The regulation mechanism of the C-terminus of RecA proteins during DNA strand-exchange process

Fan, Hsiu-Fang; Su, Shih Bin

doi:10.1016/j.bpj.2021.06.004

Cited by 3 publications

(14 citation statements)

References 64 publications

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“…This association however needs to be transient, since a large fraction of the tails (notably the longer β-tails) are released during the process and become free to interact with microtubule-binding proteins (MAPs) [121]. Similar process has been observed by AFM when fibrin proteins assemble into fibrinogen [120], while the C-terminal tails of RecA proteins have been shown to be involved in their association process into filaments [124]. These observations indicate that the ability of the disordered protein tails to bind the protein core surface but also to unbind from it is key to their function.…”

Section: Interactions Between the C-terminal Tails Of αβ-Tubulin Dimers And The Tubulin Corementioning

confidence: 88%

“…The C-terminal tail was shown to participate in the regulation of various stages of the recombination process: the filament self-assembly, the intake of the dsDNA into the filament, and the yield of strand exchange. While all those stages can take place in the absence of the tail or with partly deleted tails, the tail has been shown to mediate the response of the process to changes in pH or in magnesium concentration [124,128,129]. Specifically, full-length tails slow the RecA self-association process but promote the formation of longer and more stable filaments on ssDNA [124].…”

Section: Role Of the Reca Protein C-terminal Tails In Homologous Recombinationmentioning

confidence: 99%

“…While all those stages can take place in the absence of the tail or with partly deleted tails, the tail has been shown to mediate the response of the process to changes in pH or in magnesium concentration [124,128,129]. Specifically, full-length tails slow the RecA self-association process but promote the formation of longer and more stable filaments on ssDNA [124]. During the search, the dsDNA intake is also slowed in the presence of the tail, but this effect is reduced by adding 2 mM free Mg 2+ ions.…”

Section: Role Of the Reca Protein C-terminal Tails In Homologous Recombinationmentioning

confidence: 99%

“…It has been proposed that in condition of low magnesium concentration, the tail may compete with the incorporated dsDNA for binding to the filament secondary binding site (site II) [128,129]. In that hypothesis, the tail may stimulate dsDNA binding to site II by disengaging from that site following changes in magnesium concentration [128]; alternatively, the tail may assist unbinding of non-homologous incorporated dsDNA, thus accelerating the search process [124]. However, site II is buried in the filament interior whereas the tail extremities are situated at the periphery of the filament [131,132] (Figure 3).…”

Section: Role Of the Reca Protein C-terminal Tails In Homologous Recombinationmentioning

confidence: 99%

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When Order Meets Disorder: Modeling and Function of the Protein Interface in Fuzzy Complexes

Sacquin-Mora

Prévost

2021

Biomolecules

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The degree of proteins structural organization ranges from highly structured, compact folding to intrinsic disorder, where each degree of self-organization corresponds to specific functions: well-organized structural motifs in enzymes offer a proper environment for precisely positioned functional groups to participate in catalytic reactions; at the other end of the self-organization spectrum, intrinsically disordered proteins act as binding hubs via the formation of multiple, transient and often non-specific interactions. This review focusses on cases where structurally organized proteins or domains associate with highly disordered protein chains, leading to the formation of interfaces with varying degrees of fuzziness. We present a review of the computational methods developed to provide us with information on such fuzzy interfaces, and how they integrate experimental information. The discussion focusses on two specific cases, microtubules and homologous recombination nucleoprotein filaments, where a network of intrinsically disordered tails exerts regulatory function in recruiting partner macromolecules, proteins or DNA and tuning the atomic level association. Notably, we show how computational approaches such as molecular dynamics simulations can bring new knowledge to help bridging the gap between experimental analysis, that mostly concerns ensemble properties, and the behavior of individual disordered protein chains that contribute to regulation functions.

