Structural heterogeneity among four subunits in pyranose 2-oxidase: A molecular dynamics simulation study

Abstract

The homotetramer pyranose 2-oxidase (P2O) from Tetrametes multicolor contains flavin adenine dinucleotide (FAD) as a cofactor, and displays two conformers with different transient fluorescence spectra and lifetimes (ca. 0.1 ps and 360 ps). The ultrashort lifetimes of isoalloxazine (Iso) are ascribed to the photoinduced electron transfer (ET) from Trp168 to the excited Iso. Here, the structural heterogeneity among the four subunits in solution was studied by means of molecular dynamics simulation (MDS). The ET donor–acceptor distances in crystal and solution were compared. The distribution of the H-bond distances between Iso and the surrounding amino acids revealed appreciable differences among the four subunits. The structural fluctuations in two distant places were examined for the Iso-P and Iso-Q distances (where P and Q are Trp or Tyr) with the correlation coefficients between Iso-P and Iso-Q distances, revealing cooperative motions even though P and Q were more than 1 nm apart and located in different subunits. Moreover, distributions of the distances between Iso and its closest ionic amino acids markedly differed among the four subunits. Electrostatic (ES) energies between the Iso anion and the ionic amino acids in the entire protein were obtained using a static dielectric constant of 1. The ES energy in each subunit was strongly influenced by the other subunits, whilst the distributions of the ES energies greatly differed among the four subunits. This heterogeneous distribution of the ES energy between subunits may contribute to the large differences in the experimentally detected ET rates.