Electrochemically induced surface-enhanced infrared difference absorption (SEIDA) spectroscopy of a protein monolayer

Revealing the Hydrogen Bonding Interaction of DNA with Unnatural Bases via Plasmonic Antenna Enhanced Infrared Spectroscopy

The incorporation of unnatural bases in DNA programming can break through the limits of Watson-Crick and Hoogsteen base pairing to expand the diversity of DNA structures. Thus, understanding the interaction between DNA and unnatural bases is of great importance in DNA nanotechnology. Here, we propose an approach of plasmonic antenna enhanced infrared spectroscopy to study the hydrogen bonding interaction between poly(thymine) DNA (poly T DNA) and melamine. The formation of multiple hydrogen bonds between melamine and thymine of poly T DNA is revealed by the appearance of a new infrared (IR) feature of the NH₂ deformation vibration at 1680 cm^-1. The binding rate constant (k_b) and the dissociation rate constant (k_d) of the affinity reaction reach 39.70 M^-1·s^-1 and 4.49 × 10^-5 s^-1, respectively. This work offers a valuable IR technique to study DNA nanostructures at the molecular level, providing unique physicochemical views of the interaction mechanism between DNA and unnatural bases in DNA programming.

Infrared Difference Spectroscopy of Proteins: From Bands to Bonds

Infrared difference spectroscopy probes vibrational changes of proteins upon their perturbation. Compared with other spectroscopic methods, it stands out by its sensitivity to the protonation state, H-bonding, and the conformation of different groups in proteins, including the peptide backbone, amino acid side chains, internal water molecules, or cofactors. In particular, the detection of protonation and H-bonding changes in a time-resolved manner, not easily obtained by other techniques, is one of the most successful applications of IR difference spectroscopy. The present review deals with the use of perturbations designed to specifically change the protein between two (or more) functionally relevant states, a strategy often referred to as reaction-induced IR difference spectroscopy. In the first half of this contribution, I review the technique of reaction-induced IR difference spectroscopy of proteins, with special emphasis given to the preparation of suitable samples and their characterization, strategies for the perturbation of proteins, and methodologies for time-resolved measurements (from nanoseconds to minutes). The second half of this contribution focuses on the spectral interpretation. It starts by reviewing how changes in H-bonding, medium polarity, and vibrational coupling affect vibrational frequencies, intensities, and bandwidths. It is followed by band assignments, a crucial aspect mostly performed with the help of isotopic labeling and site-directed mutagenesis, and complemented by integration and interpretation of the results in the context of the studied protein, an aspect increasingly supported by spectral calculations. Selected examples from the literature, predominately but not exclusively from retinal proteins, are used to illustrate the topics covered in this review.

Potassium channel blocker inhibits the formation and electroactivity of Geobacter biofilm

Bacteria in biofilms are able to utilize potassium ion channel-mediated electrical signaling to achieve cell-cell communication. However, it remains unclear whether these signals play a role in Geobacter sp. when surrounded by an intense electric field. This study used a potassium channel blocker (tetraethylammonium, TEA) that interfered with the release of K⁺ but not bacterial growth to demonstrate that potassium ion channel-mediated electrical signaling affected the formation and electroactivity of Geobacter sulfurreducens. The results showed that 5 mM TEA slowed the formation of Geobacter sulfurreducens biofilm, and the current density was ~50% lower than in the control. The electrochemical analyses showed that the electroactivity of the biofilms with TEA addition was inferior. In particular, the micrometer- scale biofilm with TEA exhibited fewer high current peaks, and the species of outermost groups that participated in the electron transfer in Geobacter sulfurreducens biofilms was different from the control. This work provides initial evidence to reveal the role of potassium channels in Geobacter sulfurreducens electroactive biofilms.

