Electrochemical scanning tunneling microscopy as a tool for probing protein function: from electron transfer to molecular recognition and chemosensation
- Josep Samitier1,2,3
- Anna Lagunas1,3*corresponding author
- 1Nanobioengineering Group, Institute for Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- 2Department of Electronics and Biomedical Engineering, Faculty of Physics, University of Barcelona (UB), Barcelona, Spain
- 3CIBER-BBN, ISCIII, Madrid, Spain
Abstract
Electron transfer (ET) is involved in many fundamental biological processes. While spectroscopic and electrochemical techniques have established the theoretical framework governing protein ET, they typically capture average responses across large populations or characterize ET in fixed molecular arrangements. Electrochemical scanning tunneling microscopy (EC-STM) has emerged as a unique single-molecule technique that combines atomic-scale spatial resolution with electrochemical control, enabling direct investigation of charge transport in proteins within a dynamic framework. Initially focused on redox proteins, EC-STM has evolved from imaging to spectroscopic measurements, including current-distance, current-voltage, and break-junction approaches, revealing electrochemically regulated transport pathways and dynamic fluctuations. More recently, EC-STM has been extended to non-redox proteins and to the study of charge transport in increasingly complex biological systems, such as inter-protein ET and molecular recognition. These studies have demonstrated that ligand binding can modulate the electrical response of proteins, providing a direct readout of the conformational and electronic changes associated with biological recognition events. These observations reinforce EC-STM as a powerful approach for studying protein function beyond classical ET systems, bridging the gap between nanoscale biophysics and molecular recognition. This mini review traces the evolution of EC-STM applied to protein ET from its origins in intraprotein ET of redox proteins to its development into a versatile tool for studying protein function through molecular recognition. We analyze how EC-STM has provided new insights into ET mechanisms, protein-protein interactions, and ligand-induced electrical responses, and we conclude by considering its potential for the development of protein-based biosensors and bioelectronic technologies.
Keywords
1 Introduction
Electron transfer (ET) reactions in proteins are key steps in a wide range of biological processes, having a fundamental role in energy conversion, from photosynthesis to aerobic respiration. ET can take place within and between proteins. Intra-protein ET through redox protein centers and cofactors has been extensively studied using a range of experimental and theoretical techniques, including time-resolved spectroscopy (Bashir et al., 2011; Wherland and Pecht, 2015), electrochemistry (Algov and Alfonta, 2022), or computational modelling (Mostajabi Sarhangi and Matyushov, 2026). These studies have been largely interpreted within the framework of Marcus theory, and its quantum-mechanical extensions, which provide the basis for understanding the mechanisms and kinetics of biological ET reactions (Gray and Winkler, 1996).
According to Marcus semiclassical theory (Marcus and Sutin, 1985), the rate of ET (k *ET*) from an electron donor (A) to an acceptor (B) with fixed separation and orientation depends on the driving force of the ET reaction (-ΔG°), the nuclear reorganization energy (λ) required for ET, and the electronic coupling strength between A and B at the transition state (H *AB*) (Equation 1):
k E T = 4 π 3 h 2 λ k B T H A B 2 exp − Δ G 0 + λ 2 4 λ k B T (1)
Where k B and h stand for the Boltzmann and Planck constants, respectively, and T for temperature. When the driving force equals the reorganization energy, k *ET* reaches its maximum value, which is ultimately limited by the electronic coupling term, HAB that decreases exponentially with the donor-acceptor distance (d AB). Accordingly, k *ET* can be approximated as:
k E T ∝ exp − β d A B (2)
The key parameter in this relationship is the distance decay factor (β), characteristic of the ET mechanism, and the medium in between A and B. Because the probability of electron tunneling decreases exponentially with distance, direct tunneling becomes highly unlikely at donor-acceptor separations exceeding ∼30 Å under physiological conditions (Mostajabi Sarhangi and Matyushov, 2023).
