Functional Vibrational Spectroscopy of a CytochromecMonolayer: SEIDAS Probes the Interaction with Different Surface-Modified Electrodes

Microbial biofilms for self-powered noncontact sensing

Noncontact sensing technology plays a vital role in the intelligent human-machine interface, as the essential medium for exchanging information between human and electronic devices. To date, several inorganic materials-based noncontact sensing techniques have been used to accurately detect touch, electrical property, and physical motion. However, limited available materials, dependence on additional power supplies, and poor power production performance, have seriously obstructed the practical applications of noncontact sensing technology. Here, we developed simple self-powered noncontact sensors (SNSs) assembled using a typical G. sulfurreducens biofilm as the core component. In noncontact mode, the sensor demonstrated excellent self-powered sensing performance with maximum voltage output of 10 V and a current of 60 nA, a maximum sensing range of 40 cm which is the farthest reported to date. Depending on its excellent sensing characteristic, the SNSs was used to monitor human breathing in this work. Furthermore, an array of united SNSs was able to localize external electric fields and effectively extend the sensing area by increasing the number of devices. Compared to traditional inorganic materials, microbial biofilms have the advantages of wide existence, self-proliferation, low cost, environmental friendliness, and ultra-fast self-healing property (seconds level). The proposed biofilm SNSs in our work provides new insights for noncontact power generation of biomaterials and self-driven sensing.

Charge Transfer Surface-Enhanced Raman and Absorption Spectra of the Zwitterionic Form of Cysteine Adsorbed on M@Au12 (M = Au, Ag, Pt, and Pd) Nanoclusters

The effect of the core atom type of the M@Au₁₂ nanocluster (M = Au, Ag, Pt, and Pd) on the normal (NR) and charge-transfer surface-enhanced Raman spectroscopy (CT-SERS) of the zwitterion form of l-cysteine (ZWCYS) adsorbed on two different sites (D1 and D2) of the nanocluster is investigated separately in the gas phase and water. Because SERS requires the calculation of the absorption spectrum, the effect of the core atom type on the absorption spectrum of M@Au₁₂ and its complex with the ZWCYS has also been investigated. The vibrational bands that show the intensity enhancement in the CT-SERS of the ZWCYS interacting with the D1 site of M@Au₁₂ nanocluster in water are O─C═O asymmetric stretching (M = Au and Ag), NH₂ bending (M = Ag), S-H stretching (M = Ag, Pt, and Pd), CH₂ bending (M = Pt), and CH₂ symmetric stretching (M = Pt and Pd). The ZWCYS at the D₂ site of the M@Au₁₂ nanocluster in water exhibits intensity enhancement for O─C═O asymmetric stretching (M = Pt), NH₃ wagging (M = Au), and S-H stretching (M = Pd). The intensity of the vibrational bands of ZWCYS does not increase for M = Ag but decreases for O─C═O asymmetric stretching, S-H stretching, CH₂ symmetric stretching, CH₂ asymmetric stretching, and especially NH₂ symmetric stretching.

Excellent removal performance of 4,4'-biphenyldicarboxaldehyde m-phenylenediamine Schiff base magnetic polymer towards phenanthrene and 9-phenanthrol: Experimental, modeling and DFT calculations studies

Phenanthrene (PTH) and 9-phenanthrol (9-PTH) exhibited severe health threats and ecological hazards, for this reason, exploring a high-efficient removing strategy for PTH and 9-PTH could be considered of great urgency. Herein the 4,4'-biphenyldicarboxaldehyde m-phenylenediamine Schiff base magnetic polymer (magnetic BIPH-PHEN) was successfully fabricated via Schiff base polycondensation reaction and the subsequently one-pot embedded method. The mutual aromatic nucleus of BIPH-PHEN polymer and PTH/9-PTH could form π-π interaction, thus improving the capture ability, the embedded Fe₃O₄ nanoparticles provided the possibility for rapid separation. The physical and chemical properties of the magnetic BIPH-PHEN were systematically characterized. The removal rate of magnetic BIPH-PHEN towards PTH and 9-PTH was 85.65 % and 98.52 %, respectively (PTH or 9-PTH: 8 mg/L; Adsorbent: 0.2 g/L). The DFT calculations including energy calculations and electrostatic potential distribution analyzed the different bonding modes and proposed the most possible bonding modes in the adsorbent/adsorbate system. Moreover, the LUMO and HOMO orbits combined with energy gaps analysis proved the existence and specific types of the π-π interaction. The monolayer adsorption occurred on the homogeneous magnetic BIPH-PHEN surface, simultaneously the chemisorption was dominant. This work not only proposed new sights on assembling magnetic Schiff base polymer for removing polycyclic aromatic hydrocarbons, but also provided a deeper understanding of intramolecular interactions.