Biphasic Formation of 2D Nanomembranes by Photopolymerization of Diacetylene Lipids as Revealed by Infrared Difference Spectroscopy

Two-dimensional nanomembranes are promising materials for filtration or separation by providing the basis for controlled and rapid transport between two compartments. The polymerization by UV light of diacetylene-containing lipids at an interface produces free-standing 2D nanomembranes. Here, we analyzed in situ the nanomembrane formation of 1,2-bis(10,12-tricosadiynoyl)-sn-glycero-3-phosphocholine (DiynePC) and 1-palmitoyl-2-(10,12-tricosadiynoyl)-sn-glycero-3-phosphoethanolamine (PTPE) on germanium using light-induced infrared difference spectroscopy with attenuated total reflection to obtain insights into the kinetics and mechanism of the polymerization process. Our interpretation is supported by atomic force microscopy and density functional theory. Formation of the polymer network is evidenced by changes in the frequency of C═O stretches acting as infrared probes. However, spectral and kinetic analysis revealed a biphasic process in the monolayer. In both phases, losses in signal of CH₂ stretches are observed which are not in agreement with the accepted mechanism of chain propagation for diacetylene polymerization. These signals are dominant in the second phase and are assigned to termination reactions with some contributions from intramolecular consecutive reactions. This finding now provides a spectroscopic measure for the identity and integrity of the nanomembrane complementary to microscopic analysis. We deduce that limited 2D mobility on the solid support promotes intramolecular termination, leading to smaller domains.

Accelerating the start-up of the cathodic biofilm by adding acyl-homoserine lactone signaling molecules

Electroactive biofilms (EABs) are essential for bioelectrochemical systems, however, the formation of cathodic EABs is more time-consuming than anodic EABs. This study aims to evaluate whether acyl-homoserine lactones (AHLs) could facilitate the start-up of cathodic Geobacter soli EABs. With AHL addition, the biomass, cell viability, and extracellular polymeric substance (EPS) abundance of cathode-associated G. soli EABs were increased. Likewise, redox activities of EPS and outermost proteins in the cathodic EABs were enhanced in the presence of AHLs, which consequently led to better start-up performance of biofilms. Compared to the control without AHLs, start-up lag periods were reduced by approximately 50%, electron uptakes were enhanced by 1.3-2.0 times, and denitrification rates were more than doubled with AHL addition in the start-up cycle, which were comparable to those of mature G. soli cathodic EABs. These findings open up an opportunity for accelerating the start-up of cathodic biofilms via AHLs.

Transcriptomic, Proteomic, and Bioelectrochemical Characterization of an Exoelectrogen Geobacter soli Grown With Different Electron Acceptors

The ability of Geobacter species to transfer electrons outside cells enables them to play an important role in biogeochemical and bioenergy processes. Our knowledge of the extracellular electron transfer (EET) process in the genus Geobacter is mainly from the study of G. sulfurreducens, and in order to fully investigate the EET mechanisms in the genus Geobacter, other Geobacter species should also be considered. This study focused on the EET of Geobacter soli GSS01, which exhibited a capability of reducing insoluble Fe(III) oxides and generating electrical current comparable with G. sulfurreducens PCA. Electrochemical characterization, including cyclic voltammetry, differential pulse voltammetry, and electrochemical in situ FTIR spectra, revealed that different redox proteins contributed to the electrochemical behaviors of G. soli and G. sulfurreducens. Based on comparative transcriptomic and proteomic analyses, OmcS was the most upregulated protein in both G. soli and G. sulfurreducens cells grown with insoluble Fe(III) oxides vs. soluble electron acceptor. However, the proteins including OmcE and PilA that were previously reported as being important for EET in G. sulfurreducens were downregulated or unchanged in G. soli cells grown with insoluble electron acceptors vs. soluble electron acceptor, and many proteins that were upregulated in G. soli cells grown with insoluble electron acceptors vs. soluble electron acceptor, such as OmcN, are not important for EET in G. sulfurreducens. We also identified 30 differentially expressed small RNAs (sRNAs) in G. soli cells grown with different acceptors. Taken together, these findings help to understand the versatile EET mechanisms that exist in the genus Geobacter and point to the possibility of sRNA in modulating EET gene expression.

Disc Antenna Enhanced Infrared Spectroscopy: From Self-Assembled Monolayers to Membrane Proteins

Plasmonic surfaces have emerged as a powerful platform for biomolecular sensing applications and can be designed to optimize the plasmonic resonance for probing molecular vibrations at utmost sensitivity. Here, we present a facile procedure to generate metallic microdisc antenna arrays that are employed in surface-enhanced infrared absorption (SEIRA) spectroscopy of biomolecules. Transmission electron microscopy (TEM) grids are used as shadow mask deployed during physical vapor deposition of gold. The resulting disc-shaped antennas exhibit enhancement factors of the vibrational bands of 4 × 10⁴ giving rise to a detection limit <1 femtomol (10^-15 mol) of molecules. Surface-bound monolayers of 4-mercaptobenzoic acid show polyelectrolyte behavior when titrated with cations in the aqueous medium. Conformational rigidity of the self-assembled monolayer is validated by density functional theory calculations. The membrane protein sensory rhodopsin II is tethered to the disc antenna arrays and is fully functional as inferred from the light-induced SEIRA difference spectra. As an advance to previous studies, the accessible frequency range is improved and extended into the fingerprint region.