The incorporation of conformational dynamics into ET theory, as proposed by Beratan and co-workers (Beratan et al., 2015), introduced a significant conceptual shift to the classical Marcus framework. ET through proteins can occur via several mechanisms, including coherent tunneling and multistep or multirange hopping, which are not mutually exclusive but represent functional regimes that can coexist and interconvert depending on the instantaneous protein conformation. This dynamic interplay, known as flickering resonance, arises from transient conformational fluctuations that modulate electronic parameters and facilitate ET pathways that would not be predicted from the average protein structure alone.
Although spectroscopic, electrochemical, and computational methods have provided invaluable insights into biological ET, they often yield ensemble-averaged results or demonstrate ET within predefined molecular architectures. Techniques such as scanning tunneling microscopy (STM) are particularly attractive in this context because they directly probe charge transport through individual proteins or protein complexes under electrochemical control, enabling the label-free observation of functional heterogeneity, intermittent transport behavior, and conformationally dependent charge-transfer pathways under near-physiological conditions.
Scanning Tunneling Microscopy (STM) was first introduced in 1981 (Binnig and Rohrer, 1983), revolutionizing surface science by enabling imaging with atomic-scale resolution, well beyond the diffraction limit of light. STM operates through quantum tunneling between a sharp conductive probe and a conductive sample positioned in very close proximity. Upon application of a bias potential, a tunneling current is generated and continuously monitored by a feedback system that adjusts the probe-sample distance to maintain the current constant. As the probe scans across the surface, variations in height are recorded and used to reconstruct high-resolution three-dimensional topographic images. STM can detect extremely small quantities of biomolecules, including single proteins, under vacuum, air, inert atmospheres, or liquid environments (Nichols, 2021; Kim et al., 2023). The ability to operate in aqueous media is particularly valuable for biological studies, as it enables the investigations to be performed under conditions that closely resemble physiological environments.
Electrochemical Scanning Tunneling Microscopy (EC-STM) extends the capabilities of STM by integrating electrochemical control through a four-electrode configuration consisting of the sample and probe as independent working electrodes, together with a reference and counter electrode (Figure 1A). Using a bipotentiostat, the potentials of the sample and probe can be independently controlled while maintaining a defined bias voltage, enabling simultaneous regulation of both electrochemical and tunneling conditions (Itaya and Tomita, 1988). This setup requires specially insulated probes to minimize faradaic currents and ensure reliable tunneling current measurements (Güell et al., 2004; Kim et al., 2023; Kurczak et al., 2024). EC-STM combines single-molecule spatial resolution with precise electrochemical control, making it a powerful technique for studying redox-active biomolecules and ET processes in general. Beyond high-resolution imaging, EC-STM enables spectroscopic measurements providing detailed information on charge transport, conductance, and ET mechanisms (Alessandrini et al., 2006).

2 EC-STM as a tool for studying ET mechanisms in single redox proteins
Early EC-STM studies focused on ET proteins, particularly cytochrome c and azurin, whose well-characterized redox cofactors provided ideal model systems for validating electrochemical imaging and spectroscopy.
2.1 Electrochemical imaging
The visualization of ET proteins with EC-STM was pioneered by Ulstrup and coworkers (Andersen et al., 1995; Friis et al., 1997), who provided the first in situ submolecular resolution images of Pseudomonas aeruginosa azurin. The blue copper protein azurin was immobilized by direct covalent binding on Au (111), exploiting the protein’s surface disulfide bridge opposite the copper atom. This immobilization strategy led to effective electrical contact with the electrode, providing facile tunneling routes to the copper atom while still preserving the protein’s functional configuration. Regular arrays of molecular structures with dimensions consistent with the azurin crystallographic data appeared on the surface of the gold electrode at bipotentiostatic EC-STM voltages applied at either side of the protein’s reduction potential in constant-current mode. Each molecular structure had the shape of a cone standing on its base with a central region of brighter contrast, which corresponded to high tunneling probability near the copper atom (Friis et al., 1999). Facci et al. demonstrated that the molecular contrast of azurin could be dynamically gated by sweeping the electrochemical potential across its redox midpoint (Facci et al., 2001) (Figure 1B). In analogy with electronic transistors, a protein may be switched on or off, as a function of the applied potential.