Anaerobic ammonium oxidation driven by dissimilatory iron reduction in autotrophic Anammox consortia

Feammox has been applied to wastewater biological nitrogen removal. However, few studies have reported that Fe(III)(hydr)oxides induced Anammox consortia to remove NH4+ via the Feammox pathway. In this study, Fe(OH)3 was added to Anammox systems to investigate its effect on nitrogen removal via Feammox. The specific Anammox activity increased by 39 % by Fe(OH)3. Ammonia oxidation was observed to occur along with Fe(III) reduction and Fe(II) generation, which was further confirmed by the isotope test with feeding 15NH4+-N to detect 30N2. The cyclic voltammetry test showed that electron-storage capacity of Anammox sludge increased with Fe(OH)3. In situ Fourier transform infrared spectroscopy suggested that Fe(OH)3 enhanced the polarization of functional groups of outer membrane cytochrome of Anammox consortia to benefit extracellular electron transfer. This study demonstrated that Fe(OH)3 could induce Anammox consortia to perform extracellular respiration to enhance NH4+-N removal in the Anammox sludge system.

Water evaporation-induced electricity with Geobacter sulfurreducens biofilms

Water evaporation-induced electricity generators (WEGs) have recently attracted extensive research attention as an emerging renewable energy-harvesting technology that harvests electricity directly from water evaporation. However, the low power output, limited available material, complicated fabrication process, and extremely high cost have restricted wide applications of this technology. Here, a facile and efficient WEG prototype based on Geobacter sulfurreducens biofilm was demonstrated. The device can generate continuous electric power with a maximum output power density of ~685.12 μW/cm², which is two orders of magnitude higher than that of previously reported analogous devices. The superior performance of the device is attributed to the intrinsic properties of the G. sulfurreducens biofilm, including its hydrophilicity, porous structure, conductivity, etc. This study not only presents the unprecedented evaporating potential effect of G. sulfurreducens biofilms but also paves the way for developing hydrovoltaic technology with biomaterials.

Modulating the pro-apoptotic activity of cytochrome c at a biomimetic electrified interface

Programmed cell death via apoptosis is a natural defence against excessive cell division, crucial for fetal development to maintenance of homeostasis and elimination of precancerous and senescent cells. Here, we demonstrate an electrified liquid biointerface that replicates the molecular machinery of the inner mitochondrial membrane at the onset of apoptosis. By mimicking in vivo cytochrome c (Cyt c) interactions with cell membranes, our platform allows us to modulate the conformational plasticity of the protein by simply varying the electrochemical environment at an aqueous-organic interface. We observe interfacial electron transfer between an organic electron donor decamethylferrocene and O₂, electrocatalyzed by Cyt c. This interfacial reaction requires partial Cyt c unfolding, mimicking Cyt c in vivo peroxidase activity. As proof of concept, we use our electrified liquid biointerface to identify drug molecules, such as bifonazole, that can potentially down-regulate Cyt c and protect against uncontrolled neuronal cell death in neurodegenerative disorders.

Amino Acid Substitutions in the Non-Ordered Ω-Loop 70–85 Affect Electron Transfer Function and Secondary Structure of Mitochondrial Cytochrome c

