Surface-Enhanced Raman Scattering Studies of Human Transcriptional Coactivator p300

Biophysical and spectroscopical insights into structural modulation of species in the aggregation pathway of superoxide dismutase 1

Superoxide dismutase 1 (SOD1) aggregation is implicated in the development of Amyotrophic Lateral Sclerosis (ALS). Despite knowledge of the role of SOD1 aggregation, the mechanistic understanding remains elusive. Our investigation aimed to unravel the complex steps involved in SOD1 aggregation associated with ALS. Therefore, we probed the aggregation using ThT fluorescence, size-exclusion chromatography, and surface-enhanced Raman spectroscopy (SERS). The removal of metal ions and disulfide bonds resulted in the dimers rapidly first converting to an extended monomers then coming together slowly to form non-native dimers. The rapid onset of oligomerization happens above critical non-native dimer concentration. Structural features of oligomer was obtained through SERS. The kinetic data supported a fragmentation-dominant mechanism for the fibril formation. Quercetin acts as inhibitor by delaying the formation of non-native dimer and soluble oligomers by decreasing the elongation rate. Thus, results provide significant insights into the critical steps in oligomer formation and their structure.

Trace Detection of Adulterants in Illicit Opioid Samples Using Surface-Enhanced Raman Scattering and Random Forest Classification

The detection of trace adulterants in opioid samples is an important aspect of drug checking, a harm reduction measure that is required as a result of the variability and unpredictability of the illicit drug supply. While many analytical methods are suitable for such analysis, community-based approaches require techniques that are amenable to point-of-care applications with minimal sample preparation and automated analysis. We demonstrate that surface-enhanced Raman spectroscopy (SERS), combined with a random forest classifier, is able to detect the presence of two common sedatives, bromazolam (0.32-36% w/w) and xylazine (0.15-15% w/w), found in street opioid samples collected as a part of a community drug checking service. The Raman predictions, benchmarked against mass spectrometry results, exhibited high specificity (88% for bromazolam, 96% for xylazine) and sensitivity (88% for bromazolam, 92% for xylazine) for the compounds of interest. We additionally provide evidence that this exceeds the performance of a more conventional approach using infrared spectral data acquired on the same samples. This demonstrates the feasibility of SERS for point-of-care analysis of challenging multicomponent samples containing trace adulterants.

Differences between surfactant-free Au@Ag and CTAB-stabilized Au@Ag star-like nanoparticles in the preparation of nanoarrays to improve their surface-enhanced Raman scattering (SERS) performance

In this study, we assessed the controlled synthesis and efficacy of surface-enhanced Raman scattering (SERS) on two distinct types of star-like Au@Ag core-shell nanoarrays. These nanoarrays were designed based on gold nanostars (AuNSs), which were synthesized with and without CTAB surfactant (AuNSs-CTAB and AuNSs-FS, respectively). The AuNS-FS nanoparticles were synthesized via a novel modification process, which helped overcome the previous limitations in the free-surfactant preparation of AuNSs by significantly increasing the number of branches, increasing the sharpness of the branches and minimizing the adsorption of the surfactant on the surface of AuNSs. Furthermore, the differences in the size and morphology of these AuNSs in the created nanoarrays were studied. To create the nanoarrays, a three-step method was employed, which involved the controlled synthesis of gold nanostars, covering them with a silver layer (AuNSs-FS@Ag and AuNSs-CTAB@Ag), and finally self-assembling the AuNS@Ag core-shelled nanoparticles via the liquid/liquid self-assembly method. AuNSs-FS@Ag showed higher ability in forming self-assembled nanoarrays than the nanoparticles prepared using CTAB, which can be attributed to the decrease in the repulsion between the nanoparticles at the interface. The nano-substrates developed with AuNSs-FS@Ag possessed numerous "hot spots" on their surface, resulting in a highly effective SERS performance. AuNSs-FS featured a significantly higher number of sharp branches than AuNSs-CTAB, making it the better choice for creating nanoarrays. It is worth mentioning that AuNSs-CTAB did not exhibit the same benefits as AuNSs-FS. The morphology of AuNSs with numerous branches was formed by controlling the seed boiling temperature and adding a specific amount of silver ions. To compare the SERS activity between the as-prepared nano-substrates, i.e., AuNS-CTAB@Ag and AuNS-FS@Ag self-assembled nanoarrays, low concentrations of crystal violet aqueous solution were characterized. The results showed that the developed AuNSs-FS@Ag could detect CV at trace concentrations ranging from 1.0 ng mL-1 to 10 ng mL-1 with a limit of detection (LOD) of 0.45 ng mL-1 and limit of quantification (LOQ) of 1.38 ng mL-1. The nano-substrates remained stable for 42 days with a decrease in the intensity of the characteristic Raman peaks of CV by less than 7.0% after storage. Furthermore, the spiking method could detect trace amounts of CV in natural water from the Dong Nai River with concentrations as low as 1 to 100 ng mL-1, with an LOD of 6.07 ng mL-1 and LOQ of 18.4 ng mL-1. This method also displayed good reproducibility with an RSD value of 5.71%. To better understand the impact of CTAB stabilization of the Au@Ag star-like nanoparticles on their surface-enhanced Raman scattering (SERS) performance, we conducted density functional theory (DFT) calculations. Our research showed that the preparation of AuNSs-FS@Ag via self-assembly is an efficient, simple, and fast process, which can be easily performed in any laboratory. Furthermore, the research and development results presented herein on nanoarrays have potential application in analyzing and determining trace amounts of organic compounds in textile dyeing wastewater.

