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Journal ArticleDOI

Protein Conformational Dynamics Probed by Single-Molecule Electron Transfer

TL;DR: By probing the fluorescence lifetime of the single flavin on a photon-by-photon basis, the variation of flavin-tyrosine distance over time is observed, suggesting the existence of multiple interconverting conformers related to the fluctuating catalytic reactivity.
Abstract: Electron transfer is used as a probe for angstrom-scale structural changes in single protein molecules. In a flavin reductase, the fluorescence of flavin is quenched by a nearby tyrosine residue by means of photo-induced electron transfer. By probing the fluorescence lifetime of the single flavin on a photon-by-photon basis, we were able to observe the variation of flavin-tyrosine distance over time. We could then determine the potential of mean force between the flavin and the tyrosine, and a correlation analysis revealed conformational fluctuation at multiple time scales spanning from hundreds of microseconds to seconds. This phenomenon suggests the existence of multiple interconverting conformers related to the fluctuating catalytic reactivity.
Citations
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28 Jul 2005
TL;DR: PfPMP1)与感染红细胞、树突状组胞以及胎盘的单个或多个受体作用,在黏附及免疫逃避中起关键的作�ly.
Abstract: 抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1(PfPMP1)与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用,在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员,通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

18,940 citations

Journal ArticleDOI
TL;DR: Fractional dynamics has experienced a firm upswing during the past few years, having been forged into a mature framework in the theory of stochastic processes as mentioned in this paper, and a large number of research papers developing fractional dynamics further, or applying it to various systems have appeared since our first review article on the fractional Fokker-Planck equation.
Abstract: Fractional dynamics has experienced a firm upswing during the past few years, having been forged into a mature framework in the theory of stochastic processes. A large number of research papers developing fractional dynamics further, or applying it to various systems have appeared since our first review article on the fractional Fokker–Planck equation (Metzler R and Klafter J 2000a, Phys. Rep. 339 1–77). It therefore appears timely to put these new works in a cohesive perspective. In this review we cover both the theoretical modelling of sub- and superdiffusive processes, placing emphasis on superdiffusion, and the discussion of applications such as the correct formulation of boundary value problems to obtain the first passage time density function. We also discuss extensively the occurrence of anomalous dynamics in various fields ranging from nanoscale over biological to geophysical and environmental systems.

2,119 citations


Cites background from "Protein Conformational Dynamics Pro..."

  • ...Compelling evidence for broad time-scale distributions in protein conformational dynamics was reported recently, and modelled on the basis of the fractional Fokker–Planck equation (Yang et al 2003, Yang and Xie 2002)....

    [...]

Journal ArticleDOI
12 Dec 2007-Nature
TL;DR: The dream is to 'watch' proteins in action in real time at atomic resolution, which requires addition of a fourth dimension, time, to structural biology so that the positions in space and time of all atoms in a protein can be described in detail.
Abstract: Because proteins are central to cellular function, researchers have sought to uncover the secrets of how these complex macromolecules execute such a fascinating variety of functions. Although static structures are known for many proteins, the functions of proteins are governed ultimately by their dynamic character (or 'personality'). The dream is to 'watch' proteins in action in real time at atomic resolution. This requires addition of a fourth dimension, time, to structural biology so that the positions in space and time of all atoms in a protein can be described in detail.

2,109 citations

Journal ArticleDOI
TL;DR: The lifetime of a photophysical process is the time required by a population of N electronically excited molecules to be reduced by a factor of e via the loss of energy through fluorescence and other non-radiative processes and the average length of time τ is called the mean lifetime, or simply lifetime.
Abstract: When a molecule absorbs a photon of appropriate energy, a chain of photophysical events ensues, such as internal conversion or vibrational relaxation (loss of energy in the absence of light emission), fluorescence, intersystem crossing (from singlet state to a triplet state) and phosphorescence, as shown in the Jablonski diagram for organic molecules (Fig. 1). Each of the processes occurs with a certain probability, characterized by decay rate constants (k). It can be shown that the average length of time τ for the set of molecules to decay from one state to another is reciprocally proportional to the rate of decay: τ = 1/k. This average length of time is called the mean lifetime, or simply lifetime. It can also be shown that the lifetime of a photophysical process is the time required by a population of N electronically excited molecules to be reduced by a factor of e. Correspondingly, the fluorescence lifetime is the time required by a population of excited fluorophores to decrease exponentially to N/e via the loss of energy through fluorescence and other non-radiative processes. The lifetime of photophycal processes vary significantly from tens of femotoseconds for internal conversion1,2 to nanoseconds for fluorescence and microseconds or seconds for phosphorescence.1 Open in a separate window Figure 1 Jablonski diagram and a timescale of photophysical processes for organic molecules.

