Salt-Mediated Electrostatics in the Association of TATA Binding Proteins to DNA: A Combined Molecular Mechanics/Poisson-Boltzmann Study

@article{citeulike:3042448, 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. 10.1529/biophysj.107.125609}, author = {Bredenberg, Johan H. and Russo, Cristina and Fenley, Marcia O. }, citeulike-article-id = {3042448}, doi = {http://dx.doi.org/10.1529/biophysj.107.125609}, journal = {Biophys. J.}, keywords = {electrostatics, protein-nucleic\_acid\_interactions, solvation}, month = {June}, number = {12}, pages = {4634--4645}, posted-at = {2008-07-25 11:56:28}, priority = {0}, title = {Salt-Mediated Electrostatics in the Association of TATA Binding Proteins to DNA: A Combined Molecular Mechanics/Poisson-Boltzmann Study}, url = {http://dx.doi.org/10.1529/biophysj.107.125609}, volume = {94}, year = {2008} }

TY - JOUR ID - citeulike:3042448 L3 - citeulike-article-id:3042448 TI - Salt-Mediated Electrostatics in the Association of TATA Binding Proteins to DNA: A Combined Molecular Mechanics/Poisson-Boltzmann Study JF - Biophys. J. VL - 94 IS - 12 SP - 4634 EP - 4645 N2 - 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. 10.1529/biophysj.107.125609 KW - electrostatics KW - protein-nucleic_acid_interactions KW - solvation AU - Bredenberg, Johan AU - Russo, Cristina AU - Fenley, Marcia PY - 2008/06/15/ UR - http://dx.doi.org/10.1529/biophysj.107.125609 ER -