How do DNA-bound proteins leave their binding sites? The role of facilitated dissociation

Erbaş, Aykut; Marko, John F.

doi:10.1016/j.cbpa.2019.08.007

Cited by 27 publications

(34 citation statements)

References 54 publications

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“…A similar phenomenon, where the simultaneous binding of proteins from solution increases the rate of bound protein dissociation, has been observed in many other systems (50). The signature of facilitated protein dissociation, as discussed in ( 50 ), is its progressive enhancement proportional to increasing bulk protein concentration. In contrast, our experiments display an increased rate of dissociation even in the absence of free protein.…”

Section: Resultsmentioning

confidence: 99%

Multiprotein E. coli SSB–ssDNA complex shows both stable binding and rapid dissociation due to interprotein interactions

Naufer

Morse

Möller

et al. 2021

Nucleic Acids Research

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Escherichia coli SSB (EcSSB) is a model single-stranded DNA (ssDNA) binding protein critical in genome maintenance. EcSSB forms homotetramers that wrap ssDNA in multiple conformations to facilitate DNA replication and repair. Here we measure the binding and wrapping of many EcSSB proteins to a single long ssDNA substrate held at fixed tensions. We show EcSSB binds in a biphasic manner, where initial wrapping events are followed by unwrapping events as ssDNA-bound protein density passes critical saturation and high free protein concentration increases the fraction of EcSSBs in less-wrapped conformations. By destabilizing EcSSB wrapping through increased substrate tension, decreased substrate length, and protein mutation, we also directly observe an unstable bound but unwrapped state in which ∼8 nucleotides of ssDNA are bound by a single domain, which could act as a transition state through which rapid reorganization of the EcSSB–ssDNA complex occurs. When ssDNA is over-saturated, stimulated dissociation rapidly removes excess EcSSB, leaving an array of stably-wrapped complexes. These results provide a mechanism through which otherwise stably bound and wrapped EcSSB tetramers are rapidly removed from ssDNA to allow for DNA maintenance and replication functions, while still fully protecting ssDNA over a wide range of protein concentrations.

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Section: Resultsmentioning

confidence: 99%

Multiprotein E. coli SSB–ssDNA complex shows both stable binding and rapid dissociation due to interprotein interactions

Naufer

Morse

Möller

et al. 2021

Nucleic Acids Research

View full text Add to dashboard Cite

show abstract

“…The ability of these proteins to identify and bind to specific DNA target sites among the vast excess of non-target DNA is crucial for many fundamental cellular functions, including recruitment of transcription factors to promoter sequences, of DNA repair proteins to DNA lesions, or of DNA topoisomerases to supercoiled DNA strands. In all organisms, diffusion is the primary mechanism by which DNA-binding proteins locate their targets ( Erbaş and Marko, 2019 ; Erbaş et al., 2019 ; Schavemaker et al., 2018 ). The diffusion coefficient of a particle in a dilute solution is determined by its size and the viscosity and temperature of the medium.…”

Section: Introductionmentioning

confidence: 99%

Transient non-specific DNA binding dominates the target search of bacterial DNA-binding proteins

et al. 2021

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Summary Despite their diverse biochemical characteristics and functions, all DNA-binding proteins share the ability to accurately locate their target sites among the vast excess of non-target DNA. Toward identifying universal mechanisms of the target search, we used single-molecule tracking of 11 diverse DNA-binding proteins in living Escherichia coli . The mobility of these proteins during the target search was dictated by DNA interactions rather than by their molecular weights. By generating cells devoid of all chromosomal DNA, we discovered that the nucleoid is not a physical barrier for protein diffusion but significantly slows the motion of DNA-binding proteins through frequent short-lived DNA interactions. The representative DNA-binding proteins (irrespective of their size, concentration, or function) spend the majority (58%–99%) of their search time bound to DNA and occupy as much as ∼30% of the chromosomal DNA at any time. Chromosome crowding likely has important implications for the function of all DNA-binding proteins.

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“…More recently, in vitro single-molecule fluorescence studies with surface-immobilized 22-bp binding sites confirmed that FD can occur at a single binding site level [7]. The computational models also supported these observations [11, 12]. Similar dissociation patterns occur when competing Fis was replaced by competing nucleic acid segments [28], in accord with chromosome compaction-dependent dissociation of several metalloregulator TFs [12].…”

Section: Introductionmentioning

confidence: 76%

Facilitated Dissociation of Nucleoid Associated Proteins from DNA in the Bacterial Confinement

Koşar

Attar

Erbaş

2021

Preprint

Self Cite

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Transcription machinery ultimately depends on the temporal formation of protein-DNA complexes. Recent experimental studies demonstrate that residence time (i.e., inverse off-rate) of a transcription factor protein can be a contributor to the functional diversity of the protein. In the meantime, single-molecule experiments showed that the off-rates of a wide array of DNA-binding proteins accelerate as the bulk concentration of the protein increases via a concentration-dependent mechanism (i.e., facilitated dissociation, FD). In this study, inspired by the previous single-molecule studies on the factor for inversion stimulation (Fis) protein of \textit{E. coli}, which is a dual-purpose protein with a diverse functionality, we model the unbinding of Fis from specific bindings sites along a high-molecular-weight circular DNA in a cylindrical structure mimicking the cellular confinement of chromosome. Our simulations show that FD of Fis can well occur in confinement at physiological concentrations. Particularly, when nutrient-rich conditions are emulated with Fis concentrations around micromolar levels, the off-rates increase one order of magnitude compared to the lower Fis levels. However, Fis significantly changes the chromosome structure at higher concentrations by forming dense protein clusters bridging specific sites and juxtaposing remote DNA segments. As a result, at the physiologically observed maximum levels of Fis, the off-rates significantly slow down. Overall, our results indicate that cellular-concentration levels of a structural DNA-binding protein is intermingled with the genome architecture and DNA residence times, thereby providing a basis for understanding the complex effects of dynamic protein-DNA interactions on gene regulation.

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How do DNA-bound proteins leave their binding sites? The role of facilitated dissociation

Cited by 27 publications

References 54 publications

Multiprotein E. coli SSB–ssDNA complex shows both stable binding and rapid dissociation due to interprotein interactions

Multiprotein E. coli SSB–ssDNA complex shows both stable binding and rapid dissociation due to interprotein interactions

Transient non-specific DNA binding dominates the target search of bacterial DNA-binding proteins

Facilitated Dissociation of Nucleoid Associated Proteins from DNA in the Bacterial Confinement

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