Topological and Electron-Transfer Properties of Yeast Cytochrome c Adsorbed on Bare Gold Electrodes

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.

Use of bioconjugation with cytochrome P450 enzymes

Bioconjugation, defined as chemical modification of biomolecules, is widely employed in biological and biophysical studies. It can expand functional diversity and enable applications ranging from biocatalysis, biosensing and even therapy. This review summarizes how chemical modifications of cytochrome P450 enzymes (P450s or CYPs) have contributed to improving our understanding of these enzymes. Genetic modifications of P450s have also proven very useful but are not covered in this review. Bioconjugation has served to gain structural information and investigate the mechanism of P450s via photoaffinity labeling, mechanism-based inhibition (MBI) and fluorescence studies. P450 surface acetylation and protein cross-linking have contributed to the investigation of protein complexes formation involving P450 and its redox partner or other P450 enzymes. Finally, covalent immobilization on polymer surfaces or electrodes has benefited the areas of biocatalysis and biosensor design. This article is part of a Special Issue entitled: Cytochrome P450 biodiversity and biotechnology, edited by Erika Plettner, Gianfranco Gilardi, Luet Wong, Vlada Urlacher, Jared Goldstone.

Optical properties of Yeast Cytochrome c monolayer on gold: an in situ spectroscopic ellipsometry investigation

The adsorption of Yeast Cytochrome c (YCC) on well defined, flat gold substrates has been studied by Spectroscopic Ellipsometry (SE) in the 245-1000 nm wavelength range. The investigation has been performed in aqueous ambient at room temperature, focusing on monolayer-thick films. In situ δΨ and δΔ difference spectra have shown reproducibly well-defined features related to molecular optical absorptions typical of the so-called heme group. The data have been reproduced quantitatively by a simple isotropic optical model, accounting for the molecular absorption spectrum and film-substrate interface effects. The simulations allowed a reliable estimate of the film thickness and the determination of the position and the shape of the so-called Soret absorption peak that, within the experimental uncertainty, is the same found for molecules in liquid. These findings suggest that YCC preserves its native structure upon adsorption. The same optical model was able to reproduce also ex situ results on rinsed and dried samples, dominated by the spectral features associated to the polypeptide chain that tend to overwhelm the heme absorption features.

Force modulation and electrochemical gating of conductance in a cytochrome

Scanning probe methods have been used to measure the effect of electrochemical potential and applied force on the tunnelling conductance of the redox metalloprotein yeast iso-1-cytochrome c (YCC) at a molecular level. The interaction of a proximal probe with any sample under test will, at this scale, be inherently perturbative. This is demonstrated with conductive probe atomic force microscopy (CP-AFM) current-voltage spectroscopy in which YCC, chemically adsorbed onto pristine Au(111) via its surface cysteine residue, is observed to become increasingly compressed as applied load is increased, with concomitant decrease in junction resistance. Electrical contact at minimal perturbation, where probe-molecule coupling is comparable to that in scanning tunnelling microscopy, brings with it the observation of negative differential resistance, assigned to redox-assisted probe-substrate tunnelling. The role of the redox centre in conductance is also resolved in electrochemical scanning tunnelling microscopy assays where molecular conductance is electrochemically gateable through more than an order of magnitude.

Folding control and unfolding free energy of yeast iso-1-cytochrome c bound to layered zirconium phosphate materials monitored by surface plasmon resonance

