Real-time Surface Plasmon Resonance Research Articles

Binding of the Unorthodox Transcription Activator, Crl, to the Components of the Transcription Machinery

The small regulatory protein Crl binds to sigmaS, the RNA polymerase stationary phase sigma factor. Crl facilitates the formation of the sigmaS-associated holoenzyme (EsigmaS) and thereby activates sigmaS-dependent genes. Using a real time surface plasmon resonance biosensor, we characterized in greater detail the specificity and mode of action of Crl. Crl specifically forms a 1:1 complex with sigmaS, which results in an increase of the association rate of sigmaS to core RNA polymerase without any effect on the dissociation rate of EsigmaS. Crl is also able to associate with preformed EsigmaS with a higher affinity than with sigmaS alone. Furthermore, even at saturating sigmaS concentrations, Crl significantly increases EsigmaS association with the katN promoter and the productive isomerization of the EsigmaS-katN complex, supporting a direct role of Crl in transcription initiation. Finally, we show that Crl does not bind to sigma70 itself but is able at high concentrations to form a weak and transient 1:1 complex with both core RNA polymerase and the sigma70-associated holoenzyme, leaving open the possibility that Crl might also exert a side regulatory role in the transcriptional activity of additional non-sigmaS holoenzymes.

Conformational Dynamics of Poly(acrylic acid)‐Bovine Serum Albumin Polycomplexes at Different pH Conditions

AbstractThis work presents the real time surface plasmon resonance (SPR) and fluorescence spectroscopy observation of cooperative interactions between aggregate‐forming bovine serum albumin (BSA) and oppositely charged linear macromolecule poly(acrylic) acid (PAA). Interactions between protein and polymer result in formation of polyelectrolyte‐protein polycomplexes, which exhibit expressed conformational transformations, especially at low pH. The rate constants of observed kinetic transformations were calculated and found to vary in the range from 0.8 × 10−3 to 6.7 × 10−3 for different pH values. The processes of aggregation, sedimentation and conformation of BSA‐PAA complex are discussed.

The Structure and Binding Behavior of the Bacterial Cell Surface Layer Protein SbsC

Surface layers (S-layers) comprise the outermost cell envelope component of most archaea and many bacteria. Here we present the structure of the bacterial S-layer protein SbsC from Geobacillus stearothermophilus, showing a very elongated and flexible molecule, with strong and specific binding to the secondary cell wall polymer (SCWP). The crystal structure of rSbsC((31-844)) revealed a novel fold, consisting of six separate domains, which are connected by short flexible linkers. The N-terminal domain exhibits positively charged residues regularly spaced along the putative ligand binding site matching the distance of the negative charges on the extended SCWP. Upon SCWP binding, a considerable stabilization of the N-terminal domain occurs. These findings provide insight into the processes of S-layer attachment to the underlying cell wall and self-assembly, and also accommodate the observed mechanical strength, the polarity of the S-layer, and the pronounced requirement for surface flexibility inherent to cell growth and division.

Sensitivity Enhancement of Surface Plasmon Resonance Imaging Using Periodic Metallic Nanowires

A nanowire-mediated surface plasmon resonance (SPR) imaging is numerically investigated for enhanced sensitivity. The results calculated by rigorous coupled-wave analysis present that interplays between localized surface plasmons and surface plasmon polaritons contribute to sensitivity enhancement. Compared to conventional thin film-based SPR imaging measurement, an optimal nanowire structure can provide sensitivity enhancement by 3.44 times as well as highly linear detection property for quantification of surface reactions of interests. This paper demonstrates the potential and limitation for a highly sensitive, label-free, and real-time SPR imaging sensor based on periodic metallic nanowires.

