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Ribosome motions modulate electrostatic properties
Author(s) -
Trylska Joanna,
Konecny Robert,
Tama Florence,
Brooks Charles L.,
McCammon J. Andrew
Publication year - 2004
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.20093
Subject(s) - thermus thermophilus , chemistry , ribosome , electrostatics , biophysics , ionic strength , crystallography , chemical physics , aqueous solution , biochemistry , rna , biology , escherichia coli , gene
The electrostatic properties of the 70S ribosome of Thermus thermophilus were studied qualitatively by solving the Poisson–Boltzmann (PB) equation in aqueous solution and with physiological ionic strength. The electrostatic potential was calculated for conformations of the ribosome derived by recent normal mode analysis (Tama, F., et al. Proc Natl Acad Sci USA 2003 100, 9319–9323) of the ratchet‐like reorganization that occurs during translocation (Frank, J.; Agrawal, R. K. Nature 2000 406, 318–322). To solve the PB equation, effective parameters (charges and radii), applicable to a highly charged backbone model of the ribosome, were developed. Regions of positive potential were found at the binding site of the elongation factors G and Tu, as well as where the release factors bind. Large positive potential areas are especially pronounced around the L11 and L6 proteins. The region around the L1 protein is also positively charged, supporting the idea that L1 may interact with the E‐site tRNA during its release from the ribosome after translocation. Functional rearrangement of the ribosome leads to electrostatic changes which may help the translocation of the tRNAs during the elongation stage. © 2004 Wiley Periodicals, Inc. Biopolymers, 2004