Mechanism of Facilitated Diffusion of DNA Repair Proteins in Crowded Environment: Case Study with Human Uracil DNA Glycosylase

Dey, Pinki; Bhattacherjee, Arnab

doi:10.1021/acs.jpcb.9b07342

Cited by 18 publications

(26 citation statements)

References 90 publications

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“…This effect of crowding might actually compensate for the negative impact of the intracellular ionic conditions on OGG1 motion along the DNA [110]. Therefore, by promoting low-dimensionality diffusion phases, crowding could actually accelerate the search phase of repair factors [111]. Nevertheless, theoretical work demonstrates that efficient search by facilitated diffusion requires a trade-off between 1D and 3D diffusion phases [112].…”

Section: Does Macromolecular Crowding Facilitate or Impair Ogg1 Dynamics Within The Nucleus?mentioning

confidence: 99%

“…Nevertheless, there is a huge gap between our precise understanding of these mechanisms of facilitated diffusion in in vitro reconstituted assays and their actual poor description in a living cell context. Yet, abundant evidence indicates that the high density of the nuclear environment and its ionic conditions may actually significantly impact the efficiency of the facilitated diffusion kinetics observed in a more dilute environment [110,111,129].…”

Section: Does Facilitated Diffusion Of Ogg1 Indeed Occur In the Cell Nucleus?mentioning

confidence: 99%

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Lost in the Crowd: How Does Human 8-Oxoguanine DNA Glycosylase 1 (OGG1) Find 8-Oxoguanine in the Genome?

D’Augustin

Huet

Campalans

et al. 2020

IJMS

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The most frequent DNA lesion resulting from an oxidative stress is 7,8-dihydro-8-oxoguanine (8-oxoG). 8-oxoG is a premutagenic base modification due to its capacity to pair with adenine. Thus, the repair of 8-oxoG is critical for the preservation of the genetic information. Nowadays, 8-oxoG is also considered as an oxidative stress-sensor with a putative role in transcription regulation. In mammalian cells, the modified base is excised by the 8-oxoguanine DNA glycosylase (OGG1), initiating the base excision repair (BER) pathway. OGG1 confronts the massive challenge that is finding rare occurrences of 8-oxoG among a million-fold excess of normal guanines. Here, we review the current knowledge on the search and discrimination mechanisms employed by OGG1 to find its substrate in the genome. While there is considerable data from in vitro experiments, much less is known on how OGG1 is recruited to chromatin and scans the genome within the cellular nucleus. Based on what is known of the strategies used by proteins searching for rare genomic targets, we discuss the possible scenarios allowing the efficient detection of 8-oxoG by OGG1.

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Section: Does Macromolecular Crowding Facilitate or Impair Ogg1 Dynamics Within The Nucleus?mentioning

confidence: 99%

Section: Does Facilitated Diffusion Of Ogg1 Indeed Occur In the Cell Nucleus?mentioning

confidence: 99%

Lost in the Crowd: How Does Human 8-Oxoguanine DNA Glycosylase 1 (OGG1) Find 8-Oxoguanine in the Genome?

D’Augustin

Huet

Campalans

et al. 2020

IJMS

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“…We adopted a coarse-grained representation of protein, where each amino acid is represented by a single bead placed at the respective Cα position (34). The energetics of the protein is described by a structure-based potential (35) (for details, see the Supporting text), which represents the funnel-like energy landscape for protein folding (35) and has been used extensively in studying protein-protein (36) and protein-nucleic acid interactions (37)(38)(39)(40)(41)(42)(43). The resolution of the ssDNA molecule is three beads per nucleotide (phosphate, sugar and nitrogenous base), placed at their respective geometric centers.…”