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Section: Interactions Between the C-terminal Tails Of αβ-Tubulin Dimers And The Tubulin Corementioning

confidence: 88%

Section: Role Of the Reca Protein C-terminal Tails In Homologous Recombinationmentioning

confidence: 99%

Section: Role Of the Reca Protein C-terminal Tails In Homologous Recombinationmentioning

confidence: 99%

Section: Role Of the Reca Protein C-terminal Tails In Homologous Recombinationmentioning

confidence: 99%

See 2 more Smart Citations

When Order Meets Disorder: Modeling and Function of the Protein Interface in Fuzzy Complexes

Sacquin-Mora

Prévost

2021

Biomolecules

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“…[34][35][36][37][38] Over the years, it has been applied to investigate the reaction behaviors of RNA polymerase, [33,39] the formation of DNA looping, [37,[40][41][42][43][44][45][46][47][48][49][50][51] the hybridization of DNA, [52] the bending of DNA, [53][54][55] the formation of Holliday junction [34] and the reaction behaviors of helicases. [39,56,57] Recently, we have successfully adapted the TPM assay to investigate DNA metabolism, including RecA-mediated strand exchange process, [28,[58][59][60] site-specific recombination, [18,[61][62][63][64][65][66] DNA packaging, and nucleosome remodeling. [14,67,68] Experimental design algorithms and the experimental information obtained will be presented here.…”

Section: Introductionmentioning

confidence: 99%

Single‐molecule tethered particle motion to study protein‐DNA interaction

Fan

2023

J Chinese Chemical Soc

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Single‐molecule techniques have been demonstrated as powerful tools to investigate individual protein‐DNA interactions that are difficult to access by conventional biochemical techniques. These methods are popularly used to obtain valuable and detailed molecular mechanisms of enzyme functions. Currently, we have used single‐molecule tethered particle motion to investigate protein‐DNA interactions, including homologous recombination, site‐specific recombination, DNA package, and the nucleosome remodeling process, and useful information was obtained. Here, we will describe the experimental designs and present the information obtained.

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Human Rad51 Protein Requires Higher Concentrations of Calcium Ions for D-Loop Formation than for Oligonucleotide Strand Exchange

Renodon-Corniere,

Mikawa,

Kuwabara

et al. 2024

IJMS

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Human Rad51 protein (HsRad51)-promoted DNA strand exchange, a crucial step in homologous recombination, is regulated by proteins and calcium ions. Both the activator protein Swi5/Sfr1 and Ca2+ ions stimulate different reaction steps and induce perpendicular DNA base alignment in the presynaptic complex. To investigate the role of base orientation in the strand exchange reaction, we examined the Ca2+ concentration dependence of strand exchange activities and structural changes in the presynaptic complex. Our results show that optimal D-loop formation (strand exchange with closed circular DNA) required Ca2+ concentrations greater than 5 mM, whereas 1 mM Ca2+ was sufficient for strand exchange between two oligonucleotides. Structural changes indicated by increased fluorescence intensity of poly(dεA) (a poly(dA) analog) reached a plateau at 1 mM Ca2+. Ca2+ > 2 mM was required for saturation of linear dichroism signal intensity at 260 nm, associated with rigid perpendicular DNA base orientation, suggesting a correlation with the stimulation of D-loop formation. Therefore, Ca2+ exerts two different effects. Thermal stability measurements suggest that HsRad51 binds two Ca2+ ions with KD values of 0.2 and 2.5 mM, implying that one step is stimulated by one Ca2+ bond and the other by two Ca2+ bonds. Our results indicate parallels between the Mg2+ activation of RecA and the Ca2+ activation of HsRad51.

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The regulation mechanism of the C-terminus of RecA proteins during DNA strand-exchange process

Cited by 3 publications

References 64 publications

When Order Meets Disorder: Modeling and Function of the Protein Interface in Fuzzy Complexes

When Order Meets Disorder: Modeling and Function of the Protein Interface in Fuzzy Complexes

Single‐molecule tethered particle motion to study protein‐DNA interaction

Human Rad51 Protein Requires Higher Concentrations of Calcium Ions for D-Loop Formation than for Oligonucleotide Strand Exchange

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