Unraveling the interplay of backbone rigidity and electron rich side-chains on electron transfer in peptides: the realization of tunable molecular wires

Secondary structure determines electron transport in peptides

Proteins play a key role in biological electron transport, but the structure-function relationships governing the electronic properties of peptides are not fully understood. Despite recent progress, understanding the link between peptide conformational flexibility, hierarchical structures, and electron transport pathways has been challenging. Here, we use single-molecule experiments, molecular dynamics (MD) simulations, nonequilibrium Green's function-density functional theory (NEGF-DFT), and unsupervised machine learning to understand the role of secondary structure on electron transport in peptides. Our results reveal a two-state molecular conductance behavior for peptides across several different amino acid sequences. MD simulations and Gaussian mixture modeling are used to show that this two-state molecular conductance behavior arises due to the conformational flexibility of peptide backbones, with a high-conductance state arising due to a more defined secondary structure (beta turn or 310 helices) and a low-conductance state occurring for extended peptide structures. These results highlight the importance of helical conformations on electron transport in peptides. Conformer selection for the peptide structures is rationalized using principal component analysis of intramolecular hydrogen bonding distances along peptide backbones. Molecular conformations from MD simulations are used to model charge transport in NEGF-DFT calculations, and the results are in reasonable qualitative agreement with experiments. Projected density of states calculations and molecular orbital visualizations are further used to understand the role of amino acid side chains on transport. Overall, our results show that secondary structure plays a key role in electron transport in peptides, which provides broad avenues for understanding the electronic properties of proteins.

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.

An interesting possibility of forming special hole stepping stones with high-stacking aromatic rings in proteins: three-π five-electron and four-π seven-electron resonance bindings

Long-range hole transfer of proteins plays an important role in many biological processes of living organisms. Therefore, it is highly useful to examine the possible hole stepping stones, which can facilitate hole transfer in proteins. However, the structures of stepping stones are diverse because of the complexity of the protein structures. In the present work, we proposed a series of special stepping stones, which are instantaneously formed by three and four packing aromatic side chains of amino acids to capture a hole, corresponding to three-π five-electron (π:π∴π↔π∴π:π) and four-π seven-electron (π:π∴π:π↔π:π:π∴π) resonance bindings with appropriate binding energies. The aromatic amino acids include histidine (His), phenylalanine (Phe), tyrosine (Tyr) and tryptophan (Trp). The formations of these special stepping stones can effectively reduce the local ionization potential of the high π-stacking region to efficiently capture the migration hole. The quick formations and separations of them promote the efficient hole transfer in proteins. More interestingly, we revealed that a hole cannot delocalize over infinite aromatic rings along the high π-π packing structure at the same time and the micro-surroundings of proteins can modulate the formations of π:π∴π↔π∴π:π and π:π∴π:π↔π:π:π∴π bindings. These results may contribute a new avenue to better understand the potential hole transfer pathway in proteins.

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.

Constructing Dual-Molecule Junctions to Probe Intermolecular Crosstalk

Understanding and controlling charge transport across multiple parallel molecules are fundamental to the creation of innovative functional electronic components, as future molecular devices will likely be multimolecular. The smallest possible molecular ensemble to address this challenge is a dual-molecule junction device, which has potential to unravel the effects of intermolecular crosstalk on electronic transport at the molecular level that cannot be elucidated using either conventional single-molecule or self-assembled monolayer (SAM) techniques. Herein, we demonstrate the fabrication of a scanning tunneling microscopy (STM) dual-molecule junction device, which utilizes noncovalent interactions and allows for direct comparison to the conventional STM single-molecule device. STM-break junction (BJ) measurements reveal a decrease in conductance of 10% per molecule from the dual-molecule to the single-molecule junction device. Quantum transport simulations indicate that this decrease is attributable to intermolecular crosstalk (i.e., intermolecular π-π interactions), with possible contributions from substrate-mediated coupling (i.e., molecule-electrode). This study provides the first experimental evidence to interpret intermolecular crosstalk in electronic transport at the STM-BJ level and translates the experimental observations into meaningful molecular information to enhance our fundamental knowledge of this subject matter. This approach is pertinent to the design and development of future multimolecular electronic components and also to other dual-molecular systems where such crosstalk is mediated by various noncovalent intermolecular interactions (e.g., electrostatic and hydrogen bonding).

Unravelling electron transfer in peptide-cation complexes: a model for mimicking redox centres in proteins

We provide evidence that bound zinc promotes electron transfer in a peptide by changing the electronic properties of the peptide.

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.

