ElectrostaticInteractions betweenprotein and DNA play key roles in many biological functions, such astranscription, translation and recombination. The transcription factor may bindto DNA in two different modes: non-specific binding which the protein randomlybinds to a DNA sequence, and a specific one which the protein interacts with aspecific sequence of DNA. The interactions between protein and DNA can lead to switchbetween these two binding modes. In order to insight into this interactionmechanism, lactose repressor and its mutant Y17F were used to study the specificand non-specific binding to DNA with molecular dynamics simulations andexperimental evaluation. The results show that electrostatic interactions andhydrogen bonding can stabilize both binding modes, while the hydrophobic interactiononly exists in specific binding. In specific binding, the protein structure ismore compact, the C-terminal of the dimer can form a helix. The DNA chain is bendedabout 40�, the minor groove in the binding surface is opened about 10 �. Fornon-specific binding, the two monomers nearly depart from each other, theC-terminal is disordered, and the distance between protein and DNA is largerthan that of the specific binding. The non-specific binding may have a�pre-recognition� process. At first protein binds to DNA, the angle of DNA mightbecome smaller, the monomer of protein gets close to the DNA, then DNA bendsover. This relies on electrostatic interactions and hydrogen bonding. The complexbecomes tight, however the interactions between protein and DNA can't apply enoughforce to maintain this compact configuration. Finally the complex returns tothe loose state. Therefore, the specific interactions can stabilize this tightconfiguration. The sequence CGCTCA located in the central region of DNA mightbe the specific sequence for binding. Mutant experiment evaluates this point.These results can insight into the recognition mechanism between protein andDNA.

Electrostatic interaction on specific recognition between protein and DNA

248th National Meeting (2014)

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