Multiplexed Discrimination of Single Amino Acid Residues in Polypeptides in a Single SERS Hot Spot

The SERS-based detection of protein sequences with single-residue sensitivity suffers from signal dominance of aromatic amino acid residues and backbones, impeding detection of non-aromatic amino acid residues. Herein, we trap a gold nanoparticle in a plasmonic nanohole to generate a single SERS hot spot for single-molecule detection of 2 similar polypeptides (vasopressin and oxytocin) and 10 distinct amino acids that constitute the 2 polypeptides. Significantly, both aromatic and non-aromatic amino acids are detected and discriminated at the single-molecule level either at individual amino acid molecules or within the polypeptide chains. Correlated with molecular dynamics simulations, our results suggest that the signal dominance due to large spatial occupancy of aromatic rings of the polypeptide sidechains on gold surfaces can be overcome by the high localization of the single hot spot. The superior spectral and spatial discriminative power of our approach can be applied to single-protein analysis, fingerprinting, and sequencing.     

Rolling‐Circle Amplification Detection of Thrombin Using Surface‐Enhanced Raman Spectroscopy with Core‐Shell Nanoparticle Probe

An ultrasensitive surface‐enhanced Raman spectroscopy (SERS) sensor based on rolling‐circle amplification (RCA)‐increased “hot‐spot” was developed for the detection of thrombin. The sensor contains a SERS gold nanoparticle@Raman label@SiO₂ core‐shell nanoparticle probe in which the Raman reporter molecules are sandwiched between a gold nanoparticle core and a thin silica shell by a layer‐by‐layer method. Thrombin aptamer sequences were immobilized onto the magnetic beads (MBs) through hybridization with their complementary strand. In the presence of thrombin, the aptamer sequence was released; this allowed the remaining single‐stranded DNA (ssDNA) to act as primer and initiate in situ RCA reaction to produce long ssDNAs. Then, a large number of SERS probes were attached on the long ssDNA templates, causing thousands of SERS probes to be involved in each biomolecular recognition event. This SERS method achieved the detection of thrombin in the range from 1.0×10^?12 to 1.0×10^?8 M and a detection limit of 4.2×10^?13 M , and showed good performance in real serum samples.     

Electrochemical detection of amino acids based on cucurbit[7]uril-mediated three-dimensional gold nanoassemblies

In this paper, cucurbit[7]uril (CB[7])-mediated three-dimensional gold nanoassemblies were successfully prepared to increase the loaded amount of CB[7] and enhance the electrochemical detection of amino acids. Particle sizes of gold nanoparticles (AuNPs) significantly affect stability and detection sensitivity of nanoassemblies. The volume of gold nanoassemblies first increased and then decreased with the increase of CB[7] concentration. The 3D gold nanoassemblies composed of 16 nm AuNPs and 100 µmol/L CB[7] had excellent stability and maximum volume, exhibiting more sensitive detection for a variety of amino acids. And the detection limits of aromatic amino acids are lower in virtue of the higher binding constant between aromatic amino acids and CB[7]. This study will develop and deepen our understanding of molecular recognition in amino acids detection.     

Aromatic amino acids providing characteristic motifs in the Raman and SERS spectroscopy of peptides

Raman and surface-enhanced Raman spectroscopies (SERS) are potentially important tools in the characterization of biomolecules such as proteins and DNA. In this work, SERS spectra of three cysteine-containing aromatic peptides: tryptophan-cysteine, tyrosine-cysteine, and phenylalanine-cysteine, bound to Au nanoshell substrates, were obtained, and compared to their respective normal Raman spectra. While the linewidths of the SERS peaks are significantly broadened (up to 70%), no significant spectral shifts (<6 cm (-1)) of the major Stokes modes were observed between the two modalities. We show that the Raman and SERS spectra of penetratin, a cell-penetrating peptide oligomer, can be comprised quite reliably from the spectra of its constituent aromatic amino acids except in the backbone regions where the spectral intensities are critically dependent on the length and conformations of the probed molecules. From this study we conclude that, together with protein backbone groups, aromatic amino acid residues provide the overwhelmingly dominant features in the Raman and SERS spectra of peptides and proteins when present. It follows that the Raman modes of these three small constructed peptides may likely apply to the assignment of Raman and SERS features in the spectra of other peptides and proteins.     

