Shangbo Ning
Current Organizations / Institutes
The organizations/institutes from the scholar's latest article
Shangbo Ning has a total of 5 co-authors. Here are the top co-authors by number of shared publications:
- Chengwei Zeng
Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan 430079, China
1 shared publication - Huiwen Wang
School of Physics and Engineering, Henan University of Science and Technology, Luoyang 471023, China
1 shared publication - Junfeng Zhang
Luoyang Key Laboratory of Animal Bacterial Infectious Disease Prevention and Control Technology, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471000, China
1 shared publication - Yun Xue
College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang 471023, China
1 shared publication - Yunjie Zhao
Institute of Biophysics and Department of Physics, Central China Normal University , Wuhan 430079
1 shared publication
Latest Publications
- Open Access
- 10 January 2026
- Published by MDPI AG in Pharmaceuticals
- Vol. 19 (1) , 124
The Allosteric Regulation of the DNA-Binding Domain of p53 by the Intrinsically Disordered C-Terminal Domain
Background: Intrinsically disordered regions (IDRs) within proteins often act as pivotal linkage units for the interaction of functional domains. The p53 tumor suppressor protein contains intrinsically disordered N-terminal and C-terminal domains (NTD and CTD), playing crucial regulatory roles in cellular processes. Furthermore, experimental approaches have encountered challenges in elucidating the structural regulation by the IDRs. Methods: In this work, we employed microsecond-scale molecular dynamics simulations to explore the allosteric regulation mechanism of the p53 DNA binding domain (DBD) induced by the CTD and the DNA binding. Subsequently, we integrated dynamic cross-correlation analysis with binding free energy calculations to evaluate the interaction between the CTD and DNA. Results: The free energy landscapes (FELs) were utilized to identify the conformational ensemble of the p53 DBD. The FELs revealed that the CTD enhances the allosteric regulatory mechanisms. Conclusions: Firstly, the conformation of DBD changes on the S6-S7 loop and L1 upon DNA binding. Then the CTD directly interacts with DNA and further regulates the allosteric network (involving the S6-S7 loop, L1 loop, S4, S10, H1, and H3) to promote the binding of DBD to DNA. The allosteric mechanisms presented in this work will provide new insights into the functional mechanisms of the p53 CTD and inform the rational design of p53-targeted drugs.
- 10 January 2026
- Published by MDPI AG in Pharmaceuticals
- Vol. 19 (1) , 124
Open AccessThe Allosteric Regulation of the DNA-Binding Domain of p53 by the Intrinsically Disordered C-Terminal Domain
Background: Intrinsically disordered regions (IDRs) within proteins often act as pivotal linkage units for the interaction of functional domains. The p53 tumor suppressor protein contains intrinsically disordered N-terminal and C-terminal domains (NTD and CTD), playing crucial regulatory roles in cellular processes. Furthermore, experimental approaches have encountered challenges in elucidating the structural regulation by the IDRs. Methods: In this work, we employed microsecond-scale molecular dynamics simulations to explore the allosteric regulation mechanism of the p53 DNA binding domain (DBD) induced by the CTD and the DNA binding. Subsequently, we integrated dynamic cross-correlation analysis with binding free energy calculations to evaluate the interaction between the CTD and DNA. Results: The free energy landscapes (FELs) were utilized to identify the conformational ensemble of the p53 DBD. The FELs revealed that the CTD enhances the allosteric regulatory mechanisms. Conclusions: Firstly, the conformation of DBD changes on the S6-S7 loop and L1 upon DNA binding. Then the CTD directly interacts with DNA and further regulates the allosteric network (involving the S6-S7 loop, L1 loop, S4, S10, H1, and H3) to promote the binding of DBD to DNA. The allosteric mechanisms presented in this work will provide new insights into the functional mechanisms of the p53 CTD and inform the rational design of p53-targeted drugs.