Sodium Ion‐Induced Structural Transition on the Surface of a DNA‐Interacting Protein

Protein surfaces have pivotal roles in interactions between proteins and other biological molecules. However, the structural dynamics of protein surfaces have rarely been explored and are poorly understood. Here, the surface of a single-stranded DNA (ssDNA) binding protein (SSB) with four DNA binding domains that bind ssDNA in binding site sizes of 35, 56, and 65 nucleotides per tetramer is investigated. Using oligonucleotides as probes to sense the charged surface, NaCl induces a two-state structural transition on the SSB surface even at moderate concentrations. Chelation of sodium ions with charged amino acids alters the network of hydrogen bonds and/or salt bridges on the surface. Such changes are associated with changes in the electrostatic potential landscape and interaction mode. These findings advance the understanding of the molecular mechanism underlying the enigmatic salt-induced transitions between different DNA binding site sizes of SSBs. This work demonstrates that monovalent salt is a key regulator of biomolecular interactions that not only play roles in non-specific electrostatic screening effects as usually assumed but also may configure the surface of proteins to contribute to the effective regulation of biomolecular recognition and other downstream events.

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Publication Details

Journal
Advanced Science
Published
2024-09-20
DOI
https://doi.org/10.1002/advs.202401838
Citations
1
Primary Topic
DNA and Nucleic Acid Chemistry
Type
article
Field-Weighted Citation Impact
0.23

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article

Sodium Ion‐Induced Structural Transition on the Surface of a DNA‐Interacting Protein

Shuaikang Yuan, Chang Liu, Shuxin Hu, Jianbing Ma et al.
1 citations
Advanced Science
DNA and Nucleic Acid Chemistry
0.23
article

Sodium Ion‐Induced Structural Transition on the Surface of a DNA‐Interacting Protein

Shuaikang Yuan, Chang Liu, Shuxin Hu, Jianbing Ma, Chunhua Xu, Libang Wang, Wenfei Li, Ying Lü, Yue Lu, Ming Li, Hao Wang, Hang Fu, Yi Peng, Yichao Wu, Xuan Yu, Tao Wei, Yunliang Li, Hao Zhang
article en
1 citations

Abstract

Protein surfaces have pivotal roles in interactions between proteins and other biological molecules. However, the structural dynamics of protein surfaces have rarely been explored and are poorly understood. Here, the surface of a single-stranded DNA (ssDNA) binding protein (SSB) with four DNA binding domains that bind ssDNA in binding site sizes of 35, 56, and 65 nucleotides per tetramer is investigated. Using oligonucleotides as probes to sense the charged surface, NaCl induces a two-state structural transition on the SSB surface even at moderate concentrations. Chelation of sodium ions with charged amino acids alters the network of hydrogen bonds and/or salt bridges on the surface. Such changes are associated with changes in the electrostatic potential landscape and interaction mode. These findings advance the understanding of the molecular mechanism underlying the enigmatic salt-induced transitions between different DNA binding site sizes of SSBs. This work demonstrates that monovalent salt is a key regulator of biomolecular interactions that not only play roles in non-specific electrostatic screening effects as usually assumed but also may configure the surface of proteins to contribute to the effective regulation of biomolecular recognition and other downstream events.

Advanced ScienceVol. 11(42)
Chinese Academy of Sciences (CN), Songshan Lake Materials Laboratory (CN), Institute of Physics (CN), University of Chinese Academy of Sciences (CN), Nanjing University (CN)
National Natural Science Foundation of China, Chinese Academy of Sciences, Youth Innovation Promotion Association of the Chinese Academy of Sciences, Youth Innovation Promotion Association
Openalex Percentile: Top 42%
DNA and Nucleic Acid Chemistry
0.23
DOIOpen Access PDFOpenAlex
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