Molecular mechanism of DNA association with single-stranded DNA binding protein

Aksimentiev, Aleksei

doi:10.1093/nar/gkx917

Cited by 43 publications

(40 citation statements)

References 73 publications

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“…Too small or large bulges are energetically unstable. The result is in agreement with the previous studies done on ssDNA and RPA protein (23,24). To probe if the formation of bulges on ssDNA helps it to associate with RPA, we studied the time evolution of all phosphate residues that appear first when a bulge forms.…”

Section: Molecular Determinants Of Dynamic Binding Of Rpa To Ssdnasupporting

confidence: 89%

“…Intuitively this is a long time-scale problem. Previous studies have rather investigated the translocation of ssDNA on protein in bound states only (23,24). The analyses based on crystal structures of ssDNA bound E. coli SSB and RPA proteins demonstrate that short ssDNA segments(1-7nt) erect over the protein surface and form bulges due to defects in interactions between nucleobases of ssDNA and interfacial protein residues.…”

Section: Molecular Determinants Of Dynamic Binding Of Rpa To Ssdnamentioning

confidence: 99%

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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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Section: Molecular Determinants Of Dynamic Binding Of Rpa To Ssdnasupporting

confidence: 89%

Section: Molecular Determinants Of Dynamic Binding Of Rpa To Ssdnamentioning

confidence: 99%

Mechanism of Dynamic Binding of Replication Protein A to ssDNA

Bhattarcharjee

Mondal

2020

Preprint

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“…In general, the DNA strands were found to be stabilized by a mixture of electrostatic and co‐planar stacking interactions. For the case of E. coli SSB, our own all‐atom simulations support this view . We found that patches of the SSB surface rich in arginine residues interact with the DNA through both electrostatic and stacking interactions, contributing to the stability of the complex.…”

Section: Computer Simulations Of Dna Replication and Repair Machinerysupporting

confidence: 55%

“…The simulations revealed the formation and resolution of small ssDNA bulges that are believed to provide a mechanism for SSB diffusion along DNA. Adapted with permission . Oxford University Press.…”

Section: Computer Simulations Of Dna Replication and Repair Machinerymentioning

confidence: 99%

Molecular Mechanisms of DNA Replication and Repair Machinery: Insights from Microscopic Simulations

Chou

Aksimentiev

2019

Advcd Theory and Sims

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Reproduction, the hallmark of biological activity, requires making an accurate copy of the genetic material to allow the progeny to inherit parental traits. In all living cells, the process of DNA replication is carried out by a concerted action of multiple protein species forming a loose protein-nucleic acid complex, the replisome. Proofreading and error correction generally accompany replication but also occur independently, safeguarding genetic information through all phases of the cell cycle. Advances in biochemical characterization of intracellular processes, proteomics, and the advent of single-molecule biophysics have brought about a treasure trove of information awaiting to be assembled into an accurate mechanistic model of the DNA replication process. This review describes recent efforts to model elements of DNA replication and repair processes using computer simulations, an approach that has gained immense popularity in many areas of molecular biophysics but has yet to become mainstream in the DNA metabolism community. It highlights the use of diverse computational methods to address specific problems of the fields and discusses unexplored possibilities that lie ahead for the computational approaches in these areas.

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“…In case that comparatively long or extensive MD simulations have been conducted, one recent study concentrates on association processes of a chromatin protein with DNA (29), but not yet the protein movements. For exemplary all-atom simulation studies on the protein movements along DNA, however, the proteins of concerns are motor proteins such as RNA polymerases (30,31), or the single-stranded DNA-binding protein (32). In this work, we focus on a model TF and present all-atom microseconds equilibrium simulations of the diffusion dynamics of the TF protein along the double stranded (ds) DNA.…”

Section: Introductionmentioning

confidence: 99%

Revealing Atomic-scale Molecular Diffusion of a Plant Transcription Factor WRKY domain protein along DNA

Dai

et al. 2020

Preprint

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designed the study. Liqiang Dai conducted the MD simulations and coarse-grained simulations and analyzed the related data. Yongping Xu solved the crystal structure of WRKY-DNA complex and conducted ITC experiment. Zhenwei Du conducted the single-molecule fluorescence experiments of WRKY diffusing on DNA. AbstractTranscription factor (TF) target search on genome is highly essential for gene expression and regulation. High-resolution determination of TF diffusion along DNA remains technically challenging. Here we constructed a TF model system of the plant WRKY domain protein in complex with DNA from crystallography and demonstrated microsecond diffusion dynamics of WRKY on the DNA employing all-atom molecular dynamics (MD) simulations. Notably, we found that WRKY preferentially binds to the Crick strand of DNA with significantly stronger energetic association than to the Watson strand. The preferential binding becomes highly prominent from non-specific to specific DNA binding, but less distinct from static binding to diffusive movements of WRKY on the DNA. Remarkably, without employing acceleration forces or bias, we captured a complete one-base pair (bp) stepping cycle of WRKY tracking along major groove of DNA with homogenous (AT)n sequence, as individual protein-DNA contacts break and reform at the binding interface. Continuous tracking of WRKY forward or backward, with occasional sliding as well as strand crossing to the minor groove of DNA, have also been captured in the simulation. The processive diffusion of WRKY had been confirmed by accompanied single-molecule fluorescence assays and coarsegrained (CG) structural simulations. The study thus provides unprecedented structural dynamics details on the TF diffusion, suggests how TF possibly approaches to gene target, and supports further high-precision experimental follow-up. The stochastic movements revealed in the TF diffusion also provide general clues on how other nucleic acid walkers step and slide along DNA. Significance StatementHow transcription factors search for target genes impact on how quickly and accurately the genes are transcribed and expressed. To locate target sufficiently fast, 1D diffusion of the protein along DNA appears essential. Experimentally, it remains challenging to determine diffusional steps of protein on DNA. Here, we report all-atom equilibrium simulations of a WRKY protein binding and diffusing on DNA, revealing structural dynamics details which have not been identified previously. We unprecedently demonstrate a complete stepping cycle of the protein for one base pair on DNA within microseconds, along with stochastic stepping or sliding, directional switching, and strand crossing. Additionally, we have found preferential DNA strand association of WRKY. These suggest how protein factors approach toward target DNA sequences.

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Molecular mechanism of DNA association with single-stranded DNA binding protein

Cited by 43 publications

References 73 publications

Mechanism of Dynamic Binding of Replication Protein A to ssDNA

Mechanism of Dynamic Binding of Replication Protein A to ssDNA

Molecular Mechanisms of DNA Replication and Repair Machinery: Insights from Microscopic Simulations

Revealing Atomic-scale Molecular Diffusion of a Plant Transcription Factor WRKY domain protein along DNA

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