The secondary structure of horse cytochrome c with mutations in the P76GTKMIFA83 site of the Ω-loop, exhibiting reduced efficiency of electron transfer, were studied. CD spectroscopy studies showed that the ordering of mutant structure increases by 3–6% compared to that of the WT molecules due to the higher content of β-structural elements. The IR spectroscopy data are consistent with the CD results and demonstrate that some α-helical elements change into β-structures, and the amount of the non-structured elements is decreased. The analysis of the 1H-NMR spectra demonstrated that cytochrome c mutants have a well-determined secondary structure with some specific features related to changes in the heme microenvironment. The observed changes in the structure of cytochrome c mutants are likely to be responsible for the decrease in the conformational mobility of the P76GTKMIFA83 sequence carrying mutations and for the decline in succinate:cytochrome c-reductase and cytochrome c-oxidase activities in the mitoplast system in the presence of these cytochromes c. We suggest that the decreased efficiency of the electron transfer of the studied cytochromes c may arise due to: (1) the change in the protein conformation in sites responsible for the interaction of cytochrome c with complexes III and IV and (2) the change in the heme conformation that deteriorates its optimal orientation towards donor and acceptor in complexes III and IV therefore slows down electron transfer. The results obtained are consistent with the previously proposed model of mitochondrial cytochrome c functioning associated with the deterministic mobility of protein globule parts.

Lessons from combined experimental and theoretical examination of the FTIR and 2D-IR spectroelectrochemistry of the amide I region of cytochrome c

Amide I difference spectroscopy is widely used to investigate protein function and structure changes. In this article, we show that the common approach of assigning features in amide I difference signals to distinct secondary structure elements in many cases may not be justified. Evidence comes from Fourier transform infrared (FTIR) and 2D-IR spectroelectrochemistry of the protein cytochrome c in the amide I range, in combination with computational spectroscopy based on molecular dynamics (MD) simulations. This combination reveals that each secondary structure unit, such as an alpha-helix or a beta-sheet, exhibits broad overlapping contributions, usually spanning a large part of the amide I region, which in the case of difference absorption experiments (such as in FTIR spectroelectrochemistry) may lead to intensity-compensating and even sign-changing contributions. We use cytochrome c as the test case, as this small electron-transferring redox-active protein contains different kinds of secondary structure units. Upon switching its redox-state, the protein exhibits a different charge distribution while largely retaining its structural scaffold. Our theoretical analysis suggests that the change in charge distribution contributes to the spectral changes and that structural changes are small. However, in order to confidently interpret FTIR amide I difference signals in cytochrome c and proteins in general, MD simulations in combination with additional experimental approaches such as isotope labeling, the insertion of infrared labels to selectively probe local structural elements will be required. In case these data are not available, a critical assessment of previous interpretations of protein amide I 1D- and 2D-IR difference spectroscopy data is warranted.

Is the Use of Surface-Enhanced Infrared Spectroscopy Justified in the Selection of Peptide Fragments That Play a Role in Substrate-Receptor Interactions? Adsorption of Amino Acids and Neurotransmitters on Colloidal Ag and Au Nanoparticles

This paper describes an application of attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR) and surface-enhanced infrared spectroscopy (SEIRA) to characterize the selective adsorption of four peptides present in body fluids such as neuromedin B (NMB), bombesin (BN), neurotensin (NT), and bradykinin (BK), which are known as markers for various human carcinomas. To perform a reliable analysis of the SERIA spectra of these peptides, curve fitting of these spectra in the spectral region above 1500 cm^–1 and SEIRA measurements of sulfur-containing and aromatic amino acids were performed. On the basis of the analyses of the spectral profiles, specific conclusions were drawn regarding specific molecule–metal interactions and changes in the interaction during the substrate change from the surface of silver nanoparticles (AgNPs) to gold nanoparticles (AuNPs).

In Situ Spectroelectrochemical Investigations of Electrode-Confined Electron-Transferring Proteins and Redox Enzymes

This perspective analyzes recent advances in the spectroelectrochemical investigation of redox proteins and enzymes immobilized on biocompatible or biomimetic electrode surfaces. Specifically, the article highlights new insights obtained by surface-enhanced resonance Raman (SERR), surface-enhanced infrared absorption (SEIRA), protein film infrared electrochemistry (PFIRE), polarization modulation infrared reflection-absorption spectroscopy (PMIRRAS), Förster resonance energy transfer (FRET), X-ray absorption spectroscopy (XAS), electron paramagnetic resonance (EPR), and differential electrochemical mass spectrometry (DMES)-based spectroelectrochemical methods on the structure, orientation, dynamics, and reaction mechanisms for a variety of immobilized species. This includes small heme and copper electron shuttling proteins, large respiratory complexes, hydrogenases, multicopper oxidases, alcohol dehydrogenases, endonucleases, NO-reductases, and dye decolorizing peroxidases, among other enzymes. Finally, I discuss the challenges and foreseeable future developments toward a better understanding of the functioning of these complex macromolecules and their exploitation in technological devices.