Modeling of vapor sorption in polymeric film studied by surface plasmon resonance spectroscopy

Sorption process by surface plasmon resonance (SPR) was studied by exposing polymeric film made from anthracene labeled poly(methyl methacrylate) (An-PMMA) chains to various concentrations of saturated chloroform vapor. It was observed that the reflectivity changes were fast and reversible. The changes in reflectivity implied the swelling behavior of polymeric film during adsorbtion and can be explained by capturing of chloroform molecules. When clean air is introduced into gas cell similar behavior is observed but this time in the opposite direction as a result of desorption. Fick's law for diffusion was used to quantify real time SPR data for the swelling and desorption processes. It was observed that diffusion coefficients ( D s ) for swelling obeyed the t 1 / 2 law and found to be correlated with the amount of chloroform content in the cell. Diffusion coefficients ( D d ) during desorption were also measured and found to be increased as the saturated chloroform vapor content is increased in the cell.

Characterization of SV40 T‐antigen G‐quadruplex Helicase Activity Using SPR

Simian Virus 40 (SV40) is a double stranded DNA virus helpful as a model system for eukaryotic cellular DNA replication. It encodes a Large T‐antigen (T‐ag) protein, which is essential for viral genome replication and regulation of the host cell cycle. Acting as a helicase enzyme, T‐ag is able to unwind various forms of DNA. Guanine rich sequences of DNA capable of forming G‐quadruplex knot‐like structures have been identified in several eukaryotic oncogene promoter regions, as well as in the SV40 virus genome, and may possibly influence transcription activity. T‐ag forms an active hexameric unit in the presence of ATP, and was demonstrated to bind single‐strand, duplex, and G‐quadruplex DNA using real time surface plasmon resonance (SPR). Probing with single strand binding protein (SSB) confirmed that T‐ag activity resulted in the unwinding of an intermolecular quadruplex.

Surface Plasmon Resonance Based Assay for the Detection and Characterization of Promiscuous Inhibitors

Promiscuous binders achieve enzyme inhibition using a nonspecific aggregation-type binding mechanism to proteins. These compounds are a source of false-positive hits in biochemical inhibition assays and should be removed from screening hit lists because they are not good candidates to initiate medicinal chemistry programs. We introduce a robust approach to identify these molecules early in the lead generation process using real time surface plasmon resonance based biosensors to observe the behavior of the binding interactions between promiscuous compounds and proteins. Furthermore, the time resolution of the assay reveals a number of distinct mechanisms that promiscuous compounds employ to inhibit enzyme function and indicate that the type of mechanism can vary depending on the protein target. A classification scheme for these compounds is presented that can be used to rapidly characterize the hits from high-throughput screens and eliminate compounds with a nonspecific mechanism of inhibition.

Full-field and real-time surface plasmon resonance imaging thermometry

The feasibility of surface plasmon resonance (SPR) imaging thermometry is tested as a potential tool for full-field and real-time temperature field mapping for thermally transient liquid mediums. Using the well-known Kretschmann's analysis [Physik 241, 313 (1971)]. parametric examinations are performed to delineate the effects of important optical properties, including seven different prism materials with different refractive index values and seven different measured dielectric constants for thin gold (Au) films (approximately 47.5 nm in thickness), on the temperature dependence of SPR reflectance intensity variations. Furthermore, a laboratory-implemented real-time SPR thermometry system demonstrates the full-field mapping capabilities for transient temperature field developments in the near-wall region when a hot water droplet (80 degrees C) contacts the Au metal surface (20 degrees C) and spreads either in an air- or in a water-surrounded environment.

A photoswitchable ITAM peptidomimetic: Synthesis and real time surface plasmon resonance (SPR) analysis of the effects of cis– trans isomerization on binding

The Syk protein plays an important role in immune receptor signaling. The Syk tandem SH2 domain (tSH2)–ITAM interaction is important for recruiting Syk to the receptor complex and for Syk kinase activation. A peptidomimetic ligand for tSH2 was synthesized in which a photoswitchable azobenzene moiety was incorporated. Such a photoswitchable moiety may regulate the distance between the two phosphotyrosine containing ITAM sequences, which bind to tSH2. Different affinities of the cis and trans isomer of the ligand were found by surface plasmon resonance (SPR). By in situ irradiation during SPR measurements the effect of the cis– trans isomerization on binding could be monitored in real time.