Divalent Ion-Induced Switch in DNA Cleavage of KpnI Endonuclease Probed through Surface-Enhanced Raman Spectroscopy

We demonstrate the remarkable ability of surface-enhanced Raman spectroscopy (SERS) to track the allosteric changes in restriction endonuclease KpnI (R.KpnI) caused by metal ions. R.KpnI binds and promiscuously cleaves DNA upon activation by Mg²⁺ ions. However, the divalent ion Ca²⁺ induces high fidelity cleavage, which can be overcome by higher concentrations of Mg²⁺ ions. In the absence of any 3D crystal structure, for the first time, we have elucidated the structural underpinnings of such a differential effect of divalent ions on the endonuclease activity. A combined SERS and molecular dynamics (MD) approach showed that Ca²⁺ ion activates an enzymatic switch in the active site, which is responsible for the high fidelity activity of the enzyme. Thus, SERS in combination with MD simulations provides a powerful tool for probing the link between the structure and activity of enzyme molecules that play vital roles in DNA transactions.

Surface-Enhanced Raman Spectroscopy as a Tool for Distinguishing Extracellular Vesicles under Autophagic Conditions: A Marker for Disease Diagnostics

Extracellular vesicles (EVs) laden with lipids, proteins, DNA, and micro-RNAs play important biological functions in intercellular communication and have pivotal roles in pathophysiological conditions. Characterization of the EVs has always been a multistep process involving large volumes, and they are heterogeneous in size and properties. A multitude of approaches is used to distinguish the EVs. Here, we report simple citrate reduced silver nanoparticles assisted surface-enhanced Raman spectroscopy (SERS) as a tool to distinguish EVs extracted from several cell lines isolated under autophagic conditions (nitrogen starvation). This study is the first report of its kind in characterizing EVs from cells under autophagic conditions using SERS. We used two cancerous cell lines, HeLa, its corresponding autophagy-deficient cell line (Atg5^-/-), and a noncancerous cell line, HEK293, to isolate EVs. Our study helps in the facile detection and differentiation of EVs isolated between two closely related human cell lines that differ by their autophagic ability. The principal component analysis (PCA) of the SERS spectra of these EVs consistently showed the presence of distinct chemical compositions of the EVs. SERS of EVs can help in probing more into the molecular level information from EVs and could become a powerful tool once coupled with improved microscopy techniques for diagnosis and therapy.

Optical Detection of Degraded Therapeutic Proteins

The quality of therapeutic proteins such as hormones, subunit and conjugate vaccines, and antibodies is critical to the safety and efficacy of modern medicine. Identifying malformed proteins at the point-of-care can prevent adverse immune reactions in patients; this is of special concern when there is an insecure supply chain resulting in the delivery of degraded, or even counterfeit, drug product. Identification of degraded protein, for example human growth hormone, is demonstrated by applying automated anomaly detection algorithms. Detection of the degraded protein differs from previous applications of machine-learning and classification to spectral analysis: only example spectra of genuine, high-quality drug products are used to construct the classifier. The algorithm is tested on Raman spectra acquired on protein dilutions typical of formulated drug product and at sample volumes of 25 µL, below the typical overfill (waste) volumes present in vials of injectable drug product. The algorithm is demonstrated to correctly classify anomalous recombinant human growth hormone (rhGH) with 92% sensitivity and 98% specificity even when the algorithm has only previously encountered high-quality drug product.