Modulating the biological function of protein by tailoring the adsorption orientation on nanoparticles

Protein orientation in nanoparticle-protein conjugates plays a crucial role in binding to cell receptors and ultimately, defines their targeting efficiency. Therefore, understanding fundamental aspects of the role of protein orientation upon adsorption on the surface of nanoparticles (NPs) is vital for the development of clinically important protein-based nanomedicines. In this work, new insights on the effect of the different orientation of cytochrome c (cyt c) bound to gold nanoparticles (GNPs) using various ligands on its apoptotic activity is reported. Time-of-Flight Secondary-Ion Mass Spectrometry (ToF-SIMS), electrochemical and circular dichroism (CD) analyses are used to investigate the characteristics of cyt c orientation and structure on functionalized GNPs. These studies indicate that the orientation and position of the heme ring inside the cyt c structure can be altered by changing the surface chemistry on the GNPs. A difference in the apoptosis inducing capability because of different orientation of cyt c bound to the GNPs is observed. These findings indicate that the biological activity of a protein can be modulated on the surface of NPs by varying its adsorption orientation. This study will impact on the rational design of new nanoscale biosensors, bioelectronics, and nanoparticle-protein based drugs.

Extracellular polymeric substances trigger an increase in redox mediators for enhanced sludge methanogenesis

Artificial redox mediators can be employed to improve the electron transfer efficiency during sludge methanogenesis, whereas these artificial redox mediators have possible deficiencies, such as high cost and non-biodegradability. For large-scale commercial applications, more cost-effective and environmentally friendly alternatives should be developed. Herein, the potential of extracellular polymeric substances (EPS) as natural redox mediators to improve methanogenesis was investigated. Compared to the control test without EPS addition, the methane (CH₄) production yield was increased by 83.5 ± 2.4% with an EPS dosage of 0.50 g/L and the lag phase duration was shortened by 45.6 ± 7.0%, along with the enhanced sludge dewaterability. Spectroelectrochemical measurements implied that EPS addition notably changed the intensities of different redox-active groups, which decreased the charge transfer resistance and enhanced the extracellular electron transfer efficiency. These redox-active groups were mainly from the solubilization and hydrolysis of sludge protein due to increased protease activities, thereby leading to a higher acetate concentration during the acidification step. Further investigation showed that EPS addition also improved the activities of both acetotrophic and hydrogenotrophic methanogens, as indicated by a higher abundance of alpha subunit of methyl coenzyme M reductase (mcrA) genes, enhancing CH₄ production. This work provides an innovative strategy for improving sludge anaerobic digestion with efficient additives.

A Novel Cysteine-Functionalized MxOy Material as Support for Laccase Immobilization and a Potential Application in Decolorization of Alizarin Red S

Immobilization process improves the enzyme properties, like stability, activity, selectivity or specificity. In the study, a novel cysteine-functionalized MxOy (ZrO2, SiO2) material was used as a support for the immobilization of laccase from Trametes versicolor. The proposed matrix was prepared using a simple sol-gel method. The cysteine was introduced during the synthesis of a sample. Additionally, the obtained supports were modified with glutaraldehyde. The basic properties of the prepared cysteine functionalized ZrO2 and SiO2 were determined using spectroscopic, thermal, porous, electrostatic and elemental analysis. Furthermore, the obtained biocatalytic systems were used as catalysts in the oxidation of sulfonic acid. Catalytic and kinetic parameters were determined based on the proposed model reaction. Next, laccase immobilized on ZrO2- and SiO2-based materials were, for the first time, utilized in the decolorization of Alizarin Red S. In that process, the influence of duration, pH and temperature on the efficiency of decolorization was evaluated. The results show that the proposed biocatalytic systems offer good specific activity (ca. 19 U/mg) and activity retention (ca. 77%). Importantly, they can be successfully used in the decolorization of Alizarin Red S with high efficiency (above 95%).

