Dynamics of firefly luciferase inhibition by general anesthetics: Gaussian and anisotropic network analyses.
The new crystal structures of the product-bound firefly luciferase combined with the previously determined substrate-free structures allow for a detailed analysis of the dynamics basis for the luciferase enzymatic activities. Using the Gaussian network model and the anisotropic network model, we show here that the superposition of the three slowest anisotropic network model modes, consisting of the bending, rotating, and rocking motions of the C-domain, accounts for large rearrangement of domains from the substrate-free (open) to product-bound (closed) conformation and thus constitutes a critical component of the enzyme's functions. The analysis also offers a unique platform to reexamine the molecular mechanism of the anesthetic inhibition of the firefly luciferase. Through perturbing the protein backbone network by introducing additional nodes to represent anesthetics, we found that the presence of two representative anesthetics, halothane and n-decanol, in different regions of luciferase had distinctively different effects on the protein's global motion. Only at the interface of the C- and N-domains did the anesthetics cause the most profound reduction in the overall flexibility of the C-domain and the concomitant increase in the flexibility of the loop, where the substitution of a conserved lysine residue was found experimentally to lead to >2-3 orders of magnitude reduction in activity. These anesthetic-induced dynamics changes can alter the normal function of the protein, appearing as an epiphenomenon of an "inhibition". The implication of the study is that a leading element for general anesthetic action on proteins is to disrupt the modes of motion essential to protein functions.
Szarecka
Agnieszka
A
Departments of Anesthesiology, Pharmacology, and Computational Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA.
Xu
Yan
Y
Tang
Pei
P
D018681:Anesthetics, General / Q000494:pharmacology*; D000818:Animals; D016880:Anisotropy; D001665:Binding Sites; D055592:Biophysical Phenomena; D001703:Biophysics; D018360:Crystallography, X-Ray; D005233:Fatty Alcohols / Q000494:pharmacology; D006221:Halothane / Q000494:pharmacology; D066298:In Vitro Techniques; D049409:Luciferases, Firefly / Q000037:antagonists & inhibitors* / Q000737:chemistry; D008958:Models, Molecular; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D013816:Thermodynamics
D018681:Anesthetics, General; D005233:Fatty Alcohols; C029383:n-decyl alcohol; D049409:Luciferases, Firefly; D006221:Halothane