title: Binding Site Configurations Probe the Structure and Dynamics of the Zinc Finger of NEMO (NF-κB Essential Modulator).
abstract: Zinc-finger proteins are regulators of critical signaling pathways for various cellular functions, including apoptosis and oncogenesis. Here, we investigate how binding site protonation states and zinc coordination influence protein structure, dynamics, and ultimately function, as these pivotal regulatory proteins are increasingly important for protein engineering and therapeutic discovery. To better understand the thermodynamics and dynamics of the zinc finger of NEMO (NF-κB essential modulator), as well as the role of zinc, we present results of 20 μs molecular dynamics trajectories, 5 μs for each of four active site configurations. Consistent with experimental evidence, the zinc ion is essential for mechanical stabilization of the functional, folded conformation. Hydrogen bond motifs are unique for deprotonated configurations yet overlap in protonated cases. Correlated motions and principal component analysis corroborate the similarity of the protonated configurations and highlight unique relationships of the zinc-bound configuration. We hypothesize a potential mechanism for zinc binding from results of the thiol configurations. The deprotonated, zinc-bound configuration alone predominantly maintains its tertiary structure throughout all 5 μs and alludes rare conformations potentially important for (im)proper zinc-finger-related protein-protein or protein-DNA interactions.
authors.affiliation: Department of Physics, Wake Forest University , Winston-Salem, North Carolina 27106, United States.
authors.forename: Ryan C
authors.initials: RC
authors.lastname: Godwin
authors.affiliation: Department of Physics, Wake Forest University , Winston-Salem, North Carolina 27106, United States.
authors.forename: Ryan L
authors.initials: RL
authors.lastname: Melvin
authors.affiliation: Department of Cancer Biology, Wake Forest University Health Sciences , Winston-Salem, North Carolina 27107, United States.
authors.forename: William H
authors.initials: WH
authors.lastname: Gmeiner
authors.affiliation: Department of Physics, Wake Forest University , Winston-Salem, North Carolina 27106, United States.
authors.forename: Freddie R
authors.identifier: 0000-0002-2699-829X
authors.initials: FR
authors.lastname: Salsbury
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D002413:Cations, Divalent; D015870:Gene Expression; D006801:Humans; D006860:Hydrogen Bonding; D051550:I-kappa B Kinase / Q000737:chemistry* / Q000235:genetics; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D000072417:Protein Domains; D017510:Protein Folding; D017433:Protein Structure, Secondary; D013816:Thermodynamics; D015032:Zinc / Q000737:chemistry*; D016335:Zinc Fingers / Q000235:genetics*
chemical_list: D002413:Cations, Divalent; C491731:IKBKG protein, human; D051550:I-kappa B Kinase; D015032:Zinc