Block Copolymer Derived Vertically Coupled Plasmonic Arrays for Surface-Enhanced Raman Spectroscopy

A surface-enhanced Raman spectroscopy sensing template consisting of gold-covered nanopillars is developed. The plasmonic slab consists of a perforated gold film at the base of the nanopillars and a Babinet complementary dot array on top of the pillars. The nanopillars were fabricated by the incorporation of an iron salt precursor into a self-assembled block copolymer thin film and subsequent reactive ion etching. The preparation is easy, scalable, and cost-effective. We report on the increase in surface-enhanced Raman scattering efficiency for smaller pillar heights and stronger coupling between the dot array and perforated gold film with average enhancement factors as high as 10⁷. In addition, the block copolymer-derived templates show an excellent relative standard deviation of 8% in the measurement of the Raman intensity. Finite difference time domain simulations were performed to investigate the nature of the electromagnetic near-field enhancement and to identify plasmonic hot spots.

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.

Antenna array-enhanced attenuated total reflection IR analysis in an aqueous solution

Attenuated total reflection surface-enhanced infrared absorption spectroscopy (ATR-SEIRAS) is a powerful technique that provides structural and functional information during dynamic reactions in aqueous solutions. One existing limitation is the sensitivity to extract the signals of trace-level analytes from the background water in situ and in real time. Here, we proposed a novel ATR-SEIRAS platform that integrated a large-scale triangle gold antenna array onto a conventional ATR-IR platform to increase the sensitivity of this analytical technique. A square centimeter level well-ordered gold antenna array was fabricated onto an Si prism via nanosphere lithography. The size-dependent antenna array resonance had weak correlation with the incident polarization and antenna orientation, allowing antenna array-enhanced IR detection without the requirement of a microscope. In addition, the antenna resonance shift that occurred due to analyte adsorption-induced refractive index variation could be minimized benefiting from the high refractive index of Si (3.4). As a demonstration, we dynamically monitored the adsorption of the trace levels of proteins on top of the antenna array with a real signal enhancement factor larger than 300. Our platform opens an avenue to apply antenna array-enhanced IR spectroscopy in an aqueous environment measured via commercial IR instruments, which is extremely promising for the interfacial applications that require signal enhancement.

Graphite-assisted electro-fermentation methanogenesis: Spectroelectrochemical and microbial community analyses of cathode biofilms

The stimulatory effect of conductive particles on anaerobic digestion has been demonstrated in recent years. However, it is yet to be determined whether and how conductive particles affect methanogenesis via electro-fermentation (electro-fermentation methanogenesis). In this study, it was demonstrated, for the first time, that conductive graphite boosted the methane production yield by 54.3% and increased the maximum methane production rate by 72.2% during electro-fermentation methanogenesis. Graphite significantly affected the composition of cathode biofilms, with more live and large aggregates being observed. Spectroelectrochemical analyses further showed that the kinds and intensities of biocatalytic active sites and redox groups on the cathode biofilms increased during graphite-assisted electro-fermentation methanogenesis. Particularly, c-type cytochromes, humic acid-like substances, and humic substances improved the long-range electron transport to methanogens such as Methanobacterium and Methanosarcina. The results have implications for the improvement of electro-fermentation process and the use of conductive materials for biofuel recovery.

Water as a Universal Infrared Probe for Bioanalysis in Aqueous Solution by Attenuated Total Reflection-Surface Enhanced Infrared Absorption Spectroscopy

Monitoring the properties and reactions of biomolecules at their interface has attracted ever-growing interest. Here, we propose an approach of infrared analysis technique that utilizes water molecule as a universal probe for in situ and label free monitoring of interfacial bioevents in aqueous solution with high sensitivity. The strong infrared (IR) signal of O-H stretching vibrations from the repelled water is used to sensitively reveal the kinetics of interfacial bioevents at molecular level based on the steric displacement of water using an attenuated total reflection-surface enhanced infrared absorption spectroscopy. Using interfacial immuno-recognition and DNA hybridization as demonstrations, water IR probe offers 26 and 34 times higher sensitivity and even 200 and 86 times lower detection limit for immunosensing and DNA sensing, respectively, as compared to the traditional IR molecular fingerprints.

