Book of Abstracts: Albany 2011

category image Albany 2011
Conversation 17
June 14-18 2011
©Adenine Press (2010)

The Role of Electrostatics in Protein-DNA Interactions in Phage Lambda

Physical properties of DNA are known to be essential for RNA polymerase-promoter recognition. Especially electrostatic interactions between promoter DNA and RNA polymerase is of considerable importance in regulating promoter function (1-5), just like the electrostatic interactions between histones and DNA determine the positioning of the nucleosomes and the expression of the genome (6, 7).

One of the elements that may play a crucial role in the promoter strength regulation is the so-called “up-element”, which interacts with the alpha-subunit of the RNA polymerase and thus facilitates its binding to the promoter. It was shown earlier that the T4 phage strong promoters with pronounced “up-element” have high levels of the electrostatic potential within it (3). Using DEPPDB – DNA Electrostatic Potential Properties Database (5) – we studied electrostatic properties of the lambda phage genome DNA. We observed that the strong lambda phage promoters have pronounced “up-element” compared to the absence of it in weak promoters. Promoters with intermediate strength possess weak “up-element” (fig. 1).

Figure 1: Electrostatic profile of a strong (3), weak (2) and intermediate-strength (1) promoters of the phage lambda. The “up-element” area is highlighted with gray.

Strong promoters also have the characteristic heterogeneity of the electrostatic profile, known to differentiate promoters and coding regions. Pseudopromoters are located in the region of high potential value with a prominent electrostatic trap. It is reported that RNA polymerase binds them frequently and rests there for a long time (8).

Not only promoters are marked with peculiarities in the electrostatic properties. Regulator proteins binding sites within the operators also have electrostatic features that correlate with binding ability of the corresponding regulatory proteins. Apparently the sequence text itself shows weaker correlations. Another region that shows a considerable increase in the electrostatic potential value is the attachment site where the initial integration to the host genome DNA occurs.

The role of electrostatics in the DNA-protein interaction is directly confirmed by the rigorous experiment evidence described in ref. 8. Using the visualization of the individual molecules of RNA polymerase and phage DNA observed is the spatial non-homogeneity of their interactions. The frequency of binding correlates with the absolute value of the electrostatic potential along the DNA molecule.

These data highlight the universal role of electrostatics in the protein interactions with the genome DNA.


  1. R. V. Polozov, T. R. Dzhelyadin, A. A. Sorokin, N. N. Ivanova, V. S. Sivozhelezov, S. G. Kamzolova, J. Biomol. Struct. Dyn. 16, 1135-43 (1999).
  2. S.G. Kamzolova, A.A. Sorokin, T.D. Dzhelyadin P.M., Beskaravainy, A.A. Osypov, J. Biomol. Struct. Dyn. 23, 341-346 (2005).
  3. S. G. Kamzolova, V. S. Sivozhelezov, A. A. Sorokin, T. R Dzhelyadin, N. N. Ivanova, R. V. Polozov, J. Biomol. Struct. Dyn. 18, 325-334 (2000).
  4. A. A. Sorokin, A. A. Osypov, T. R. Dzhelyadin, P. M. Beskaravainy, S. G. Kamzolova, J. Bioinform. Comput. Biol. 4(2), 455-467 (2006).
  5. A. A. Osypov, G. G. Krutinin, S. G. Kamzolova, J. Bioinform. Comput. Biol. 8(3), 413-425 (2010).
  6. S.M. West, R. Rohs, R. S. Mann, B. Honig, J Biomol Struct Dyn 27, 861-866 (2010).
  7. D. Wang, N. B. Ulyanov, V. B. Zhurkin, J Biomol Struct Dyn 27, 843-859 (2010).
  8. Y. Harada, T. Funatsu, K. Murakami, Y. Nonoyama, A. Ishihama, T. Yanagida, Biophys. J. 76, 709–715 (1999).

Gleb G. Krutinin
Eugenia A. Krutinina,
Svetlana G. Kamzolova
Alexander A. Osypov*

Institute of Cell Biophysics
Russian Academy of Sciences
Moscow Region, 142290 Russia