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The biology of boundary conditions: cellular reconstitution in one, two, and three dimensionsAn integrated model of transcription factor diffusion shows the importance of intersegmental transfer and quaternary protein structure for target site finding.Method for the analysis of contribution of sliding and hopping to a facilitated diffusion of DNA-binding protein: Application to in vivo data.Computational models for large-scale simulations of facilitated diffusionThe dynamic interplay between DNA topoisomerases and DNA topology.Dynamic strategies for target-site search by DNA-binding proteins.How landscape heterogeneity frames optimal diffusivity in searching processesTheory on the dynamics of feedforward loops in the transcription factor networksTheory on the coupled stochastic dynamics of transcription and splice-site recognitionIn vivo facilitated diffusion model.Rapid search for specific sites on DNA through conformational switch of nonspecifically bound proteins.Exploring protein-DNA interactions in 3D using in situ construction, manipulation and visualization of individual DNA dumbbells with optical traps, microfluidics and fluorescence microscopy.Theoretical and computational modeling of target-site search kinetics in vitro and in vivoOn the minimization of fluctuations in the response times of autoregulatory gene networks.Concentration- and chromosome-organization-dependent regulator unbinding from DNA for transcription regulation in living cells.A new approach to the problem of bulk-mediated surface diffusion.Dancing on DNA: kinetic aspects of search processes on DNAVariance-corrected Michaelis-Menten equation predicts transient rates of single-enzyme reactions and response times in bacterial gene-regulation.DNA concentration-dependent dissociation of EcoRI: direct transfer or reaction during hopping.Proteins searching for their target on DNA by one-dimensional diffusion: overcoming the "speed-stability" paradox.Pluralistic and stochastic gene regulation: examples, models and consistent theory.Fungal genes in context: genome architecture reflects regulatory complexity and function.A mathematical model for scanning and catalysis on single-stranded DNA, illustrated with activation-induced deoxycytidine deaminaseQuantitative influence of macromolecular crowding on gene regulation kinetics.Multiple-binding-site mechanism explains concentration-dependent unbinding rates of DNA-binding proteins.Foundations for modeling the dynamics of gene regulatory networks: a multilevel-perspective review.Proteins Recognizing DNA: Structural Uniqueness and Versatility of DNA-Binding Domains in Stem Cell Transcription Factors.Physical constraints determine the logic of bacterial promoter architectures.Rad4 recognition-at-a-distance: Physical basis of conformation-specific anomalous diffusion of DNA repair proteins.What matters for lac repressor search in vivo--sliding, hopping, intersegment transfer, crowding on DNA or recognition?Efficient search of multiple types of targets.Extracting enzyme processivity from kinetic assays.Obstacles may facilitate and direct DNA search by proteins.Real sequence effects on the search dynamics of transcription factors on DNA.Signal focusing through active transport.Transcription factor clusters regulate genes in eukaryotic cells.Theory of site-specific DNA-protein interactions in the presence of conformational fluctuations of DNA binding domains.A comprehensive computational model of facilitated diffusion in prokaryotes.Geometry-induced bursting dynamics in gene expression.Generalized facilitated diffusion model for DNA-binding proteins with search and recognition states
P2860
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P2860
description
article científic
@ca
article scientifique
@fr
articolo scientifico
@it
artigo científico
@pt
bilimsel makale
@tr
scientific article published on 06 May 2009
@en
vedecký článok
@sk
vetenskaplig artikel
@sv
videnskabelig artikel
@da
vědecký článek
@cs
name
Facilitated diffusion with DNA coiling.
@en
Facilitated diffusion with DNA coiling.
@nl
type
label
Facilitated diffusion with DNA coiling.
@en
Facilitated diffusion with DNA coiling.
@nl
prefLabel
Facilitated diffusion with DNA coiling.
@en
Facilitated diffusion with DNA coiling.
@nl
P2860
P50
P356
P1476
Facilitated diffusion with DNA coiling
@en
P2093
Gijs J L Wuite
Svenja-Marei J Kalisch
P2860
P304
P356
10.1073/PNAS.0903293106
P407
P577
2009-05-06T00:00:00Z