Cooperative binding of DNA and CBFbeta to the Runt domain of the CBFalpha studied via MD simulations.

Printer-friendly versionPrinter-friendly versionPDF versionPDF version
TitleCooperative binding of DNA and CBFbeta to the Runt domain of the CBFalpha studied via MD simulations.
Publication TypeJournal Article
Year of Publication2005
AuthorsHabtemariam, B, Anisimov, VM, Mackerell, AD
JournalNucleic Acids Res
Volume33
Issue13
Pagination4212-22
Date Published2005
ISSN1362-4962
KeywordsAmino Acids, Binding Sites, Computer Simulation, Core Binding Factor alpha Subunits, Core Binding Factors, DNA, DNA-Binding Proteins, Models, Molecular, Neoplasm Proteins, Protein Binding, Protein Structure, Tertiary, Transcription Factor AP-2, Transcription Factors
Abstract

The Runt domain (RD) is the DNA-binding region of the Runx genes. A related protein, known as core binding factor beta (CBFbeta) also binds to the RD to enhance RD-DNA interaction by 6- to 10-fold. Here, we report results from molecular dynamics (MD) simulations of RD alone, as a dimer in complexes with DNA and CBFbeta and in a ternary complex with DNA and CBFbeta. Consistent with the experimental findings, in the presence of CBFbeta the estimated free energy of binding of RD to the DNA is more favorable, which is shown to be due to more favorable intermolecular interactions and desolvation contributions. Also contributing to the enhanced binding are favorable intramolecular interactions between the 'wing' residues (RD residues 139-145) and the 'wing1' residues (RD residues 104-116). The simulation studies also indicate that the RD-CBFbeta binding is more favorable in the presence of DNA due to a more favorable RD-CBFbeta interaction energy. In addition, it is predicted that long-range interactions involving ionic residues contribute to binding cooperativity. Results from the MD calculations are used to interpret a variety of experimental mutagenesis data. A novel role for RD Glu116 to the RD-CBFbeta interaction is predicted.

DOI10.1093/nar/gki724
Alternate JournalNucleic Acids Res.
PubMed ID16049027
PubMed Central IDPMC1180745
Grant ListR01 GM051501 / GM / NIGMS NIH HHS / United States
R29 GM051501 / GM / NIGMS NIH HHS / United States
CA 95350 / CA / NCI NIH HHS / United States
GM 51501 / GM / NIGMS NIH HHS / United States