Site-Selective Surface-Enhanced Raman Detection of Proteins

Strategies for protein detection via surface-enhanced Raman spectroscopy (SERS) currently exploit the formation of randomly generated hot spots at the interfaces of metal colloidal nanoparticles, which are clustered together by intrusive chemical or physical processes in the presence of the target biomolecule. We propose a different approach based on selective and quantitative gathering of protein molecules at regular hot spots generated on the corners of individual silver nanocubes in aqueous medium at physiological pH. Here, the protein, while keeping its native configuration, experiences an intense local E-field, which boosts SERS efficiency and detection sensitivity. Uncontrolled signal fluctuations caused by variable molecular adsorption to different particle areas or inside clustered nanoparticles are circumvented. Advanced electron microscopy analyses and computational simulations outline a strategy relying on a site-selective mechanism with superior Raman signal enhancement, which offers the perspective of highly controlled and reproducible routine SERS detection of proteins.

Differentiation of digestive system cancers by using serum protein‐based surface‐enhanced Raman spectroscopy

The aim of this study is to develop a more robust surface‐enhanced Raman spectroscopy method for the simultaneous differentiation of two or more different types of cancer. For this, the periodical reversal of current directions is imposed on electrophoresis for the fast purification of serum proteins, and the serum proteins were then mixed with silver nanoparticles for surface‐enhanced Raman spectroscopy spectral measurement. The Raman spectra of serum proteins from healthy subjects (n = 85) and three types of digestive system cancer – colorectal cancer (n = 109), gastric cancer (n = 133), and liver cancer (n = 38) – were measured for analyses. Principal component analysis and linear discriminant analysis yield diagnostic sensitivities of 94.5, 97.0, and 89.1% and specificities of 98.1, 92.7, and 99.2% in the differentiation of colorectal, gastric, and liver cancers, respectively. This work marks a promising step toward the potential applications of Raman spectroscopic blood analysis in multi‐type cancer screening. Copyright © 2016 John Wiley & Sons, Ltd.

Using surface enhanced Raman scattering to analyze the interactions of protein receptors with bacterial quorum sensing modulators

Many members of the LuxR family of quorum sensing (QS) transcriptional activators, including LasR of Pseudomonas aeruginosa, are believed to require appropriate acyl-homoserine lactone (acyl-HSL) ligands to fold into an active conformation. The failure to purify ligand-free LuxR homologues in nonaggregated form at the high concentrations required for their structural characterization has limited the understanding of the mechanisms by which QS receptors are activated. Surface-enhanced Raman scattering (SERS) is a vibrational spectroscopy technique that can be applied to study proteins at extremely low concentrations in their active state. The high sensitivity of SERS has allowed us to detect molecular interactions between the ligand-binding domain of LasR (LasRLBD) as a soluble apoprotein and modulators of P. aeruginosa QS. We found that QS activators and inhibitors produce differential SERS fingerprints in LasRLBD, and in combination with molecular docking analysis provide insight into the relevant interaction mechanism. This study reveals signal-specific structural changes in LasR upon ligand binding, thereby confirming the applicability of SERS to analyze ligand-induced conformational changes in proteins.

Gold nanoaggregates for probing single-living cell based on surface-enhanced Raman spectroscopy

Gold nanoparticles are delivered into living cells by transient electroporation method to obtain intracellular surface-enhanced Raman spectroscopy (SERS). The subcellular localization of gold nanoparticles is characterized by transmission electron microscopy, and the forming large gold nanoaggregates are mostly found in the cytoplasm. The SERS detection of cells indicates that this kind of gold nanostructures induces a high signal enhancement of cellular chemical compositions, in addition to less cellular toxicity than that of silver nanoparticles. These results demonstrate that rapid incorporation of gold nanoparticles by electroporation into cells has great potential applications in the studies of cell biology and biomedicine.