Dynamic relaying properties of a β-turn peptide in long-range electron transfer

The relay stations play a significant role in long-range charge hopping transfer in proteins. Although studies have clarified that many more protein structural motifs can function as relays in charge hopping transfers by acting as intermediate charge carriers, the relaying properties are still poorly understood. In this work, taking a β-turn oligopeptide as an example, we report a dynamic character of a relay with tunable relaying properties using the density functional theory calculations. Our main finding is that a β-turn peptide can serve as an effective electron relay in facilitating long-range electron migration and its relay properties is vibration-tunable. The vibration-induced structural transient distortions remarkably affect the lowest occupied molecular orbital (LUMO) energy, vertical electron affinity and electron-binding mode of the β-turn oligopeptide and the singly occupied molecular orbital (SOMO) energy of the corresponding electron adduct and thus the relaying properties. Different vibration modes lead to different structural distortions and thus have different effects on the relaying properties and ability of the β-turn peptide. For the relaying properties, there approximately is a linear negative correlation of electron affinity with the LUMO energy of the β-turn or the SOMO energy of its electron adduct. Besides, such relaying properties also vary in the vibration evolution process, and the electron-binding modes may be tunable. As an important addition to the known static charge relaying properties occurring in various protein structural motifs, this work reports the dynamic electron-relaying characteristics of a β-turn oligopeptide with variable relaying properties governed by molecular vibrations which can be applied to different proteins in mediating long-range charge transfers. Clearly, this work reveals molecular vibration effects on the electron relaying properties of protein structural motifs and provides new insights into the dynamics of long-range charge transfers in proteins. © 2018 Wiley Periodicals, Inc.

Mechanistic insight into protein supported biosorption complemented by kinetic and thermodynamics perspectives

In this review, we discussed the micro-level aspects of protein supported biosorption. The mechanism, surface chemistry in terms of energy interactions and electron transfer process (ETP) of peptide systems within protein are three important areas that provide mechanistic insight into protein supported biosorption. The functional groups in proteinous material like hydroxyl (-OH), carbonyl (>C=O), carboxyl (-COOH) and sulfhydryl (-SH) play a significant role in the biosorption of variety of pollutants such as metal ions, metalloids, and organic matters in wastewaters. The mechanistic aspects of biosorption are crucial not only for the separation process but also they contribute towards stoichiometric considerations and mathematical modelling process. The surface chemistry of applied biosorbents relies on interfacial components whose interaction energies are estimated with help of classical Derjaguin, Landau, Verwey, and Overbeek (DLVO) theory mathematically. Proteins are the fundamental molecules of many biomaterial used for the biosorption of contaminents and peptide bond is considered as the backbone of proteins. The charge variations on peptide bonding is the result of ETP whose discussion was made part of this review for understaning number of biological and technological processes of vital interests. In addition, this review was complemented by exhaustive overview of kinetic and thermodynamics perspectives of biosorption process.

Peptides as Bio-Inspired Electronic Materials: An Electrochemical and First-Principles Perspective

Molecular electronics is at the forefront of interdisciplinary research, offering a significant extension of the capabilities of conventional silicon-based technology as well as providing a possible stand-alone alternative. Bio-inspired molecular electronics is a particularly intriguing paradigm, as charge transfer in proteins/peptides, for example, plays a critical role in the energy storage and conversion processes for all living organisms. However, the structure and conformation of even the simplest protein is extremely complex, and therefore, synthetic model peptides comprising well-defined geometry and predetermined functionality are ideal platforms to mimic nature for the elucidation of fundamental biological processes while also enhancing the design and development of single-peptide electronic components. In this Account, we first present intramolecular electron transfer within two synthetic peptides, one with a well-defined helical conformation and the other with a random geometry, using electrochemical techniques and computational simulations. This study reveals two definitive electron transfer pathways (mechanisms), the natures of which are dependent on secondary structure. Following on from this, electron transfer within a series of well-defined helical peptides, constrained by either Huisgen cycloaddition, ring-closing metathesis, or a lactam bridge, was determined. The electrochemical results indicate that each constrained peptide, in contrast to a linear counterpart, exhibits a remarkable shift of the formal potential to the positive (>460 mV) and a significant reduction of the electron transfer rate constant (up to 15-fold), which represent two distinct electronic "on/off" states. High-level calculations demonstrate that the additional backbone rigidity provided by the side-bridge constraints leads to an increased reorganization energy barrier, which impedes the vibrational fluctuations necessary for efficient intramolecular electron transfer through the peptide backbone. Further calculations reveal a clear mechanistic transition from hopping to superexchange (tunneling) stemming from side-bridge gating. We then extended our research to fine-tuning of the electronic properties of peptides through both structural and chemical manipulation, to reveal an interplay between electron-rich side chains and backbone rigidity on electron transfer. Further to this, we explored the possibility that the side-bridge constraints present in our synthetic peptides provide an additional electronic transport pathway, which led to the discovery of two distinct forms of quantum interferometer. The effects of destructive quantum interference appear essentially through both the backbone and an alternative tunneling pathway provided by the side bridge in the constrained β-strand peptide, as evidenced by a correlation between electrochemical measurements and conductance simulations for both linear and constrained β-strand peptides. In contrast, an interplay between quantum interference effects and vibrational fluctuations is revealed in the linear and constrained 3₁₀-helical peptides. Collectively, these exciting findings augment our fundamental knowledge of charge transfer dynamics and kinetics in peptides and also open up new avenues to design and develop functional bio-inspired electronic devices, such as on/off switches and quantum interferometers, for practical applications in molecular electronics.

