Worm Model for Electron Tunneling in Proteins:  Consolidation of the Pathway Model and the Dutton Plot

Abstract

We present a novel method for selecting important electron tunneling pathways in proteins by connecting important interatomic tunneling currents. Then, we constituted an electron tunneling route, called a “worm”, which is formed by averaging over all of the interatomic tunneling currents. The method is applied to six kinds of Ru-modified azurins where the electron transfer takes place from the copper ion to the ruthenium ion linked to the surface of the azurin. We found that the worm is not straight but winds, reflecting the specific role of the microenvironment of the protein structure and ligands in the electron tunneling pathway and rather narrow radius of the worm, ca. 1.5 Å at most. The donor−acceptor distance dependence of the electron-transfer rate k e is examined by taking into account the one-dimensional atomic density in the worm. We found that the Dutton plot, in which the logarithm of k e is in a linear relation with the donor−acceptor distance, which, in turn, depends somewhat on the one-dimensional atom density, is reproduced for a certain level of analysis by the worm model. Thus, we can consolidate the electron tunneling pathway model with the Dutton plot by using the worm model.

Generation of adenosyl radical from S-adenosylmethionine (SAM) in biotin synthase

“…The rate of electron transfer is proportional to the square of the electron coupling matrix element. Many theoretical studies [98][99][100][101][102][103][104][105][106][107] highlighted the importance of the electronic coupling interactions because H DA is expected to decay exponentially with the distance between the donor and acceptor. For thermal electron transfer, H DA represents the one-half splitting between the adiabatic states associated with the D − and A − at the transition state [108][109][110][111].…”

Electron transfer between cofactors in protein domains linked by a flexible tether

“…Transition rates are defined for conformational transitions among geometries. The ET rate constant is assumed to be geometry dependent [21,[30][31][32][33][34][35][36][37][38][39] and we neglect the back ET reaction. We first sample the inter-domain potential surface and calculate the distribution of reaction pathways.…”

Gated Electron Transfers and Electron Pathways in Azurin: A NMR Dynamic Study at Multiple Fields and Temperatures

“…lower than 2.98-1.43Z1.55. Five of these residues (11,(47)(48)(49)120) are spatially close (the longest distance is 9.2 Å ) to the copper ion and participate in a tight hydrogen bond network around the metal site. 32 Residues 47-49 extend from the two copper ligands Gly45 and His46 and lead to a b-strand.…”

“…Another approach chosen by several groups induces artificial ET from a ruthenium complex 47 attached to azurin; of particular interest here is the attachment to His83. [19][20][21]48,49 Experiments and calculations yield again a network of ET pathways, containing in a central position the b-sheet including the strands with residues 46-49 and 111-112. Essential interference in the network of pathways is achieved through interstrand hydrogen bonds.…”