Surpassingly competitive electromagnetic field enhancement at the silica/silver interface for selective intracellular surface enhanced Raman scattering detection

A thin plasmonic nanofilm is formed by preformed silver nanoparticles (30 nm) in the matrix of poly(vinyl alcohol) adsorbed on silica microparticles (1.5 μm) (SiO2@Ag-PVA). By applying finite element method (FEM) analysis the surface enhanced Raman spectroscopy (SERS) enhancement factors (EFs) can reach 10(5) with higher values from 10(9) to 10(11) in the silver layer of 5 nm thickness. Nanoparticles in the SiO2@Ag-PVA nanofilm need at least 15 nm radius to exhibit SERS EFs greater than 10(7). High values of this enhancement at the silver/silica interface of spherical geometry can be reached faster by using a 532 nm compared to 785 nm excitation wavelength. By this approach different SERS spectral features can be distinguished between live fibroblasts with spread ("healthy" state) or round ("unhealthy" state) shapes. Characteristic features of secondary protein structures, detection of different acidic conditions and cholesterol with at least a 3-fold higher sensitivity are examined. Moreover, a greater amount of glucose (glucogen) and also tyrosine can be monitored in real time. This is important in identification of higher risk of diabetes as well as in several genetic metabolic disorders (e.g., phenylketonuria, tyrosinaemia type II and tyrosinosis).

Replacing heme with paclitaxel to prepare drug-loaded globin nanoassembles for CD163 targeting

Protein-based nanoparticles hold great promises in both preclinical and clinical practices, such as oncology diagnosis and treatment, because of their high biocompatibility and biodegradability. However, the complicated preparation and lack of targeting specific cells or tissues may limit their further uses. To overcome these limitations, we developed a novel replacing method for preparing dual-functional protein nanocarrier, such that one function is capable of encapsulating small molecule into protein, whereas the other function is cable of recognizing CD163 receptor [hemoglobin (Hb) scavenger receptor]. In this study, Hb was chosen as the targeting drug carrier. First, the heme group in the Hb was removed and replaced by paclitaxel (PTX) to form nanoparticles (Gb-NPs-PTX). The resulted Gb-NPs-PTX showed spherical shape and their diameter could be controlled in the range of 120-160 nm by altering the ratio of PTX to Hb. The binding activity of Gb-NPs-PTX to CD163 was confirmed by cell uptake in CD163(+) Chinese hamster ovary cells. Results in vivo also showed a CD163-dependent tissue accumulation of Gb-NPs-PTX in mice. In summary, by using the novel replacing method, PTX could be easily encapsulated into Hb nanoparticles and the targeting effects of Hb could also be kept.

Concave gold nanocube assemblies as nanotraps for surface-enhanced Raman scattering-based detection of proteins

SERS detection of proteins is typically performed by using labeling agents with stable and high Raman scattering cross sections. This is a valuable approach for trace detection and quantification of a target protein but is unsuitable for inspecting its inherent structural and functional properties. On the other hand, direct SERS of proteins has been mainly devoted to the study of short peptides and aminoacid sequences or of prosthetic groups with intense Raman signals, which is of scarce interest for a thorough characterization of most proteins. Here we try to overcome these limitations by setting-up an effective platform for the structural SERS analysis of proteins. The platform consists of an extended bidimensional array of gold concave nanocubes (CNCs) supported on a PDMS film. CNCs are closely-packed through face-face and face-corner interactions generating a monolayered arrangement featuring well distributed nanoholes. Here the protein homogeneously experiences an E-field enhancement outward from the metal surfaces surrounding it, which causes a large number of vibrations to be contemporarily amplified. The proposed platform provides stable and detailed SERS spectra and confers rapidity and reproducibility to the analysis.

Label-free detection of serum proteins using surface-enhanced Raman spectroscopy for colorectal cancer screening

Surface-enhanced Raman scattering (SERS) spectra of serum proteins purified from human serum samples were employed to detect colorectal cancer. Acetic acid as a new aggregating agent was introduced to increase the magnitude of the SERS enhancement. High-quality SERS spectra of serum proteins were acquired from 103 cancer patients and 103 healthy volunteers. Tentative assignments of SERS bands reflect that some specific biomolecular contents and protein secondary structures change with colorectal cancer progression. Principal component analysis combined with linear discriminant analysis was used to assess the capability of this approach for identifying colorectal cancer, yielding diagnostic accuracies of 100% (sensitivity: 100%; specificity: 100%) based on albumin SERS spectroscopy and 99.5% (sensitivity: 100%; specificity: 99%) based on globulin SERS spectroscopy, respectively. A partial least squares (PLS) approach was introduced to develop diagnostic models. An albumin PLS model successfully predicted the unidentified subjects with a diagnostic accuracy of 93.5% (sensitivity: 95.6%; specificity: 91.3%) and the globulin PLS model gave a diagnostic accuracy of 93.5% (sensitivity: 91.3%; specificity: 95.6%). These results suggest that serum protein SERS spectroscopy can be a sensitive and clinically powerful means for colorectal cancer detection.