Rational Design of a 310 -Helical PIP-Box Mimetic Targeting PCNA, the Human Sliding Clamp

The human sliding clamp (PCNA) controls access to DNA for many proteins involved in DNA replication and repair. Proteins are recruited to the PCNA surface by means of a short, conserved peptide motif known as the PCNA-interacting protein box (PIP-box). Inhibitors of these essential protein-protein interactions may be useful as cancer therapeutics by disrupting DNA replication and repair in these highly proliferative cells. PIP-box peptide mimetics have been identified as a potentially rapid route to potent PCNA inhibitors. Here we describe the rational design and synthesis of the first PCNA peptidomimetic ligands, based on the high affinity PIP-box sequence from the natural PCNA inhibitor p21. These mimetics incorporate covalent i,i+4 side-chain/side-chain lactam linkages of different lengths, designed to constrain the peptides into the 3₁₀ -helical structure required for PCNA binding. NMR studies confirmed that while the unmodified p21 peptide had little defined structure in solution, mimetic ACR2 pre-organized into 3₁₀ -helical structure prior to interaction with PCNA. ACR2 displayed higher affinity binding than most known PIP-box peptides, and retains the native PCNA binding mode, as observed in the co-crystal structure of ACR2 bound to PCNA. This study offers a promising new strategy for PCNA inhibitor design for use as anti-cancer therapeutics.

Protein bioelectronics: a review of what we do and do not know

We review the status of protein-based molecular electronics. First, we define and discuss fundamental concepts of electron transfer and transport in and across proteins and proposed mechanisms for these processes. We then describe the immobilization of proteins to solid-state surfaces in both nanoscale and macroscopic approaches, and highlight how different methodologies can alter protein electronic properties. Because immobilizing proteins while retaining biological activity is crucial to the successful development of bioelectronic devices, we discuss this process at length. We briefly discuss computational predictions and their connection to experimental results. We then summarize how the biological activity of immobilized proteins is beneficial for bioelectronic devices, and how conductance measurements can shed light on protein properties. Finally, we consider how the research to date could influence the development of future bioelectronic devices.

Electronic structure of dipeptides in the gas-phase and as an adsorbed monolayer

UPS and DFT reveal how frontier energy levels and molecular orbitals of peptides are modified upon peptide binding to a gold substrate.

Peptides as Bio-inspired Molecular Electronic Materials

Understanding the electronic properties of single peptides is not only of fundamental importance to biology, but it is also pivotal to the realization of bio-inspired molecular electronic materials. Natural proteins have evolved to promote electron transfer in many crucial biological processes. However, their complex conformational nature inhibits a thorough investigation, so in order to study electron transfer in proteins, simple peptide models containing redox active moieties present as ideal candidates. Here we highlight the importance of secondary structure characteristic to proteins/peptides, and its relevance to electron transfer. The proposed mechanisms responsible for such transfer are discussed, as are details of the electrochemical techniques used to investigate their electronic properties. Several factors that have been shown to influence electron transfer in peptides are also considered. Finally, a comprehensive experimental and theoretical study demonstrates that the electron transfer kinetics of peptides can be successfully fine tuned through manipulation of chemical composition and backbone rigidity. The methods used to characterize the conformation of all peptides synthesized throughout the study are outlined, along with the various approaches used to further constrain the peptides into their geometric conformations. The aforementioned sheds light on the potential of peptides to one day play an important role in the fledgling field of molecular electronics.

A controllable mechanistic transition of charge transfer in helical peptides: from hopping to superexchange

A controllable mechanistic transition of charge transfer in helical peptides is demonstrated as a direct result of side-bridge gating.

