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Protein Science, Vol 5, Issue 1 62-71, Copyright © 1996 by Cold Spring Harbor Laboratory Press

ARTICLE

Simulations of CRP:(cAMP)(2) in noncrystalline environments show a subunit transition from the open to the closed conformation

A. E. GARCIA and J. G. HARMAN
Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545

The CRP:cAMP complex functions as a transcription factor that facilitates RNA polymerase recognition of several bacterial promoters. Detailed crystal structure information is available for CRP:(cAMP)(2) and for CRP:(cAMP)(2) complexed with DNA. In the crystalline environment, CRP:(cAMP)(2) subunits are asymmetrically related; one subunit has a closed conformation and the other has an open conformation. The CRP:(cAMP)(2) complexed with DNA shows both subunits in a closed conformation. We have studied the molecular dynamics of CRP:(cAMP)(2) in noncrystalline environments. CRP:(cAMP)(2) was simulated for 625 ps in vacuo and for 140 ps in solution. The crystal structure of CRP:(cAMP)(2) in the absence of DNA was used as the initial conformation. Molecule optimal dynamic coordinates (MODCs) (Garcia A, 1992, Phys Rev Lett 68:2696) were used to analyze protein conformations sampled during the course of the simulations. Two MODCs define a transition of the open subunit to a closed subunit conformation during the first 125 ps of simulation in vacuo; the resulting subunit conformation is similar to that observed in CRP:(cAMP)(2):DNA crystals. Simulation of CRP:(cAMP)(2) in solution showed that a transition from the open to the closed state also occurs when water is explicitly included in the calculations. These calculations suggest that the asymmetric conformation of CRP:(cAMP)(2) is stabilized by crystal lattice interactions. The predicted solution conformation is more symmetric, with both subunits in a closed conformation.
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