Protein Film Infrared Electrochemistry Demonstrated for Study of H2 Oxidation by a [NiFe] Hydrogenase

Understanding the chemistry of redox proteins demands methods that provide precise control over redox centers within the protein. The technique of protein film electrochemistry, in which a protein is immobilized on an electrode surface such that the electrode replaces physiological electron donors or acceptors, has provided functional insight into the redox reactions of a range of different proteins. Full chemical understanding requires electrochemical control to be combined with other techniques that can add additional structural and mechanistic insight. Here we demonstrate a technique, protein film infrared electrochemistry, which combines protein film electrochemistry with infrared spectroscopic sampling of redox proteins. The technique uses a multiple-reflection attenuated total reflectance geometry to probe a redox protein immobilized on a high surface area carbon black electrode. Incorporation of this electrode into a flow cell allows solution pH or solute concentrations to be changed during measurements. This is particularly powerful in addressing redox enzymes, where rapid catalytic turnover can be sustained and controlled at the electrode allowing spectroscopic observation of long-lived intermediate species in the catalytic mechanism. We demonstrate the technique with experiments on E. coli hydrogenase 1 under turnover (H2 oxidation) and non-turnover conditions.

The Grateful Infrared: Sequential Protein Structural Changes Resolved by Infrared Difference Spectroscopy

The catalytic activity of proteins is a function of structural changes. Very often these are as minute as protonation changes, hydrogen bonding changes, and amino acid side chain reorientations. To resolve these, a methodology is afforded that not only provides the molecular sensitivity but allows for tracing the sequence of these hierarchical reactions at the same time. This feature article showcases results from time-resolved IR spectroscopy on channelrhodopsin (ChR), light-oxygen-voltage (LOV) domain protein, and cryptochrome (CRY). All three proteins are activated by blue light, but their biological role is drastically different. Channelrhodopsin is a transmembrane retinylidene protein which represents the first light-activated ion channel of its kind and which is involved in primitive vision (phototaxis) of algae. LOV and CRY are flavin-binding proteins acting as photoreceptors in a variety of signal transduction mechanisms in all kingdoms of life. Beyond their biological relevance, these proteins are employed in exciting optogenetic applications. We show here how IR difference absorption resolves crucial structural changes of the protein after photonic activation of the chromophore. Time-resolved techniques are introduced that cover the time range from nanoseconds to minutes along with some technical considerations. Finally, we provide an outlook toward novel experimental approaches that are currently developed in our laboratories or are just in our minds ("Gedankenexperimente"). We believe that some of them have the potential to provide new science.

Recent developments in methodology employed to study the interactions between nanomaterials and model lipid membranes

With the boom of nanotechnology, nanomaterials (NMs) have been widely utilized in diverse applications, especially in biological and biomedical fields. Understanding how NMs interact with biomolecules, including proteins, DNA, and lipids, is of great importance for revealing the limitations posed and opportunities offered. Model lipid membrane, as a simplified cell membrane model, has been widely used to study the nanomaterial-lipid membrane interactions. In this article, current and emerging techniques, both experimental and theoretical, to investigate the interactions between NMs and model lipid membrane are summarized with each tool's capacities and limitations, along with future directions and challenges in this exciting area. This critical information will provide methodological guidance for researchers in this field.

Revealing the Nature of Interaction between Graphene Oxide and Lipid Membrane by Surface-Enhanced Infrared Absorption Spectroscopy

Revealing the nature of interaction between graphene oxide (GO) and lipid membrane is a crucial issue but still remains challenging. Here, we describe our recent effort toward this direction by studying the GO-induced vibrational changes of interfacial water and lipid membrane with surface-enhanced infrared absorption (SEIRA) spectroscopy. The experimental results provide evidence that overcoming the electrostatic repulsion of phosphate group, its hydrogen bonding attraction as well as the electrostatic and hydrophobic interaction of choline group are the driving forces for the effective adsorption of GO on lipid membrane. This work will open exciting new avenues to explore the use of SEIRA spectroscopy technique in probing nanobio interface.