The free energy change (Delta G degrees ) for the unfolding of immobilized yeast iso-1-cytochrome c (Cyt c) at nanoassemblies was measured by surface plasmon resonance (SPR) spectroscopy. Data show that SPR is sensitive to protein conformational changes, and protein solid interface exerts a major influence on bound protein stability. First, Cyt c was self-assembled on the Au film via the single thiol of Cys-102. Then, crystalline sheets of layered alpha-Zr(O(3)POH)(2).H(2)O (alpha-ZrP) or Zr(O(3)PCH(2)CH(2)COOH)(2).xH(2)O (alpha-ZrCEP) were adsorbed to construct alpha-ZrP/Cyt c/Au or alpha-ZrCEP/Cyt c/Au nanoassemblies. The construction of each layer was monitored by SPR, in real time, and the assemblies were further characterized by atomic force microscopy and electrochemical studies. Thermodynamic stability of the protein nanoassembly was assessed by urea-induced unfolding. Surprisingly, unfolding is reversible in all cases studied here. Stability of Cyt c in alpha-ZrP/Cyt c/Au increased by approximately 4.3 kJ/mol when compared to the unfolding free energy of Cyt c/Au assembly. In contrast, the protein stability decreased by approximately 1.5 kJ/mol for alpha-ZrCEP/Cyt c/Au layer. Thus, OH-decorated surfaces stabilized the protein whereas COOH-decorated surfaces destabilized it. These data quantitate the role of specific functional groups of the inorganic layers in controlling bound protein stability.

Nanoscopic and redox characterization of engineered horse cytochrome C chemisorbed on a bare gold electrode

In this paper, we exploit the potential offered by site-directed mutagenesis to achieve direct adsorption of horse cyt c on a bare gold electrode surface. To this issue, the side chain T102 has been replaced by a cysteine. T102 is close to the surface exposed C-terminal residue (E104), therefore the T102C mutation is expected to generate an exposed cysteine side chain able to facilitate protein binding to the electrode via the sulphur atom (analogously to what observed for yeast iso-1-cyt c). Scanning Tunnelling and Tapping Mode Atomic Force Microscopy measurements show that the T102C mutant stably adsorbs on an Au(111) surface and retains the morphological characteristics of the native form. Cyclic voltammetry reveals that the adsorbed variant is electroactive; however, the heterogeneous electron transfer with the electrode surface is slower than that observed for yeast iso-1-cyt c. We ascribe it to differences in the tertiary architecture of the two proteins, characterized by different flexibility and stability. In particular, the region where the N- and C-terminal helices get in contact (and where the mutation occurs) is analyzed in detail, since the interactions between these two helices are considered crucial for the stability of the overall protein fold.

Specific vectorial immobilization of oligonucleotide-modified yeast cytochrome C on carbon nanotubes

Iso-1-cytochrome c from the yeast Saccharomyces cerevisiae (YCC) contains a surface cysteine residue, Cys102, that is located opposite to the lysine-rich side containing the exposed heme edge, which is the docking site for enzymes. Site-specific vectorial immobilization of YCC via Cys102 on single-walled carbon nanotubes (SWNT) thus provides a selective interface between nanoscopic electronic devices and complex enzymes. We have achieved this by modification of Cys102 with an oligonucleotide (dT(18)). Atomic force microscopy, fluorescence imaging, and cyclic voltammetry show the specific adsorption of YCC, modified with dT(18), on the SWNT sidewall with retention of its native properties. Pretreatment of the SWNT with Triton-X405 blocks the nonspecific binding of untreated YCC but does not interfere with binding of the oligonucleotide-modified YCC.

Cytochrome c self-assembly on alkanethiol monolayer electrodes as characterized by AFM, IR, QCM, and direct electrochemistry

With the advantage of carbodiimide coupling chemistry, horse heart cytochrome c (cyt c) has been covalently immobilized onto self-assembled monolayers (SAMs) from 11-mercaptoundecanoic acid (MUDA) developed on single-crystal or polycrystalline gold substrate surfaces. The cyt c immobilized substrates thus prepared have been characterized by atomic force microscopy (AFM); we have succeeded in obtaining surface topographical images down to single-protein resolution. AFM imaging has also shown densely packed, uniform protein monolayer formation that is highly suggestive of self-assembly of cyt c molecules on MUDA SAMs. Covalent attachment of cyt c has been further evidenced by reflection-absorption FT-IR as well as microgravimetric analysis using a quartz crystal microbalance (QCM). In the latter, the specific MUDA and cyt c surface concentrations were determined to be 0.86 +/- 0.11 nmol cm-2 (n = 5) and 28 +/- 12 pmol cm-2 (n = 5), both of which agree fairly well with their theoretical counterparts. The obtained QCM chips having the cyt c/MUDA/Au interfacial structure were found to be capable of the direct electrochemistry of the surface-attached cyt c molecules. Cyclic voltammetric measurements on the chips gave particular redox waves showing characteristics of surface process. The electroactive protein surface concentration was determined to be 7.2 +/- 4.8 pmol cm-2 (n = 6); it was almost consistent with values found in literature, while it was limited to 26% in magnitude for the QCM data. This was deemed to have arisen from the orientation variation of the surface-confined cyt c molecules and is discussed briefly.

