ArticleJournal of molecular modeling2019
Molecular mechanisms of the protein-protein interaction-regulated binding specificity of basic-region leucine zipper transcription factors.
Article in Journal of molecular modeling, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed, 9 citations in OpenAlex.
- Structure-guided design and cloning of peptide inhibitors targeting CDK9/cyclin T1 protein-protein interaction.Frontiers in pharmacology · 2024Article
- Optimizing the Calculation of Free Energy Differences in Nonequilibrium Work SQM/MM Switching Simulations.The journal of physical chemistry. B · 2022Article
- Insight into the bZIP gene family inFrontiers in plant science · 2022Article
- Genome-Wide Identification of bZIP Transcription Factor Genes and Functional Analyses of Two Members inJournal of fungi (Basel, Switzerland) · 2021Article
- Molecular mechanism of methyl-dependent and spatial-specific DNA recognition of c-Jun homodimer.Journal of molecular modeling · 2021Article
- Comparison of the binding characteristics of SARS-CoV and SARS-CoV-2 RBDs to ACE2 at different temperatures by MD simulations.Briefings in bioinformatics · 2021Article
- Insight into theInternational journal of molecular sciences · 2020Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
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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