Paper Citing NAMD - Abstract
Satpati, Priyadarshi; Simonson, Thomas
Conformational selection through electrostatics: Free energy simulations of gtp and gdp binding to archaeal initiation factor 2
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 80:1264-1282, MAR 2012
Archaeal Initiation Factor 2 is a GTPase involved in protein biosynthesis. In its GTP-bound, ON conformation, it binds an initiator tRNA and carries it to the ribosome. In its GDP-bound, OFF conformation, it dissociates from tRNA. To understand the specific binding of GTP and GDP and their dependence on the conformational state, molecular dynamics free energy simulations were performed. The ON state specificity was predicted to be weak, with a GTP/GDP binding free energy difference of -1 kcal/mol, favoring GTP. The OFF state specificity is larger, 4 kcal/mol, favoring GDP. The overall effects result from a competition among many interactions in several complexes. To interpret them, we use a simpler, dielectric continuum model. Several effects are robust with respect to the model details. Both nucleotides have a net negative charge, so that removing them from solvent into the binding pocket carries a desolvation penalty, which is large for the ON state, and strongly disfavors GTP binding compared to GDP. Short-range interactions between the additional GTP phosphate group and ionized sidechains in the binding pocket offset most, but not all of the desolvation penalty; more distant groups also contribute significantly, and the switch 1 loop only slightly. The desolvation penalty is lower for the more open, wetter OFF state, and the GTP/GDP difference much smaller. Short-range interactions in the binding pocket and with more distant groups again make a significant contribution. Overall, the simulations help explain how conformational selection is achieved with a single phosphate group. Proteins 2012; 2011 (c) Wiley Periodicals, Inc.