This potential-dependent behavior aligns with the sequential two-step electron transfer framework established by Kuznetsov and Ulstrup, (2000), highlighting how optimized interface coupling minimizes the reorganization energy required for long-range electron transport. By using functionalized self-assembled monolayers (SAMs) or genetic engineering to insert specific anchoring tags, researchers can systematically control the distance and coupling strength between the electrode and the protein’s internal redox centers (Halliwell et al., 2004; Chi et al., 2005; Delia Pia et al., 2011).
2.2 Electrochemical spectroscopy
Intra-protein ET between redox sites proceeds by combination of electron tunneling steps and conduction through covalent and hydrogen bonds in the protein matrix (Curry et al., 1995). By coupling electrostatic control of a protein’s redox state with spectroscopic measurements of charge transport, EC-STM allows researchers to study electronic properties and biophysics of individual proteins. Ulstrup and coworkers were the first to probe the direct catalytic activity of single redox enzymes using this approach (Albrecht et al., 2006; Gwyer et al., 2006). They were able to successfully image Escherichia coli cytochrome c nitrite reductase (NrfA) on the Au (111) EC-STM electrode surface with bipotentiostatic control and under conditions where the enzyme preserved its electrocatalytical activity (Gwyer et al., 2006).
Early demonstrations of spectroscopic measurements using EC-STM were reported by Gorostiza’s group establishing a method to determine β via EC-STM current-distance (Iz) tunneling spectroscopy (Nagy and Wandlowski, 2003) of individual redox proteins (Artés et al., 2011). Exponential current decays were obtained from the initial set point till the onset of the faradaic leakage current of the EC-STM probe departed from the sample surface. Based on Equation 2, β was calculated from the fitting of semilogarithmic Iz plots. Electrochemical gating of β was reported for azurin, which decreased from the value measured on bare Au (β ≈ 11 nm−1) to 5.4 and 4.4 nm−1 for the reduced and oxidized protein, respectively (Figure 1C). The resulting redox-dependent β values supported a two-step tunneling mechanism and highlighted the unique ability of EC-STM to determine β as a function of protein redox state, exploiting electrochemical control unavailable in previous fixed-orientation approaches (Gray and Winkler, 2003). This concept has since been extended to more complex membrane-bound electron-transfer proteins such as Photosystem I (PSI), for which a contribution of electrochemically gated long current decays (β < 4 nm-1) have been described (López-Martínez et al., 2019; López-Ortiz et al., 2022).
In addition to Iz spectroscopy, EC-STM enables current-voltage (IV) measurements under electrochemical control, allowing to determine protein conductance and probe the energetic alignment of transport states. At a current set point, a swiping bias voltage ramp is applied to the STM probe and the current recorded. IV characteristics were first reported for individual azurin molecules, revealing a rectifying behavior, for which a transition voltage (TV) of 0.4 V was determined, in agreement with previously measured β (β ≈ CTV1/2, with C = 1.05 Å−1 V−1/2) (Figure 1D). The introduction of TV spectroscopy (TVS) further enabled the extraction of characteristic transport energies from wired junction configuration, revealing an unusually low TV = 0.06 V, and demonstrating TV is strongly regulated by the electronic coupling with the probe (Artés et al., 2012b).
