BIOPHYSICAL THEORY AND MODELING |
Spontaneous conformational changes in the E. coli GroEL subunit from all-atom molecular dynamics simulations
Yelena Sliozberg 1 and Cameron Abrams 1*
1 Drexel University
* To whom correspondence should be addressed. E-mail: cfa22{at}drexel.edu.
Submitted on March 6, 2007
Revised on April 22, 2007
Accepted on 10 May 2007
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Abstract |
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The E. coli GroEL chaperonin is a complex of identical subunit proteins (57 kDa each) arranged in a back-to-back stacking of two heptameric rings. Its hallmarks include nested positive intraring and negative interring cooperativity in ATP binding and the ability to mediate the folding of newly transcribed and/or denatured substrate proteins. We performed unbiased molecular dynamics simulations of the GroEL subunit protein in explicit water both with and without the nucleotide KMgATP to understand better the details of the structural transitions that enable these behaviors. Placing KMgATP in the equatorial domain binding pocket of a t state subunit, which corresponds to a low ATP-affinity state, produced a short-lived (6 ns) state that spontaneously transitioned to the high ATP-affinity r state. The important feature of this transition is a large-scale rotation of the intermediate domain's helix M to close the ATP binding pocket. Pivoting of helix M is accompanied by counterclockwise rotation and slight deformation of the apical domain, important for lowering the affinity for substrate protein. Aligning simulation conformations into model heptamer rings demonstrates that the t
r transition in one subunit is not sterically hindered by t state neighbors, but requires breakage of Arg197-Glu386 intersubunit salt bridges which are important for interring positive cooperativity. Lowest-frequency quasi-harmonic modes of vibration computed pre- and post-transition clearly show that natural vibrations facilitate the transition. Finally, we propose a novel mechanism for interring cooperativity in ATP binding inspired by the observation of spontaneous insertion of the side-chain of Ala480 into the empty nucleotide pocket.
Key Words:
ATP, GroEL, allostery, chaperonin, molecular dynamics
