Probing Charge Transport through Peptide Bonds

Coherent spin transport in a copper protein

CONTEXT

The coherent electron/spin transport in azurin, a species of copper protein, was calculated based on the Landauer model. The research is motivated by the fast electron transport and spin selectivity/polarization in azurin, which have been reported in relation to the chiral-induced spin selectivity of the peptide structure. The calculated spin polarization of copper proteins was large. This phenomenon was strongly influenced by the spin density of the atoms in the ligand group, whereas the contribution of copper was negligible. The results suggest that spin polarization in copper proteins is enhanced by that of the ligand groups. The predicted spin polarization aligns primarily with the scanning tunneling microscope-based break-junction technique to study the electronic properties of single-molecule junctions.

METHODS

Computational techniques employed in this study are nonequilibrium Green's functions (NEGF) and density functional theory (DFT) based on the Landauer model, implemented using the QuantumATK software (Synopsys Inc.). The Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional was adopted for spin-polarized generalized gradient approximation (SGGA). The valence atomic orbitals were constructed using the wavefunctions of the SIESTA package, which was based on the norm-conserving Troullier-Martins relativistic pseudopotentials for describing core electrons. The mesh used for real-space integration was 150 Ha.

Single-Molecule Electrical Profiling of Peptides and Proteins

In recent decades, there has been a significant increase in the application of single-molecule electrical analysis platforms in studying proteins and peptides. These advanced analysis methods have the potential for deep investigation of enzymatic working mechanisms and accurate monitoring of dynamic changes in protein configurations, which are often challenging to achieve in ensemble measurements. In this work, the prominent research progress in peptide and protein-related studies are surveyed using electronic devices with single-molecule/single-event sensitivity, including single-molecule junctions, single-molecule field-effect transistors, and nanopores. In particular, the successful commercial application of nanopores in DNA sequencing has made it one of the most promising techniques in protein sequencing at the single-molecule level. From single peptides to protein complexes, the correlation between their electrical characteristics, structures, and biological functions is gradually being established. This enables to distinguish different molecular configurations of these biomacromolecules through real-time electrical monitoring of their life activities, significantly improving the understanding of the mechanisms underlying various life processes.

Effect of Hydrodynamic Interactions and Flow on Charge Transport in Redox-Active Polymer Solutions

Redox-active polymers (RAPs) are a subclass of polyelectrolytes that can store charge and undergo redox self-exchange reactions. RAPs are of great interest in the field of redox flow batteries (RFBs) due to their ability to quickly charge and discharge, their chemical modularity, and their molecular size. However, designing RAPs for efficient charge transport at the molecular level requires a fundamental understanding of the charge transport mechanisms that occur in RFBs. Previous work from our group has explored these mechanisms, and in this paper, we seek to improve upon the previous model by incorporating both hydrodynamic interactions (HIs) and out-of-equilibrium dynamics, which are both highly pertinent to flow battery systems. We use a hybrid Brownian dynamics and Monte Carlo simulation to model redox-active polymer chains in both dilute and semidilute solutions. This model is used to show that HI is an important feature when charge hopping is not the major mechanism for charge displacement and leads to more rapid segmental and translational motion of polymer chains that expedites charge transport at low polymer concentrations. We demonstrate that strong extensional flows may result in either enhanced or decreased transport depending on the fraction of charges present on the RAP chain. We show that flow not only can promote charge transport by extending polymer conformations but can also suppress nonadjacent charge hopping processes that are important for transport at high charge fractions. Shear flows can similarly enhance charge transport through chain extension, but tumbling dynamics lead to oscillatory displacements that become dominant features with high charge fractions and strong flows.

Electron Spin-Dependent Electrocatalysis for the Oxygen Reduction Reaction in a Chiro-Self-Assembled Iron Phthalocyanine Device

The chiral-induced spin selectivity effect (CISS) is a breakthrough phenomenon that has revolutionized the field of electrocatalysis. We report the first study on the electron spin-dependent electrocatalysis for the oxygen reduction reaction, ORR, using iron phthalocyanine, FePc, a well-known molecular catalyst for this reaction. The FePc complex belongs to the non-precious catalysts group, whose active site, FeN4, emulates catalytic centers of biocatalysts such as Cytochrome c. This study presents an experimental platform involving FePc self-assembled to a gold electrode surface using chiral peptides (L and D enantiomers), i.e., chiro-self-assembled FePc systems (CSAFePc). The chiral peptides behave as spin filters axial ligands of the FePc. One of the main findings is that the peptides' handedness and length in CSAFePc can optimize the kinetics and thermodynamic factors governing ORR. Moreover, the D-enantiomer promotes the highest electrocatalytic activity of FePc for ORR, shifting the onset potential up to 1.01 V vs. RHE in an alkaline medium, a potential close to the reversible potential of the O2 /H2 O couple. Therefore, this work has exciting implications for developing highly efficient and bioinspired catalysts, considering that, in biological organisms, biocatalysts that promote O2 reduction to water comprise L-enantiomers.

