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Molecular mechanisms of the protein-protein interaction–regulated binding specificity of basic-region leucine zipper transcription factors

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Abstract

It is well known that the DNA-binding specificity of transcription factors (TFs) is influenced by protein-protein interactions (PPIs). However, the underlying molecular mechanisms remain largely unknown. In this work, we adopted the cAMP-response element-binding protein (CREB) of the basic leucine zipper (bZIP) TF family as a model system, and a workflow of combined bioinformatics and molecular modeling analysis of protein-DNA interaction was tested. First, the multiple sequence alignment and SDPsite method were used to find potential bZIP family binding specificity determining positions (SDPs) within the protein-protein interaction region. Second, the mutation system was analyzed using molecular dynamics simulation. Molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) free energy calculations confirmed the enhancement of the binding affinity of the mutation, which was in agreement with experimental results. The root mean square fluctuation (RMSF) and hydrogen bonding changes suggested an open and close protein dimerization process after the system was mutated, which resulted in the change of the hydrogen bonding of the protein-DNA interface and a slight conformational change. We believe that this work will contribute to understanding the protein-protein interaction–regulated binding specificity of bZIP transcription factors.

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Funding

This work was supported by the National Key R&D Program of China (Grant No. 2017YFB0203405), National Natural Science Foundation of China (Nos. 21873034, 31670779), Fundamental Research for the Central Universities (Project 2662018JC027), and Huazhong Agricultural University Scientific & Technological Self Innovation Foundation (Program No. 2015RC008).

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  1. Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, People’s Republic of China

    Qing Li, Le Xiong, Jun Gao & Hong-Yu Zhang

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  1. Qing Li
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  4. Hong-Yu Zhang
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Correspondence to Jun Gao or Hong-Yu Zhang.

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Li, Q., Xiong, L., Gao, J. et al. Molecular mechanisms of the protein-protein interaction–regulated binding specificity of basic-region leucine zipper transcription factors. J Mol Model 25, 246 (2019). https://doi.org/10.1007/s00894-019-4138-9

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