Mutation-Induced Population Shift in the MexR Conformational Ensemble Disengages DNA Binding: A Novel Mechanism for MarR Family Derepression

Madhanagopal Anandapadamanaban; Robert Pilstål; Cecilia Andresen; Jill Trewhella; Martin Moche; Björn Wallner; Maria Sunnerhagen

doi:10.1016/j.str.2016.06.008

Mutation-Induced Population Shift in the MexR Conformational Ensemble Disengages DNA Binding: A Novel Mechanism for MarR Family Derepression

Structure. 2016 Aug 2;24(8):1311-1321. doi: 10.1016/j.str.2016.06.008. Epub 2016 Jul 14.

Authors

Madhanagopal Anandapadamanaban¹, Robert Pilstål², Cecilia Andresen¹, Jill Trewhella³, Martin Moche⁴, Björn Wallner², Maria Sunnerhagen⁵

Affiliations

¹ Division of Chemistry, Department of Physics, Chemistry and Biology, Linköping University, 581 83 Linköping, Sweden.
² Division of Bioinformatics, Department of Physics, Chemistry and Biology, Linköping University, 581 83 Linköping, Sweden.
³ Division of Chemistry, Department of Physics, Chemistry and Biology, Linköping University, 581 83 Linköping, Sweden; School of Molecular Bioscience, The University of Sydney, Sydney, NSW 2006, Australia.
⁴ Department of Medical Biochemistry and Biophysics, Protein Science Facility, Karolinska Institutet, 171 77 Stockholm, Sweden.
⁵ Division of Chemistry, Department of Physics, Chemistry and Biology, Linköping University, 581 83 Linköping, Sweden. Electronic address: [email protected].

PMID: 27427478
DOI: 10.1016/j.str.2016.06.008

Abstract

MexR is a repressor of the MexAB-OprM multidrug efflux pump operon of Pseudomonas aeruginosa, where DNA-binding impairing mutations lead to multidrug resistance (MDR). Surprisingly, the crystal structure of an MDR-conferring MexR mutant R21W (2.19 Å) presented here is closely similar to wild-type MexR. However, our extended analysis, by molecular dynamics and small-angle X-ray scattering, reveals that the mutation stabilizes a ground state that is deficient of DNA binding and is shared by both mutant and wild-type MexR, whereas the DNA-binding state is only transiently reached by the more flexible wild-type MexR. This population shift in the conformational ensemble is effected by mutation-induced allosteric coupling of contact networks that are independent in the wild-type protein. We propose that the MexR-R21W mutant mimics derepression by small-molecule binding to MarR proteins, and that the described allosteric model based on population shifts may also apply to other MarR family members.

MeSH terms

Allosteric Regulation
Allosteric Site
Amino Acid Sequence
Bacterial Proteins / chemistry*
Bacterial Proteins / genetics
Bacterial Proteins / metabolism
Binding Sites
Cloning, Molecular
Crystallography, X-Ray
DNA, Bacterial / chemistry*
DNA, Bacterial / genetics
DNA, Bacterial / metabolism
Escherichia coli / genetics
Escherichia coli / metabolism
Gene Expression
Gene Expression Regulation, Bacterial*
Molecular Dynamics Simulation
Mutation*
Operon
Protein Binding
Protein Conformation, alpha-Helical
Protein Conformation, beta-Strand
Protein Interaction Domains and Motifs
Pseudomonas aeruginosa / genetics*
Pseudomonas aeruginosa / metabolism
Recombinant Proteins / chemistry
Recombinant Proteins / genetics
Recombinant Proteins / metabolism
Repressor Proteins / chemistry*
Repressor Proteins / genetics
Repressor Proteins / metabolism
Scattering, Small Angle
Sequence Alignment
Sequence Homology, Amino Acid
X-Ray Diffraction

Substances

Bacterial Proteins
DNA, Bacterial
MexR protein, Pseudomonas aeruginosa
Recombinant Proteins
Repressor Proteins