Dynamics of Firefly Luciferase Inhibition by General Anesthetics: Gaussian and Anisotropic Network Analyses

¹ University of Pittsburgh School of Medicine

^* To whom correspondence should be addressed. E-mail: tangp{at}anes.upmc.edu.

Submitted on December 7, 2006
Revised on January 14, 2007
Accepted on 10 May 2007

	Abstract

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 Gaussian Network Model (GNM) and Anisotropic Network Model (ANM), we show here that the superposition of the three slowest ANM 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 (close) 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 impact on the protein 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 activities. 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.

Key Words: ANM, GNM, elastic network models, general anesthesia, luciferase, mechanism of general anesthesia

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