Dynamics of the protein structure of T169S pyranose 2-oxidase in solution: Molecular dynamics simulation

Abstract

Pyranose 2-oxidase (P2O) from Trametes multicolor contains FAD as cofactor, and forms a tetramer. The protein structure of a mutated P2O, T169S (Thr169 is replaced by Ser), in solution was studied by means of molecular dynamics simulation and analyses of photoinduced electron transfer (ET) from Trp168 to excited isoalloxazine (Iso*), and was compared with wild type (WT) P2O. Hydrogen bonding between Iso and nearby amino acids was very similar as between T169S and WT protein. Distances between Iso and Tyr456 were extremely heterogeneous among the subunits, 1.7 (1.5 in WT) in subunit A (Sub A), 0.97 (2.2 in WT) in Sub B, 1.3 (2.1 in WT) in Sub C, 1.3 nm (2.0 in WT) in Sub D. Mean values of root of mean square fluctuation over all residues were greater by four times than those in WT. This suggests that the protein structure of T169S is much more flexible than that of WT. Electrostatic (ES) energies between Iso anion in one subunit and ionic groups in the entire protein were evaluated. It was found that more than 50% of the total ES energy in each subunit is contributed from other subunits. Reported fluorescence decays were analyzed by a method as WT, previously reported. Electron affinities of Iso* in T169S were appreciably higher than those in WT. Static dielectric constants near Iso and Trp168 were also quite higher in T169S than those in WT.

Ultrafast photoinduced flavin dynamics in the unusual active site of the tRNA methyltransferase TrmFO

“…19 Similar ET phenomena from aromatic amino acids (Tyr and Trp) to the excited isoalloxazine, resulting in ultrashort excited-state lifetimes, have been previously reported in numerous other flavoproteins. [20][21][22][23][24][25][26][27][28][29][30] Such ET is very sensitive to the distance of the reactive centers and can reciprocally be considered as reporter of their relative position, as for instance formerly used to explore the structural flexibility of ThyX. 31 Ultrafast spectroscopy is a particularly suited tool for probing such reactions, which Nag et al recently applied to investigate the quenching dynamics of two variants of TtTrmFO, C51A and C51A/Y343F.…”

Equivalence between inverted regions of the energy gap law and inverted regions of donor–acceptor distances in photoinduced electron transfer processes in flavoproteins

“…The third term is the ES energy between the ion-pair and ionic groups in the protein, which is described elsewhere. [28][29][30][31] DG 0 (t) is dependent on the environment near a donor and an acceptor molecule as in anoxygenic photosynthetic bacteria. 42 Tyr residues (termed YZ and YD) in Photosystem II of the bacteria display the difference in redox potential despite that they are also symmetrically arranged in the vicinity of the same electron donor (P680).…”

“…[21][22][23][24][25][26][27] The ET rate from the individual donor has been evaluated with an ET theory and MDS structures, using uorescence lifetimes or decays in these avoproteins. [24][25][26][27][28][29][30][31] Logarithmic ET rates (ln Rates) linearly decrease with the donor-acceptor distances (Rc), known as the Dutton law. 32 However, the ln Rate vs. Rc relationship oen displays parabolic functions with Rc in avoproteins, when the rates are faster than ca.…”

“…1 ps À1 . [28][29][30][31] In these donors, the values of ln Rate become smaller with Rc, which is called the inverted region of Rc (Rc-inverted region). [28][29][30][31] In the present study, we call the ln Rate vs. Rc relationship the extend Dutton law (EXDL).…”

“…[28][29][30][31] In these donors, the values of ln Rate become smaller with Rc, which is called the inverted region of Rc (Rc-inverted region). [28][29][30][31] In the present study, we call the ln Rate vs. Rc relationship the extend Dutton law (EXDL). However, it is also known that the ln Rate vs. standard free energy gap (SFEG) relationship displays parabolic functions, which is called the energy gap law (SEGL).…”