Water organization between oppositely charged surfaces: implications for protein sliding along DNA.
Water molecules are abundant in protein-DNA interfaces, especially in their nonspecific complexes. In this study, we investigated the organization and energetics of the interfacial water by simplifying the geometries of the proteins and the DNA to represent them as two equally and oppositely charged planar surfaces immersed in water. We found that the potential of mean force for bringing the two parallel surfaces into close proximity comprises energetic barriers whose properties strongly depend on the charge density of the surfaces. We demonstrated how the organization of the water molecules into discretized layers and the corresponding energetic barriers to dehydration can be modulated by the charge density on the surfaces, salt, and the structure of the surfaces. The 1-2 layers of ordered water are tightly bound to the charged surfaces representing the nonspecific protein-DNA complex. This suggests that water might mediate one-dimensional diffusion of proteins along DNA (sliding) by screening attractive electrostatic interactions between the positively charged molecular surface on the protein and the negatively charged DNA backbone and, in doing so, reduce intermolecular friction in a manner that smoothens the energetic landscape for sliding, and facilitates the 1D diffusion of the protein.
Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel.
Amir
A
Marcovitz
Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel.
Aviv
A
Naftaly
Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel.
Yaakov
Y
Levy
D004247:DNA / Q000737:chemistry*; D004058:Diffusion; D007477:Ions / Q000737:chemistry; D008956:Models, Chemical; D008957:Models, Genetic; D011506:Proteins / Q000737:chemistry*; D012492:Salts / Q000737:chemistry; D012964:Sodium / Q000737:chemistry; D012997:Solvents / Q000737:chemistry; D013499:Surface Properties; D014867:Water / Q000737:chemistry*
D007477:Ions; D011506:Proteins; D012492:Salts; D012997:Solvents; D014867:Water; D004247:DNA; D012964:Sodium