Response of enhanced sludge methanogenesis by red mud to temperature: Spectroscopic and electrochemical elucidation of endogenous redox mediators

Adding conductive materials can promote methanogenesis via facilitating electron exchange between syntrophic bacteria and methanogenic archaea. However, little is known about how temperature would interact with such an addition and thus affect the compositions and characteristics of endogenous redox mediators (ERMs). In particular, it is of strong interest to understand how the temperature variation would affect the improvement on methanogenesis induced by ERMs with conductive materials. Herein, we have investigated the response of sludge methanogenesis to temperature variation (from 15 to 35 °C) and spectroscopically detected the ERMs induced by conductive red mud. It was demonstrated that the increasing temperature enhanced the stimulating effect of conductive red mud on methane accumulation, and the methane production potential showed a linear relationship with redox parameters such as areal capacitance (C_a), free charges (R₂) and electron exchange capacity (EEC). 2DCOS spectra further indicated that ν_(C-O) and δ_(O-H) in humic acids, β-turn type III amide I ν_s(C=O) in Cytochrome c, and δ_(C-H) in amines and lipids became the main redox groups in ERMs at 35 °C with the addition of red mud. The model revealed that the contribution of ERMs to the CO₂ reduction to CH₄ increased from 35.2 ± 1.4% to 58.6 ± 1.5% when the temperature increased from 15 to 35 °C. Our finding that conductive materials stimulated the formation and electroactivity of ERMs with the increasing temperature during anaerobic digestion can have important implications for the improvement of engineered methanogenic processes.

Layer-by-Layer-Assembled AuNPs-Decorated First-Generation Poly(amidoamine) Dendrimer with Reduced Graphene Oxide Core as Highly Sensitive Biosensing Platform with Controllable 3D Nanoarchitecture for Rapid Voltammetric Analysis of Ultratrace DNA Hybridization

The structure and electrochemical properties of layer-by-layer-assembled gold nanoparticles (AuNPs)-decorated first-generation (G1) poly(amidoamine) dendrimer (PD) with reduced graphene oxide (rGO) core as a highly sensitive and label-free biosensing platform with a controllable three-dimensional (3D) nanoarchitecture for the rapid voltammetric analysis of DNA hybridization at ultratrace levels were characterized. Mercaptopropinoic acid (MPA) was self-assembled onto Au substrate, then GG1PD formed by the covalent functionalization between the amino terminals of G1PD and carboxyl terminals of rGO was covalently linked onto MPA, and finally AuNPs were decorated onto GG1PD by strong physicochemical interaction between AuNPs and -OH of rGO in GG1PD, which was characterized through different techniques and confirmed by computational calculation. This 3D controllable thin-film electrode was optimized and evaluated using [Fe(CN)₆]^3-/4- as the redox probe and employed to covalently immobilize thiol-functionalized single-stranded DNA as biorecognition element to form the DNA nanobiosensor, which achieved fast, ultrasensitive, and high-selective differential pulse voltammetric analysis of DNA hybridization in a linear range from 1 × 10^-6 to 1 × 10^-13 g m^-1 with a low detection limit of 9.07 × 10^-14 g m^-1. This work will open a new pathway for the controllable 3D nanoarchitecture of the layer-by-layer-assembled metal nanoparticles-functionalized lower-generation PD with two-dimensional layered nanomaterials as cores that can be employed as ultrasensitive and label-free nanobiodevices for the fast diagnosis of specific genome diseases in the field of biomedicine.

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.

Surface enhanced infrared absorption spectroscopy based on gold nanostars and spherical nanoparticles