REACTIVITY OF SINGLET OXYGEN TOWARD LARGE PEPTIDES

Abstract— The reactions of singlet oxygen, ¹O₂, with amino acids and their derivatives have been studied previously. It was found that only five amino acid residues interact readily with ¹O₂. Here we describe its reactions with the large peptides melittin, neuropeptide Y (NPY) and insulin in their native and in their denatured forms. The singlet oxygen quenching by a polypeptide was compared with that of a solution at the same concentration as those of its constituent amino acids, which are known to react efficiently with ¹O₂. It was found that the quenching rate by such a mixture exceeded that of the polypeptides in their native form. The ratio of the rate constants for NPY to that of the corresponding amino acid mixture in solution was 0.75. For melittin in its monomeric form it was 0.83 and for a tetramer of melittin (at high ionic strength) it was 0.70. For native insulin the ratio of the rate constants was 0.55. For oxidized insulin with its -S-S- bridges opened the figure became 0.80. However, the quenching by all the polypeptides in their fully denatured form (in the presence of 6 M urea) equalled that of the corresponding amino acid mixtures. Although polypeptides are generally supposed not to possess a stable secondary structure in solution the effects are explained by shielding of some of the reactive amino acid residues in the chain by temporary folding or incipient secondary structures of the native polypeptide.
It is shown that the kinetics for a homogeneous solution of quenchers applies also to measurements in a polypeptide solution where the quenchers are localized along the polypeptide backbone and thus form clusters in solution.     

Catalytic Molecular Imaging of MicroRNA in Living Cells by DNA‐Programmed Nanoparticle Disassembly

Molecular imaging is an essential tool for disease diagnostics and treatment. Direct imaging of low‐abundance nucleic acids in living cells remains challenging because of the relatively low sensitivity and insufficient signal‐to‐background ratio of conventional molecular imaging probes. Herein, we report a class of DNA‐templated gold nanoparticle (GNP)–quantum dot (QD) assembly‐based probes for catalytic imaging of cancer‐related microRNAs (miRNA) in living cells with signal amplification capacity. We show that a single miRNA molecule could catalyze the disassembly of multiple QDs with the GNP through a DNA‐programmed thermodynamically driven entropy gain process, yielding significantly amplified QD photoluminescence (PL) for miRNA imaging. By combining the robust PL of QDs with the catalytic amplification strategy, three orders of magnitude improvement in detection sensitivity is achieved in comparison with non‐catalytic imaging probe, which enables facile and accurate differentiation between cancer cells and normal cells by miRNA imaging in living cells.     

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.     

鸭肉中环丙沙星残留的表面增强拉曼光谱测定

为实现鸭肉中环丙沙星(CIP)残留的快速检测,建立了一种鸭肉中CIP残留的表面增强拉曼光谱(SERS)快速检测方法。进行了增强基底的紫外-可见吸收光谱分析和鸭肉中CIP残留检测的SERS可行性分析。通过单因素实验,确定了金胶加入量、含CIP的鸭肉提取液加入量、氯化钠溶液加入量和吸附时间。在最佳实验条件下,建立了鸭肉中CIP残留的SERS检测的标准工作曲线,决定系数(R2)为0.987 9,预测样本中CIP的平均回收率为97.0%~111.7%。实验结果表明,鸭肉中CIP残留的SERS快速检测方法是可行的。     

The dehydroalanine effect in the fragmentation of ions derived from polypeptides

The fragmentation of peptides and proteins upon collision‐induced dissociation (CID) is highly dependent on sequence and ion type (e.g. protonated, deprotonated, sodiated, odd electron, etc.). Some amino acids, for example aspartic acid and proline, have been found to enhance certain cleavages along the backbone. Here, we show that peptides and proteins containing dehydroalanine, a non‐proteinogenic amino acid with an unsaturated side‐chain, undergo enhanced cleavage of the N—Cα bond of the dehydroalanine residue to generate c‐ and z‐ions. Because these fragment ion types are not commonly observed upon activation of positively charged even‐electron species, they can be used to identify dehydroalanine residues and localize them within the peptide or protein chain. While dehydroalanine can be generated in solution, it can also be generated in the gas phase upon CID of various species. Oxidized S‐alkyl cysteine residues generate dehydroalanine upon activation via highly efficient loss of the alkyl sulfenic acid. Asymmetric cleavage of disulfide bonds upon collisional activation of systems with limited proton mobility also generates dehydroalanine. Furthermore, we show that gas‐phase ion/ion reactions can be used to facilitate the generation of dehydroalanine residues via, for example, oxidation of S‐alkyl cysteine residues and conversion of multiply‐protonated peptides to radical cations. In the latter case, loss of radical side‐chains to generate dehydroalanine from some amino acids gives rise to the possibility for residue‐specific backbone cleavage of polypeptide ions. Copyright © 2016 John Wiley & Sons, Ltd.     