Breaking of the phosphodiester bond: a key factor that induces hemolysis

In-depth understanding the toxicity of nanomaterials in red blood cells (RBCs) is of great interest, because of the importance of RBCs in transporting oxygen in blood circulation. Although the toxic effects of nanoparticles in RBCs have been revealed, the conclusions from the literature are conflicting, and in particular, the toxic mechanism is still at the infant stage. Herein, we investigated the size-dependent toxicity of well-known CdTe semiconductor quantum dots (QDs) and revealed the exact toxic mechanism at the molecular level by confocal microscopy and Fourier transform infrared (FT-IR) spectroscopy techniques. We found that smaller mercaptosuccinic acid-capped CdTe QDs (MSA-QDs) with the green-emitting color could cause hemagglutination whereas the middle-size yellow-emitting MSA-QDs induced the formation of stomatocytes and echinocytes and the bigger size red-emitting MSA-QDs induced heavy hemolysis and the formation of lots of ghost cells. The FT-IR data proved that all the MSA-QDs were likely to bond to the RBCs membranes and caused the structural changes of lipid and protein in RBCs. But only the red-emitting MSA-QDs caused the breakage of the phosphodiester bond, which might cause the heavy hemolysis. To some extent, this is the first example that reveals the hemolysis mechanism at the molecular level.

Toxicity mechanism of graphene oxide and nitrogen-doped graphene quantum dots in RBCs revealed by surface-enhanced infrared absorption spectroscopy

GO can extract the lipid bilayer of RBCs membranes, resulting in hemolysis and aberrant forms. In contrast, GQDs just disturb the structure and conformation of the lipid, resulting in only aberrant cells.

Surface enhanced vibrational spectroscopic evidence for an alternative DNA-independent redox activation of endonuclease III

Redox activation of the [4Fe–4S] cluster in DNA repair enzyme endonuclease III does not exclusively rely on interaction with DNA.

Infrared spectroscopic studies on the V-ATPase

V-ATPase is an ATP-driven rotary motor that vectorially transports ions. Together with F-ATPase, a homologous protein, several models on the ion transport have been proposed, but their molecular mechanisms are yet unknown. V-ATPase from Enterococcus hirae forms a large supramolecular protein complex (total molecular weight: ~700,000) and physiologically transports Na⁺ and Li⁺ across a hydrophobic lipid bilayer. Stabilization of these cations in the binding site has been discussed on the basis of X-ray crystal structures of a membrane-embedded domain, the K-ring (Na⁺ and Li⁺ bound forms). Sodium or lithium ion binding-induced difference FTIR spectra of the intact E. hirae V-ATPase have been measured in aqueous solution at physiological temperature. The results suggest that sodium or lithium ion binding induces the deprotonation of Glu139, a hydrogen-bonding change in the tyrosine residue and rigid α-helical structures. Identical difference FTIR spectra between the entire V-ATPase complex and K-ring strongly suggest that protein interaction with the I subunit does not cause large structural changes in the K-ring. This result supports the previously proposed Na⁺ transport mechanism by V-ATPase stating that a flip-flop movement of a carboxylate group of Glu139 without large conformational changes in the K-ring accelerates the replacement of a Na⁺ ion in the binding site. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems.

In-situ ultra-sensitive infrared absorption spectroscopy of biomolecule interactions in real time with plasmonic nanoantennas

Infrared absorption spectroscopy is a powerful biochemical analysis tool as it extracts detailed molecular structural information in a label-free fashion. Its molecular specificity renders the technique sensitive to the subtle conformational changes exhibited by proteins in response to a variety of stimuli. Yet, sensitivity limitations and the extremely strong absorption bands of liquid water severely limit infrared spectroscopy in performing kinetic measurements in biomolecules’ native, aqueous environments. Here we demonstrate a plasmonic chip-based technology that overcomes these challenges, enabling the in-situ monitoring of protein and nanoparticle interactions at high sensitivity in real time, even allowing the observation of minute volumes of water displacement during binding events. Our approach leverages the plasmonic enhancement of absorption bands in conjunction with a non-classical form of internal reflection. These features not only expand the reach of infrared spectroscopy to a new class of biological interactions but also additionally enable a unique chip-based technology.