SERS and MD simulation studies of a kinase inhibitor demonstrate the emergence of a potential drug discovery tool

We demonstrate the use of surface-enhanced Raman spectroscopy (SERS) as an excellent tool for identifying the binding site of small molecules on a therapeutically important protein. As an example, we show the specific binding of the common antihypertension drug felodipine to the oncogenic Aurora A kinase protein via hydrogen bonding interactions with Tyr-212 residue to specifically inhibit its activity. Based on SERS studies, molecular docking, molecular dynamics simulation, biochemical assays, and point mutation-based validation, we demonstrate the surface-binding mode of this molecule in two similar hydrophobic pockets in the Aurora A kinase. These binding pockets comprise the same unique hydrophobic patches that may aid in distinguishing human Aurora A versus human Aurora B kinase in vivo. The application of SERS to identify the specific interactions between small molecules and therapeutically important proteins by differentiating competitive and noncompetitive inhibition demonstrates its ability as a complementary technique. We also present felodipine as a specific inhibitor for oncogenic Aurora A kinase. Felodipine retards the rate of tumor progression in a xenografted nude mice model. This study reveals a potential surface pocket that may be useful for developing small molecules by selectively targeting the Aurora family kinases.

Allosteric transition induced by Mg²⁺ ion in a transactivator monitored by SERS

We demonstrate the utility of the surface-enhanced Raman spectroscopy (SERS) to monitor conformational transitions in protein upon ligand binding. The changes in protein's secondary and tertiary structures were monitored using amide and aliphatic/aromatic side chain vibrations. Changes in these bands are suggestive of the stabilization of the secondary and tertiary structure of transcription activator protein C in the presence of Mg(2+) ion, whereas the spectral fingerprint remained unaltered in the case of a mutant protein, defective in Mg(2+) binding. The importance of the acidic residues in Mg(2+) binding, which triggers an overall allosteric transition in the protein, is visualized in the molecular model. The present study thus opens up avenues toward the application of SERS as a potential tool for gaining structural insights into the changes occurring during conformational transitions in proteins.

Naphthoquinone-mediated inhibition of lysine acetyltransferase KAT3B/p300, basis for non-toxic inhibitor synthesis

Hydroxynaphthoquinone-based inhibitors of the lysine acetyltransferase KAT3B (p300), such as plumbagin, are relatively toxic. Here, we report that free thiol reactivity and redox cycling properties greatly contribute to the toxicity of plumbagin. A reactive 3rd position in the naphthoquinone derivatives is essential for thiol reactivity and enhances redox cycling. Using this clue, we synthesized PTK1, harboring a methyl substitution at the 3rd position of plumbagin. This molecule loses its thiol reactivity completely and its redox cycling ability to a lesser extent. Mechanistically, non-competitive, reversible binding of the inhibitor to the lysine acetyltransferase (KAT) domain of p300 is largely responsible for the acetyltransferase inhibition. Remarkably, the modified inhibitor PTK1 was a nearly non-toxic inhibitor of p300. The present report elucidates the mechanism of acetyltransferase activity inhibition by 1,4-naphthoquinones, which involves redox cycling and nucleophilic adduct formation, and it suggests possible routes of synthesis of the non-toxic inhibitor.

pH changes the aggregation propensity of amyloid-β without altering the monomer conformation

Decoupling conformational changes from aggregation will help us understand amyloids better. Here we attach Alzheimer's amyloid-β(1-40) monomers to silver nanoparticles, preventing their aggregation, and study their conformation under aggregation-favoring conditions using SERS. Surprisingly, the α-helical character of the peptide remains unchanged between pH 10.5 and 5.5, while the solubility changes >100×. Amyloid aggregation can therefore start without significant conformational changes.