Mixed Monolayers to Promote G-Protein Adsorption: α2A-Adrenergic Receptor-Derived Peptides Coadsorbed with Formyl-Terminated Oligopeptides

Pure and mixed monolayers of a synthetic peptide, GPR-i3n, derived from the third intracellular loop of the alpha2 adrenergic receptor and a shorter inactive oligopeptide, N-formyl-(Gly)3-(Cys) (called 3GC), were prepared on gold surfaces. The mixing ratio of the GPR-i3n and 3GC was used to control G-protein binding capability. The GPR-i3n peptide is specially designed for bovine G-protein selectivity and has been proven to have high affinity to G-proteins [Vahlberg, C.; Petoral, R. M., Jr.; Lindell, C.; Broo, K.; Uvdal, K. Langmuir 2006, 22 (17), 7260-7264]. Pure 3GC monolayers show very low protein adsorption capability. In this study, 3GC is chosen as a coadsorbent, with the aim to induce molecular conformational changes during monolayer formation to enhance G-protein adsorption. A full characterization of the mixed monolayers was done. The monolayer thickness and the mass-related surface coverage for both GPR-i3n and 3GC were investigated using radio labeling. The GPR-i3n was labeled by 125I-targeting tyrosine, and the activity was measured by using radioimmunoassay (RIA). The formation and chemical composition of GPR-i3n and 3GC monolayers were investigated using X-ray photoelectron spectroscopy, and it is shown that both GPR-i3n and 3GC bind chemically to the gold surface. The interaction between the mixed monolayers and G-proteins was investigated by means of real-time surface plasmon resonance. There is a higher protein binding capacity to the monolayer when the GPR-i3n peptide is intermixed with the 3GC coadsorbent, despite the fact that the 3GC itself has a very low G-protein binding capability. This supports a molecular reorientation at the surface, while 3GC is intermixed with GPR-i3n.

A Bioorganometallic Approach for the Electrochemical Detection of Proteins: A Study on the Interaction of Ferrocene–Peptide Conjugates with Papain in Solution and on Au Surfaces

In this paper, a new bioorganometallic approach for the detection of proteins using surface-bound ferrocene-peptide conjugates is presented. Specifically, a series of peptide conjugates of 1'-aminoferrocene-1-carboxylic acid (ferrocene amino acid, Fca) is synthesized: Boc-Fca-Gly-Gly-Tyr(Bzl)-Arg(NO2)-OMe (2), Thc-Fca-Gly-Gly-Tyr(Bzl)-Arg(NO2)-OMe (3), Thc-Fca-Gly-Gly-Tyr(Bzl)-Arg(NO2)-OH (4), Boc-Fca-Gly-Gly-Arg(Mtr)-Tyr-OMe (7), Thc-Fca-Gly-Gly-Arg(Mtr)-Tyr-OMe (8), Thc-Fca-Gly-Gly-Arg(Mtr)-Tyr-OH (9), Thc-Fca-Gly-Gly-Arg-Tyr-OH (10). The peptide is conjugated to the C-terminal side of Fca and compounds 4, 7-10 possess a thiostic acid linked to the N-terminal side of Fca in order to facilitate formation of thin films on gold substrates. Competitive inhibition towards papain was determined for Thc-Fca-Gly-Gly-Tyr(Bzl)-Arg(NO2)-OH (4), Thc-Fca-Gly-Gly-Arg(Mtr)-Tyr-OH (9) and Thc-Fca-Gly-Gly-Arg-Tyr-OH (10). The binding interaction between the peptide modified substrates and papain enzyme was studied using real-time surface plasmon resonance (SPR) imaging. Peptide 10 showed the strongest binding affinity to papain. Adsorption/desorption rate constants were ka = 1.75+/-0.05 x 10(5) M(-1) s(-1) and kd = 2.90 +/- 0.05 x 10(-2) s(-1). Interactions of papain with Fca-peptide 10 were investigated by cyclic voltammetry. The interaction results were also verified by measuring the electrochemical response of the peptide-papain interaction as function of increasing enzyme concentration. A linear relationship was observed for papain concentration of up to 80 nM. Shifting to higher potentials as well as decrease in the overall signal intensity was observed. The detection limit was 4 x 10(-9) M.