Tuning the conformation of synthetic co‐polypeptides of serine and glutamic acid through control over polymer composition

Ring opening polymerization (ROP) of N‐carboxy anhydride (NCA) amino acids presents a rapid way to synthesize high molecular weight polypeptides with different amino acid compositions. The compositional and functional versatility of polypeptides make these materials an attractive choice for biomaterials. The functional performance of polypeptide materials is equally linked to their conformation which is determined by the amino acid sequence in the polymer chains. Here, the interplay between composition and conformation of synthetic polypeptides obtained by NCA polymerization was explored. Various copolypeptides from Glu(Bzl) and Ser(Bzl) were prepared to investigate how polypeptide composition affected the conformation of the resulting copolymer. Polymerization kinetics indicated that the copolymerization of Glu(Bzl) and Ser(Bzl) preferentially yielded alternating copolymers. Both the polydispersity and the conformation of the polypeptides were dependent on the Ser(Bzl) content in the polymer, demonstrating that polypeptide functionalities could be tuned directly by altering the relative amounts of amino acids in the chain. This work presents the first step toward an improved understanding and control over polypeptide conformation through modulating the amino acid composition of the material. Understanding this sequence–functionality relationship is essential to advancing the use of ROP as a technique to design smart polypeptide based materials with specific functions. © 2016 The Authors. Journal of Polymer Science Part A: Polymer Chemistry Published by Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2016 , 54, 2331–2336     

梅花鹿茸多肽的化学结构及生物活性

在马鹿茸活性多肽结构与功能研究基础上, 从新鲜梅花鹿茸中分离纯化了活性单体多肽, 确定了其化学结构, 并与马鹿茸多肽进行结构与活性比较. 利用离子交换层析、 凝胶过滤层析及反相高效液相色谱层析等生物化学技术, 从梅花鹿茸中分离得到1个新多肽, SDS-PAGE电泳显示为一条带, HPLC图谱为单一峰, MALDI-TOF MS给出该多肽的精确分子量为3263.4, 其等电点pI=8.15. 一级结构研究表明, 该多肽是由32个氨基酸残基组成的直链多肽, 不含半胱氨酸, 富含缬氨酸、 赖氨酸、 亮氨酸和甘氨酸, 氨基酸序列为VLSATDKTNVLAAWGKVGGNAPAFGAEALERM. 生物活性检测结果表明, 该多肽可促进原代培养的表皮细胞和软骨细胞增殖, 也能刺激NIH3T3成纤维细胞株的分裂. 梅花鹿茸多肽与马鹿茸多肽在结构上均为32个氨基酸残基组成的直链多肽, 但第5, 8, 11和30位氨基酸残基不同. 2种多肽结构上的变化并未影响其促细胞增殖生物活性.     

A quantitative, real-time assessment of binding of peptides and proteins to gold surfaces

Interactions of peptides and proteins with inorganic surfaces are important to both natural and artificial systems; however, a detailed understanding of such interactions is lacking. In this study, we applied new approaches to quantitatively measure the binding of amino acids and proteins to gold surfaces. Real‐time surface plasmon resonance (SPR) measurements showed that TEM1‐β‐lactamase inhibitor protein (BLIP) interacts only weakly with Au nanoparticles (NPs). However, fusion of three histidine residues to BLIP (3H‐BLIP) resulted in a significant increase in the binding to the Au NPs, which further increased when the histidine tail was extended to six histidines (6H‐BLIP). Further increasing the number of His residues had no effect on the binding. A parallel study using continuous (111)‐textured Au surfaces and single‐crystalline, (111)‐oriented, Au islands by ellipsometry, FTIR, and localized surface plasmon resonance (LSPR) spectroscopy further confirmed the results, validating the broad applicability of Au NPs as model surfaces. Evaluating the binding of all other natural amino acid homotripeptides fused to BLIP (except Cys and Pro) showed that aromatic and positively‐charged residues bind preferentially to Au with respect to small aliphatic and negatively charged residues, and that the rate of association is related to the potency of binding. The binding of all fusions was irreversible. These findings were substantiated by SPR measurements of synthesized, free, soluble tripeptides using Au‐NP‐modified SPR chips. Here, however, the binding was reversible allowing for determination of binding affinities that correlate with the binding potencies of the related BLIP fusions. Competition assays performed between 3H‐BLIP and the histidine tripeptide (3 His) suggest that Au binding residues promote the adsorption of proteins on the surface, and by this facilitate the irreversible interaction of the polypeptide chain with Au. The binding of amino acids to Au was simulated by using a continuum solvent model, showing agreement with the experimental values. These results, together with the observed binding potencies and kinetics of the BLIP fusions and free peptides, suggest a binding mechanism that is markedly different from biological protein–protein interactions.     