Rather than relying on individual IV curves, single-molecule conductance can be determined statistically from thousands of repeated junction formation events acquired using EC-STM break-junction approach, operated either in dynamic tapping or static blinking modes (Artés et al., 2012a; Ruiz et al., 2017). In dynamic tapping, the STM probe is repeatedly approached and retracted to/from the sample, and the formed single-protein junctions appear as conductance plateaus in the Iz traces. However, in this mode the mechanical force exerted during junction rupture can perturb the protein structure leading to transport misinterpretations. This limitation is solved in static blinking where current-versus-time (It) is recorded at an applied bias and current set point. It traces exhibit a characteristic telegraph-like noise in which spontaneous contact between the probe and the sample results in current jumps (blinks). By collecting the blinking features with subtracted tunneling background and setting them to a common time origin, 2D blinking maps of the conductance dispersion in the single-protein junction are constructed. This statistical spectroscopic approach allowed the observation of the thermodynamic dispersion of red-ox states from single-molecule perspective (Artés et al., 2014), and to determine the most probable transport mechanisms depending on protein orientation, electrode coupling, redox state and electrochemical potential in the azurin model (Ruiz et al., 2017; Romero-Muñiz et al., 2018; 2021) (Figure 1E).
3 EC-STM probing of ET and molecular recognition in membrane proteins
EC-STM studies have progressively evolved to address increasingly complex biological questions providing insights into charge transport between ET protein partners and probing ligand-induced modulation of charge transport in non-redox proteins.
3.1 Interprotein electron transport (ETp)
Charge transport in biological systems involves consecutive ET events through redox proteins, resulting in a tightly regulated flow of electrons. Interprotein ET drives vital energy conversion systems like cellular respiration and photosynthesis. The process requires the two proteins to conformationally align in a competent ET complex while still maintaining the high turnover rate necessary for their biological function. The distance dependence of interprotein ET has been explored through protein partners and engineered mutants that perturb the geometry of the native complex, providing valuable insights into donor-acceptor distances and coupling mechanisms (Nocek et al., 1996). However, these studies are largely restricted to the final bound state and do not capture the dynamic nature of biological ET (Beratan et al., 2015).
In collaboration with Gorostiza and co-workers, we have demonstrated electrochemically gated, long-distance interprotein ET within protein partners of the mitochondrial respiratory chain through the aqueous solution, using EC-STM (Lagunas et al., 2018). The ETp was studied between cytochrome c (Cc) and the membrane-bound cytochrome bc 1 (Complex III). Both proteins were selectively immobilized through Cys-based covalent bonding on the probe and the sample electrodes of EC-STM, with their redox active sites facing each other, while still providing rotational freedom and good electrical contact. The soluble domain of plant cytochrome c 1 (Cc 1) was bound through its native N-terminal Cys10 to the Au (111) sample electrode, and the E104C mutant of human Cc was attached to the STM probe. Iz measurements were conducted at a positive bias to promote unidirectional electron flow from Cc 1 to Cc, thus mimicking physiological ET. EC gating experiments displayed a minimum β = 0.5 nm-1 with current spanning up to 10 nm for US close to the midpoint redox potentials of the proteins (Figure 2A). Note that in this long-range context, β represents an apparent decay length rather than a classical tunneling coupling decay. Long-range ETp was successfully reproduced in forward Iz curves recorded 100 nm away from the initial set-point, ruling out any artifacts from structural modifications during interaction, and inhibited by adding wild-type Cc, in Cc-Cc junctions, as well as by using the phosphomimetic mutant Y48pCMF Cc (Cc 1- Y48pCMF Cc) (Gomila et al., 2022).

MD simulations showed that the lysine ring of Cc accumulates anions, whereas cations are depleted from the hydrophobic patch, creating a confined region between the two proteins with weak electrical screening. This allows the potential profile to extend over several nanometers. The similar spatial extent of the potential profile and the measured current indicates that the long-range current is driven by the diffuse double layer. Thus, the Gouy-Chapman region may act as a charge conduit for ET through the aqueous solution, enabling protein partners to reconcile high specificity with weak binding while maintaining high turnover rates (Lagunas et al., 2018; Gomila et al., 2022).
