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Allosteric transition pathways in the lactose repressor protein core domains: Asymmetric motions in a homodimer

¹ Department of Bioengineering,
² Department of Biochemistry and Cell Biology, and
³ W.M. Keck Center for Computational Biology, Rice University, Houston, Texas 77005, USA
⁴ Graduate Program of Structural and Computational Biology and Molecular Biophysics and
⁵ Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA

Reprint requests to: Jianpeng Ma, 1 Baylor Plaza, BCM-125, Baylor College of Medicine, Houston, TX 77030, USA; e-mail: jpma{at}bcm.tmc.edu; fax: (713) 796-9438.

The crystal structures of lactose repressor protein (LacI) provide static endpoint views of the allosteric transition between DNA- and IPTG-bound states. To obtain an atom-by-atom description of the pathway between these two conformations, motions were simulated with targeted molecular dynamics (TMD). Strikingly, this homodimer exhibited asymmetric dynamics. All asymmetries observed in this simulation are reproducible and can begin on either of the two monomers. Asymmetry in the simulation originates around D149 and was traced back to the pre-TMD equilibrations of both conformations. In particular, hydrogen bonds between D149 and S193 adopt a variety of configurations during repetitions of this process. Changes in this region propagate through the structure via noncovalent interactions of three interconnected pathways. The changes of pathway 1 occur first on one monomer. Alterations move from the inducer-binding pocket, through the N-subdomain ß-sheet, to a hydrophobic cluster at the top of this region and then to the same cluster on the second monomer. These motions result in changes at (1) side chains that form an interface with the DNA-binding domains and (2) K84 and K84’, which participate in the monomer–monomer interface. Pathway 2 reflects consequent reorganization across this subunit interface, most notably formation of a H74-H74rsquo; -stacking intermediate. Pathway 3 extends from the rear of the inducer-binding pocket, across a hydrogen-bond network at the bottom of the pocket, and transverses the monomer–monomer interface via changes in H74 and H74rsquo;. In general, intermediates detected in this study are not apparent in the crystal structures. Observations from the simulations are in good agreement with biochemical data and provide a spatial and sequential framework for interpreting existing genetic data.

Keywords: Gene regulation; allosteric mechanism; structural flexibility; conformational transition pathway; targeted molecular dynamics

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