纸质空心金纳米笼SERS传感器的制备及对非小细胞肺癌患者痰液中miRNAs的快速高灵敏检测

利用油水界面自组装法获得了单层空心金纳米笼(HGNCs)阵列基底. 通过时域有限差分方法, 证明HGNCs间隙可提供大量“热点”, 从而使基底表现出优异的表面增强拉曼散射(SERS)性能. 同时, 将拉曼信号分子标记的发夹结构DNA与基底链接, 在与目标miRNAs互补杂交后进行SERS信号检测. 结果表明, 基于单层HGNCs阵列基底的SERS传感器具有优良的灵敏度、 可重复性和特异性, 对痰液中miR-196a和miR-21的检出限分别为10.00和36.15 amol/L. 为了验证该SERS传感器在临床检测中的准确性, 利用其对非小细胞肺癌(NSCLC)患者痰液中miR-196a和miR-21进行检测, 并将结果与实时定量多聚核苷酸链式反应技术(qRT-PCR)的检测结果进行了比较. 2种检测方法均显示NSCLC患者痰液中miR-196a和miR-21的表达高于健康人, 检测结果间没有统计学差异, 且相对标准偏差均低于10%. 因此, 纸质空心金纳米笼SERS传感器在NSCLC诊断中具有应用价值, 可能成为生物医学诊断领域miRNAs研究的一个替代工具.     

Highly Reproducible Surface‐Enhanced Raman Spectra on Semiconductor SnO2 Octahedral Nanoparticles

Highly reproducible surface‐enhanced Raman scattering (SERS) spectra are obtained on the surface of SnO₂ octahedral nanoparticles. The spot‐to‐spot SERS signals show a relative standard deviation (RSD) consistently below 20 % in the intensity of the main Raman peaks of 4‐mercaptobenzoic acid (4‐MBA) and 4‐nitrobenzenethiol (4‐NBT), indicating good spatial uniformity and reproducibility. The SERS signals are believed to mainly originate from a charge‐transfer (CT) mechanism. Time‐dependent density functional theory (TD‐DFT) is used to simulate the SERS spectrum and interpret the chemical enhancement mechanism in the experiment. The research extends the application of SERS and also establishes a new uniform SERS substrate.     

Determination of Saxitoxin by Aptamer-Based Surface-Enhanced Raman Scattering

Saxitoxin is one of the most harmful paralytic shellfish toxins due to its high toxicity and adverse effects on the environment and human health. Aptasensors provide simple detection procedures because they have the advantages of chemical stability, easy synthesis and modification, and high convenience in signal transformation. Surface-enhanced Raman scattering (SERS) is an analytical technique that amplifies the analytical signals of molecules at extremely low concentrations, or even at the single molecule level, when the analyte is very close to rough metal surfaces or nanostructures. In this study, an SERS aptasensor is reported for the determination of saxitoxin for the first time. The optimized saxitoxin aptamer (M-30f) was modified on gold nanoparticles and served as the recognition element. Crystal violet was used as the Raman reporter without chemical bounding. The analytical principles of the aptasensor are that saxitoxin destabilized the conformations of the aptamer at high temperature conditions and altered the binding of crystal violet on the gold nanoparticles. In the presence of saxitoxin, the conformation of aptamer containing the G-quadruplex that selectively bound crystal violet unfolded to a large extent and hence the crystal violet molecules were released from gold nanoparticles with a reduced SERS signal. The effects of the gold nanoparticle size, the amount of DNA, aptamer density, sodium chloride concentration, and operation temperature upon the SERS determination were optimized. The resulting simple SERS aptasensor was developed with a satisfactory limit of detection (11.7?nM) and selectivity. The application for the analysis of real shellfish samples with simple procedures demonstrates that this SERS aptasensor is promising for on-site applications.     

Conformationally Constrained Peptidomimetics as Inhibitors of the Protein Arginine Methyl Transferases

Protein arginine N‐methyl transferases (PRMTs) belong to a family of enzymes that modulate the epigenetic code through modifications of histones. In the present study, peptides emerging from a phage display screening were modified in the search for PRMT inhibitors through substitution with non‐proteinogenic amino acids, N‐alkylation of the peptide backbone, and incorporation of constrained dipeptide mimics. One of the modified peptides ( 23 ) showed an increased inhibitory activity towards several PRMTs in the low μm range and the conformational preference of this peptide was investigated and compared with the original hit using circular dichroism and NMR spectroscopy. Introducing two constrained tryptophan residue mimics (l ‐Aia) spaced by a single amino acid was found to induce a unique turn structure stabilized by a hydrogen bond and aromatic π‐stacking interaction between the two l ‐Aia residues.     