Plasmonic anisotropic nanoparticles possess a number of hot spots on their surface due to the presence of sharp edges, tips or vertices, leading to a high electric field strength surrounding the nanostructures. In this paper, we explore different plasmonic nanostructures, including anisotropic gold nanostars (AuNSts) and spherical gold nanoparticles, in surface-enhanced infrared absorption spectroscopy (SEIRAS) in an attenuated total reflection (ATR) configuration. In our experiments, we observed up to 10-times enhancement of the infrared (IR) absorption of thioglycolic acid (TGA) and up to 2-times enhancement of signals for bovine serum albumin (BSA) protein on plasmonic nanostructure-based films deposited on a silicon (Si) internal reflection element (IRE) compared to bare Si IRE. The dependence of the observed enhancement on the amount of AuNSts present at the surface of the IRE has been demonstrated. Quantitative studies with both, TGA and BSA were performed, observing that the SEIRA signal can be correlated to the concentration of analyte molecules present within the evanescent field. The calibration curves in the presence of the AuNSts showed enhanced sensitivity as compared with the bare Si IRE. We finally compare efficiencies of anisotropic AuNSts and spherical citrate-capped and "bare" laser-synthesized gold nanoparticles as SEIRAS substrates for the detection of TGA and BSA. The signal obtained from AuNSts was at least 2 times higher for TGA molecules in comparison with spherical gold nanoparticles, which was explained by a more efficient generation of hot spots on anisotropic surface due to the presence of sharp edges, tips or vertices, leading to a high electric field strength surrounding the AuNSts.

Revealing the Effect of Protein Weak Adsorption to Nanoparticles on the Interaction between the Desorbed Protein and its Binding Partner by Surface-Enhanced Infrared Spectroelectrochemistry

In recent years, the properties of protein corona have attracted intense interest in the field of nanobio interface, but a long-ignored research issue is how the desorbed proteins suffering from conformational change upon weak association with nanoparticles affect their functional properties when further interacting with their downstream protein partners. In this Article, surface-enhanced infrared absorption spectroscopy (SEIRAS) and electrochemical cyclic voltammetry were used to study the adsorption and redox properties of the soluble cytochrome c (cyt c) on 11-mercaptoundecanoic acid (MUA) self-assembled monolayer (SAM) after weakly binding to and then desorbed from nano-TiO₂. For the first time, our study reveals that the weak interaction between cyt c and nano-TiO₂ induces the protein to undergo a heterogeneous conformational change. More importantly, the cyt c with a largely unfolded conformation exhibits a weaker interaction with its binding partner mimics than the native-like cyt c but a faster adsorption rate even at a concentration that is much lower than that of native-like cyt c. Correspondingly, the cyt c with a large unfolding shows a greatly positive-shifted formal potential (E_f) relative to the native-like protein possibly due to the disruption of the pocket structure of heme in the vicinity of Met80. These properties could enable the largely unfolded cyt c to undergo a favorable binding but an unavailable electron transfer to cytochrome c oxidase even in the presence of high-concentration native cyt c, probably causing the disruption of electron flow.

Mid-infrared spectroscopy for protein analysis: potential and challenges

Mid-infrared (MIR) spectroscopy investigates the interaction of MIR photons with both organic and inorganic molecules via the excitation of vibrational and rotational modes, providing inherent molecular selectivity. In general, infrared (IR) spectroscopy is particularly sensitive to protein structure and structural changes via vibrational resonances originating from the polypeptide backbone or side chains; hence information on the secondary structure of proteins can be obtained in a label-free fashion. In this review, the challenges for IR spectroscopy for protein analysis are discussed as are the potential and limitations of different IR spectroscopic techniques enabling protein analysis. In particular, the amide I spectral range has been widely used to study protein secondary structure, conformational changes, protein aggregation, protein adsorption, and the formation of amyloid fibrils. In addition to representative examples of the potential of IR spectroscopy in various fields related to protein analysis, the potential of protein analysis taking advantage of miniaturized MIR systems, including waveguide-enhanced MIR sensors, is detailed.

Molecular simulations of cytochrome c adsorption on positively charged surfaces: the influence of anion type and concentration

The influence of anion type and concentration on the adsorption of cytochrome c onto the positively charged NH₂-SAM surface.

2nd coordination sphere controlled electron transfer of iron hangman complexes on electrodes probed by surface enhanced vibrational spectroscopy

Surface enhanced vibrational spectroscopy shows the correlation between electron transfer kinetics and protonation degree of Fe Hangman complexes on electrodes.