Surface Reactivity of Pulsed-Plasma Polymerized Pentafluorophenyl Methacrylate (PFM) toward Amines and Proteins in Solution

Pulsed-plasma polymerization has been used to deposit ultrathin layers of pentafluorophenyl methacrylate by using low duty cycles and low power input. The monomer structure can be retained such that the chemical reactivity of the active ester group could be studied using the reaction with a simple amine. The film properties in aqueous phosphate buffer have been investigated using Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, and real time surface plasmon resonance spectroscopy. The films react readily with diaminohexane and immunoglobulin (IgG), yet the reactivity shows a dependence on the extent of hydrolysis of the ester group.

Effect of oxazaborolidines on immobilized fructosyltransferase analyzed by surface plasmon resonance

Dental diseases are among the most prevalent afflictions of humankind. These diseases are associated with the formation of biofilms harboring pathogenic bacteria. Fructosyltransferases (FTF) are extra cellular enzymes of several oral bacteria. FTF are associated with the formation of extracellular polysaccharide matrix (fructans) which play a role in biofilm formation and oral bacteria physiology. Oxazaborolidines have been shown to inhibit biofilm formation. The purpose of this study was to examine if the anti-biofilm effect is, in part, an effect on the immobilized enzymes synthesizing the extra cellular polysaccharide participating in biofilm formation. Eight different oxazaborolidines (BNO1-BNO8) were synthesized and evaluated for their affect on the synthesis of fructans by FTF using the biomolecular interaction analysis (BIAcore) system which involves the use of real-time surface plasmon resonance (SPR) technique. The tested oxazaborolidines demonstrated a significant and immediate inhibitory effect on immobilized FTF activity. This effect was reversible. Our results show that oxazaborolidines can act as enzymatic inhibitors of FTF immobilized on the surface, also at levels lower than their MIC. Part of the anti-biofilm effect of BNOs may be accounted for this enzymatic inhibition.

On-Chip Enzyme Immunoassay of a Cardiac Marker Using a Microfluidic Device Combined with a Portable Surface Plasmon Resonance System

This paper reports a miniaturized immunosensor designed to determine a trace level cardiac marker, B-type natriuretic peptide (BNP), using a microfluidic device combined with a portable surface plasmon resonance (SPR) sensor system. Sample BNP solution was introduced into the microchannel after an immunoreaction with acetylcholine esterase-labeled antibody (conjugate), and only unbound conjugate was trapped on the BNP-immobilized surface in the flow channel. Then, the thiol compound generated by the enzymatic reaction with the trapped conjugate was accumulated on a gold thin film located downstream in the microchannel to monitor the real-time SPR angle shift. We achieved a detectable concentration range of 5 pg/mL-100 ng/mL by monitoring the SPR angle shift, which covers the required detection range for the BNP concentrations found in blood. This success resulted from the use of a T-shaped microfluidic device structure, which prevents the sample solution from flowing over the gold film used for SPR detection. We were able to measure trace levels of BNP peptide (15 fg) within 30 min since the procedure with our immunosensor is simpler than a multistep immunoassay through the simultaneous use of a labeled enzymatic reaction and the real-time monitoring of enzymatic product accumulation in the microfluidic device. We employed the procedure to detect serum BNP by using spiked samples in human serum and achieved satisfactory recovery for heat-treated samples to denature the esterase in the serum before the immunoreaction.

