Acquiring a nano-view of single molecules in actions

In 1959, Nobel laureate Richard Feynman suggested that ‘there is plenty of room at the bottom,’ predicting the possibility of single-molecule detection and studies. Over the last 20 years, we have witnessed a rapid development in single-molecule spectroscopy. Single-molecule spectroscopy and imaging have been demonstrated to be a powerful molecular analytical approach to studying the complex and inhomogeneous chemical, biological, and physical processes involved in protein dynamics, protein-protein interactions, protein-DNA interaction dynamics, biological and chemical catalyses, and interfacial dynamics. The discipline of single-molecule spectroscopy has been expanded across a broad range, including optical imaging, optical spectroscopy of fluorescence and Raman, atomic force spectroscopy, and various forms of scanning probe microscopy. A significant feature of this exciting development is that single-molecule spectroscopy is developing hand-in-hand with the recent advancements in nanotechnology, imaging technologies, ultrafast dynamics technologies, theoretical modeling and analyses, and computational technologies

Exploring the Mechanism of Flexible Biomolecular Recognition with Single Molecule Dynamics

Combining a single-molecule study of protein binding with a coarse grained molecular dynamics model including solvent (water molecules) effects, we find that biomolecular recognition is determined by flexibilities in addition to structures. Our single-molecule study shows that binding of CBD (a fragment of Wiskott-Aldrich syndrome protein) to Cdc42 involves bound and loosely bound states, which can be quantitatively explained in our model as a result of binding with large conformational changes. Our model identified certain key residues for binding consistent with mutational experiments. Our study reveals the role of flexibility and a new scenario of dimeric binding between the monomers: first bind and then fold. © 2007 The American Physical Society

2d Regional Correlation Analysis Of Single-molecule Time Trajectories

We report a new approach of 2D regional correlation analysis capable of analyzing fluctuation dynamics of complex multiple correlated and anticorrelated fluctuations under a noncorrelated noise background. Using this new method, by changing and scanning the start time and end time along a pair of fluctuation trajectories, we are able to map out any defined segments along the fluctuation trajectories and determine whether they are correlated, anticorrelated, or noncorrelated; after which, a cross-correlation analysis can be applied for each specific segment to obtain a detailed fluctuation dynamics analysis. We specifically discuss an application of this approach to analyze single-molecule fluorescence resonance energy transfer (FRET) fluctuation dynamics where the fluctuations are often complex, although this approach can be useful for analyzing other types of fluctuation dynamics of various physical variables as well

Bunching Effect In Single-molecule T4 Lysozyme Nonequilibrium Conformational Dynamics Under Enzymatic Reactions

The bunching effect, implying that conformational motion times tend to bunch in a finite and narrow time window, is observed and identified to be associated with substrate enzyme complex formation in T4 lysozyme conformational dynamics under enzymatic reactions. Using single-molecule fluorescence spectroscopy, we have probed T4 lysozyme conformational motions under the hydrolysis reaction of polysaccharide of E. coli 13 cell walls by monitoring the fluorescence resonant energy transfer (FRET) between a donor acceptor probe pair tethered to T4 lysozyme domains involving open close hinge-bending motions. On the basis of the single-molecule spectroscopic results, molecular dynamics simulation, and a random walk model analysis, multiple intermediate states have been estimated in the evolution of T4 lysozyme enzymatic reaction active complex formation (Chen, Y.; Hu, D.; Vorpagel, E. R.; Lu, H. P. Probing single-molecule T4 lysozyme conformational dynamics by intramolecular fluorescence energy transfer. J. Phys. Chem. B 2003, 107, 7947-7956). In this Article, we report progress on the analysis of the reported experimental results, and we have identified the bunching effect of the substrate enzyme active complex formation time in T4 lysozyme enzymatic reactions. We show that the bunching effect, a dynamic behavior observed for the catalytic hinge-bending conformational motions of T4 lysozyme, is a convoluted outcome of multiple consecutive Poisson rate processes that are defined by protein functional motions under substrate enzyme interactions; i.e., convoluted multiple Poisson rate processes give rise to the bunching effect in the enzymatic reaction dynamics. We suggest that the bunching effect is likely common in protein conformational dynamics involved in conformation-gated protein functions

Single-Molecule Dynamics Reveals Cooperative Binding-Folding in Protein Recognition

The study of associations between two biomolecules is the key to understanding molecular function and recognition. Molecular function is often thought to be determined by underlying structures. Here, combining a single-molecule study of protein binding with an energy-landscape–inspired microscopic model, we found strong evidence that biomolecular recognition is determined by flexibilities in addition to structures. Our model is based on coarse-grained molecular dynamics on the residue level with the energy function biased toward the native binding structure (the Go model). With our model, the underlying free-energy landscape of the binding can be explored. There are two distinct conformational states at the free-energy minimum, one with partial folding of CBD itself and significant interface binding of CBD to Cdc42, and the other with native folding of CBD itself and native interface binding of CBD to Cdc42. This shows that the binding process proceeds with a significant interface binding of CBD with Cdc42 first, without a complete folding of CBD itself, and that binding and folding are then coupled to reach the native binding state. The single-molecule experimental finding of dynamic fluctuations among the loosely and closely bound conformational states can be identified with the theoretical, calculated free-energy minimum and explained quantitatively in the model as a result of binding associated with large conformational changes. The theoretical predictions identified certain key residues for binding that were consistent with mutational experiments. The combined study identified fundamental mechanisms and provided insights about designing and further exploring biomolecular recognition with large conformational changes