Amide I vibrational mode suppression in surface (SERS) and tip (TERS) enhanced Raman spectra of protein specimens

Surface- and tip-enhanced Raman spectroscopy (SERS and TERS) are modern spectroscopic techniques, which are becoming widely used and show a great potential for the structural characterisation of biological systems. Strong enhancement of the Raman signal through localised surface plasmon resonance enables chemical detection at the single-molecule scale. Enhanced Raman spectra collected from biological specimens, such as peptides, proteins or microorganisms, were often observed to lack the amide I band, which is commonly used as a marker for the interpretation of the secondary protein structure. The cause of this phenomenon was unclear for many decades. In this work, we investigated this phenomenon for native insulin and insulin fibrils using both TERS and SERS and compared these spectra to the spectra of well-defined homo peptides. The results indicate that the appearance of the amide I Raman band does not correlate with the protein aggregation state, but is instead determined by the size of the amino acid side chain. For short model peptides, the absence of the amide I band in TERS and SERS spectra correlates with the presence of a bulky side chain. Homo-glycine and -alanine, which are peptides with small side chain groups (H and CH(3), respectively), exhibited an intense amide I band in almost 100% of the acquired spectra. Peptides with bulky side chains, such as tyrosine and tryptophan, exhibited the amide I band in 70% and 31% of the acquired spectra, respectively.

Serum albumin and globulin analysis for hepatocellular carcinoma detection avoiding false-negative results from alpha-fetoprotein test negative subjects

Surface-enhanced Raman spectroscopy (SERS) of serum albumin and globulin were employed to detect hepatocellular carcinoma (HCC). Tentative assignments of SERS bands show specific biomolecular changes associated with cancer development. These changes include a decrease in relative amounts of tryptophan, glutamine, glycine, and serine, indicating excessive consumption of amino acids for protein duplication. Principal component analysis was also introduced to analyze the obtained spectra, resulting in both diagnostic sensitivity and specificity of 100%. More importantly, it reveals that this method can detect HCC patients with alpha-fetoprotein negative test results, suggesting its great potential as a new alternative to detect HCC.

Analysis of protein acetyltransferase structure-function relation by surface-enhanced raman scattering (SERS): a tool to screen and characterize small molecule modulators

Among the different posttranslational modifications (PTMs) that significantly regulate the protein function, lysine acetylation has become the major focus, especially to understand the epigenetic role of the acetyltransferases, in cellular physiology. Furthermore, dysfunction of these acetyltransferases is well documented under pathophysiological conditions. Therefore, it is important to understand the dynamic structure-function relationship of acetyltransferases in a relatively less complicated and faster method, which could be efficiently exploited to design and synthesis of small molecule modulators (activators/inhibitors) of these enzymes for in vivo functional analysis and therapeutic purposes. We have developed surface-enhanced Raman scattering (SERS) method, for acetyltransferases towards this goal. By employing SERS, we have not only demonstrated the autoacetylation induced structural changes of p300 enzyme but also could use this technique to characterize and design potent, specific inhibitors as well as activators of the p300. In this chapter we shall describe the methods in detail which could be highly useful for other classes of HATs and PTM enzymes.

Charge density distribution and the electrostatic moments of CTPB in the active site of p300 enzyme: a DFT and charge density study

A molecular docking and charge density analysis have been carried out to understand the conformational change, charge distribution and electrostatic properties of N-(4-chloro-3-trifluoromethyl-phenyl)-2-ethoxy-6-pentadecyl-benzamide (CTPB) in the active site of p300. The nearest neighbors, shortest intermolecular contacts between CTPB-p300 and the lowest binding energy of CTPB have been analyzed from the docking analysis. Further, a charge density analysis has been carried out for the molecule in gas phase and for the corresponding molecule lifted from the active site of p300. Due to the intermolecular interaction between CTPB and the amino acids of active site, the conformation of the CTPB has been significantly altered (particularly the pentadecyl chain). CTPB forms strong interaction with the amino acid residues Tyr1397 and Trp1436 at the distance 2.12 and 2.72Å, respectively. However, the long pentadecyl alkyl chain of CTPB produces a barrier and reducing the chance of forming hydrogen bonding with p300. The electron density ρbcp(r) of the polar bonds (C-O, C-N, C-F and C-Cl) of CTPB are increased when it present in the active site. The dipole moment of CTPB in the active site is significantly less (5.73D) when compared with the gas phase (8.16D) form. In the gas phase structure, a large region of negative electrostatic potential (ESP) is found at the vicinity of O(2) and CF3 group, which is less around the O(1) atom. Whereas, in the active site, the negative ESP around the CF3 group is decreased and increased at the O(1) and O(2)-atoms. The ESP modifications of CTPB in the active site are mainly attributed to the effect of intermolecular interaction. The gas phase and active site study insights the molecular flexibility and the electrostatic properties of CTPB in the active site.

