Efficiency of Charge Transport in a Polypeptide Chain: The Isolated System

A model for ultra-fast charge transport in membrane proteins

Isolated proteins have recently been observed to transport charge and reactivity over very long distances with extraordinary rates and near perfect efficiencies in spite of their site. This is not the case if the peptide is in water, where the efficiency of charge hopping to the next site is reduced to approximately 2%. Here, water is not an ideal solvent for charge transport. The issue at hand is how to explain such enormous charge transfer quenching in water compared to another typical medium, namely lipid. We performed molecular dynamics simulations to computationally substantiate the novel long-distance charge transfer yield of the polypeptides in lipids. This is characterized by the charge transfer persistent-distance decay constant and not by the rate, which is seldom, if ever, measured and hence not directly addressed here. This model can encompass an extremely wide range of yields over very long distances in peptides in various media. The calculations here demonstrate the good charge transport efficiency in lipids in contrast to the poor efficiency in water. The protein charge transport also exhibits a very strong anisotropic effect in lipids. The peptide secondary structure effect of charge transfer in membranes is analyzed in contrast to that in water. These results suggest that this model can be useful for the prediction of charge transfer efficiency in various environments of interest and indicate that the charge transfer is highly efficient in membrane proteins.

Electron delocalization and charge transfer in polypeptide chains

In this work, the electron structure and charge-transfer mechanism in polypeptide chains are investigated according to natural bond orbitals (NBO) analysis at the level of B3LYP/6-311++G**. The results indicate that the delocalization of electrons between neighboring peptide subgroups can occur in two opposite directions, and the delocalization effect in the direction from the carboxyl end to the amino end has an obvious advantage. As a result of a strong hyperconjugative interaction, the lowest unoccupied NBO of the peptide subgroup, pi*C-O, has significant delocalization to neighboring subgroups, and the energies of these NBOs decrease from the carboxyl end to the amino end. The formation of intramolecular O...H-N type hydrogen bonds also helps to delocalize the electron from the carboxyl end to the amino end. Thus, the electron will flow to the amino end. The superexchange mechanism is suggested in the electron-transfer process.

Probing Ultrafast Purely Electronic Charge Migration in Small Peptides

A pump–probe experiment that can examine a pure charge migration on a time scale short compared to the onset of nuclear motion is discussed. The mass spectrometric studies of Schlag et al. suggest that short peptide terminated by an aromatic amino acid are particularly suitable test compounds. The pump pulse needs to ionize the molecule on a time scale short compared to the period of the electronic motion, typically sub-fs. However, ionization occurs preferentially when the electrical field of the light is maximal so that the duration of the pulse envelope can be somewhat longer. Detection by photoelectron spectrometry of the peptide cation, to produce a dication, is shown to be able to probe the electronic rearrangement.

Electron transfers in proteins: investigations with a modified through-bond coupling model

By integrating the merits of previous models, a modified through-bond coupling (MTBC) model is proposed in this work and shows obvious improvement compared with previous models. With the MTBC model, the dominant electron coupling pathways in the polypeptide chains were identified, where the N-H bonds were found to be essential to the electron couplings. The local structures of peptides and proteins were finely characterized by the electron couplings and decay factors since they are structure sensitive. The neighboring carbonyl O-O distances are qualitatively correlated with the decay factors, and the deviations from the transconfigurations will weaken the coupling interactions. When the two amino acids being studied are not close in sequence, the couplings through hydrogen bonds are probably the main pathway because the electron transfers in this way save many steps, albeit the decay factor is less than that of per bond, consistent with the classical electron-tunneling model developed by Beratan [Science 252, 1285 (1991)]. It was found that the MTBC model can be effectively extended to study the electron transfers in complex biological systems with the combination of the fragment approach, which takes into account the contributions of key hydrogen bonds.

Charge Transfer in Polypeptides: Effect of Secondary Structures on Charge-Transfer Integral and Site Energies

We have theoretically studied the charge transfer in glycine polypeptide using quantum mechanical models based on a tight-binding Hamiltonian approach. The charge-transfer integrals and site energies involved in the transport of positive charge through the peptide bond in glycine polypeptide have been calculated. The charge-transfer integrals and site energies have been calculated directly from the matrix elements of the Kohn-Sham Hamiltonian defined in terms of the molecular orbitals of the individual fragments of the glycine polypeptide. In addition to this, we have calculated the rate of charge transfer between a neighboring amino acid subgroup through the Marcus rate equation. These calculations have been performed for the different secondary structures of the glycine model peptide such as linear, alpha-helix, 3(10)-helix, and antiparallel beta-sheet by varying the dihedral angles omega, varphi, and psi along the Calpha-carbon of amino acid subgroup. Present theoretical results confirm that the charge transfer through the peptide bond is strongly affected by the conformations of the oligopeptide.

Peptide electron transfer: more questions than answers

Nature has specifically designed proteins, as opposed to DNA, for electron transfer. There is no doubt about the electron transfer within proteins compared with the uncertain and continuing debate about charge transfer through DNA. However, the exact mechanism of electron transfer within peptide systems has been a source of controversy. Two different mechanisms for electron transfer between a donor and an acceptor, electron hopping and bridge-assisted superexchange, have been proposed, and are supported by experimental evidence and theoretical calculations. Several factors were found to affect the kinetics of this process, including peptide chain length, secondary structure and hydrogen bonding. Electrochemical measurements of surface-supported peptides have contributed significantly to the debate. Here we summarize the current approaches to the study of electron transfer in peptides with a focus on surface measurements and comment on these results in light of the current and often controversial debate on electron transfer mechanisms in peptides.

Understanding Electron Transfer across Negatively-Charged Aib Oligopeptides

The physicochemical effects modulating the conformational behavior and the rate of intramolecular dissociative electron transfer in phthalimide-Aibn-peroxide peptides (n = 0-3) have been studied by an integrated density functional/continuum solvent model. We found that three different orientations of the phthalimide ring are possible, labeled Phihel, PhiC7, and PhipII. In the condensed phase, they are very close in energy when the system is neutral and short. When the peptide chain length increases and the system is negatively charged, Phihel becomes instead the most stable conformer. Our calculations confirm that the 3(10)-helix is the most stable secondary structure for the peptide bridge. However, upon charge injection in the phthalimide end of the phthalimide-Aib3-peroxide, the peptide bridge can adopt an alpha-helix conformation as well. The study of the dependence of the frontier orbitals on the length and on the conformation of the peptide bridge (in agreement with experimental indications) suggests that for n = 3 the process could be influenced by a 3(10) --> alpha-helix conformational transition of the peptide chain.