The spatial range and electrochemical gating of the current were found to depend on solvent properties, decreasing at higher pH, in deuterated water, and under low oxygen concentration. These observations identified protons and superoxide ions as the most likely mediators of the long-range Cc 1-Cc ET (Figure 2A). The measured kinetic isotope effects (KIEs, 1–10) indicate that proton transfer is involved in the rate-limiting step, compatible with a proton-coupled ET (PCET) mechanism. PCET could be initiated by ionizable residues at tunneling distances from the heme, whose pKa depends on the redox state. The transferred protons may either drift along the Gouy-Chapman conduit or propagate through the aqueous phase via Grotthuss proton-hopping (Lagunas et al., 2025b). While these pioneering studies establish a foundation for long-range ET in protein complexes, further exploration by the broader biophysics community will be valuable to expand these insights to other systems.
Long-range currents have also been observed for ETp between photosystem I (PSI) and its soluble partner plastocyanin (Pc), selectively immobilized on EC-STM electrodes. Interestingly, apo-Pc exhibited lower β values and higher conductance than holo-Pc, whereas the latter produced narrower conductance distributions. These findings suggest that, in the absence of the Cu center, ETp can proceed through multiple, non-preferential pathways within the protein matrix, while the native redox-active protein funnels charge through specific pathways involving the metal center (López-Ortiz et al., 2023).
3.2 EC-STM of non-redox proteins: molecular recognition and chemosensation
Although proteins are generally considered electrical insulators, unexpectedly high conductance has also been reported for electrochemically inactive proteins. Early STM studies demonstrated the imaging of IgG and γ-gliadin in air (Leatherbarrow et al., 1991; Thomson et al., 1992), while temperature-dependent ETp was later reported for apo-azurin and bacteriorhodopsin in solid-state junctions (Sepunaru et al., 2011; 2012). In solution, zinc-free insulin and several other non-redox proteins have been investigated by EC-STM, highlighting the critical role of the protein-electrode interface (Welinder et al., 2010; Zhang et al., 2017). Lindsay and co-workers further demonstrated that measurable currents require specific binding to at least one electrode and that recognition-ligand contacts produce higher conductance, revealing that protein conductance is highly sensitive to both the chemical nature of the electrical contact and local conformational changes (Zhang and Lindsay, 2019; Zhang et al., 2019) (Figure 2B). These findings have enabled EC-STM to probe conductance pathways in individual proteins and their modulation by ligand binding, thus providing valuable information on conformational states related to biological processes and offering novel modes of protein biosensing and bioelectronics (Tang et al., 2022; Zhang et al., 2022).
Chemosensation is the ability of biological systems to detect chemical cues through the selective binding of ligands to chemoreceptor proteins, enabling organisms to recognize and discriminate against a wide variety of molecules. Signal transduction has been proposed to arise from ligand-induced conformational and electronic changes in the receptor that modulate its electrical conductance (Reggiani et al., 2012; Alfinito and Reggiani, 2016). Using EC-STM, we recently demonstrated that binding of the cognate ligand dihydrojasmone to the human olfactory receptor 1A1 (hOR1A1) induces a dose-dependent conductance increase and a shift toward lower open-circuit voltages, revealing changes in the receptor’s capacitive properties (Lagunas et al., 2022) (Figure 2C). hOR1A1 was selectively immobilized on the surface of Au (111) electrode of the EC-STM through a half-antibody against a Rho1D4 C-terminal tag, thus exposing the binding site towards the solution. Consistent with previous observations by Lindsay and co-workers, ligand binding induced an increase in the measured conductance, which was around 11% and also a 30% decrease in the capacitive response. Building on these findings, the same experimental configuration enabled the discrimination of hOR1A1 agonists according to their potency by impedance measurements. MD simulations attributed the ligand-induced specific capacitance drop to changes in the magnitude and orientation of the receptor’s electric dipole (Figure 2C), thereby modulating its response to the applied electric field (Lagunas et al., 2025a). Although preliminary, this work highlights the potential of label-free capacitive biosensors based on intrinsic receptor dynamics (such as dipole modulation) rather than simple double-layer thickness variations (Huang et al., 2024), offering a promising route to discriminate ligands by potency. To fully establish the scope of this approach, further systematic studies will be necessary to evaluate sensitivity and selectivity with lower-affinity ligands and across other olfactory receptors.
