ArticleNucleic acids research2009
Experimentally based contact energies decode interactions responsible for protein-DNA affinity and the role of molecular waters at the binding interface.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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14 citing papers in PubMed, 23 citations in OpenAlex.
- Article
- The role of zinc finger linkers in zinc finger protein binding to DNA.Journal of computer-aided molecular design · 2021Article
- Optimal affinity ranking for automated virtual screening validated in prospective D3R grand challenges.Journal of computer-aided molecular design · 2018Article
- "Solvent hydrogen-bond occlusion": A new model of polar desolvation for biomolecular energetics.Journal of computational chemistry · 2017Article
- Structure-based modeling of protein: DNA specificity.Briefings in functional genomics · 2015Review
- Probing the role of interfacial waters in protein-DNA recognition using a hybrid implicit/explicit solvation model.Proteins · 2013Article
- Atomistic modeling of protein-DNA interaction specificity: progress and applications.Current opinion in structural biology · 2012Review
- Characterization and prediction of the binding site in DNA-binding proteins: improvement of accuracy by combining residue composition, evolutionary conservation and structural parameters.Nucleic acids research · 2012Article
- Improved modeling of side-chain--base interactions and plasticity in protein--DNA interface design.Journal of molecular biology · 2012Article
- Article
- Extensive protein and DNA backbone sampling improves structure-based specificity prediction for C2H2 zinc fingers.Nucleic acids research · 2011Article
- On the analysis of protein-protein interactions via knowledge-based potentials for the prediction of protein-protein docking.Protein science : a publication of the Protein Society · 2011Article
- Electrostatic hot spot on DNA-binding domains mediates phosphate desolvation and the pre-organization of specificity determinant side chains.Nucleic acids research · 2010Article
- Optimization of minimum set of protein-DNA interactions: a quasi exact solution with minimum over-fitting.Bioinformatics (Oxford, England) · 2010Article
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2 authors at 1 institution in 1 country.
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Abstract
A major obstacle towards understanding the molecular basis of transcriptional regulation is the lack of a recognition code for protein-DNA interactions. Using high-quality crystal structures and binding data on the promiscuous family of C(2)H(2) zinc fingers (ZF), we decode 10 fundamental specific interactions responsible for protein-DNA recognition. The interactions include five hydrogen bond types, three atomic desolvation penalties, a favorable non-polar energy, and a novel water accessibility factor. We apply this code to three large datasets containing a total of 89 C(2)H(2) transcription factor (TF) mutants on the three ZFs of EGR. Guided by molecular dynamics simulations of individual ZFs, we map the interactions into homology models that embody all feasible intra- and intermolecular bonds, selecting for each sequence the structure with the lowest free energy. These interactions reproduce the change in affinity of 35 mutants of finger I (R(2) = 0.998), 23 mutants of finger II (R(2) = 0.96) and 31 finger III human domains (R(2) = 0.94). Our findings reveal recognition rules that depend on DNA sequence/structure, molecular water at the interface and induced fit of the C(2)H(2) TFs. Collectively, our method provides the first robust framework to decode the molecular basis of TFs binding to DNA.
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