Functional Metalloproteins Integrated with Conductive Substrates: Detecting Single Molecules and Sensing Individual Recognition Events

In the past decade, there has been significant interest in the integration of biomaterials with electronic elements: combining biological functions of biomolecules with nanotechnology offers new perspectives for implementation of ultrasensitive hybrid nanodevices. In particular, great attention has been devoted to redox metalloproteins, since they possess unique characteristics, such as electron-transfer capability, possibility of gating redox activity, and nanometric size, which make them appealing for bioelectronics applications at the nanoscale. The reliable connection of redox proteins to electrodes, aimed at ensuring good electrical contact with the conducting substrate besides preserving protein functionality, is a fundamental step for designing a hybrid nanodevice and calls for a full characterization of the immobilized proteins, possibly at the single-molecule level. Here, we describe how a multitechnique approach, based on several scanning probe microscopy techniques, may provide a comprehensive characterization of different metalloproteins on metal electrodes, disclosing unique information not only about morphological properties of the adsorbed molecules but also about the effectiveness of electrical coupling with the conductive substrate, or even concerning the preserved biorecognition capability upon adsorption. We also show how the success of an immobilization strategy, which is of primary importance for optimal integration of metalloproteins with a metal electrode, can be promptly assessed by means of the proposed approach. Besides the characterization aspect, the complementary employment of the proposed techniques deserves major potentialities for ultrasensitive detection of adsorbed biomolecules. In particular, it is shown how sensing of single metalloproteins may be optimized by monitoring the most appropriate observable. Additionally, we suggest how the combination of several experimental techniques might offer increased versatility, real-time response, and wide applicability as a detection method, once a reproducible correlation among signals coming from different single-molecule techniques is established.

Preserved enzymatic activity of glucose oxidase immobilized on unmodified electrodes for glucose detection

Glucose sensing electrodes have been realized by immobilizing glucose oxidase (GOx) on unmodified edge plane of highly oriented pyrolytic graphite (epHOPG) and the native oxide of heavily doped silicon (SiO2/Si). Both kinds of electrode show direct interfacial electron transfer due to the redox process of the immobilized GOx. The measured formal potential of the redox process agrees with that of the native enzyme, suggesting that the immobilized GOx has retained its enzymatic activity. The electron transfer rates of the GOx immobilized electrode are 2s(-1) for GOx/epHOPG electrode and 7.9s(-1) for GOx/SiO2/Si electrode, which are greater than those for which GOx is immobilized on modified electrodes, probably due to the fact that the enzyme makes direct contact to electrode surface. The preservation of the enzymatic activity of the immobilized GOx has been confirmed by observing the response of the GOx/epHOPG and GOx/SiO2/Si electrodes to glucose with a detection limit of 0.050 mM. The response signals the catalyzed oxidation of glucose and, therefore, confirms that the immobilized GOx retained its enzymatic activity. The properties of the electrode as a glucose sensor are presented.

