Solution phase refinement of active site structure using 2D NMR and judiciously 13C-labeled cytochrome P450

Abstract

The Cytochrome P450 (CYP450) superfamily has been the subject of intense research for over six decades. Here the HU227 strain of E. coli, lacking the δ-aminolevulinic acid (δ-ALA) synthase gene, was employed, along with [5-¹³C] δ-ALA, in the heterologous expression of P450cam harboring a prosthetic group labeled with ¹³C at the four methine carbons (C_m) and pyrrole C_α positions. The product was utilized as a proof of principle strategy for defining and refining solution phase active site structure in cytochrome P450cam, providing proton-to-proton distances from ¹³C_mH to protons on bound substrate or nearby amino acid residues, using short mixing time 2D or 3D NOESY-HMQC methods. The results reveal the interesting finding that 2D ¹³C-filtered NOESY-HMQC can be used to obtain distances between protons on labeled ¹³C to positions of protons nearby in the active site, confirming the utility of this NMR-based approach to probing active site structure under physiological conditions. Such ¹³C-heme-filtered NOE data complement X-ray crystallographic and T1-based NMR measurements; and, may also be of potentially significant utility in furnishing experimental distance constraints in validations of docking routines commonly employed for determining the relative affinities and binding orientations of drug candidates with CYP450s.

Keywords: 2D (13)C-filtered NOESY-HMQC; ALA synthesis; Cytochrome P450; Docking procedures; HU227 E. coli strain; Heme proteins.