Bidirectional Electron-Transfer in Polypeptides with Various Secondary Structures

Ping Han,Lishan Yao,Chengbu Liu,Ruiyou Guo,Yefei Wang

doi:10.1038/s41598-017-16678-7

Abstract

The protein-mediated bidirectional electron transfer (ET) is the foundation of protein molecular wire, and plays an important role in the rapid detection of oxo-guanine-adenine DNA mismatches by MutY glycosylase. However, the influences of structural transitions on bidirectional ET are still not clear. In this work, the modified through-bond coupling (MTBC) model was further refined to correlate the structural transition and ET rate more quantitatively. With this model, various polyglycine structures (310-helix, α-helix, β-sheets, linear, polyproline helical I and II) were studied to explore the influences of structural transitions on bidirectional ET. It was found that the HOMO-LUMO gaps (ΔE) in CN (from the carboxyl to amino terminus) direction are much lower than that in opposite direction, except for polypro I. However, with the equal tunneling energy, the differences between bidirectional ET rates are slight for all structures. In structural transitions, we found that the ET rates are not only affected by the Ramachandran angles, but also correlated to the alignment of C = O vectors, the alignment of peptide planes and the rearrangement of other structure factors. The detailed information can be used to rationalize the inhomogeneous ET across different protein structures and design more efficient protein molecular wires.

Highlights

The assaults of endogenous and exogenous oxidative agents often lead to the oxidation of genomic DNA, which may cause aging, cancers, and neurological syndromes such as Alzheimer’s disease and amyotrophic lateral sclerosis[1,2,3,4,5,6]
The modified through-bond coupling (MTBC) model was further refined to reflect the influences of structural transitions on ET rate more quantitatively
In order to eliminate the influence of terminal groups, the relative decay factor through a glycine unit can be obtained as[40,41] εave,Gly εT otal, (n + 2)Gly εT otal, nGly where n and n+2 represent the number of glycine units in the polypeptide models

Summary

Introduction

The assaults of endogenous and exogenous oxidative agents often lead to the oxidation of genomic DNA, which may cause aging, cancers, and neurological syndromes such as Alzheimer’s disease and amyotrophic lateral sclerosis[1,2,3,4,5,6]. The more strongly binding between the DNA duplex and the MutY in reduced state increases the likelihood of the enzyme approaching and repairing the lesion In this model, the protein-mediated ET occurs in direction CN (from the carboxyl to amino terminus) or NC when MutY binds to or dissociates from DNA duplex. The protein-mediated ET occurs in direction CN (from the carboxyl to amino terminus) or NC when MutY binds to or dissociates from DNA duplex It indicates that the bidirectional ET in protein would play an important role in the recognizing and repairing process. The bifunctional model proposed by Schlag et al.[32,33,34] indicated that the ET in polypeptides should be controlled by the internal rotations of Ramachandran angles This influence was further confirmed by a recent electrochemical study[35]. By analyzing the electronic structures and ET rates, the effects of structural transitions on bidirectional ET are discussed as well

Methods

Results

Conclusion