NMR Investigation of the Interaction between the RecQ C-Terminal Domain of Human Bloom Syndrome Protein and G-Quadruplex DNA from the Human c-Myc Promoter

Lee, Sung‐Jin; Lee, Ae-Ree; Ryu, Kyoung‐Seok; Lee, Joon‐Hwa; Park, Chin‐Ju

doi:10.1016/j.jmb.2019.01.010

Cited by 11 publications

(30 citation statements)

References 32 publications

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“…Most recently, the Thermus oshimai PIF1-G4 complex was submited, showing a G4-recognizing surface ( Figure 4E ) ( Dai et al, 2021 ), which is different from DHX36. In terms of RecQ family helicases, the RQC interaction with G4 DNA was studied by NMR ( Lee et al, 2019 ), and the crystal structure of a Cronobacter sakazakii RecQ, bound to unfolded G4 DNA, was achived ( Figure 4F ), showing that a guanine-specific pocket is essential for G4 resolution ( Voter et al, 2018 ). Interestingly, the G4s in these complexes are parallel structures with short loop lengths ( Bugaut and Balasubramanian, 2008 ), which have higher melting temperature.…”

Section: Representative Research Methods To Reveal Molecular Mechanismsmentioning

confidence: 99%

The Cellular Functions and Molecular Mechanisms of G-Quadruplex Unwinding Helicases in Humans

Liu

Zhu

Wang

et al. 2021

Front. Mol. Biosci.

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G-quadruplexes (G4s) are stable non-canonical secondary structures formed by G-rich DNA or RNA sequences. They play various regulatory roles in many biological processes. It is commonly agreed that G4 unwinding helicases play key roles in G4 metabolism and function, and these processes are closely related to physiological and pathological processes. In recent years, more and more functional and mechanistic details of G4 helicases have been discovered; therefore, it is necessary to carefully sort out the current research efforts. Here, we provide a systematic summary of G4 unwinding helicases from the perspective of functions and molecular mechanisms. First, we provide a general introduction about helicases and G4s. Next, we comprehensively summarize G4 unfolding helicases in humans and their proposed cellular functions. Then, we review their study methods and molecular mechanisms. Finally, we share our perspective on further prospects. We believe this review will provide opportunities for researchers to reach the frontiers in the functions and molecular mechanisms of human G4 unwinding helicases.

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Section: Representative Research Methods To Reveal Molecular Mechanismsmentioning

confidence: 99%

The Cellular Functions and Molecular Mechanisms of G-Quadruplex Unwinding Helicases in Humans

Liu

Zhu

Wang

et al. 2021

Front. Mol. Biosci.

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“…The G4 unfolding mediated by helicases contains several steps that accompany structural rearrangements of both G4 and proteins [49,50]. The c-MYC G4 interaction with two human RecQ helicases (Werner syndrome protein (WRN) and Bloom syndrome protein (BLM)) was studied independently [51,52]. The RecQ C-terminal (RQC) domain of WRN was subjected to titration with non-G4 DNA or G4 DNA, and the residues which showed G4-specific responses were identified [51].…”

Section: G4-protein Interactionmentioning

confidence: 99%

“…In the case of BLM RQC, titration with up to 2 molar equivalents of DNA was performed, and CSPs could be observed, while only a few peaks disappeared upon addition of G4 [52]. Interestingly, the significantly perturbed residues were partially overlapped with the known duplex DNA binding surfaces [52,54].…”

Section: G4-protein Interactionmentioning

confidence: 99%

Dynamics Studies of DNA with Non-canonical Structure Using NMR Spectroscopy

Kim

Park

Lee

2020

IJMS

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The non-canonical structures of nucleic acids are essential for their diverse functions during various biological processes. These non-canonical structures can undergo conformational exchange among multiple structural states. Data on their dynamics can illustrate conformational transitions that play important roles in folding, stability, and biological function. Here, we discuss several examples of the non-canonical structures of DNA focusing on their dynamic characterization by NMR spectroscopy: (1) G-quadruplex structures and their complexes with target proteins; (2) i-motif structures and their complexes with proteins; (3) triplex structures; (4) left-handed Z-DNAs and their complexes with various Z-DNA binding proteins. This review provides insight into how the dynamic features of non-canonical DNA structures contribute to essential biological processes.

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“…Combined amide chemical shift perturbations were calculated using the equation: Δδ = [(Δδ HN ) 2 + (Δδ N /5) 2 ] 1/2 [67]. In order to apply a consensus approach for the identification of shifts that are large enough to be considered as indicators of the binding site in more than 10 interaction studies between MAYV MD and small molecules or RNA oligos, we always applied the widely used method to calculate a threshold value [68][69][70][71]. This threshold is based on the calculation of the average CSP value and the SD σ and sets an unbiased criterion to detect the residues that are significantly involved in an interaction.…”

Section: N-relaxation Studiesmentioning

confidence: 99%

Deciphering the Nucleotide and RNA Binding Selectivity of the Mayaro Virus Macro Domain

Tsika

Melekis

Tsatsouli

et al. 2019

Journal of Molecular Biology

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Mayaro virus (MAYV) is a member of Togaviridae family, which also includes Chikungunya virus as a notorious member. MAYV recently emerged in urban areas of the Americas, and this emergence emphasized the current paucity of knowledge about its replication cycle. The macro domain (MD) of MAYV belongs to the N-terminal region of its non-structural protein 3, part of the replication complex. Here, we report the first structural and dynamical characterization of a previously unexplored Alphavirus MD investigated through high-resolution NMR spectroscopy, along with data on its ligand selectivity and binding properties. The structural analysis of MAYV MD reveals a typical "macro" (ββαββαβαβα) fold for this polypeptide, while NMR-driven interaction studies provide in-depth insights into MAYV MD-ligand adducts. NMR data in concert with thermodynamics and biochemical studies provide convincing experimental evidence for preferential binding of adenosine diphosphate ribose (ADP-r) and adenine-rich RNAs to MAYV MD, thus shedding light on the structure-function relationship of a previously unexplored viral MD. The emerging differences with any other related MD are expected to enlighten distinct functions.

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NMR Investigation of the Interaction between the RecQ C-Terminal Domain of Human Bloom Syndrome Protein and G-Quadruplex DNA from the Human c-Myc Promoter

Cited by 11 publications

References 32 publications

The Cellular Functions and Molecular Mechanisms of G-Quadruplex Unwinding Helicases in Humans

The Cellular Functions and Molecular Mechanisms of G-Quadruplex Unwinding Helicases in Humans

Dynamics Studies of DNA with Non-canonical Structure Using NMR Spectroscopy

Deciphering the Nucleotide and RNA Binding Selectivity of the Mayaro Virus Macro Domain

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