1,829 citations

Journal ArticleDOI
TL;DR: This Perspective is intended as a guidebook for both experimentalists and theorists working on systems, which exhibit anomalous diffusion, and pays special attention to the ergodicity breaking parameters for the different anomalous stochastic processes.
Abstract: Modern microscopic techniques following the stochastic motion of labelled tracer particles have uncovered significant deviations from the laws of Brownian motion in a variety of animate and inanimate systems. Such anomalous diffusion can have different physical origins, which can be identified from careful data analysis. In particular, single particle tracking provides the entire trajectory of the traced particle, which allows one to evaluate different observables to quantify the dynamics of the system under observation. We here provide an extensive overview over different popular anomalous diffusion models and their properties. We pay special attention to their ergodic properties, highlighting the fact that in several of these models the long time averaged mean squared displacement shows a distinct disparity to the regular, ensemble averaged mean squared displacement. In these cases, data obtained from time averages cannot be interpreted by the standard theoretical results for the ensemble averages. Here we therefore provide a comparison of the main properties of the time averaged mean squared displacement and its statistical behaviour in terms of the scatter of the amplitudes between the time averages obtained from different trajectories. We especially demonstrate how anomalous dynamics may be identified for systems, which, on first sight, appear to be Brownian. Moreover, we discuss the ergodicity breaking parameters for the different anomalous stochastic processes and showcase the physical origins for the various behaviours. This Perspective is intended as a guidebook for both experimentalists and theorists working on systems, which exhibit anomalous diffusion.

1,390 citations

References
More filters
28 Jul 2005
TL;DR: PfPMP1)与感染红细胞、树突状组胞以及胎盘的单个或多个受体作用,在黏附及免疫逃避中起关键的作�ly.
Abstract: 抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1(PfPMP1)与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用,在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员,通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

18,940 citations

Journal ArticleDOI
TL;DR: In this paper, the electron transfer reactions between ions and molecules in solution have been the subject of considerable experimental study during the past three decades, including charge transfer, photoelectric emission spectra, chemiluminescent electron transfer, and electron transfer through frozen media.

7,155 citations

Journal ArticleDOI
31 Mar 1995-Science
TL;DR: The onset of a sharp change in ddT( is the Debye-Waller factor and T is temperature) in proteins, which is controversially indentified with the glass transition in liquids, is shown to be general for glass formers and observable in computer simulations of strong and fragile ionic liquids, where it proves to be close to the experimental glass transition temperature.
Abstract: Glasses can be formed by many routes. In some cases, distinct polyamorphic forms are found. The normal mode of glass formation is cooling of a viscous liquid. Liquid behavior during cooling is classified between "strong" and "fragile," and the three canonical characteristics of relaxing liquids are correlated through the fragility. Strong liquids become fragile liquids on compression. In some cases, such conversions occur during cooling by a weak first-order transition. This behavior can be related to the polymorphism in a glass state through a recent simple modification of the van der Waals model for tetrahedrally bonded liquids. The sudden loss of some liquid degrees of freedom through such first-order transitions is suggestive of the polyamorphic transition between native and denatured hydrated proteins, which can be interpreted as single-chain glass-forming polymers plasticized by water and cross-linked by hydrogen bonds. The onset of a sharp change in d dT( is the Debye-Waller factor and T is temperature) in proteins, which is controversially indentified with the glass transition in liquids, is shown to be general for glass formers and observable in computer simulations of strong and fragile ionic liquids, where it proves to be close to the experimental glass transition temperature. The latter may originate in strong anharmonicity in modes ("bosons"), which permits the system to access multiple minima of its configuration space. These modes, the Kauzmann temperature T(K), and the fragility of the liquid, may thus be connected.

4,016 citations

Journal ArticleDOI
13 Dec 1991-Science
TL;DR: The concepts that emerge from studies of the conformational substates and the motions between them permit a quantitative discussion of one simple reaction, the binding of small ligands such as carbon monoxide to myoglobin.
Abstract: Recent experiments, advances in theory, and analogies to other complex systems such as glasses and spin glasses yield insight into protein dynamics. The basis of the understanding is the observation that the energy landscape is complex: Proteins can assume a large number of nearly isoenergetic conformations (conformational substates). The concepts that emerge from studies of the conformational substates and the motions between them permit a quantitative discussion of one simple reaction, the binding of small ligands such as carbon monoxide to myoglobin.

2,902 citations

Journal ArticleDOI
12 Mar 1999-Science
TL;DR: The progress in applying single-molecule detection and single-Molecule spectroscopy at room temperature by laser-induced fluorescence with the use of fluorophores that are site-specifically attached to macromolecules is reviewed.
Abstract: Recent advances in single-molecule detection and single-molecule spectroscopy at room temperature by laser-induced fluorescence offer new tools for the study of individual macromolecules under physiological conditions. These tools relay conformational states, conformational dynamics, and activity of single biological molecules to physical observables, unmasked by ensemble averaging. Distributions and time trajectories of these observables can therefore be measured during a reaction without the impossible need to synchronize all the molecules in the ensemble. The progress in applying these tools to biological studies with the use of fluorophores that are site-specifically attached to macromolecules is reviewed.

2,053 citations