Molecular Mechanism of Facilitated Dissociation of Fis Protein from DNA

Tsai, Ming-Yen; Zhang, Bin; Zheng, Weihua; Wolynes, Peter G.

doi:10.1021/jacs.6b08416

Cited by 51 publications

(96 citation statements)

References 22 publications

(55 reference statements)

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“…6, we show the simulation results for the explicit electrostatic simulations only for various nonelectrostatic binding energies, since we have shown in the previous sections that implicit treatment cannot provide correct physical environment for unbinding. In the simulation, we vary the strength of the non-electrostatic binding energy per bead so that we can scan energy ranges around 10 k B T total, which is the typical molecular binding energies [10,34,46]. Our simulations reveal various regimes for unbinding events.…”

Section: Short-ranged Non-electrostatic Interactions Modulate the Ratmentioning

confidence: 99%

Effects of electrostatic interactions on ligand dissociation kinetics

2018

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We study unbinding of multivalent cationic ligands from oppositely charged polymeric binding sites sparsely grafted on a flat neutral substrate. Our molecular dynamics (MD) simulations are suggested by single-molecule studies of protein-DNA interactions. We consider univalent salt concentrations spanning roughly a thousandfold range, together with various concentrations of excess ligands in solution. To reveal the ionic effects on unbinding kinetics of spontaneous and facilitated dissociation mechanisms, we treat electrostatic interactions both at a Debye-Hückel (DH, or 'implicit' ions, i.e., use of an electrostatic potential with a prescribed decay length) level, as well as by the more precise approach of considering all ionic species explicitly in the simulations. We find that the DH approach systematically overestimates unbinding rates, relative to the calculations where all ion pairs are present explicitly in solution, although many aspects of the two types of calculation are qualitatively similar. For facilitated dissociation (FD, acceleration of unbinding by free ligands in solution) explicit ion simulations lead to unbinding at lower free ligand concentrations. Our simulations predict a variety of FD regimes as a function of free ligand and ion concentrations; a particularly interesting regime is at intermediate concentrations of ligands where non-electrostatic binding strength controls FD. We conclude that explicit-ion electrostatic modeling is an essential component to quantitatively tackle problems in molecular ligand dissociation, including nucleicacid-binding proteins.

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Section: Short-ranged Non-electrostatic Interactions Modulate the Ratmentioning

confidence: 99%

Effects of electrostatic interactions on ligand dissociation kinetics

2018

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“…The standard picture of protein-DNA interactions assumes binding via concentration-dependent association and concentration-independent "spontaneous dissociation" kinetics, with net affinity neatly described by the ratio of the off-rate, off , to the association rate constant, , i.e., D = off / . Experiments that resolve dynamics of individual molecules are starting to challenge this classical picture: lifetimes of DNA-protein complexes have been found to be appreciably shortened by nearby proteins that compete for space on DNA (10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20). However, the molecular mechanisms underlying this "facilitated dissociation" (FD) effect remain unclear.…”

