ArticleBiophysical journal2008
Salt-mediated electrostatics in the association of TATA binding proteins to DNA: a combined molecular mechanics/Poisson-Boltzmann study.
Article in Biophysical journal, 2008. 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, 22 citations in OpenAlex.
- A Newton-like iterative method implemented in the DelPhi for solving the nonlinear Poisson-Boltzmann equation.Mathematical biosciences and engineering : MBE · 2020Article
- DelPhi Suite: New Developments and Review of Functionalities.Journal of computational chemistry · 2019Article
- Dynamic structure mediates halophilic adaptation of a DNA polymerase from the deep-sea brines of the Red Sea.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2018Article
- Problems of robustness in Poisson-Boltzmann binding free energies.Journal of chemical theory and computation · 2015Article
- Theoretical assessment of the oligolysine model for ionic interactions in protein-DNA complexes.The journal of physical chemistry. B · 2011Article
- A Fast and Robust Poisson-Boltzmann Solver Based on Adaptive Cartesian Grids.Journal of chemical theory and computation · 2011Article
- Revisiting the association of cationic groove-binding drugs to DNA using a Poisson-Boltzmann approach.Biophysical journal · 2010Article
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
The TATA-binding protein (TBP) is a key component of the archaea ternary preinitiation transcription assembly. The archaeon TBP, from the halophile/hyperthermophile organism Pyrococcus woesei, is adapted to high concentrations of salt and high-temperature environments. Although most eukaryotic TBPs are mesophilic and adapted to physiological conditions of temperature and salt, they are very similar to their halophilic counterparts in sequence and fold. However, whereas the binding affinity to DNA of halophilic TBPs increases with increasing salt concentration, the opposite is observed for mesophilic TBPs. We investigated these differences in nonspecific salt-dependent DNA-binding behavior of halophilic and mesophilic TBPs by using a combined molecular mechanics/Poisson-Boltzmann approach. Our results are qualitatively in good agreement with experimentally observed salt-dependent DNA-binding for mesophilic and halophilic TBPs, and suggest that the distribution and the total number of charged residues may be the main underlying contributor in the association process. Therefore, the difference in the salt-dependent binding behavior of mesophilic and halophilic TBPs to DNA may be due to the very unique charge and electrostatic potential distribution of these TBPs, which consequently alters the number of repulsive and attractive electrostatic interactions.
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