Surface-Enhanced Raman Scattering: A Technique of Choice for Molecular Detection

Although surface-enhanced Raman scattering (SERS) has crossed its infancy long ago, it is yet to persuade different challenges to make it available in day-to-day applications. SERS is being criticized mainly due to the quality of the SERS analyses that uses substrates to get the giant enhancement for respective Raman signal of the target molecule. Hence, understanding the phenomena behind substrates, cost-effective development and optimization of such substrates for routine analytical purposes and utilization of modern modalities to get the insights out has become a very wide-spreading and interesting area of research. In this piece of work, several key terminologies related to SERS have been presented in brief. Since SERS is a localized surface plasmon resonance (LSPR) mediated signal-enhancing phenomena, it is indispensable to understand the correlation between LSPR excitations originated from substrate and SERS signal originated from molecules. A wide range of SERS-active substrates including scattered nanoaggregates, anisotropic assembly, two-dimensional nanostructure, multi-layered nanostructure of gold nanoparticles and colloidal approach have been used to interpret such correlation between LSPR excitations and SERS characteristics. Few exemplary applications of SERS have been also mentioned followed by typical simulative work how nanoobject behaves at different excitations and polarizations.

Universal metal-semiconductor hybrid nanostructured SERS substrate for biosensing

We demonstrate here a novel high surface area GaN nanowall network substrate with plasmonic Ag nanodroplets, that can be employed as a highly sensitive, reproducible, and charge independent SERS substrate. The uniformity of the size and distribution of the Ag droplets and the absence of linker ligands result in large near-field intensity, while the GaN nanowall network morphology provides multiple reflections for signal enhancement. FDTD calculations simulate the observed hot-spot distribution and reiterate the higher performance of this hybrid substrate over conventional ones. Our studies on oppositely charged proteins provide a proof of concept for employing this as a versatile charge independent label free SERS substrate for trace biomolecule detection.

Quantitative surface enhanced Raman scattering detection based on the "sandwich" structure substrate

A sandwich structured substrate was designed for quantitative molecular detection using surface enhanced Raman scattering (SERS), in which the probe molecule was sandwiched between silver nanoparticles (SNPs) and silver nanoarrays. The SNPs was prepared using Lee-Meisel method, and the silver nanoarrays was fabricated on porous anodic aluminum oxide (AAO) using electrodepositing method. The SERS studies show that the sandwich structured substrate exhibits good stability and reproducibility, and the detection sensitivity of Rhodamine 6G (R6G) and Melamine can respectively reach up to 10(-19) M and 10(-9) M, which is improved greatly as compared to other SERS substrates. The improved SERS sensitivity is closely associated with the stronger electromagnetic field enhancement, which stems from localized surface plasmon (LSP) coupling between the two silver nanostructures. Furthermore, the SERS intensity increased almost linearly as the mother concentration increased, which indicates that such a sandwich structure may be used as a good SERS substrate for quantitative analysis.

Detection of proteins on silica-silver core-shell substrates by surface-enhanced Raman spectroscopy

We have employed the proposed Silica-Silver Core-Shell (SSCS) SERS-active substrates to detect four model proteins: lysozyme (a protein without chromophore), cytochrome c (a protein with chromophore of heme), fluorescein isothiocyanate (FITC)-anti human IgG (labeled with FITC) and atto610-biotin/avidin (recognition with labeled small molecules). SERS spectra of these proteins and Raman labels on the SSCS substrates show both high sensitivity and reproducibility, which are due to electromagnetic SERS enhancement with additional localization field within closely packed Ag nanoparticles decorated on the SiO(2) nanoparticles and the aggregation of SiO(2)@Ag particles. We have found that the SERS intensities of atto610-biotin/avidin adsorbed on the SSCS substrates are about 20 times stronger than those from Ag plating on Au-decorated substrate. Moreover, the broad surface plasmon resonance (SPR) of the proposed substrates will extend SERS applications to more biological molecules with different laser excitations.