Infrared absorption spectroscopy provides important information about molecules, but is hampered by the absorption of water. Adato and Altug exploit the plasmonic enhancement from nanoantennas to overcome this, enabling chip-based monitoring of biological samples in aqueous environments.

Recent applications of ATR FTIR spectroscopy and imaging to proteins

Attenuated Total Reflection (ATR) Fourier Transform Infrared (FTIR) spectroscopy is a label-free, non-destructive analytical technique that can be used extensively to study a wide variety of different molecules in a range of different conditions. The aim of this review is to discuss and highlight the recent advances in the applications of ATR FTIR spectroscopic imaging to proteins. It briefly covers the basic principles of ATR FTIR spectroscopy and ATR FTIR spectroscopic imaging as well as their advantages to the study of proteins compared to other techniques and other forms of FTIR spectroscopy. It will then go on to examine the advances that have been made within the field over the last several years, particularly the use of ATR FTIR spectroscopy for the understanding and development of protein interaction with surfaces. Additionally, the growing potential of Surface Enhanced Infrared Spectroscopy (SEIRAS) within this area of applications will be discussed. The review includes the applications of ATR FTIR imaging to protein crystallisation and for high-throughput studies, highlighting the future potential of the technology within the field of protein structural studies and beyond.

Label-free strategy for in-situ analysis of protein binding interaction based on attenuated total reflection surface enhanced infrared absorption spectroscopy (ATR-SEIRAS)

A versatile ATR-SEIRAS methodology is described herein for highly sensitive analysis of immunoglobulin (IgG) recognition. This strategy allows in situ tracking of specific protein binding at the liquid-solid interface. Most importantly, interferential signal from environmental molecules (e.g., water, nonspecific binding molecules, and bulk molecules) can be eliminated to negligible levels by using the ATR analysis mode, and the sensitive IR structural information of target proteins is obtained simultaneously. A simplified numerical model has been established to quantitatively describe the kinetics and thermodynamics of protein recognition processes at surfaces. Compared with conventional label-free methods for protein binding study, experimental results obtained from IR spectroscopic information are more reliable. The presented ATR-SEIRAS method is powerful in studying surface limited protein binding reactions.

Analyzing the catalytic processes of immobilized redox enzymes by vibrational spectroscopies

Analyzing the structure and function of redox enzymes attached to electrodes is a central challenge in many fields of fundamental and applied life science. Electrochemical techniques such as cyclic voltammetry which are routinely used do not provide insight into the molecular structure and reaction mechanisms of the immobilized proteins. Surface-enhanced infrared absorption (SEIRA) and surface-enhanced resonance Raman (SERR) spectroscopy may fill this gap, if nanostructured Au or Ag are used as conductive support materials. In this account, we will first outline the principles of the methodology including a description of the most important strategies for biocompatible protein immobilization. Subsequently, we will critically review SERR and SEIRA spectroscopic approaches to characterize the protein and active site structure of the immobilized enzymes. Special emphasis is laid on the combination of surface-enhanced vibrational spectroscopies with electrochemical methods to analyze equilibria and dynamics of the interfacial redox processes. Finally, we will assess the potential of SERR and SEIRA spectroscopy for in situ investigations on the basis of the first promising studies on human sulfite oxidase and hydrogenases under turnover conditions.

Surface-enhanced vibrational spectroscopy for probing transient interactions of proteins with biomimetic interfaces: electric field effects on structure, dynamics and function of cytochrome c

Most of the biochemical and biophysical processes of proteins take place at membranes, and are thus under the influence of strong local electric fields, which are likely to affect the structure as well as the reaction mechanism and dynamics. To analyse such electric field effects, biomimetic interfaces may be employed that consist of membrane models deposited on nanostructured metal electrodes. For such devices, surface-enhanced resonance Raman and IR absorption spectroscopy are powerful techniques to disentangle the complex interfacial processes of proteins in terms of rotational diffusion, electron transfer, and protein and cofactor structural changes. The present article reviews the results obtained for the haem protein cytochrome c, which is widely used as a model protein for studying the various reaction steps of interfacial redox processes in general. In addition, it is shown that electric field effects may be functional for the natural redox processes of cytochrome c in the respiratory chain, as well as for the switch from the redox to the peroxidase function, one of the key events preceding apoptosis.