Single-molecular protein-based bioelectronics via electronic transport: fundamentals, devices and applications

Biomolecular electronics is a rapidly growing multidisciplinary field that combines biology, nanoscience, and engineering to bridge the two important fields of life sciences and molecular electronics. Proteins are remarkable for their ability to recognize molecules and transport electrons, making the integration of proteins into electronic devices a long sought-after goal and leading to the emergence of the field of protein-based bioelectronics, also known as proteotronics. This field seeks to design and create new biomolecular electronic platforms that allow for the understanding and manipulation of protein-mediated electronic charge transport and related functional applications. In recent decades, there have been numerous reports on protein-based bioelectronics using a variety of nano-gapped electrical devices and techniques at the single molecular level, which are not achievable with conventional ensemble approaches. This review focuses on recent advances in physical electron transport mechanisms, device fabrication methodologies, and various applications in protein-based bioelectronics. We discuss the most recent progress of the single or few protein-bridged electrical junction fabrication strategies, summarise the work on fundamental and functional applications of protein bioelectronics that enable high and dynamic electron transport, and highlight future perspectives and challenges that still need to be addressed. We believe that this specific review will stimulate the interdisciplinary research of topics related to protein-related bioelectronics, and open up new possibilities for single-molecule biophysics and biomedicine.

Electron transport via tyrosine-doped oligo-alanine peptide junctions: role of charges and hydrogen bonding

A way of modulating the solid-state electron transport (ETp) properties of oligopeptide junctions is presented by charges and internal hydrogen bonding, which affect this process markedly. The ETp properties of a series of tyrosine (Tyr)-containing hexa-alanine peptides, self-assembled in monolayers and sandwiched between gold electrodes, are investigated in response to their protonation state. Inserting a Tyr residue into these peptides enhances the ETp carried via their junctions. Deprotonation of the Tyr-containing peptides causes a further increase of ETp efficiency that depends on this residue's position. Combined results of molecular dynamics simulations and spectroscopic experiments suggest that the increased conductance upon deprotonation is mainly a result of enhanced coupling between the charged C-terminus carboxylate group and the adjacent Au electrode. Moreover, intra-peptide hydrogen bonding of the Tyr hydroxyl to the C-terminus carboxylate reduces this coupling. Hence, the extent of such a conductance change depends on the Tyr-carboxylate distance in the peptide's sequence.

Charge Transport Across Dynamic Covalent Chemical Bridges

Relationships between chemical structure and conductivity in ordered polymers (OPs) are difficult to probe using bulk samples. We propose that conductance measurements of appropriate molecular-scale models can reveal trends in electronic coupling(s) between repeat units that may help inform OP design. Here, we apply the scanning tunneling microscope-based break-junction (STM-BJ) method to study transport through single-molecules comprising OP-relevant imine, imidazole, diazaborole, and boronate ester dynamic covalent chemical bridges. Notably, solution-stable boron-based compounds dissociate in situ unless measured under a rigorously inert glovebox atmosphere. We find that junction conductance negatively correlates with the electronegativity difference between bridge atoms, and corroborative first-principles calculations further reveal a different nodal structure in the transmission eigenchannels of boronate ester junctions. This work reaffirms expectations that highly polarized bridge motifs represent poor choices for the construction of OPs with high through-bond conductivity and underscores the utility of glovebox STM-BJ instrumentation for studies of air-sensitive materials.

Constrained DFT for Molecular Junctions

We have explored the use of constrained density functional theory (cDFT) for molecular junctions based on benzenediamine. By elongating the junction, we observe that the energy gap between the ionization potential and the electronic affinity increases with the stretching distance. This is consistent with the trend expected from the electrostatic screening. A more detailed analysis shows how this influences the charge distribution of both the individual metal layers and the molecular atoms. Overall, our work shows that constrained DFT is a powerful tool for studying screening effects in molecular junctions.

Single-Molecule Junction Formation in Break-Junction Measurements

The scanning tunneling microscope-based break-junction (STM-BJ) technique is the most common method used to study the electronic properties of single-molecule junctions. It relies on repeatedly forming and rupturing a Au contact in an environment of the target molecules. The probability of junction formation is typically very high (∼70-95%), prompting questions relating to how the nanoscale structure of the Au electrode before the metal point contact ruptures alters junction formation. Here we analyze conductance traces measured with the STM-BJ setup by combining correlation analysis and multiple machine learning tools, including gradient-boosted trees and neural networks. We show that two key features describing the Au-Au contact prior to rupture determine the extent of contact relaxation (snapback) and the probability of junction formation. Importantly, our data strongly indicate that molecular junctions are formed prior to the rupture of the Au-Au contact, explaining the high probability of junction formation observed in room-temperature solution measurements.

