Improving selectivity of DNA–RNA binding zinc finger using directed evolution

Sulej, Agata

doi:10.1186/s13104-019-4833-8

Cited by 2 publications

(2 citation statements)

References 17 publications

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“…Numerous studies have reported that ZnF containing proteins are generally involved in protein–protein, protein-DNA, and protein-RNA interactions (Eom et al . 2016 ; Sulej 2019 ). To the best of our knowledge, the biochemical function of nsp2 is unknown.…”

Section: Resultsmentioning

confidence: 99%

Structure and Function of N-Terminal Zinc Finger Domain of SARS-CoV-2 NSP2

Chen

et al. 2021

Virol. Sin.

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SARS-CoV-2 has become a global pandemic threatening human health and safety. It is urgent to find effective therapeutic agents and targets with the continuous emergence of novel mutant strains. The knowledge of the molecular basis and pathogenesis of SARS-CoV-2 in host cells requires to be understood comprehensively. The unknown structure and function of nsp2 have hindered our understanding of its role in SARS-CoV-2 infection. Here, we report the crystal structure of the N-terminal of SARS-CoV-2 nsp2 to a high resolution of 1.96 Å. This novel structure contains three zinc fingers, belonging to the C2H2, C4, and C2HC types, respectively. Structure analysis suggests that nsp2 may be involved in binding nucleic acids and regulating intracellular signaling pathways. The binding to single or double-stranded nucleic acids was mainly through the large positively charged region on the surface of nsp2, and K111, K112, K113 were key residues. Our findings lay the foundation for a better understanding of the relationship between structure and function for nsp2. It is helpful to make full use of nsp2 as further research and development of antiviral targets and drug design. Supplementary Information The online version contains supplementary material available at 10.1007/s12250-021-00431-6.

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Section: Resultsmentioning

confidence: 99%

Structure and Function of N-Terminal Zinc Finger Domain of SARS-CoV-2 NSP2

Chen

et al. 2021

Virol. Sin.

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“…S9.6 is commonly used to detect and characterize R-loops in situ [12][13][14] and to obtain genome-wide R-loop sequence profiles [15,16]. Other hybrid binders include a protein based on the Zinc finger motif [17], and a neomycin-methidium conjugate binds hybrids in a sequence-nonspecific manner, forming complexes with sub-nanomolar (K D ) affinities [18].…”

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confidence: 99%

Multivalent forms of the ribonuclease H1 hybrid binding domain are high‐affinity binders of RNA–DNA hybrids

Stopar

Nicholson

2022

FEBS Letters

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The hybrid binding domain (HBD) is a conserved fold present in ribonucleases H1 that selectively recognizes RNA-DNA hybrids, which are structures present in cellular R-loops and participate in diverse biological processes. We engineered multivalent HBD proteins to create high-affinity hybrid binders. Using EMSA-and SPR-based analyses, we showed that the triple-HBD protein exhibits a ~22 000-fold increase in hybrid affinity (K D 370 pM) relative to the single HBD (K D 8.29 lM), with the length and sequence of the linkers enabling optimal function. These findings provide a framework for testing models that correlate multivalency and affinity to understand how multivalent proteins function and also can serve to guide applications that exploit multivalency as a strategy to enhance binding affinity.

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Improving selectivity of DNA–RNA binding zinc finger using directed evolution

Cited by 2 publications

References 17 publications

Structure and Function of N-Terminal Zinc Finger Domain of SARS-CoV-2 NSP2

Structure and Function of N-Terminal Zinc Finger Domain of SARS-CoV-2 NSP2

Multivalent forms of the ribonuclease H1 hybrid binding domain are high‐affinity binders of RNA–DNA hybrids

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