabine Bernauer, Marino Zerial, Bianca H. Habermann, Rebecca C Wade
    Abstract:

    BackgroundRab GTPases constitute the largest subfamily of the Ras protein superfamily. Rab proteins regulate organelle biogenesis and transport, and display distinct Binding preferences for effector and activator proteins, many of which have not been elucidated yet. The underlying Molecular recognition motifs, Binding partner preferences and selectivities are not well understood. Methodology/Principal FindingsComparative analysis of the amino acid sequences and the three-dimensional electrostatic and hydrophobic Molecular interaction fields of 62 human Rab proteins revealed a wide range of Binding properties with large differences between some Rab proteins. This analysis assists the functional annotation of Rab proteins 12, 14, 26, 37 and 41 and provided an explanation for the shared function of Rab3 and 27. Rab7a and 7b have very different electrostatic potentials, indicating that they may bind to different effector proteins and thus, exert different functions. The subfamily V Rab GTPases which are associated with endosome differ subtly in the interaction properties of their switch regions, and this may explain exchange factor specificity and exchange kinetics. Conclusions/SignificanceWe have analysed conservation of sequence and of Molecular interaction fields to cluster and annotate the human Rab proteins. The analysis of three dimensional Molecular interaction fields provides detailed insight that is not available from a sequence-based approach alone. Based on our results, we predict novel functions for some Rab proteins and provide insights into their divergent functions and the determinants of their Binding partner selectivity.

S Carniato - One of the best experts on this subject based on the ideXlab platform.

  • unveiling residual Molecular Binding in triply charged hydrogen bromide
    Journal of Physics: Conference Series, 2012
    Co-Authors: Francis Penent, G Gamblin, P. Lablanquie, Jérôme Palaudoux, Ljiljana Andric, Yasumasa Hikosaka, S Carniato
    Abstract:

    Double Auger decay following HBr(3d) inner-shell ionization by synchrotron radiation has been used to investigate HBr3+ potential energy curves. The direct double Auger decay reveals the residual Binding energy sustained by theoretical calculation. Sequential processes are also observed and are characterized through observation of Br+* autoionizing states following HBr2+ fragmentation.

  • unveiling residual Molecular Binding in triply charged hydrogen bromide
    Physical Review Letters, 2011
    Co-Authors: Francis Penent, G Gamblin, P. Lablanquie, Jérôme Palaudoux, Ljiljana Andric, Yasumasa Hikosaka, S Carniato
    Abstract:

    We present an experimental and theoretical study of triply charged hydrogen bromide ions formed by photoionization of the inner 3d shell of Br. The experimental results, obtained by detecting the 3d photoelectron in coincidence with the two subsequent Auger electrons, are analyzed using calculated potential energy curves of HBr{sup 3+}. The competition between the short-range chemical Binding potential and the Coulomb repulsion in the dissociative process is shown. Two different mechanisms are observed for double Auger decay: one, a direct process with simultaneous ejection of two Auger electrons to final HBr{sup 3+} ionic states and the other, a cascade process involving double Auger decay characterized by the autoionization of Br*{sup +} ion subsequent to the HBr{sup 2+} fragmentation.

Rebecca C Wade - One of the best experts on this subject based on the ideXlab platform.

  • The Interaction Properties of the Human Rab GTPase Family – A Comparative Analysis Reveals Determinants of Molecular Binding Selectivity
    2013
    Co-Authors: Matthias Stein, Manohar Pilli, Sabine Bernauer, Marino Zerial, Bianca H. Habermann, Rebecca C Wade
    Abstract:

    Background: Rab GTPases constitute the largest subfamily of the Ras protein superfamily. Rab proteins regulate organelle biogenesis and transport, and display distinct Binding preferences for effector and activator proteins, many of which have not been elucidated yet. The underlying Molecular recognition motifs, Binding partner preferences and selectivities are not well understood. Methodology/Principal Findings: Comparative analysis of the amino acid sequences and the three-dimensional electrostatic and hydrophobic Molecular interaction fields of 62 human Rab proteins revealed a wide range of Binding properties with large differences between some Rab proteins. This analysis assists the functional annotation of Rab proteins 12, 14, 26, 37 and 41 and provided an explanation for the shared function of Rab3 and 27. Rab7a and 7b have very different electrostatic potentials, indicating that they may bind to different effector proteins and thus, exert different functions. The subfamily V Rab GTPases which are associated with endosome differ subtly in the interaction properties of their switch regions, and this may explain exchange factor specificity and exchange kinetics. Conclusions/Significance: We have analysed conservation of sequence and of Molecular interaction fields to cluster and annotate the human Rab proteins. The analysis of three dimensional Molecular interaction fields provides detailed insight that is not available from a sequence-based approach alone. Based on our results, we predict novel functions for some Ra

  • the interaction properties of the human rab gtpase family a comparative analysis reveals determinants of Molecular Binding selectivity
    PLOS ONE, 2012
    Co-Authors: Matthias Stein, Manohar Pilli, Sabine Bernauer, Bianca Habermann, Marino Zerial, Rebecca C Wade
    Abstract:

    Background Rab GTPases constitute the largest subfamily of the Ras protein superfamily. Rab proteins regulate organelle biogenesis and transport, and display distinct Binding preferences for effector and activator proteins, many of which have not been elucidated yet. The underlying Molecular recognition motifs, Binding partner preferences and selectivities are not well understood. Methodology/Principal Findings Comparative analysis of the amino acid sequences and the three-dimensional electrostatic and hydrophobic Molecular interaction fields of 62 human Rab proteins revealed a wide range of Binding properties with large differences between some Rab proteins. This analysis assists the functional annotation of Rab proteins 12, 14, 26, 37 and 41 and provided an explanation for the shared function of Rab3 and 27. Rab7a and 7b have very different electrostatic potentials, indicating that they may bind to different effector proteins and thus, exert different functions. The subfamily V Rab GTPases which are associated with endosome differ subtly in the interaction properties of their switch regions, and this may explain exchange factor specificity and exchange kinetics. Conclusions/Significance We have analysed conservation of sequence and of Molecular interaction fields to cluster and annotate the human Rab proteins. The analysis of three dimensional Molecular interaction fields provides detailed insight that is not available from a sequence-based approach alone. Based on our results, we predict novel functions for some Rab proteins and provide insights into their divergent functions and the determinants of their Binding partner selectivity.

  • The Interaction Properties of the Human Rab GTPase Family – A Comparative Analysis Reveals Determinants of Molecular Binding Selectivity
    2012
    Co-Authors: Matthias Stein, Manohar Pilli, Sabine Bernauer, Marino Zerial, Bianca H. Habermann, Rebecca C Wade
    Abstract:

    BackgroundRab GTPases constitute the largest subfamily of the Ras protein superfamily. Rab proteins regulate organelle biogenesis and transport, and display distinct Binding preferences for effector and activator proteins, many of which have not been elucidated yet. The underlying Molecular recognition motifs, Binding partner preferences and selectivities are not well understood. Methodology/Principal FindingsComparative analysis of the amino acid sequences and the three-dimensional electrostatic and hydrophobic Molecular interaction fields of 62 human Rab proteins revealed a wide range of Binding properties with large differences between some Rab proteins. This analysis assists the functional annotation of Rab proteins 12, 14, 26, 37 and 41 and provided an explanation for the shared function of Rab3 and 27. Rab7a and 7b have very different electrostatic potentials, indicating that they may bind to different effector proteins and thus, exert different functions. The subfamily V Rab GTPases which are associated with endosome differ subtly in the interaction properties of their switch regions, and this may explain exchange factor specificity and exchange kinetics. Conclusions/SignificanceWe have analysed conservation of sequence and of Molecular interaction fields to cluster and annotate the human Rab proteins. The analysis of three dimensional Molecular interaction fields provides detailed insight that is not available from a sequence-based approach alone. Based on our results, we predict novel functions for some Rab proteins and provide insights into their divergent functions and the determinants of their Binding partner selectivity.