Section: Introductionmentioning

confidence: 99%

Facilitated Dissociation of Transcription Factors from Single DNA Binding Sites

Kamar

Banigan

Erbaş

et al. 2017

Preprint

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The binding of transcription factors (TFs) to DNA controls most aspects of cellular function, making the understanding of their binding kinetics imperative. The standard description of bimolecular interactions posits TF off-rates are independent of TF concentration in solution. However, recent observations have revealed that proteins in solution can accelerate the dissociation of DNA-bound proteins. To study the molecular basis of facilitated dissociation (FD), we have used single-molecule imaging to measure dissociation kinetics of Fis, a key E. coli TF and major bacterial nucleoid protein, from single dsDNA binding sites. We observe a strong FD effect characterized by an exchange rate ~1 × 10 4 M −1 s −1 , establishing that FD of Fis occurs at the single-binding-site level, and we find that the off-rate saturates at large Fis concentrations in solution. While spontaneous (i.e., competitorfree) dissociation shows a strong salt dependence, we find that facilitated dissociation depends only weakly on salt. These results are quantitatively explained by a model in which partially dissociated bound proteins are susceptible to invasion by competitor proteins in solution. We also report FD of NHP6A, a yeast TF whose structure differs significantly from Fis. We further perform molecular dynamics simulations, which indicate that FD can occur for molecules that interact far more weakly than those we have studied. Taken together, our results indicate that FD is a general mechanism assisting in the local removal of TFs from their binding sites and does not necessarily require cooperativity, clustering, or binding site overlap. SIGNIFICANCE STATEMENTTranscription factors (TFs) control biological processes by binding and unbinding to DNA. Therefore it is crucial to understand the mechanisms that affect TF binding kinetics. Recent studies challenge the standard picture of TF binding kinetics by demonstrating cases of proteins in solution accelerating TF dissociation rates through a facilitated dissociation (FD) process. Our study shows that FD can occur at the level of single binding sites, without the action of large protein clusters or long DNA segments. Our results quantitatively support a model of FD in which competitor proteins invade partially dissociated states of DNA-bound TFs. FD is expected to be a general mechanism for modulating gene expression by altering the occupancy of TFs on the genome.. CC-BY-NC 4.0 International license peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/135947 doi: bioRxiv preprint first posted online May. 9, 2017; 3 \body INTRODUCTION Protein-DNA interactions ultimately control all aspects of cellular function through their actions as "transcription factors" (TFs) by regulating gene transcription, folding DNA into chromosomes, and modifying the structure of chromatin; these regulatory and structural functions are often interwoven (1-9). Understanding protein-DNA interaction kinetics is ...

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“…This hybrid AWSEM/3SPN.2C scheme has already been used for a variety of protein-DNA systems. 8,27,35 The details of the force field models can be found elsewhere. 8…”

Section: Coarse-grained Models For Proteins and Dnasmentioning

confidence: 99%

Multiple Binding Configurations of Fis Protein Pairs on DNA: Facilitated Dissociation versus Cooperative Dissociation

Tsai

Zheng

Chen

et al. 2019

Preprint

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As a master transcription regulator, Fis protein influences over two hundred genes of E-coli . Fis protein's non-specific binding to DNA is widely acknowledged, and its kinetics of dissociation from DNA is strongly influenced by its surroundings: the dissociation rate increases as the concentration of Fis protein in the solution-phase increases. In this study, we use computational methods to explore the global binding energy landscape of the Fis1:Fis2:DNA ternary complex. The complex contains a binary-Fis molecular dyad whose formation relies on complex structural rearrangements. The simulations allow us to distinguish several different pathways for the dissociation of the protein from DNA with different functional outcomes, and involving different protein stoichiometries: 1. Simple exchange of proteins and 2. Cooperative unbinding of two Fis proteins to yield bare DNA. In the case of exchange, the protein on the DNA is replaced by solution-phase protein through competition for DNA binding sites. This process seen in fluorescence imaging experiments has been called facilitated dissociation. In the latter case of cooperative unbinding of pairs, two neighboring Fis proteins on DNA form a unique binary-Fis configuration via protein-protein interactions, which in turn leads to the co-dissociation of both molecules simultaneously, a process akin to the "molecular stripping" seen in the NFκB/IκB genetic broadcasting system. This simulation shows that the existence of multiple binding configurations of transcription factors can have a significant impact on the kinetics and outcome of transcription factor dissociation from DNA, with important implications for the systems biology of gene regulation by Fis.

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Molecular Mechanism of Facilitated Dissociation of Fis Protein from DNA

Cited by 51 publications

References 22 publications

Effects of electrostatic interactions on ligand dissociation kinetics

Effects of electrostatic interactions on ligand dissociation kinetics

Facilitated Dissociation of Transcription Factors from Single DNA Binding Sites

Multiple Binding Configurations of Fis Protein Pairs on DNA: Facilitated Dissociation versus Cooperative Dissociation

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