The electrostatic profile of bacterial promoter: influence of temperature and ion strength
Institute of Cell Biophysics RAS, Russia, 142290, Pushchino, Institutskaya. 3, Tel.:(4967)739165, E-mail: email@example.com pp. (accepted)
The electrostatic force is the most far-reaching from intermolecular interaction ones. It plays a special role in protein-DNA recognition, because the DNA molecule in solution has extremely high charge density. This role was experimentally proven by observation of “molecular mimicry” effect, when phage protein blocks the bacterial restriction system by emulation of DNA charge distribution.
We have developed simple algorithm of calculation of electrostatic profile of long DNA fragmens based upon Coulomb formula [2-3]. The main deficiency of the method is that it gives profile values in arbitrary units, so it is possible to compare profile of several DNA fragments, but difficult to assess the significance of observed differences.
To address that problem we have used APBS software , to calculated electrostatic potential around 700 E.coli promoter regions for three different temperature values and four different ionic strendths. The 1-D profile of electrostatic potential was obtained from simulation results by algorithm provided in .
It was show that for normal conditions coulomb method gives profile where position of peaks and throws are identical to those obtained from APBS simulations. The values of profile in extremes were close to the average by 3-5%. With profiles obtained from two method we have created recalculation algorithm,which is able to convert coulomb arbitrary unints into APBS kT values with reasonable accurasy.
The research was partially supported by RFBR, research project No. 14-44-03679-р_центр_а.
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