Analyzing Protein-DNA Recognition Mechanisms Export

@article{citeulike:2767709, abstract = {We present a computational algorithm that can be used to analyze the generic mechanisms involved in protein-DNA recognition. Our approach is based on energy calculations for the full set of base sequences that can be threaded onto the DNA within a protein-DNA complex. It is able to reproduce experimental consensus binding sequences for a variety of DNA binding proteins and also correlates well with the order of measured binding free energies. These results suggest that the crystal structure of a protein-DNA complex can be used to identify all potential binding sequences. By analyzing the energy contributions that lead to base sequence selectivity, it is possible to quantify the concept of direct versus indirect recognition and to identify a new concept describing whether the protein-DNA interaction and DNA deformation terms select optimal binding sites by acting in accord or in disaccord.}, author = {Paillard, Guillaume and Lavery, Richard}, citeulike-article-id = {2767709}, citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.str.2003.11.022}, citeulike-linkout-1 = {http://linkinghub.elsevier.com/retrieve/pii/S0969212603002922}, citeulike-linkout-2 = {http://www.sciencedirect.com/science/article/B6VSR-4BG8PJ8-J/1/ab887a63f6ff80e0efd52c6ceb96c069}, day = {16}, doi = {10.1016/j.str.2003.11.022}, journal = {Structure}, keywords = {dependency}, month = {March}, number = {1}, pages = {113--122}, posted-at = {2008-05-08 00:47:28}, priority = {2}, title = {Analyzing Protein-DNA Recognition Mechanisms}, url = {http://dx.doi.org/10.1016/j.str.2003.11.022}, volume = {12}, year = {2004} }

TY - JOUR ID - citeulike:2767709 L3 - citeulike-article-id:2767709 N2 - We present a computational algorithm that can be used to analyze the generic mechanisms involved in protein-DNA recognition. Our approach is based on energy calculations for the full set of base sequences that can be threaded onto the DNA within a protein-DNA complex. It is able to reproduce experimental consensus binding sequences for a variety of DNA binding proteins and also correlates well with the order of measured binding free energies. These results suggest that the crystal structure of a protein-DNA complex can be used to identify all potential binding sequences. By analyzing the energy contributions that lead to base sequence selectivity, it is possible to quantify the concept of direct versus indirect recognition and to identify a new concept describing whether the protein-DNA interaction and DNA deformation terms select optimal binding sites by acting in accord or in disaccord. IS - 1 JF - Structure EP - 122 TI - Analyzing Protein-DNA Recognition Mechanisms VL - 12 SP - 113 KW - dependency AU - Paillard, Guillaume AU - Lavery, Richard PY - 2004/03/16/ UR - http://dx.doi.org/10.1016/j.str.2003.11.022 ER -