title: Energetics of zinc-mediated interactions in the allosteric pathways of metal sensor proteins.
abstract: A metal-mediated interprotomer hydrogen bond has been implicated in the allosteric mechanism of DNA operator binding in several metal-sensing proteins. Using computational methods, we investigate the energetics of such zinc-mediated interactions in members of the ArsR/SmtB family of proteins (CzrA, SmtB, CadC, and NmtR) and the MarR family zinc-uptake repressor AdcR, which feature similar interactions, but in sites that differ widely in their allosteric responsiveness. We provide novel structural insight into previously uncharacterized allosteric forms of these proteins using computational methodologies. We find this metal-mediated interaction to be significantly stronger (∼8 kcal/mol) at functional allosteric metal binding sites compared to a nonresponsive site (CadC) and the apo-proteins. Simulations of the apo-proteins further reveal that the high interaction energy works to overcome the considerable disorder at these hydrogen-bonding sites and functions as a "switch" to lock in a weak DNA-binding conformation once metal is bound. These findings suggest a conserved functional role of metal-mediated second coordination shell hydrogen bonds at allosterically responsive sites in zinc-sensing transcription regulators.
authors.affiliation: Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, Florida 32611-8435, United States.
authors.forename: Dhruva K
authors.initials: DK
authors.lastname: Chakravorty
authors.forename: Trent M
authors.initials: TM
authors.lastname: Parker
authors.forename: Alfredo J
authors.initials: AJ
authors.lastname: Guerra
authors.forename: C David
authors.initials: CD
authors.lastname: Sherrill
authors.forename: David P
authors.initials: DP
authors.lastname: Giedroc
authors.forename: Kenneth M
authors.initials: KM
authors.lastname: Merz
mesh_terms: D000494:Allosteric Regulation; D001426:Bacterial Proteins / Q000737:chemistry / Q000378:metabolism*; D006860:Hydrogen Bonding; D008958:Models, Molecular; D009169:Mycobacterium tuberculosis / Q000737:chemistry / Q000378:metabolism; D013210:Staphylococcus / Q000737:chemistry / Q000378:metabolism; D013816:Thermodynamics; D015032:Zinc / Q000737:chemistry / Q000378:metabolism*
chemical_list: D001426:Bacterial Proteins; D015032:Zinc