Section: Methodsmentioning

confidence: 99%

Mechanism of Dynamic Binding of Replication Protein A to ssDNA

Bhattarcharjee

Mondal

2020

Preprint

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Replication protein A (RPA) serves as hub protein inside eukaryotic cells, where it coordinates crucial DNA metabolic processes and activates the DNA-damage response system. A characteristic feature of its action is to associate with ssDNA intermediates before handing over them to downstream proteins. The length of ssDNA intermediates differs for different pathways. This means RPA must have mechanisms for selective processing of ssDNA intermediates based on their length, the knowledge of which is fundamental to elucidate when and how DNA repair and replication processes are symphonized. By employing extensive molecular simulations, we investigated the mechanism of binding of RPA to ssDNA of different lengths. We show that the binding involves dynamic equilibrium with a stable intermediate, the population of which increases with the length of ssDNA. The vital underlying factors are decoded through collective variable principal component analysis. It suggests a differently orchestrated set of interactions that define the action of RPA based on the sizes of ssDNA intermediates. We further estimated the association kinetics and probed the diffusion mechanism of RPA to ssDNA. RPA diffuses on short ssDNA through progressive 'bulge' formation. With long ssDNA, we observed a conformational change in ssDNA coupled with its binding to RPA in a cooperative fashion. Our analysis explains how the 'short-lived,' long ssDNA intermediates are processed quickly in vivo. The study thus reveals the molecular basis of several recent experimental observations related to RPA binding to ssDNA and provides novel insights into the RPA functioning in DNA repair and replication. Significance StatementDespite ssDNA be the common intermediate to all pathways involving RPA, how does the latter function differently in the DNA processing events such as DNA repair, replication, and recombination just based on the length of ssDNA intermediates remains unknown. The major hindrance is the difficulty in capturing the transient interactions between the molecules. Even attempts to crystallize RPA complexes with 32nt and 62nt ssDNA have yielded a resolved structure of only 25nt ssDNA wrapped with RPA. Here, we used a state-of-the-art coarse-grained protein-ssDNA model to unravel the detailed mechanism of binding of RPA to ssDNA. Our study illustrates the molecular origin of variations in RPA action during various DNA processing events depending on the length of ssDNA intermediates.

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“…Therefore, sliding is primarily observed with short lengths of DNA (≤10 base pairs), the range of a helical turn, but this still allows for scanning of more than a single base pair [50]. In addition, the hopping mechanism of DNA translocation also shows a 35 % increase for hUNG2 enzymes containing the N-terminal tail, and an additional 13 % increase in the presence of crowding agents, for a total of 48 % increased lesion search by hopping [51]. The amplified hopping is a result of molecular crowding preventing hUNG2 from fully diffusing into the bulk solution when transferring to another site on the DNA strand [14,52].…”

Section: N-terminal Domain Of Hung Facilitates Translocation On Dnamentioning

confidence: 99%

“…S67 is also a site for serine phosphorylation, which may negatively impact conformational changes needed for DNA binding [19]. Furthermore, molecular dynamic simulations suggest the role of positively-charged residues 5-19 and 73-88, particularly R76, K78, R84, and R88 of the RPA-binding motif, in facilitating nonspecific and electrostatic interactions with DNA [19,51].…”

Section: N-terminal Domain Of Hung Facilitates Translocation On Dnamentioning

confidence: 99%

The N-terminal domain of uracil-DNA glycosylase: Roles for disordered regions

Perkins

Zhao

2021

DNA Repair

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The presence of uracil in DNA calls for rapid removal facilitated by the uracil-DNA glycosylase superfamily of enzymes, which initiates the base excision repair (BER) pathway. In humans, uracil excision is accomplished primarily by the human uracil-DNA glycosylase (hUNG) enzymes. In addition to BER, hUNG enzymes play a key role in somatic hypermutation to generate antibody diversity. hUNG has several isoforms, with hUNG1 and hUNG2 being the two major isoforms. Both isoforms contain disordered N-terminal domains, which are responsible for a wide range of functions, with minimal direct impact on catalytic efficiency. Subcellular localization of hUNG enzymes is directed by differing N-terminal sequences, with hUNG1 dedicated to mitochondria and hUNG2 dedicated to the nucleus. An alternative isoform of hUNG1 has also been identified to localize to the nucleus in mouse and human cell models. Furthermore, hUNG2 has been observed at replication forks performing both pre-and postreplicative uracil excision to maintain genomic integrity. Replication protein A (RPA) and proliferating cell nuclear antigen (PCNA) are responsible for recruitment to replication forks via protein-protein interactions with the N-terminus of hUNG2. These interactions, along with protein degradation, are regulated by various post-translational modifications within the Nterminal tail, which are primarily cellcycle dependent. Finally, translocation on DNA is also mediated by interactions between the N-terminus and DNA, which is enhanced under molecular crowding conditions by preventing diffusion events and compacting tail residues. This review summarizes recent research supporting the emerging roles of the N-terminal domain of hUNG.

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Mechanism of Facilitated Diffusion of DNA Repair Proteins in Crowded Environment: Case Study with Human Uracil DNA Glycosylase

Cited by 18 publications

References 90 publications

Lost in the Crowd: How Does Human 8-Oxoguanine DNA Glycosylase 1 (OGG1) Find 8-Oxoguanine in the Genome?

Lost in the Crowd: How Does Human 8-Oxoguanine DNA Glycosylase 1 (OGG1) Find 8-Oxoguanine in the Genome?

Mechanism of Dynamic Binding of Replication Protein A to ssDNA

The N-terminal domain of uracil-DNA glycosylase: Roles for disordered regions

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