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Tang M, Suraweera A, Nie X, Li Z, Lai P, Wells JW, O'Byrne KJ, Woods RJ, Bolderson E, Richard DJ. Mono-phosphorylation at Ser4 of barrier-to-autointegration factor (Banf1) significantly reduces its DNA binding capability by inducing critical changes in its local conformation and DNA binding surface. Phys Chem Chem Phys 2023; 25:24657-24677. [PMID: 37665626 DOI: 10.1039/d3cp02302h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Barrier-to-autointegration factor (Banf1) is a small DNA-bridging protein. The binding status of Banf1 to DNA is regulated by its N-terminal phosphorylation and dephosphorylation, which plays a critical role in cell proliferation. Banf1 can be phosphorylated at Ser4 into mono-phosphorylated Banf1, which is further phosphorylated at Thr3 to form di-phosphorylated Banf1. It was observed decades ago that mono-phosphorylated Banf1 cannot bind to DNA. However, the underlying molecular- and atomic-level mechanisms remain unclear. A clear understanding of these mechanisms will aid in interfering with the cell proliferation process for better global health. Herein, we explored the detailed atomic bases of unphosphorylated Banf1-DNA binding and how mono- and di-phosphorylation of Banf1 impair these atomic bases to eliminate its DNA-binding capability, followed by exploring the DNA-binding capability of mono- and di-phosphorylation Banf1, using comprehensive and systematic molecular modelling and molecular dynamics simulations. This work presented in detail the residue-level binding energies, hydrogen bonds and water bridges between Banf1 and DNA, some of which have not been reported. Moreover, we revealed that mono-phosphorylation of Banf1 causes its N-terminal secondary structure changes, which in turn induce significant changes in Banf1's DNA binding surface, thus eliminating its DNA-binding capability. At the atomic level, we also uncovered the alterations in interactions due to the induction of mono-phosphorylation that result in the N-terminal secondary structure changes of Banf1. Additionally, our modelling showed that phosphorylated Banf1 with their dominant N-terminal secondary structures bind to DNA with a significantly lower affinity and the docked binding pose are not stable in MD simulations. These findings help future studies in predicting effect of mutations in Banf1 on its DNA-binding capability and open a novel avenue for the development of therapeutics such as cancer drugs, targeting cell proliferation by inducing conformational changes in Banf1's N-terminal domain.
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Affiliation(s)
- Ming Tang
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, Queensland University of Technology at the Translational Research Institute Australia, Brisbane, Australia.
- Faculty of Medicine, Frazer Institute, The University of Queensland at the Translational Research Institute Australia, Brisbane, Australia
| | - Amila Suraweera
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, Queensland University of Technology at the Translational Research Institute Australia, Brisbane, Australia.
| | - Xuqiang Nie
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, Queensland University of Technology at the Translational Research Institute Australia, Brisbane, Australia.
- College of Pharmacy, Key Lab of the Basic Pharmacology of the Ministry of Education, Zunyi Medical University, Zunyi, China
| | - Zilin Li
- School of Mechanics and Safety Engineering, Zhengzhou University, Zhengzhou 450001, China
- School of Mechanical, Medical and Process Engineering, Queensland University of Technology, Brisbane, Australia
| | - Pinglin Lai
- Academy of Orthopedics Guangdong Province, Guangdong Provincial Key Laboratory of Bone and Joint Degeneration Diseases, The Third Affiliated Hospital, Southern Medical University, Guangzhou, China
| | - James W Wells
- Faculty of Medicine, Frazer Institute, The University of Queensland at the Translational Research Institute Australia, Brisbane, Australia
| | - Kenneth J O'Byrne
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, Queensland University of Technology at the Translational Research Institute Australia, Brisbane, Australia.
- Princess Alexandra Hospital, Brisbane, Australia
| | - Robert J Woods
- Complex Carbohydrate Research Centre, University of Georgia, 315 Riverbend Rd, Athens, GA, 30602, USA
| | - Emma Bolderson
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, Queensland University of Technology at the Translational Research Institute Australia, Brisbane, Australia.
| | - Derek J Richard
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, Queensland University of Technology at the Translational Research Institute Australia, Brisbane, Australia.
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Afolabi OB, Oloyede OI, Aluko BT, Johnson JA. Biosynthesis of magnesium hydroxide nanomaterials using Monodora myristica, antioxidative activities and effect on disrupted glucose metabolism in streptozotocin-induced diabetic rat. FOOD BIOSCI 2021. [DOI: 10.1016/j.fbio.2021.101023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Shang YD, Zhang JL, Wang Y, Zhang HX, Zheng QC. Molecular simulation investigation on the interaction between barrier-to-autointegration factor dimer or its Gly25Glu mutant and LEM domain of emerin. Comput Biol Chem 2014; 53PB:184-190. [PMID: 25462326 DOI: 10.1016/j.compbiolchem.2014.09.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 09/17/2014] [Accepted: 09/19/2014] [Indexed: 02/06/2023]
Abstract
The interaction between barrier-to-autointegration factor dimer (BAF2) and LEM domain of emerin (EmLEM) was studied by molecular simulation methods. Nonspecific fragment of double-strand DNA molecule was docked with each chain of BAF2 by ZDOCK program. The model of DNA2:BAF2:EmLEM was thus constructed. The mutant Gly25Glu of BAF2 was manually constructed to explore the detailed effect of the mutation on the binding of BAF2 and EmLEM. It has been experimentally suggested that point mutation Gly25Glu can disturb the binding between BAF2 and EmLEM. Then, molecular dynamics (MD) simulations were performed on DNA2:BAF2(WT):EmLEM and DNA2:BAF2(MT):EmLEM complexes. 30ns trajectories revealed that the trajectory fluctuations of MT complex are more violent than that of the WT complex. Further, the binding free energy analysis showed that the electronegative residues Asp57, Glu61 and Asp65 from chain A, glu36 from chain B of BAF2 mainly contribute to interact with EmLEM. Besides, a stable π-π stack between trp62 and phe39 from BAF2(WT) chain B is destroyed by Glu25 in BAF2(MT). As a result, trp62 forms an interaction with glu25, and phe39 converts to strengthen affinity to EmLEM. On the other hand, Trp62 from chain A also forms a strong interaction with MT Glu25. Thus, with the docking of DNA, BAF2(MT) has higher affinity with EmLEM than BAF2(WT).
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Affiliation(s)
- Yu-Dong Shang
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, Jilin 130023, PR China
| | - Ji-Long Zhang
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, Jilin 130023, PR China
| | - Yan Wang
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, Jilin 130023, PR China
| | - Hong-Xing Zhang
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, Jilin 130023, PR China
| | - Qing-Chuan Zheng
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, Jilin 130023, PR China.
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