Conformation-dependent charge transport through short peptides

We report on charge transport across single short peptides using the Mechanically Controlled Break Junction (MCBJ) method. We record thousands of electron transport events across single-molecule junctions and with an unsupervised machine learning algorithm, we identify several classes of traces with multifarious conductance values that may correspond to different peptide conformations. Data analysis shows that very short peptides, which are more rigid, show conductance plateaus at low conductance values of about 10^-3G₀ and below, with G₀ being the conductance quantum, whereas slightly longer, more flexible peptides also show plateaus at higher values. Fully stretched peptide chains exhibit conductance values that are of the same order as that of alkane chains of similar length. The measurements show that in the case of short peptides, different compositions and molecular lengths offer a wide range of junction conformations. Such information is crucial to understand mechanism(s) of charge transport in and across peptide-based biomolecules.

Large Increase in the Dielectric Constant and Partial Loss of Coherence Increases Tunneling Rates across Molecular Wires

Although the dielectric behavior of monolayers is important in a large range of applications, its role in charge transport studies involving molecular junctions is largely ignored. This paper describes a large increase in the relative static dielectric constant (ε_r) by simply increasing the thickness of well-organized monolayers of oligoglycine and oligo(ethylene glycol) from 7 up to 14. The resulting large capacitance of 3.5-5.1 μF/cm² is thickness-independent, which is highly attractive for field-effect transistor applications. This increase of ε_r results in a linear increase of the thermal activation energy by a factor of 6, which suggests that the mechanism of charge transport gradually changes from coherent to (partially) incoherent tunneling. The comparisons of oligoglycine (which readily forms hydrogen bonds with neighboring molecules) and methyl terminated oligo(ethylene glycol) (which lacks hydrogen bond donors) monolayers, kinetic isotope effects, and relative humidity-dependent measurements all indicate the importance of strong hydrogen bonds involving ionic species and strongly bonded water in the unusual dielectric behavior and the incoherent tunneling mechanism. This partial loss of coherence of the charge carriers can explain the unusually small tunneling decay coefficients across long molecular wires, and the length-dependent increase of ε_r of monolayers opens up interesting new applications.

Ubiquitous Electron Transport in Non-Electron Transfer Proteins

Many proteins that have no known role in electron transfer processes are excellent electronic conductors. This surprising characteristic is not generally evident in bulk aggregates or crystals, or in isolated, solvated peptides, because the outer hydrophilic shell of the protein presents a barrier to charge injection. Ligands that penetrate this barrier make excellent electrical contacts, yielding conductivities on the order of a S/m. The Fermi Energy of metal electrodes is aligned with the energy of internal electronic states of the protein, as evidenced by resonant transmission peaks at about 0.3V on the Normal Hydrogen Electrode scale. This energy is about 0.7 V less than the oxidation potential of aromatic amino acids, indicating a large reduction in electrostatic reorganization energy losses in the interior of the proteins. Consistent with a possible biological role for this conductance, there is a strong dependence on protein conformation. Thus, direct measurement of conductance is a powerful new way to read out protein conformation in real time, opening the way to new types of single molecule sensors and sequencing devices.

Coenzyme Coupling Boosts Charge Transport through Single Bioactive Enzyme Junctions

Oxidation of formate to CO₂ is catalyzed via the donation of electrons from formate dehydrogenase (FDH) to nicotinamide adenine dinucleotide (NAD⁺), and thus the charge transport characteristics of FDH become essential but remain unexplored. Here, we investigated the charge transport through single-enzyme junctions of FDH using the scanning tunneling microscope break junction technique (STM-BJ). We found that the coupling of NAD⁺ with FDH boosts the charge transport by ∼2,100%, and the single-enzyme conductance highly correlates with the enzyme activity. The combined flicker noise analysis demonstrated the switching of the coenzyme-mediated charge transport pathway and supported by the significantly reduced HOMO-LUMO gap from calculations. Site-specific mutagenesis analysis demonstrated that FDH-NAD⁺ stably combined own higher bioactivity and boosts charge transport, and the coupling has been optimized via the natural selection. Our work provides evidence of hydrogen bond coupling in bioactivity but also bridges the charge transport through single-enzyme junctions and enzyme activities.