Time-resolved FT-IR Spectroscopy of Membrane Proteins

Time-resolved Fourier transform infrared spectroscopy (FT-IR) offers distinct advantages concerning restrictions pertinent to biomolecules. In particular, it is possible to monitor the temporal evolution of the reaction mechanism of complex machineries as membrane proteins, where other techniques encounter significant experimental difficulties. Here, we present the classical principles and experimental realizations of time-resolved FT-IR spectroscopy together with recent developments employed in our laboratory. Examples from applications to retinal proteins are reviewed that underline the impact of time-resolved FT-IR spectroscopy on the understanding of protein reactions on the level of single bonds.

Photosynthetic hydrogen production by a hybrid complex of photosystem I and [NiFe]-hydrogenase

Nature provides key components for generating fuels from renewable resources in the form of enzymatic nanomachines which catalyze crucial steps in biological energy conversion, for example, the photosynthetic apparatus, which transforms solar power into chemical energy, and hydrogenases, capable of generating molecular hydrogen. As sunlight is usually used to synthesize carbohydrates, direct generation of hydrogen from light represents an exception in nature. On the molecular level, the crucial step for conversion of solar energy into H(2) lies in the efficient electronic coupling of photosystem I and hydrogenase. Here we show the stepwise assembly of a hybrid complex consisting of photosystem I and hydrogenase on a solid gold surface. This device gave rise to light-induced H(2) evolution. Hydrogen production is possible at far higher potential and thus lower energy compared to those of previously described (bio)nanoelectronic devices that did not employ the photosynthesis apparatus. The successful demonstration of efficient solar-to-hydrogen conversion may serve as a blueprint for the establishment of this system in a living organism with the paramount advantage of self-replication.

Bioenergetics at the gold surface: SEIRAS probes photosynthetic and respiratory reactions at the monolayer level

The present study surveys a novel approach to studies of membrane proteins whose catalytic action is driven by the redox potential or by the membrane potential. We introduce SEIRAS (surface-enhanced IR absorption spectroscopy) to probe a monolayer of membrane protein adhered to the surface of a gold electrode. SEIRAS renders high surface sensitivity by enhancing the signal of the adsorbed molecule by approximately two orders of magnitude. It is demonstrated that reaction-induced spectroscopy is applicable by recording IR differences of cytochrome c after stimulation by the electrical potential. The impact of the membrane potential on the function of a membrane protein is demonstrated by performing light-induced difference spectroscopy on a microbial rhodopsin (sensory rhodopsin II) under voltage-clamp conditions. The methodology presented opens new avenues to study the mechanism of electron-triggered and voltage-gated proteins at the level of single bonds. As many of these catalytic reactions are of vectorial nature, control on the orientation of the membrane protein is mandatory. Approaches are presented on how to specifically adhere photosynthetic and respiratory proteins to the electrode surface and reconstitute these membrane proteins in the lipid bilayer. Functionality of such biomimetic systems is assessed in situ by spectro-electrochemical methods.

Resolving voltage-dependent structural changes of a membrane photoreceptor by surface-enhanced IR difference spectroscopy

Membrane proteins are molecular machines that transport ions, solutes, or information across the cell membrane. Electrophysiological techniques have unraveled many functional aspects of ion channels but suffer from the lack of structural sensitivity. Here, we present spectroelectrochemical data on vibrational changes of membrane proteins derived from a single monolayer. For the seven-helical transmembrane protein sensory rhodopsin II, structural changes of the protein backbone and the retinal cofactor as well as single ion transfer events are resolved by surface-enhanced IR difference absorption spectroscopy (SEIDAS). Angular changes of bonds versus the membrane normal have been determined because SEIDAS monitors only those vibrations whose dipole moment are oriented perpendicular to the solid surface. The application of negative membrane potentials (DeltaV = -0.3 V) leads to the selective halt of the light-induced proton transfer at the stage of D75, the counter ion of the retinal Schiff base. It is inferred that the voltage raises the energy barrier of this particular proton-transfer reaction, rendering the energy deposited in the retinal by light excitation insufficient for charge transfer to occur. The other structural rearrangements that accompany light-induced activity of the membrane protein, are essentially unaffected by the transmembrane electric field. Our results demonstrate that SEIDAS is a generic approach to study processes that depend on the membrane potential, like those in voltage-gated ion channels and transporters, to elucidate the mechanism of ion transfer with unprecedented spatial sensitivity and temporal resolution.

