Nuclear magnetic resonance-based determination of dioxygen binding sites in protein cavities.

ABSTRACT: The location and ligand accessibility of internal cavities in cysteine-free wild-type T4 lysozyme was investigated using O₂ gas-pressure NMR spectroscopy and molecular dynamics (MD) simulation. Upon increasing the concentration of dissolved O₂ in solvent to 8.9 mM, O₂ -induced paramagnetic relaxation enhancements (PREs) to the backbone amide and side chain methyl protons were observed, specifically around two cavities in the C-terminal domain. To determine the number of O₂ binding sites and their atomic coordinates from the 1/r⁶ distance dependence of the PREs, we established an analytical procedure using Akaike's Information Criterion, in combination with a grid-search. Two O₂ -accessible sites were identified in internal c

SUBMITTER: Kitahara R 

PROVIDER: S-EPMC5818741 | biostudies-literature | 2018 Mar

REPOSITORIES: biostudies-literature