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Binding of NAD⁺ with FDH boosts the charge transport by more than 2,100%

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Single-enzyme conductance highly correlates with the enzyme activity

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Hydrogen bond bridges the charge transport and enzyme activities

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Experiments combined with calculations probe switching of charge transport pathway

Backbone-Constrained Peptides: Temperature and Secondary Structure Affect Solid-State Electron Transport

The primary sequence and secondary structure of a peptide are crucial to charge migration, not only in solution (electron transfer, ET), but also in the solid-state (electron transport, ETp). Hence, understanding the charge migration mechanisms is fundamental to the development of biomolecular devices and sensors. We report studies on four Aib-containing helical peptide analogues: two acyclic linear peptides with one and two electron-rich alkene-based side chains, respectively, and two peptides that are further rigidified into a macrocycle by a side bridge constraint, containing one or no alkene. ETp was investigated across Au/peptide/Au junctions, between 80 and 340 K in combination with the molecular dynamic (MD) simulations. The results reveal that the helical structure of the peptide and electron-rich side chain both facilitate the ETp. As temperature increases, the loss of helical structure, change of monolayer tilt angle, and increase of thermally activated fluctuations affect the conductance of peptides. Specifically, room temperature conductance across the peptide monolayers correlates well with previously observed ET rate constants, where an interplay between backbone rigidity and electron-rich side chains was revealed. Our findings provide new means to manipulate electronic transport across solid-state peptide junctions.

Electronic Decay Length in a Protein Molecule

Antibodies have two identical binding domains and can therefore form a well-defined conducting bridge by binding a pair of electrodes functionalized with an epitope. The conductance measured between these two fixed points on the antibody does not change with the size of the electrode gap. A second conduction path is via one specific attachment to an epitope and a second nonspecific attachment to the surface of the antibody. In this case, the conductance does change with gap size, yielding an estimated electronic decay length >6 nm, long enough that it is not possible to distinguish between an exponential or a hyperbolic distance dependence. This decay length is substantially greater than that measured for hopping transport in an organic molecular wire.

Doping hepta-alanine with tryptophan: A theoretical study of its effect on the electrical conductance of peptide-based single-molecule junctions

Motivated by a recent experiment [C. Guo et al., Proc. Natl. Acad. Sci. U. S. A. 113, 10785 (2016)], we carry out a theoretical study of electron transport through peptide-based single-molecule junctions. We analyze the pristine hepta-alanine and its functionalizations with a single tryptophan unit, which is placed in three different locations along the backbone. Contrary to expectations from the experiment on self-assembled monolayers, we find that insertion of tryptophan does not raise the electrical conductance and that the resulting peptides instead remain insulating in the framework of a coherent transport picture. The poor performance of these molecules as conductors can be ascribed to the strongly off-resonant transport and low electrode-molecule coupling of the frontier orbitals. Although the introduction of tryptophan increases the energy of the highest occupied molecular orbital (HOMO) of the peptides in the gas phase, the new HOMO states are localized on the tryptophan unit and therefore essentially do not contribute to coherent charge transport.

Thermoelectric properties of oligoglycine molecular wires

We have investigated the electrical and thermoelectrical properties of glycine chains with and without cysteine terminal groups. The electrical conductance of (Gly)n, (Gly)nCys and Cys(Gly)nCys molecules (where Gly, Cys represent glycine and cysteine and n = 1-3) was found to decay exponentially with length l as e-βl. Our results show that connecting the molecules to gold electrodes via the sulphur atom of the cysteine moiety leads to higher β factors of 1.57 Å-1 and 1.22 Å-1 for (Gly)nCys and Cys(Gly)nCys respectively, while β = 0.92 Å-1 for (Gly)n. We also find that replacing the peptide bond with a methylene group (-CH2-) increases the conductance of (Gly)3Cys. Furthermore, we find the (Gly)1Cys and Cys(Gly)1Cys systems show good thermoelectrical performance, because of their high Seebeck coefficients (∼0.2 mV K-1) induced by the sulphur of the cysteine(s). With the contributions of both electrons and phonons taken into consideration, a high figure of merit ZT = 0.8 is obtained for (Gly)1Cys at room temperature, which increases further with increasing temperature, suggesting that peptide-based SAM junctions are promising candidates for thermoelectric energy harvesting.

Electron Transport Through Homopeptides: Are They Really Good Conductors?

Motivated by recent experiments, we performed a theoretical study of electron transport through single-molecule junctions incorporating four kinds of homopeptides (based on alanine, glutamic acid, lysine, and tryptophan). Our results suggest that these molecules are rather insulating and operate in off-resonance tunneling as their main transport mechanism. We ascribe their poor performance as conductors to the high localization of their frontier orbitals. We found that binding scenarios in which side chains lie on the side of gold protuberances could give rise to an increase in conductance with respect to end-to-end binding configurations. These findings provide an insight into the conductance mechanism of the building blocks of proteins and identify key issues that need to be further investigated.