Electron-Transfer Reactions through the Associated Interaction between Cytochromec and Self-Assembled Monolayers of Optically Active Cobalt(III) Complexes: Molecular Recognition Ability Induced by the Chirality of the Cobalt(III) Units

Self-assembled monolayers (SAMs) of optically active Co(III) complexes ((S)-2/(R)-2) that contain (S)- or (R)-phenylalanine derivatives as a molecular recognition site were constructed on Au electrodes ((S)-2-Au/(R)-2-Au). Molecular recognition characteristics induced by the S and R configurations were investigated by measurements of electron-transfer reactions with horse heart cytochrome c (cyt c). The electrochemical studies indicate that the maximum current of cyt c reduction is obtained when the Au electrode is modified by 2 with a moderate coverage of approximately 4.0 x 10(-11) mol cm(-2). Since the Au electrode is not densely packed with the Co(III) units at this concentration, we conclude that the penetrative association process between cyt c and the Co(III) unit plays an important role in this electron-transfer system. The differences in the electron-transfer rates of (S)-2-Au and (R)-2-Au increase with increasing scan rates, a result indicating that the chiral ligand has an influence on the rate of association of the complexes with cyt c. 3-Au has a mixed monolayer composed of 2 and hexanethiol and exhibits electron-transfer behavior comparable to 2-Au. The difference in the association rates of (S)-3-Au and (R)-3-Au is larger than that between (S)-2-Au and (R)-2-Au, which indicates that the molecular recognition ability of 3-Au has been enhanced by filling the gap between molecules of 2 with hexanethiols. The differences in the oxidation rates of cyt c(II) between (S)-2-Au and (R)-2-Au and between (S)-3-Au and (R)-3-Au were larger than the differences in the rates of the reduction of cyt c(III); this suggests that the size of the heme crevice varies according to the oxidation state of cyt c.

Kinetic, Thermodynamic, and Mechanistic Patterns for Free (Unbound) Cytochromec at Au/SAM Junctions: Impact of Electronic Coupling, Hydrostatic Pressure, and Stabilizing/Denaturing Additives

Combined kinetic (electrochemical) and thermodynamic (calorimetric) investigations were performed for an unbound (intact native-like) cytochrome c (CytC) freely diffusing to and from gold electrodes modified by hydroxyl-terminated self-assembled monolayer films (SAMs), under a unique broad range of experimental conditions. Our approach included: 1) fine-tuning of the charge-transfer (CT) distance by using the extended set of Au-deposited hydroxyl-terminated alkanethiol SAMs [-S-(CH(2))(n)-OH] of variable thickness (n=2, 3, 4, 6, 11); 2) application of a high-pressure (up to 150 MPa) kinetic strategy toward the representative Au/SAM/CytC assemblies (n=3, 4, 6); 3) complementary electrochemical and microcalorimetric studies on the impact of some stabilizing and denaturing additives. We report for the first time a mechanistic changeover detected for "free" CytC by three independent kinetic methods, manifested through 1) the abrupt change in the dependence of the shape of the electron exchange standard rate constant (k(o)) versus the SAM thickness (resulting in a variation of estimated actual CT range within ca. 15 to 25 A including ca. 11 A of an "effective" heme-to-omega-hydroxyl distance). The corresponding values of the electronic coupling matrix element vary within the range from ca. 3 to 0.02 cm(-1); 2) the change in activation volume from +6.7 (n=3), to approximately 0 (n=4), and -5.5 (n=6) cm(3) mol(-1) (disclosing at n=3 a direct pressure effect on the protein's internal viscosity); 3) a "full" Kramers-type viscosity dependence for k(o) at n=2 and 3 (demonstrating control of an intraglobular friction through the external dynamic properties), and its gradual transformation to the viscosity independent (nonadiabatic) regime at n=6 and 11. Multilateral cross-testing of "free" CytC in a native-like, glucose-stabilized and urea-destabilized (molten-globule-like) states revealed novel intrinsic links between local/global structural and functional characteristics. Importantly, our results on the high-pressure and solution-viscosity effects, together with matching literature data, strongly support the concept of "dynamic slaving", which implies that fluctuations involving "small" solution components control the proteins' intrinsic dynamics and function in a highly cooperative manner as far as CT processes under adiabatic conditions are concerned.