Where Does the Electron Go? Stable and Metastable Peptide Cation Radicals Formed by Electron Transfer

Electron transfer to doubly and triply charged heptapeptide ions containing polar residues Arg, Lys, and Asp in combination with nonpolar Gly, Ala, and Pro or Leu generates stable and metastable charge-reduced ions, (M + 2H)^+●, in addition to standard electron-transfer dissociation (ETD) fragment ions. The metastable (M + 2H)^+● ions spontaneously dissociate upon resonant ejection from the linear ion trap, giving irregularly shaped peaks with offset m/z values. The fractions of stable and metastable (M + 2H)^+● ions and their mass shifts depend on the presence of Pro-4 and Leu-4 residues in the peptides, with the Pro-4 sequences giving larger fractions of the stable ions while showing smaller mass shifts for the metastables. Conversion of the Asp and C-terminal carboxyl groups to methyl esters further lowers the charge-reduced ion stability. Collisional activation and photodissociation at 355 nm of mass-selected (M + 2H)^+● results in different dissociations that give sequence specific MS³ spectra. With a single exception of charge-reduced (LKGLADR + 2H)^+●, the MS³ spectra do not produce ETD sequence fragments of the c and z type. Hence, these (M + 2H)^+● ions are covalent radicals, not ion-molecule complexes, undergoing dramatically different dissociations in the ground and excited electronic states. The increased stability of the Pro-4 containing (M + 2H)^+● ions is attributed to radicals formed by opening of the Pro ring and undergoing further stabilization by hydrogen atom migrations. UV-VIS photodissociation action spectroscopy and time-dependent density functional theory calculations are used in a case in point study of the stable (LKGPADR + 2H)^+● ion produced by ETD. In contrast to singly-reduced peptide ions, doubly reduced (M + 3H)⁺ ions are stable only when formed from the Pro-4 precursors and show all characteristics of even electron ions regarding no photon absorption at 355 nm or ion-molecule reactions, and exhibiting proton driven collision induced dissociations. Graphical Abstract ᅟ.

Electron transfer in peptides

In this review, we discuss the factors that influence electron transfer in peptides. We summarize experimental results from solution and surface studies and highlight the ongoing debate on the mechanistic aspects of this fundamental reaction. Here, we provide a balanced approach that remains unbiased and does not favor one mechanistic view over another. Support for a putative hopping mechanism in which an electron transfers in a stepwise manner is contrasted with experimental results that support electron tunneling or even some form of ballistic transfer or a pathway transfer for an electron between donor and acceptor sites. In some cases, experimental evidence suggests that a change in the electron transfer mechanism occurs as a result of donor-acceptor separation. However, this common understanding of the switch between tunneling and hopping as a function of chain length is not sufficient for explaining electron transfer in peptides. Apart from chain length, several other factors such as the extent of the secondary structure, backbone conformation, dipole orientation, the presence of special amino acids, hydrogen bonding, and the dynamic properties of a peptide also influence the rate and mode of electron transfer in peptides. Electron transfer plays a key role in physical, chemical and biological systems, so its control is a fundamental task in bioelectrochemical systems, the design of peptide based sensors and molecular junctions. Therefore, this topic is at the heart of a number of biological and technological processes and thus remains of vital interest.

Two Aromatic Rings Coupled a Sulfur-Containing Group to Favor Protein Electron Transfer by Instantaneous Formations of π∴S:π↔π:S∴π or π∴π:S↔π:π∴S Five-Electron Bindings

The cooperative interactions among two aromatic rings with a S-containing group are described, which may participate in electron hole transport in proteins. Ab initio calculations reveal the possibility for the formations of the π∴S:π↔π:S∴π and π∴π:S↔π:π∴S five-electron bindings in the corresponding microsurrounding structures in proteins, both facilitating electron hole transport as efficient relay stations. The relay functionality of these two special structures comes from their low local ionization energies and proper binding energies, which varies with the different aromatic amino acids, S-containing residues, and the arrangements of the same aromatic rings according to the local microsurroundings in proteins.

A New Type of Electron Relay Station in Proteins: Three-Piece S:Π∴S↔S∴Π:S Resonance Structure

A type of relay station for electron transfer in proteins, three-piece five-electron bonding, is introduced in this paper, which is also first proposed here. The ab initio calculations predict the formation of S:Π∴S↔S∴Π:S resonance binding with an aromatic ring located in the middle of two sulfur-containing groups, which may participate in electron-hole transport in proteins. These special structures can lower the local ionization energies to capture electron holes efficiently and may be easily formed and broken because of their proper binding energies. In addition, the UV-vis spectra provide evidence of the formations of the three-piece five-electron binding. The cooperation of three adjacent pieces may be advantage to promote electron transfer a longer distance.