Voltammetry and in situ scanning tunneling microscopy of cytochrome C nitrite reductase on Au(111) electrodes

Escherichia coli cytochrome c nitrite reductase (NrfA) catalyzes the six-electron reduction of nitrite to perform an important role in the biogeochemical cycling of nitrogen. Here we describe NrfA adsorption on single-crystal Au(111) electrodes as an electrocatalytically active film in which the enzyme undergoes direct electron exchange with the electrode. The adsorbed NrfA has been imaged to molecular resolution by in situ scanning tunneling microscopy (in situ STM) under full electrochemical potential control and under conditions where the enzyme is electrocatalytically active. Details of the density and orientational distribution of NrfA molecules are disclosed. The submonolayer coverage resolved by in situ STM is readily reconciled with the failure to detect nonturnover signals in cyclic voltammetry of the NrfA films. The molecular structures show a range of lateral dimensions. These are suggestive of a distribution of orientations that could account for the otherwise anomalously low turnover number calculated for the total population of adsorbed NrfA molecules when compared with that determined for solutions of NrfA. Thus, comparison of the voltammetric signals and in situ STM images offers a direct approach to correlate electrocatalytic and molecular properties of the protein layer, a long-standing issue in protein film voltammetry.

Topological and dynamical properties of Azurin anchored to a gold substrate as investigated by molecular dynamics simulation

A classical molecular dynamics study of the electron transfer protein azurin, covalently bound to a gold substrate through its native disulphide group, is carried out at full hydration. With the aim of investigating the effects on the protein structure and dynamics as induced by the presence of an electric field, simulations are performed on neutral, positively and negatively charged substrates. A number of parameters, such as the average structure, the root mean square deviations and fluctuations, the intraprotein hydrogen bonds and solvent accessible surface of the protein, are monitored during 10 ns of run. The orientation, the height and the lateral size of the protein, with respect to the substrate are evaluated and compared with the experimental data obtained by scanning probe nanoscopies. The electron transfer properties between the copper redox center and the disulphide bridge bound to the substrate are investigated and briefly discussed.

Single molecule recognition between cytochrome C 551 and gold-immobilized azurin by force spectroscopy

Recent developments in single molecule force spectroscopy have allowed investigating the interaction between two redox partners, Azurin and Cytochrome C 551. Azurin has been directly chemisorbed on a gold electrode whereas cytochrome c has been linked to the atomic force microscopy tip by means of a heterobifunctional flexible cross-linker. When recording force-distance cycles, molecular recognition events could be observed, displaying unbinding forces of approximately 95 pN for an applied loading rate of 10 nN/s. The specificity of molecular recognition was confirmed by the significant decrease of unbinding probability observed in control block experiments performed adding free azurin solution in the fluid cell. In addition, the complex dissociation kinetics has been here investigated by monitoring the unbinding forces as a function of the loading rate: the thermal off-rate was estimated to be approximately 14 s(-1), much higher than values commonly estimated for complexes more stable than electron transfer complexes. Results here discussed represent the first studies on molecular recognition between two redox partners by atomic force microscopy.

Bioelectrochemically functional nanohybrids through co-assembling of proteins and surfactants onto carbon nanotubes: facilitated electron transfer of assembled proteins with enhanced faradic response

Preparation and bioelectrochemical properties of functional nanohybrids through co-assembling of hemeproteins (i.e., horseradish peroxidase, hemoglobin, myoglobin and cytochrome c) and surfactants onto carbon nanotubes (CNTs) are described. The prepared protein-surfactant-CNT nanohybrids are found to possess facilitated interfacial electron transfer of the proteins with enhanced faradic responses. The enhancements are ascribed for the first time to the properties of the surfactants for facilitation of protein electrochemistry and the improved portion of electroactive proteins assembled, of which the latter assignment is closely associated with the electrochemical and structural properties of the nanotubes and the three-dimensional architecture of the CNT film confined onto the glassy carbon electrode. It is proposed that the single and/or small bundles of the nanotubes in the CNT film electrode can be rationally functionalized with surfactants to be functional nanoelectrodes capable of facilitating electron transfer of proteins. The three-dimensional confinement of these functional nanowires onto the GC electrode essentially increases the portion of electroactive proteins assembled in the nanohybrids. These properties of the protein-surfactant-CNT nanohybrids, combined with the bioelectrochemical catalytic activity, could make them useful for development of bioelectronic devices and investigation of protein electrochemistry at functional interfaces.