Surface-enhanced Raman scattering for protein detection

Proteins are essential components of organisms and they participate in every process within cells. The key characteristic of proteins that allows their diverse functions is their ability to bind other molecules specifically and tightly. With the development of proteomics, exploring high-efficiency detection methods for large-scale proteins is increasingly important. In recent years, rapid development of surface-enhanced Raman scattering (SERS)-based biosensors leads to the SERS realm of applications from chemical analysis to nanostructure characterization and biomedical applications. For proteins, early studies focused on investigating SERS spectra of individual proteins, and the successful design of nanoparticle probes has promoted great progress of SERS-based immunoassays. In this review we outline the development of SERS-based methods for proteins with particular focus on our proposed protein-mediated SERS-active substrates and their applications in label-free and Raman dye-labeled protein detection.

Nanofluidic biosensing for beta-amyloid detection using surface enhanced Raman spectroscopy

Trace detection of the conformational transition of beta-amyloid peptide (Abeta) from a predominantly alpha-helical structure to beta-sheet could have a large impact in understanding and diagnosing Alzheimer's disease. We demonstrate how a novel nanofluidic biosensor using a controlled, reproducible surface enhanced Raman spectroscopy active site was developed to observe Abeta in different conformational states during the Abeta self-assembly process as well as to distinguish Abeta from confounder proteins commonly found in cerebral spinal fluid.

Surface-enhanced Raman spectroscopic studies of coactivator-associated arginine methyltransferase 1

We report, for the first time, the surface-enhanced Raman spectra of an important enzyme, coactivator-associated arginine methyltransferase 1 (CARM1), involved in various biological activities such as tumor suppressor function and stem cell differentiation. We have employed surface-enhanced Raman scattering (SERS) to obtain insight into the structural details of CARM1 by adsorbing it to silver (Ag) nanoparticles. The enzyme retains its activity even after its adsorption onto Ag nanoparticles. We observe strong SERS modes arising from amide vibrations and aromatic ring amino acids. The SERS spectra revealed amide I bands at 1637 cm(-1) and 1666 cm(-1), which arise as a result of the alpha helix of the protein and the polypeptide backbone vibration of a random coil, respectively. In order to confirm the amide vibrations, we have performed SERS on deuterated CARM1, which exhibits a clear red shift in amide band positions. The SERS spectra may provide useful information, which could be harnessed to study the functional interactions of CARM1 with small molecule modulators.

Specific inhibition of p300-HAT alters global gene expression and represses HIV replication

Reversible acetylation of histone and nonhistone proteins plays pivotal role in cellular homeostasis. Dysfunction of histone acetyltransferases (HATs) leads to several diseases including cancer, neurodegenaration, asthma, diabetes, AIDS, and cardiac hypertrophy. We describe the synthesis and characterization of a set of p300-HAT-specific small-molecule inhibitors from a natural nonspecific HAT inhibitor, garcinol, which is highly toxic to cells. We show that the specific inhibitor selectively represses the p300-mediated acetylation of p53 in vivo. Furthermore, inhibition of p300-HAT down regulates several genes but significantly a few important genes are also upregulated. Remarkably, these inhibitors were found to be nontoxic to T cells, inhibit histone acetylation of HIV infected cells, and consequently inhibit the multiplication of HIV.

Activation of p300 Histone Acetyltransferase by Small Molecules Altering Enzyme Structure: Probed by Surface-Enhanced Raman Spectroscopy

Reversible acetylation of nucleosomal histones and nonhistone proteins play pivotal roles in the regulation of all the DNA templated phenomenon. Dysfunction of the enzymes involved in the acetylation/deacetylation leads to several diseases. Therefore, these enzymes are the targets for new generation therapeutics. Here, we report the synthesis of trifluoromethyl phenyl benzamides and their effect on histone acetyltransferase (HAT) activity of p300. One of these benzamides, CTPB (N-(4-chloro-3-trifluoromethyl-phenyl)-2-ethoxy-6-pentadecyl-benzamide), was discovered as a potent activator of the p300 HAT activity. We have found that pentadecyl hydrocarbon chain of CTPB is required to activate the HAT only under certain context. Furthermore, our results show that the relative position of -CF3 and -Cl in CTB (N-(4-chloro-3-trifluoromethyl-phenyl)-2-ethoxy-benzamide) is also very critical for the activation. Surface-enhanced Raman spectroscopy (SERS) of p300 and the HAT activator complexes evidently suggest that the activation of HAT activity is achieved by the alteration of p300 structure. Therefore, apart from elucidating the chemical basis for small molecule mediated activation of p300, this report also describes, for the first time, Raman spectroscopic analysis of the complexes of histone-modifying enzymes and their modulators, which may be highly useful for therapeutic applications.