Albany 2015:Book of Abstracts
June 9-13 2015
©Adenine Press (2012)
Spatial Organization of Electrostatic Interactions Between T7 Specific RNA Polymerase and Its Native Promoters
Electrostatic forces are of considerable importance in the multistep process of protein-DNA recognition, especially at its earliest stage. Here contribution of electrostatic interaction in protein-DNA recognition is presented by an example of complexes T7 specific RNA polymerase (RNAP) with its native promoters. Distribution of electrostatic potential around promoter binding center (PBC) of RNAP has been earlier calculated (Kamzolova et al. 2014). There are three crests of positive potential in the PBC electrostatic pattern, which correspond to three RNAP subdomains involved in promoter recognition. Here the role of each of these positively charged crests in electrostatic interaction with different T7 promoters was studied. To investigate patterns of electrostatic profiles in promoter regions and appreciate their match with spatial distribution of crests in potential of RNAP promoter recognition elements, the results of calculation of electrostatic potential distribution around all 12 T7 promoters were obtained as 2D topological maps. T7 promoters are known to be classified into two groups (class II and class III) by their location in the genome, time of their expression and functional behavior. For comparative study 2D electrostatic maps of each class promoters were averaged and the consensus maps were analyzed by their spatial match with the PBC electrostatic pattern of RNAP. There was observed a good correlation in spatial organization of positively charged crests of RNAP and negatively charged specific elements of the promoter DNA. However it is interesting that different set of electrostatic interactions were found to be involved in complex formation of RNAP with T7 promoters belonging to different classes. Differential character in the topology of electrostatic T7 RNA polymerase-promoter DNA interactions can be provided due to the presence of three different positively charged sites in the enzyme binding to different parts of the promoter DNA. The difference in the electrostatic arrangement of the primary complex formed by the different T7 promoter classes may affect the pathway and the rate of formation of the final active complex thus suggesting a reasonable explanation for the difference in strength and functional behavior of the promoters belonging to the different classes.
This research has been supported by RFBR, research project No. 14-44-03679.
Kamzolova, S.G., Beskaravainy, P.M., Osypov, A.A., Dzhelyadin, T.R., Temlyakova, E.A., Sorokin, A.A. (2014) Electrostatic map of T7 DNA: comparative analysis of functional and electrostatic properties of T7 RNA polymerase-specific promoters., Journal of Biomolecular Structure & Dynamics, 32(8), 1184-1192.
Institute of Cell Biophysics RAS