Determination of the Orientation of Adsorbed Cytochrome c on Carboxyalkanethiol Self-Assembled Monolayers by In Situ Differential Modification

The contact domain utilized by horse cytochrome c when adsorptively bound to a C(10)COOH self-assembled monolayer (SAM) was delineated using a chemical method based on differential modification of surface amino acids. Horse cytochrome c was adsorbed at low ionic strength (pH 7.0, 4.4 mM potassium phosphate) onto 10 microm diameter gold particles coated with HS(CH(2))(10)COOH SAMs. After in situ modification of lysyl groups by reductive Schiff-base methylation, the protein was desorbed, digested using trypsin, and the peptide mapped using LC/MS. Relative lysyl reactivities were ascertained by comparing the resulting peptide frequencies to control samples of solution cytochrome c modified to the same average extent. The least reactive lysines in adsorbed cytochrome c were found to be 13, 72, 73, 79, and 86-88, consistent with a contact region located up and to the left (Met-80 side) of the solvent-exposed heme edge (conventional front face view). The most reactive lysines were 39, 53, 55, and 60, located on the lower backside. The proposed orientation features a heme tilt angle of approximately 35-40 degrees with respect to the substrate surface normal. Factors that can complicate or distort data interpretation are discussed, and the generality of differential modification relative to existing in situ methods for protein orientation determination is also addressed.

Orientational Control of the Physiological Reaction of Cytochrome c Oxidase Tethered to a Gold Electrode

The physiological reaction of a membrane protein is reconstituted on a solid-supported electrode by orientational control via the position of an affinity tag. Recombinant cytochrome c oxidase (CcO) from Rhodobacter sphaeroides is immobilized on a chemically modified gold surface via the affinity of a histidine tag (His-tag) to a nickel chelating nitrilotriacetic acid surface. Control of the orientation is achieved by the adsorption of CcO through the His-tag engineered into the two opposite sites of the membrane protein surface. After reconstitution into a lipid layer, the functionality of this enzyme film electrode is probed by surface-enhanced infrared absorption spectroscopy and cyclic voltammetry. We demonstrate that cytochrome c (Cc) binds and initiates the catalytic reaction of CcO only when the latter is orientated with subunit II facing the bulk aqueous phase while Cc does not interact with the oppositely orientated CcO. We infer from the observed catalytic dioxygen reduction at potentials below 240 mV (vs a normal hydrogen electrode) that reduced Cc mediates electron input into CcO in a way similar to the physiological pathway. The quantitative analysis of the IR spectra indicates the presence of an inactive population of Cc bound to CcO at equal amounts as the redox-active population. This methodological approach demonstrates that the orientation of the membrane protein can be controlled depending on the position of the affinity tag. The approach is considered to be of general applicability as the introduction of affinity tags is routine in current biochemistry.

Use of Surface Enhanced Infrared Absorption Spectroscopy (SEIRA) to probe the functionality of a protein monolayer

We present a novel infrared method to investigate the functionality of a protein monolayer tethered to a metal substrate. The approach employs Surface Enhanced Infrared Absorption Spectroscopy (SEIRAS), which renders high surface sensitivity by enhancing the signal of the adsorbed protein by up to approximately 2 orders of magnitude. We demonstrate that the electrochemically induced absorption changes of a cytochrome c monolayer can be observed with excellent signal-to-noise ratio when the protein is adhered to a modified gold surface. To probe membrane proteins, a concept is introduced for the oriented incorporation into solid supported lipid bilayers. Recombinant cytochrome c oxidase solubilized in detergent is immobilized on a chemically modified gold surface via the affinity of its histidine (His)-tag to a nickel-chelating nitro-triacetic acid (NTA) surface. The protein monolayer is reconstituted into the lipid environment by detergent removal. Changing the orientation of the protein with respect to the metal surface is achieved by inserting the His-tag on either side of the membrane protein surface. Orientational control is mandatory for experiments in which electrons are injected from the electrode into the protein. The presented methodology opens new avenues to study the mechanism of the biomedically relevant class of electron and voltage-gated proteins on the atomic level.