Single-molecule detection of yeast cytochrome c by Surface-Enhanced Raman Spectroscopy

The giant enhancement of Raman signal near silver colloidal nanoparticles is exploited to study the Raman spectrum of Cytochrome c from Saccharomyces cerevisiae (Yeast Cytochrome c--YCc) in the limit of single-molecule. The investigation is performed on proteins both in solution and immobilised onto a glass slide using a quasi resonant laser line as exciting source with low excitation intensity. In both cases, spectra acquired at different times exhibit dramatic temporal fluctuations in both the total spectrum and in the specific line intensity, even though averaging of several individual spectra reproduces the main Raman features of bulk YCc. Analysis of the spectral intensity fluctuations from solutions reveals a multimodal distribution of some specific Raman lines, consistent with the approaching of single molecule regime. Among other results, the statistical analysis of the spectra from immobilised samples seems to indicate dynamical processes involving the reorientational of the heme with respect to the metal surface.

In situ STM imaging and direct electrochemistry of Pyrococcus furiosus ferredoxin assembled on thiolate-modified Au111 surfaces

We have addressed here electron transfer (ET) of Pyrococcus furiosus ferredoxin (PfFd, 7.5 kDa) in both homogeneous solution using edge plane graphite (EPG) electrodes and in the adsorbed state by electrochemistry on surface-modified single-crystal Au111 electrodes, This has been supported by surface microscopic structures of PfFd monolayers, as revealed by scanning tunneling microscopy under potential control (in situ STM). Direct ET between PfFd in phosphate buffer solution, pH 7.9, and EPG electrodes is observed in the presence of promoters. Neomycin gives rise to a pair of redox peaks with a formal potential of ca -430 mV (vs SCE), corresponding to [3Fe-4S]1+/0. The presence of an additional promoter, which can be propionic acid, alanine, or cysteine, induces a second pair of redox peaks at approximately -900 mV (vs SCE) arising from [3Fe-4S]0/1-. A robust neomycin-PfFd complex was detected by mass spectrometry. The results clearly favor an ET mechanism in which the promoting effect of small organic molecules is through formation of promoter-protein complexes. The interaction of PfFd with small organic molecules in homogeneous solution offers clues to confine the protein on the electrode surface modified by the same functional group monolayer and to address diffusionless direct electrochemistry, as well as surface microstructures of the protein monolayer. PfFd molecules were found to assemble on either mercaptopropionic acid (MPA) or cysteine-modified Au111 surfaces in stable monolayers or submonolayers. Highly ordered (2 radical 3 x 5)R30 degrees cluster structures with six MPA molecules in each cluster were found by in situ STM. Individual PfFd molecules on the MPA layer are well resolved by in situ STM. Under Ar protection reversible cyclic voltammograms were obtained on PfFd-MPA/Au111 and PfFd-cysteine/Au111 electrodes with redox potentials of -220 and -201 mV (vs SCE), respectively, corresponding to the [Fe3S4]1+/0 couple. These values are shifted positively by 200 mV relative to homogeneous solution due to interactions between the promoting layers and the protein molecules. Possible mechanisms for such interactions and their ET patterns are discussed.

Direct Immobilization of Native Yeast Iso-1 Cytochrome c on Bare Gold: Fast Electron Relay to Redox Enzymes and Zeptomole Protein-Film Voltammetry

Cyclic voltammetry shows that yeast iso-1-cytochrome c (YCC), chemisorbed on a bare gold electrode via Cys102, exhibits fast, reversible interfacial electron transfer (k(0) = 1.8 x 10(3) s(-1)) and retains its native functionality. Vectorially immobilized YCC relays electrons to yeast cytochrome c peroxidase, and to both cytochrome cd(1) nitrite reductase (NIR) and nitric oxide reductase from Paracoccus denitrificans, thereby revealing the mechanistic properties of these enzymes. On a microelectrode, we measured nitrite turnover by approximately 80 zmol (49 000 molecules) of NIR, coadsorbed on 0.65 amol (390 000 molecules) of YCC.