Probing Single-molecule Interfacial Geminate Electron-cation Recombination Dynamics

Interfacial electron-cation recombination in zinc-tetra (4-carboxyphenyl) porphyrin (ZnTCPP)/TiO(2) nanoparticle system has been probed at the single-molecule level by recording and analyzing photon-to-photon pair times of the ZnTCPP fluorescence. We have. developed a novel approach to reveal the hidden single-molecule interfacial electron-cation recombination dynamics by analyzing the autocorrelation function and a proposed convoluted single-molecule interfacial electron-cation recombination model. Our results suggest that the fluctuations of the interfacial electron transfer (ET) reactivity modulate the ET cycles as well as the interfacial electron-cation recombination dynamics. On the basis of this model, the single-molecule electron-cation recombination time of ZnTCPP/-TiO(2) system is deduced to be at time scale of 10(-5) s. The autocorrelation of photon-to-photon pair times as well as the convoluted ET model has been further demonstrated by simulation and interpreted in terms of the interfacial ET reactivity fluctuation and blinking. Our approach not only can effectively probe the single-molecule interfacial electron-cation dynamics but also can be applied to other single-molecule ground-state regeneration dynamics occurring at interfaces and within condensed phases

Combined Single-molecule Photon-stamping Spectroscopy And Femtosecond Transient Absorption Spectroscopy Studies Of Interfacial Electron Transfer Dynamics

The inhomogeneous interfacial electron transfer (IET) dynamics of 9-phenyl-2,3,7-trihydroxy-6-fluorone (PF)-sensitized TiO2 nanoparticles (NPs) has been probed by a single-molecule photon-stamping technique as well as ensemble-averaged femtosecond transient absorption spectroscopy. The forward electron transfer (FET) time shows a broad distribution at the single-molecule level, indicating the inhomogeneous interactions and ET reactivity of the PF/TiO2 NP system. The broad distribution of the FET time is measured to be 0.4 ± 0.1 ps in the transient absorption and picoseconds to nanoseconds in the photon-stamping measurements. The charge recombination time, having a broad distribution at the single-molecule level, clearly shows a biexponential dynamic behavior in the transient absorption: a fast component of 3.0 ± 0.1 ps and a slow component of 11.5 ± 0.5 ns. We suggest that both strong and weak interactions between PF and TiO2 coexist, and we have proposed two mechanisms to interpret the observed IET dynamics. A single-molecule photon-stamping technique and ensemble-averaged transient absorption spectroscopy provide efficient “zoom-in” and “zoom-out” approaches for probing the IET dynamics. The physical nature of the observed multiexponential or stretched-exponential ET dynamics in the ensemble-averaged experiments, often associated with dynamic and static inhomogeneous ET dynamics, can be identified and analyzed by single-molecule spectroscopy measurements

The connection between the host halo and the satellite galaxies of the Milky Way

Many properties of the Milky Way's dark matter halo, including its mass assembly history, concentration, and subhalo population, remain poorly constrained. We explore the connection between these properties of the Milky Way and its satellite galaxy population, especially the implication of the presence of the Magellanic Clouds for the properties of the Milky Way halo. Using a suite of high-resolution $N$-body simulations of Milky Way-mass halos with a fixed final Mvir ~ 10^{12.1}Msun, we find that the presence of Magellanic Cloud-like satellites strongly correlates with the assembly history, concentration, and subhalo population of the host halo, such that Milky Way-mass systems with Magellanic Clouds have lower concentration, more rapid recent accretion, and more massive subhalos than typical halos of the same mass. Using a flexible semi-analytic galaxy formation model that is tuned to reproduce the stellar mass function of the classical dwarf galaxies of the Milky Way with Markov-Chain Monte-Carlo, we show that adopting host halos with different mass-assembly histories and concentrations can lead to different best-fit models for galaxy-formation physics, especially for the strength of feedback. These biases arise because the presence of the Magellanic Clouds boosts the overall population of high-mass subhalos, thus requiring a different stellar-mass-to-halo-mass ratio to match the data. These biases also lead to significant differences in the mass--metallicity relation, the kinematics of low-mass satellites, the number counts of small satellites associated with the Magellanic Clouds, and the stellar mass of Milky Way itself. Observations of these galaxy properties can thus provide useful constraints on the properties of the Milky Way halo.Comment: 20 pages, 12 figures, accepted for publication in ApJ. A new section on the effect of host halo mass-assembly history on the central galaxy stellar mass is adde