Single-particle trajectories reveal two-state diffusion-kinetics of hOGG1 proteins on DNA

Vestergaard, Christian; Blainey, Paul C.; Flyvbjerg, Henrik

doi:10.1093/nar/gky004

Cited by 32 publications

(50 citation statements)

References 45 publications

(65 reference statements)

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“…The covariance-based estimator (CVE) introduced and demonstrated in [6,7,29] is an attractive alternative; however, away from surfaces, it estimates the bulk value of D, does that even from short segments of the trajectory, and does this optimally, provided its SNR DΔt √ /σ loc > 1 [6,7]. So, our exact MSD is probably best used with experimental MSDvalues as a fairly simple way to gauge deviation from bulk behavior as function of time-scale of measurement.…”

Section: Discussionmentioning

confidence: 99%

Confined Brownian Motion Tracked With Motion Blur: Estimating Diffusion Coefficient and Size of Confining Space

2021

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Mesoscopic environments and particles diffusing in them are often studied by tracking such particles individually while their Brownian motion explores their environment. Environments may be, e.g., a domain in a cell membrane, an interior compartment of a cell, or an engineered nanopit. Particle trajectories are typically determined from time-lapse recorded movies. These are recorded with sufficient exposure time per frame to be able to detect and localize particles in each frame. Since particles move during this exposure time, particles image with motion blur. This motion blur can compromise estimates of diffusion coefficients and the size of the confining domain if not accounted for correctly. We do that here. We give explicit and exact expressions for the variance of measured positions and the mean-squared displacement of a Brownian particle confined in, respectively, a 1D box, a 2D box, a 2D circular disc, and a 3D sphere. Our expressions are valid for all exposure times, irrespective of the size of the confining space and the value of the diffusion coefficient. They apply also in the common case where the exposure time is smaller than the time-lapse due, e.g., to “dead time” caused by the readout process in the camera. These expressions permit determination of diffusion coefficients and domain sizes for given movies for the simple geometries we consider. More important, the trends observed in our exact results when parameter values are varied are valid also for more complex geometries for which no exact analytical solutions exist. Wherever the underlying physics is the same, the exact quantitative description of its consequences provided here is portable as a qualitative and semi-quantitative understanding of its consequences in general. The results may also be useful for other types of reflected Brownian motion than those occurring in single-particle tracking, e.g., in nuclear magnetic resonance imaging techniques. For use in that particular context, we briefly discuss the effects of confinement on anisotropic Brownian motion imaged with motion blur.

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Section: Discussionmentioning

confidence: 99%

Confined Brownian Motion Tracked With Motion Blur: Estimating Diffusion Coefficient and Size of Confining Space

2021

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“…A recent reanalysis of the original single-molecule data used a new approach (known as optimal estimator of diffusion coefficients) and suggested that hOGG1 switches between two diffusive modes that more closely resemble those observed in ensemble measurements of hUNG and hOGG1 (see below). 40,133…”

Section: Dna Translocation By Dna Repair Glycosylasesmentioning

confidence: 99%

Facilitated Diffusion Mechanisms in DNA Base Excision Repair and Transcriptional Activation

Esadze

Stivers

2018

Chem. Rev.

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Preservation of the coding potential of the genome and highly regulated gene expression over the life span of a human are two fundamental requirements of life. These processes require the action of repair enzymes or transcription factors that efficiently recognize specific sites of DNA damage or transcriptional regulation within a restricted time frame of the cell cycle or metabolism. A failure of these systems to act results in accumulated mutations, metabolic dysfunction, and disease. Despite the multifactorial complexity of cellular DNA repair and transcriptional regulation, both processes share a fundamental physical requirement that the proteins must rapidly diffuse to their specific DNA-binding sites that are embedded within the context of a vastly greater number of nonspecific DNA-binding sites. Superimposed on the needle-in-the-haystack problem is the complex nature of the cellular environment, which contains such high concentrations of macromolecules that the time frame for diffusion is expected to be severely extended as compared to dilute solution. Here we critically review the mechanisms for how these proteins solve the needle-in-the-haystack problem and how the effects of cellular macromolecular crowding can enhance facilitated diffusion processes. We restrict the review to human proteins that use stochastic, thermally driven site-recognition mechanisms, and we specifically exclude systems involving energy cofactors or circular DNA clamps. Our scope includes ensemble and single-molecule studies of the past decade or so, with an emphasis on connecting experimental observations to biological function.

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“…Flanking DNA sequence around the target DNA site has also been found to modulate the search process by altering the funnel-shaped protein-DNA binding energy landscape (8). These multifaceted search mechanisms have been captured in vitro via different spectroscopic approaches (9)(10)(11)(12)(13) and also through in silico models and simulations (14)(15)(16)(17)(18)(19)(20)(21)(22)(23) at the single-molecule level. The in vivo condition is, however, entirely different because of the presence of an astounding concentration ($100-300 mg/mL) of dissolved macromolecules (24,25).…”

Section: Introductionmentioning

confidence: 99%

Structural Basis of Enhanced Facilitated Diffusion of DNA-Binding Protein in Crowded Cellular Milieu

Dey

Bhattacherjee

2020

Biophysical Journal

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Although the fast association between DNA-binding proteins (DBPs) and DNA is explained by a facilitated diffusion mechanism, in which DBPs adopt a weighted combination of three-dimensional diffusion and one-dimensional (1D) sliding and hopping modes of transportation, the role of cellular environment that contains many nonspecifically interacting proteins and other biomolecules is mostly overlooked. By performing large-scale computational simulations with an appropriately tuned model of protein and DNA in the presence of nonspecifically interacting bulk and DNA-bound crowders (genomic crowders), we demonstrate the structural basis of the enhanced facilitated diffusion of DBPs inside a crowded cellular milieu through, to our knowledge, novel 1D scanning mechanisms. In this one-dimensional scanning mode, the protein can float along the DNA under the influence of nonspecific interactions of bulk crowder molecules. The search mode is distinctly different compared to usual 1D sliding and hopping dynamics in which protein diffusion is regulated by the DNA electrostatics. In contrast, the presence of genomic crowders expedites the target search process by transporting the protein over DNA segments through the formation of a transient protein-crowder bridged complex. By analyzing the ruggedness of the associated potential energy landscape, we underpin the molecular origin of the kinetic advantages of these search modes and show that they successfully explain the experimentally observed acceleration of facilitated diffusion of DBPs by molecular crowding agents and crowderconcentration-dependent enzymatic activity of transcription factors. Our findings provide crucial insights into gene regulation kinetics inside the crowded cellular milieu.

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Single-particle trajectories reveal two-state diffusion-kinetics of hOGG1 proteins on DNA

Cited by 32 publications

References 45 publications

Confined Brownian Motion Tracked With Motion Blur: Estimating Diffusion Coefficient and Size of Confining Space

Confined Brownian Motion Tracked With Motion Blur: Estimating Diffusion Coefficient and Size of Confining Space

Facilitated Diffusion Mechanisms in DNA Base Excision Repair and Transcriptional Activation

Structural Basis of Enhanced Facilitated Diffusion of DNA-Binding Protein in Crowded Cellular Milieu

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