ArticleJournal of molecular modeling2014
Contribution of phenylalanine side chain intercalation to the TATA-box binding protein-DNA interaction: molecular dynamics and dispersion-corrected density functional theory studies.
Article in Journal of molecular modeling, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 27 citations in OpenAlex.
- Understanding the underlying language code that governs the π-π non-covalent interactions between proteins and DNA.Scientific reports · 2026Article
- The Kaposi's sarcoma-associated herpesvirus TBP mimic uses a noncanonical DNA-binding mode to promote viral late gene transcription.Nucleic acids research · 2025Article
- Review
- Substance P and Neurokinin-1 receptor are overexpressed in adamantinomatous craniopharyngioma than in the pituitary gland.Pituitary · 2024Article
- Cooperative dynamics of PARP-1 zinc-finger domains in the detection of DNA single-strand breaks.Scientific reports · 2024Article
- Substance P and Neurokinin-1 Receptor System in Thyroid Cancer: Potential Targets for New Molecular Therapies.Journal of clinical medicine · 2023Article
- C-B-A Test of DNA Force Fields.ACS omega · 2023Article
- Article
- Photon Dissipation as the Origin of Information Encoding in RNA and DNA.Entropy (Basel, Switzerland) · 2020Article
- Sequence specificity in DNA-drug intercalation: MD simulation and density functional theory approaches.Journal of computer-aided molecular design · 2020Article
- Role of indirect readout mechanism in TATA box binding protein-DNA interaction.Journal of computer-aided molecular design · 2015Article
- Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Deformation of DNA takes place quite often due to binding of small molecules or proteins with DNA. Such deformation is significant due to minor groove binding and, besides electrostatic interactions, other non-covalent interactions may also play an important role in generating such deformation. TATA-box binding protein (TBP) binds to the minor groove of DNA at the TATA box sequence, producing a large-scale deformation in DNA and initiating transcription. In order to observe the interactions of protein residues with DNA in the minor groove that produce the deformation in the DNA structure, we carried out molecular dynamics simulations of the TBP-DNA system. The results reveal consistent partial intercalation of two Phe residues, distorting stacking interactions at two dinucleotide step sites. We carried out calculations based on dispersion-corrected density functional theory to understand the source of such stabilization. We observed favorable interaction energies between the Phe residues and the base pairs with which they interact. We suggest that salt-bridge interactions between the phosphate groups and Lys or Arg residues, along with the intercalation of Phe residues between two base pair stacks, stabilize the kinked and opened-up DNA conformation.
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