Disease-related Modifications in Tau Affect the Interaction between Fyn and Tau

Microtubule-associated protein tau is the major component of the neurofibrillary tangles of Alzheimer disease (AD) and is genetically linked to frontotemporal dementias (FTDP-17). We have recently shown that tau interacts with the SH3 domain of Fyn, an Src family non-receptor tyrosine kinase, and is tyrosine-phosphorylated by Fyn on Tyr-18. Also, tyrosine-phosphorylated tau is present in the neuropathology of AD. To determine whether alterations in the tau-Fyn interaction might correlate with disease-related factors in AD and FTDP-17, we have performed real-time surface plasmon resonance studies on a panel of 21 tau constructs with Fyn SH3. We report that the interaction between Fyn SH3 and 3R-tau was 20-fold higher than that with 4R-tau. In addition, the affinity between 4R-tau and Fyn SH3 was increased 25-45-fold by phosphorylation-mimicking mutations or by FTDP-17 mutations. In vitro kinase reactions show that tau, with lower affinity SH3 interactions, exhibited a lower level of Tyr-18 phosphorylation under our reaction conditions. Lastly, we have demonstrated that tau is phosphorylated on Tyr-18 in the tau P301L mouse model for tauopathy (JNPL3). In summary, our results suggest that disease-related phosphorylation and missense mutations of tau increase association of tau with Fyn. Because these effects are mediated through the 4R component of the tau population, these results also have implications for the FTDP-17 diseases caused by increased expression of 4R-tau. Our data support a role for the Fyn-tau interaction in neurodegeneration.

Determination of Ribonuclease H Surface Enzyme Kinetics by Surface Plasmon Resonance Imaging and Surface Plasmon Fluorescence Spectroscopy

The kinetics of the ribonuclease H (RNase H) surface hydrolysis of RNA-DNA heteroduplexes formed on DNA microarrays was studied using a combination of real-time surface plasmon resonance imaging (SPRI) and surface plasmon fluorescence spectroscopy (SPFS). Time-dependent SPRI and SPFS data at various enzyme concentrations were quantitatively analyzed using a simple model that couples diffusion, enzyme adsorption, and surface enzyme kinetics. This model is characterized by a set of three rate constants, enzyme adsorption (k(a)), enzyme desorption (k(d)), enzyme catalysis (k(cat)), and one dimensionless diffusion parameter (beta). Values of k(a) = 3.15 (+/-0.20) x 10(6) M(-1).s(-1), k(d) = 0.10 (+/-0.05) s(-1), and k(cat) = 0.95 (+/-0.10) s(-1) were determined from fitting all of the SPRI and SPFS data sets. One of the most interesting kinetic parameters is the surface RNase H hydrolysis reaction rate constant (k(cat)), which was found to be approximately 10 times slower than that observed in solution, but approximately 100 times faster than that recently observed for the exonuclease III surface hydrolysis of double-stranded DNA microarrays (k(cat) = 0.009 s(-1)). Moreover, the surface coverage of the intermediate enzyme-substrate complex (ES) was found to be extremely small during the course of the reaction because k(cat) is much larger than the product of k(a) and the bulk enzyme concentration.

αvβ3-integrin-dependent activation of focal adhesion kinase mediates NF-κB activation and motogenic activity by HIV-1 Tat in endothelial cells

Once in the extracellular environment, the transactivator protein HIV-1 Tat exerts several pleiotropic effects by interacting with different cellular receptors, including integrin alpha(v)beta3. Real-time surface plasmon resonance analysis reveals that Tat/alpha(V)beta3 interaction occurs with rapid kinetics (association and dissociation rates equal to 1.16 x 10(7) M(-1) s(-1) and 3.78 x 10(-1) s(-1), respectively) and high affinity (dissociation constant = 32 nM). Through this interaction, substratum-immobilized Tat promotes adhesion and motogenic activity in endothelial cells. Also, alpha(v)beta(3)/Tat interaction triggers the activation of focal adhesion kinase, RhoA and pp60src. Overexpression of the dominant negative form of focal adhesion kinase, but not of an inactive Leu1034Ser substitution mutant isoform, impairs the activation of focal adhesion kinase and RhoA, but not that of pp60src, without affecting endothelial cell adhesion and spreading. alpha(v)beta3/Tat interaction triggers the activation of NF-kappaB in endothelial cells in a focal adhesion kinase-, RhoA- and pp60src-dependent manner, as shown in dominant negative focal adhesion kinase transfectants or using specific pharmacological inhibitors. Finally, the activation of focal adhesion kinase, RhoA, NF-kappaB and pp60src are required to mediate the motogenic activity of Tat in endothelial cells. Since Tat accumulates in an immobilized form in the extracellular matrix, these results provide new biochemical and biological insights about alpha(v)beta3/Tat interaction exploitable for the design of anti-Tat strategies.

