Entropy redistribution controls allostery in a metalloregulatory protein
- Daiana A. Capdevilaa,1,
- Joseph J. Braymera,1,2,
- Katherine A. Edmondsa,
- Hongwei Wua, and
- David P. Giedroca,3
-
Edited by Judith P. Klinman, University of California, Berkeley, CA, and approved March 2, 2017 (received for review December 15, 2016)
Significance
The immune system limits nutrient availability and releases highly reactive toxic molecules to control bacterial infections. Successful pathogens resist these host effects by using regulatory proteins that “sense” diverse environmental stressors and alter the transcription of genes required to mount an adaptive response. We demonstrate here that these regulatory proteins are capable of sensing a specific stressor in a process that relies nearly exclusively on a redistribution of atomic motions to regulate gene transcription. This work provides insights into how nature exploits a simple molecular scaffold that relies on changes in atomic motions to evolve new adaptive responses to a wide range of environmental stimuli.
Abstract
Allosteric communication between two ligand-binding sites in a protein is a central aspect of biological regulation that remains mechanistically unclear. Here we show that perturbations in equilibrium picosecond–nanosecond motions impact zinc (Zn)-induced allosteric inhibition of DNA binding by the Zn efflux repressor CzrA (chromosomal zinc-regulated repressor). DNA binding leads to an unanticipated increase in methyl side-chain flexibility and thus stabilizes the complex entropically; Zn binding redistributes these motions, inhibiting formation of the DNA complex by restricting coupled fast motions and concerted slower motions. Allosterically impaired CzrA mutants are characterized by distinct nonnative fast internal dynamics “fingerprints” upon Zn binding, and DNA binding is weakly regulated. We demonstrate the predictive power of the wild-type dynamics fingerprint to identify key residues in dynamics-driven allostery. We propose that driving forces arising from dynamics can be harnessed by nature to evolve new allosteric ligand specificities in a compact molecular scaffold.
Footnotes
-
↵1D.A.C. and J.J.B. contributed equally to this work.
-
↵2Present address: Institut für Zytobiologie, Philipps-Universität Marburg, 35032 Marburg, Germany.
- ↵3To whom correspondence should be addressed. Email: giedroc{at}indiana.edu.
-
Author contributions: D.A.C., J.J.B., and D.P.G. designed research; D.A.C., J.J.B., and K.A.E. performed research; H.W. contributed new reagents/analytic tools; D.A.C., J.J.B., and K.A.E. analyzed data; and D.A.C., J.J.B., K.A.E., and D.P.G. wrote the paper.
-
The authors declare no conflict of interest.
-
This article is a PNAS Direct Submission.
-
Data deposition: The relaxation data and order parameters have been deposited at Biological Magnetic Resonance Bank, www.bmrb.wisc.edu/ [accession nos. 26959 (apo) and 27028 (Zn)].
-
See Commentary on page 4278.
-
This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1620665114/-/DCSupplemental.