Iron hangman complexes exhibit improved catalytic properties regarding O₂ and H₂O₂ reduction, which are attributed to the presence of a proton donating group in defined vicinity of the catalytic metal centre. Surface enhanced resonance Raman (SERR) and IR (SEIRA) spectro-electrochemistry has been applied concomitantly for the first time to analyse such iron hangman porphyrin complexes attached to electrodes in aqueous solution. While the SERR spectra yield information about the redox state of the central iron, the SEIRA spectra show protonation and deprotonation events of the 2^nd coordination sphere. To investigate the influence of a proton active hanging group on the heterogeneous electron transfer between the iron porphyrin and the electrode, two hangman complexes with either an acid or ester functional group were compared. Using time resolved SERR spectroscopy the electron transfer rates of both complexes were determined. Complexes with an acid group showed a slow electron transfer rate at neutral pH that increased significantly at pH 4, while complexes with an ester group exhibited a much faster, but pH independent rate. SEIRA measurements were able to determine directly for the first time a pK_a value of 3.4 of a carboxylic hanging group in the immobilized state that shifted to 5.2 in D₂O buffer solution. The kinetic data showed an increase of the heterogeneous electron transfer rate with the protonation degree of the acid groups. From these results, we propose a PCET which is strongly modulated by the protonation state of the acid hanging group via hydrogen bond interactions.

Real-time dynamic adsorption processes of cytochrome c on an electrode observed through electrochemical high-speed atomic force microscopy

An understanding of dynamic processes of proteins on the electrode surface could enhance the efficiency of bioelectronics development and therefore it is crucial to gain information regarding both physical adsorption of proteins onto the electrode and its electrochemical property in real-time. We combined high-speed atomic force microscopy (HS-AFM) with electrochemical device for simultaneous observation of the surface topography and electron transfer of redox proteins on an electrode. Direct electron transfer of cytochrome c (cyt c) adsorbed on a self-assembled monolayers (SAMs) formed electrode is very attractive subject in bioelectrochemistry. This paper reports a real-time visualization of cyt c adsorption processes on an 11-mercaptoundecanoic acid-modified Au electrode together with simultaneous electrochemical measurements. Adsorbing cyt c molecules were observed on a subsecond time resolution simultaneously with increasing redox currents from cyt c using EC-HS-AFM. The root mean square roughness (R_RMS) from the AFM images and the number of the electrochemically active cyt c molecules adsorbed onto the electrode (Γ) simultaneously increased in positive cooperativity. Cyt c molecules were fully adsorbed on the electrode in the AFM images when the peak currents were steady. This use of electrochemical HS-AFM significantly facilitates understanding of dynamic behavior of biomolecules on the electrode interface and contributes to the further development of bioelectronics.

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 IR absorption spectroscopy of the KcsA potassium channel upon application of an electric field

Surface-enhanced IR absorption spectroscopy coupled with an electrochemical system enables the potassium-induced specific structural change of the potassium channel.

Biomimetic environment to study E. coli complex I through surface-enhanced IR absorption spectroscopy

In this study complex I was immobilized in a biomimetic environment on a gold layer deposited on an ATR-crystal in order to functionally probe the enzyme against substrates and inhibitors via surface-enhanced IR absorption spectroscopy (SEIRAS) and cyclic voltammetry (CV). To achieve this immobilization, two methods based on the generation of a high affinity self-assembled monolayer (SAM) were probed. The first made use of the affinity of Ni-NTA toward a hexahistidine tag that was genetically engineered onto complex I and the second exploited the affinity of the enzyme toward its natural substrate NADH. Experiments were also performed with complex I reconstituted in lipids. Both approaches have been found to be successful, and electrochemically induced IR difference spectra of complex I were obtained.

Investigation on the adsorption characteristics of sodium benzoate and taurine on gold nanoparticle film by ATR-FTIR spectroscopy

Fourier transform infrared (FTIR) spectroscopic studies of sodium benzoate and taurine adsorbed on gold nanoparticle (AuNp) film on silanised glass slides have been studied by attenuated total reflection technique (ATR). The surface morphology of the AuNp films has been measured by Atomic Force Microscopy. The ATR spectra of sodium benzoate and taurine deposited on AuNp film are compared with ATR spectra of their powdered bulk samples. A new red-shifted band appeared along with the symmetric and asymmetric stretches of carboxylate group of sodium benzoate leading to a broadening of the above peaks. Similar behavior is also seen in the case of symmetric and asymmetric stretches of sulphonate group of taurine. The results indicate presence of both chemisorbed and physisorbed layers of both sodium benzoate and taurine on the AuNp film with bottom layer chemically bound to AuNp through carboxylate and sulphonate groups respectively.