Structure and function analysis of protein–nucleic acid complexes

Kuznetsova, Svetlana Aleksandrovna; Oretskaya, T. S.

doi:10.1070/rcr4581

Cited by 4 publications

(2 citation statements)

References 96 publications

(119 reference statements)

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“…Protein is the product of gene expression, and gene expression depends on protein. Protein–nucleic acid interactions exist at almost all levels of gene expression [ 1 , 2 ]. In protein–nucleic acid interfaces, a residue whose mutation to alanine leads to a large reduction in the binding free energy is termed as hotspot [ 3–5 ].…”

Section: Introductionmentioning

confidence: 99%

HISNAPI: a bioinformatic tool for dynamic hot spot analysis in nucleic acid–protein interface with a case study

Mei

Wang²,

Wu³

et al. 2021

Briefings in Bioinformatics

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Protein–nucleic acid interactions play essential roles in many biological processes, such as transcription, replication and translation. In protein–nucleic acid interfaces, hotspot residues contribute the majority of binding affinity toward molecular recognition. Hotspot residues are commonly regarded as potential binding sites for compound molecules in drug design projects. The dynamic property is a considerable factor that affects the binding of ligands. Computational approaches have been developed to expedite the prediction of hotspot residues on protein–nucleic acid interfaces. However, existing approaches overlook hotspot dynamics, despite their essential role in protein function. Here, we report a web server named Hotspots In silico Scanning on Nucleic Acid and Protein Interface (HISNAPI) to analyze hotspot residue dynamics by integrating molecular dynamics simulation and one-step free energy perturbation. HISNAPI is capable of not only predicting the hotspot residues in protein–nucleic acid interfaces but also providing insights into their intensity and correlation of dynamic motion. Protein dynamics have been recognized as a vital factor that has an effect on the interaction specificity and affinity of the binding partners. We applied HISNAPI to the case of SARS-CoV-2 RNA-dependent RNA polymerase, a vital target of the antiviral drug for the treatment of coronavirus disease 2019. We identified the hotspot residues and characterized their dynamic behaviors, which might provide insight into the target site for antiviral drug design. The web server is freely available via a user-friendly web interface at http://chemyang.ccnu.edu.cn/ccb/server/HISNAPI/ and http://agroda.gzu.edu.cn:9999/ccb/server/HISNAPI/.

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Section: Introductionmentioning

confidence: 99%

HISNAPI: a bioinformatic tool for dynamic hot spot analysis in nucleic acid–protein interface with a case study

Mei

Wang²,

Wu³

et al. 2021

Briefings in Bioinformatics

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“…Methodological advances have now made it possible to comprehensively investigate such interactions by biochemical and biophysical approaches (Kuznetsova et al . 2016 ; Lin and Wu 2019 ), which usually acquire accurate quantitation of nucleoprotein complex.…”

Section: Introductionmentioning

confidence: 99%

Quantitation of nucleoprotein complexes by UV absorbance and Bradford assay

Jiang¹,

Luo²,

Mei³

et al. 2021

Biophysics Reports

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Despite the importance of studying nucleoprotein complexes, no appropriate method for quantifying them is available. Here, a UV absorbance method using the formula “ C mg/mL = 1.55 A 280 – 0.76 A 260 ” were applied to quantify nucleoprotein complexes. After modification using two paired A 260 and A 280 values, the UV-derived formula-based method could accurately quantify proteins in nucleoprotein complexes. Otherwise, by taking the target protein as a standard, the Bradford assay can accurately quantify proteins in nucleoprotein complexes without interference by nucleic acids. The above methods were successfully applied to measure the concentration of Mtu P49-CTG complexes of Mycobacterium tuberculosis . In conclusion, both the Bradford assay and the UV-derived formula-based method were appropriate for quantifying proteins in nucleoprotein complexes, which may make contributions to explore the interactions between proteins and nucleic acids at the molecular level.

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