Effects of solute–matrix interaction on monitoring the conformational changes of immobilized proteins by surface plasmon resonance sensor

A real-time and labeling-free surface plasmon resonance (SPR) sensor was used to monitor the conformational changes of immobilized globule proteins (RNase A and lysozyme) in chemical unfolding and refolding. The effects of chemical denaturants on the protein structures were investigated. The methodology in protein conformational study on the solid surface is refined through the theoretic calculations and the conformational information of native/denatured proteins in solution. Additionally, our observation illustrates that the ambient buffer solution is merit to influence the refractive index of immobilized protein films and directly be observed from the SPR resonance angle shifts.

Affibody protein capture microarrays: Synthesis and evaluation of random and directed immobilization of affibody molecules

Affibody molecules, 58-amino acid three-helix bundle proteins directed to different targets by combinatorial engineering of staphylococcal protein A, were used as capture ligands on protein microarrays. An evaluation of slide types and immobilization strategies was performed to find suitable conditions for microarray production. Two affibody molecules, Z Taq and Z IgA, binding Taq DNA polymerase and human IgA, respectively, were synthesized by solid phase peptide synthesis using an orthogonal protection scheme, allowing incorporation of selective immobilization handles. The resulting affibody variants were used for random surface immobilization (through amino groups) or oriented surface immobilization (through cysteine or biotin coupled to the side chain of Lys 58). Evaluation of the immobilization techniques was carried out using both a real-time surface plasmon resonance biosensor system and a microarray system using fluorescent detection of Cy3-labeled target protein. The results from the biosensor analyses showed that directed immobilization strategies significantly improved the specific binding activity of affibody molecules. However, in the microarray system, random immobilization onto carboxymethyl dextran slides and oriented immobilization onto thiol dextran slides resulted in equally good signal intensities, whereas biotin-mediated immobilization onto streptavidin-coated slides produced slides with lower signal intensities and higher background staining. For the best slides, the limit of detection was 3 pM for IgA and 30 pM for Taq DNA polymerase.

Surface Enzyme Kinetics for Biopolymer Microarrays: a Combination of Langmuir and Michaelis−Menten Concepts

Real-time surface plasmon resonance (SPR) imaging measurements of surface enzymatic reactions on DNA microarrays are analyzed using a kinetics model that couples the contributions of both enzyme adsorption and surface enzyme reaction kinetics. For the case of a 1:1 binding of an enzyme molecule (E) to a surface-immobilized substrate (S), the overall enzymatic reaction can be described in terms of classical Langmuir adsorption and Michaelis-Menten concepts and three rate constants: enzyme adsorption (k(a)), enzyme desorption (k(d)) and enzyme catalysis (k(cat)). In contrast to solution enzyme kinetics, the amount of enzyme in solution is in excess as compared to the amount of substrate on the surface. Moreover, the surface concentration of the intermediary enzyme-substrate complex (ES) is not constant with time, but goes to zero as the reaction is completed. However, kinetic simulations show that the fractional surface coverage of ES on the remaining unreacted sites does reach a steady-state value throughout the course of the surface reaction. This steady-state value approaches the Langmuir equilibrium value for cases where k(a)[E] >> k(cat). Experiments using the 3' --> 5' exodeoxyribonuclease activity of Exonuclease III on double-stranded DNA microarrays as a function of temperature and enzyme concentration are used to demonstrate how this model can be applied to quantitatively analyze the SPR imaging data.