α‐Helical Polypeptide Films Grown From Sulfide or Thiol Linkers on Gold Surfaces

We prepared two new linkers, S‐functionalized adamantane derivatives 2 and 3 , which bind as monolayers on polycrystalline gold. From these surface anchors, both L ‐ and D ‐isomers of alanine can be grown as thin films of α‐helical polypeptides directed from the gold surface by using the appropriate N‐carboxyalanine anhydride. FT‐IR Studies show that these layers are roughly 1000‐Å thick and that, under the same growth conditions, the L ‐polypeptide layers grow at a rate ca. 30% greater than that of the non‐natural D ‐amino acid. X‐Ray photoelectron spectroscopy studies show that, upon equilibration, all three S‐atoms of the sulfide moieties of 2 are bound to the gold surface, and that, on average, three of the four thiols of 3 are chemoadsorbed. The essential role of H₂O on the surface of these films as a necessary component in these gas‐phase polymerization reactions is demonstrated.     

SERS标记的金纳米棒探针用于免疫检测

报道了基于金纳米棒表面增强拉曼散射(SERS)的免疫检测. 将拉曼活性分子对巯基苯甲酸吸附于金纳米棒表面, 制备出SERS标记的金纳米棒探针. 该探针和蛋白抗体结合形成SERS标记抗体. 通过SERS标记抗体、待测抗原和俘获抗体(固体基底上修饰的抗体, 即俘获抗体)之间的免疫应答反应, 将金纳米棒探针组装到固体基底上, 形成SERS标记抗体-抗原-俘获抗体 “三明治”夹心复合体. 待测抗原浓度越大, 固体基底上俘获的金纳米棒探针的数目越多, 从而可通过SERS信号的强弱来检测待测抗原的浓度. 由于金纳米棒的表面等离子体共振(SPR)峰位置可以在较宽的范围内调控, 可通过激发光和SPR的耦合来提高SERS信号, 从而提高免疫检测的灵敏度. 单组分抗原可检出的浓度范围高于1×10－8 mg/mL.     

Analysis of Redox Activity of Proteins on the Carbon Screen Printed Electrodes

Direct redox activity of different proteins was investigated on the surface of carbon screen printed electrodes (SPE). The signal attributed to the electrochemical oxidation of amino acid residues (cysteine (Cys), tryptophan (Trp) and tyrosine (Tyr)) was registered at E_max from 0.6 to 0.7 V (vs. Ag/AgCl). Based on the difference in the redox behavior of L ‐tyrosine and 3‐nitro‐L ‐tyrosine, the selective electrochemical detection of native and nitrated albumins was demonstrated. It was shown that the electrochemical signal correlated with the surface density of electroactive amino acid residues on the protein molecule. A simple electrochemical method for the total protein analysis was proposed.     

Enantioselective micellar electrokinetic chromatography of dl‐amino acids using (+)‐1‐(9‐fluorenyl)‐ethyl chloroformate derivatization and UV‐induced fluorescence detection

Chiral analysis of dl ‐amino acids was achieved by micellar electrokinetic chromatography coupled with UV‐excited fluorescence detection. The fluorescent reagent (+)‐1‐(9‐fluorenyl)ethyl chloroformate was employed as chiral amino acid derivatizing agent and sodium dodecyl sulfate served as pseudo‐stationary phase for separating the formed amino acid diastereomers. Sensitive analysis of (+)‐1‐(9‐fluorenyl)ethyl chloroformate‐amino acids was achieved applying a xenon‐mercury lamp for ultraviolet excitation, and a spectrograph and charge‐coupled device for wavelength‐resolved emission detection. Applying signal integration over a 30 nm emission wavelength interval, signal‐to‐noise ratios for derivatized amino acids were up to 23 times higher as obtained using a standard photomultiplier for detection. The background electrolyte composition (electrolyte, pH, sodium dodecyl sulfate concentration, and organic solvent) was studied in order to attain optimal chemo‐ and enantioseparation. Enantioseparation of 12 proteinogenic dl ‐amino acids was achieved with chiral resolutions between 1.2 and 7.9, and detection limits for most derivatized amino acids in the 13–60 nM range (injected concentration). Linearity (coefficients of determination > 0.985) and peak‐area and migration‐time repeatabilities (relative standard deviations lower than 2.6 and 1.9%, respectively) were satisfactory. The employed fluorescence detection system provided up to 100‐times better signal‐to‐noise ratios for (+)‐1‐(9‐fluorenyl)ethyl chloroformate‐amino acids than ultraviolet absorbance detection, showing good potential for d ‐amino acid analysis.