4 Conclusions and future directions
Interpreting the electrical signatures of single proteins in electronic junctions has substantially advanced our understanding of the intrinsic properties that govern fundamental chemical and biological processes. EC-STM offers single-molecule spatial resolution with precise electrochemical control, enabling ETp investigations under conditions that closely resemble the physiological environment of proteins. Measured currents depend on the chemical environment, contact configuration, and gap distance. Although strategies have been developed to control or estimate tip-protein gap in EC-STM (Ha et al., n.d.), accurately defining it at the molecular scale remains a significant technical challenge. Other techniques such as conductive atomic force microscopy (c-AFM) and solid-state junctions, could offer more control on gap distance and also complementary insights on the electrical contact, electrode coupling, and protein hydration on the electrical measurements (Zhao et al., 2004; Li et al., 2012; Amdursky et al., 2014; Mukhopadhyay et al., 2020). In particular, c-AFM allows calibrated mechanical forces to be applied while simultaneously measuring current, providing a means to examine how contact pressure and protein deformation influence conductance (Zhao et al., 2004; Li et al., 2012).
Proteins are particularly attractive building blocks for nanoscale electronics because they can self-assemble into well-defined architectures, can be engineered with atomic precision, and display remarkable chemical diversity. These properties make them promising components for new classes of single-molecule sensors and bioelectronic devices. In chemosensory proteins, EC-STM has shown that ligand recognition can modulate both molecular conductance and the receptor capacitive response, providing an electrical readout of ligand-induced conformational and electronic changes. The ability to discriminate agonists according to their potency through capacitance measurements opens opportunities for protein-based electronic noses, multiplexed biosensing, and the rational discovery of selective odorants and therapeutics.
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Footnotes
Edited by: Melanie Koehler, Technical University of Munich, Germany
Reviewed by: Zhiyong Zheng, Université Catholique de Louvain, Belgium
Statements
- Conflict of interest
The author(s) declared that this work was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
- Funding
The author(s) declared that financial support was received for this work and/or its publication. This work was funded by the CERCA Program and the Commission for Universities and Research of the Departament d’Innovació, Universitats i Empresa, Generalitat de Catalunya (2021 SGR 01545) and supported by Networking Biomedical Research Centre (CIBER), Spain (Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina), which is funded by the VI National R&D&IPlan 2008–2011, Iniciativa Ingenio 2010, Consolider Program, CIBER Actions, and the Instituto de Salud Carlos III, with the support of the European Regional Development Fund and of ‘Plan de Recuperación, Transformación y Resiliencia (C17.I1) – Financiado por la Unión Europea – NextGenerationEU», and ‘Plan Complementario de Biotecnología aplicada a la salud’.
- Author contributions
JS: Project administration, Conceptualization, Writing – review and editing, Funding acquisition, Supervision. AL: Investigation, Project administration, Visualization, Conceptualization, Writing – review and editing, Writing – original draft, Funding acquisition.
- Acknowledgements
The authors are grateful to Pau Gorostiza for helpful discussions.
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Citation
Samitier, J. & Lagunas, A. (2026). Electrochemical scanning tunneling microscopy as a tool for probing protein function: from electron transfer to molecular recognition and chemosensation. Frontiers in Biophysics, Volume 4. https://doi.org/
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- 4 - 2026
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Copyright © 2026 Samitier and Lagunas.
License: https://creativecommons.org/licenses/by/4.0/
*Correspondence: Anna Lagunas
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