Use of surface plasmon resonance to probe the equilibrium and dynamic aspects of interactions between biological macromolecules

Cooperative and uncooperative cyclic-nucleotide-gated ion channels

Ion channels gated by cyclic nucleotides serve multiple functions in sensory signaling in diverse cell types ranging from neurons to sperm. Newly discovered members from bacteria and marine invertebrates provide a wealth of structural and functional information on this channel family. A hallmark of classical tetrameric cyclic-nucleotide-gated channels is their cooperative activation by binding of several ligands. By contrast, the new members seem to be uncooperative, and binding of a single ligand molecule suffices to open these channels. These new findings provide a fresh look at the mechanism of allosteric activation of ion channels.

A fluorescence polarization-based assay for the identification and evaluation of calmodulin antagonists

A fluorescence polarization (FP) assay was developed to identify calmodulin (CaM) antagonists. A fluorescent tracer was newly designed by covalently labeling N-(6-aminohexyl)-5-chloro-1-naphthalenesulfonamide (W-7), which is a well-known CaM antagonist, with the Cy5 dye. In the FP assay, the tracer (Cy5-W-7) was bound to CaM with a dissociation constant (K(d)) of 6.5 microM and demonstrated efficient competitive activity with other CaM antagonists, including W-7, chlorpromazine, trifluoperazine, W-5, and clozapine, indicating that Cy5-W-7 binds to the ligand-binding site of CaM in a specific manner. The inhibitory activities of Cy5-W-7 and CaM antagonists were subsequently measured by the CaM-dependent calcineurin phosphatase assay, and the results were confirmed with those of the FP assays. In addition, assay optimization for high-throughput screening was performed, and a Z' factor of 0.7 was achieved in a 1536-well format. The FP assay was found to be a simple and reliable alternative to conventional assays for evaluating CaM antagonists.

On-chip photoactivation of heterologously expressed rhodopsin allows kinetic analysis of G-protein signaling by surface plasmon resonance spectroscopy

Surface plasmon resonance spectroscopy allows the study of protein interaction dynamics in real-time. Application of this technique to G-protein coupled receptors, the largest family of receptors involved in signal transduction, has been complicated by their low level of expression and the critical dependence of their native conformation on the hydrophobic transmembrane lipid environment. Here, we investigate and compare three different strategies to immobilize rhodopsin, a prototypical G-protein coupled receptor on a sensor chip surface using antibodies and a lectin for receptor capturing. By further probing of different experimental conditions (pH, detergent type) we identified the optimal factors to maintain rhodopsin in a functional conformation and extended this approach to recombinant rhodopsin that was heterologously expressed in COS cells. Functional operation of rhodopsin on the sensor chip surface was proven by its activation and subsequent light-stimulated G-protein coupling. The influence of these experimental parameters on the association and dissociation kinetics of G-protein receptor coupling was determined. Thereby, we found that the kinetics of G(t) interaction were not changed by the strategy of immobilization or the type of detergent. Regeneration of opsin directly on a chip allowed recycling of the immobilized native and recombinant receptor. Thus, the approach provides an experimental framework for choosing the most suitable conditions for the solubilization, immobilization, and for functional tests of rhodopsin on a biosensor surface.

Application of surface plasmon resonance spectroscopy to study G-protein coupled receptor signalling

The G-protein coupled receptor rhodopsin is a classical example of a seven transmembrane helix receptor; it is photoexcited and transmits this light signal to a G-protein mediated cascade. Many components of this receptor-triggered cascade can be purified in their native forms from natural sources making this system most suitable for biophysical studies. A central aspect of cellular signal transduction routes is to understand protein-protein interactions in a quantitative way. Surface plasmon resonance (SPR) spectroscopy is a biosensor-based technique that allows investigating molecular interactions by determining kinetic parameters. We here show how dark-adapted rhodopsin can be immobilized on the sensor chip surface. A laser device implemented in the SPR system allowed us to trigger light-induced conformational changes in rhodopsin and to monitor light-dependent binding of the photoreceptor cell G-protein transducin to rhodopsin. The sensor chip surface can be regenerated and used for several rounds of interaction analysis. Furthermore, illuminated rhodopsin can be regenerated by applying 9-cis-retinal on the sensor chip surface.

2-aminoimidazole amino acids as inhibitors of the binuclear manganese metalloenzyme human arginase I

Arginase, a key metalloenzyme of the urea cycle that converts L-arginine into L-ornithine and urea, is presently considered a pharmaceutical target for the management of diseases associated with aberrant l-arginine homeostasis, such as asthma, cardiovascular diseases, and erectile dysfunction. We now report the design, synthesis, and evaluation of a series of 2-aminoimidazole amino acid inhibitors in which the 2-aminoimidazole moiety serves as a guanidine mimetic. These compounds represent a new class of arginase inhibitors. The most potent inhibitor identified in this study, 2-(S)-amino-5-(2-aminoimidazol-1-yl)pentanoic acid (A1P, 10), binds to human arginase I with K(d) = 2 microM and significantly attenuates airways hyperresponsiveness in a murine model of allergic airways inflammation. These findings suggest that 2-aminoimidazole amino acids represent new leads for the development of arginase inhibitors with promising pharmacological profiles.

Effect of ionic strength on PNA-DNA hybridization on surfaces and in solution

Peptide nucleic acids (PNAs) are mimics of oligonucleotides containing a neutral peptidelike backbone and are able to bind complementary DNA targets with high affinity and selectivity. In order to investigate the effect of the ionic strength of the buffer solution, hybridization experiments with PNAs as (catcher) probes and DNAs as target oligonucleotides were performed in different salt solutions. Surface plasmon field-enhanced fluorescence spectroscopy was employed for real-time monitoring of DNA hybridizations to surface bound PNA. Probes with three different strand lengths were immobilized by self-assembly on the sensor surface. By introducing Cy5-labeled DNA targets the affinity constants, K(A)=k(on) (association)/k(off) (dissociation), were determined for fully complementary (MM0) as well as for single base mismatched (MM1) duplexes. Furthermore, the thermal stability of each duplex was determined by measuring melting curves in solution which was then compared to the kinetic and affinity parameters determined for the surface hybridization reactions. The results indicate that ions do not play a significant role for the PNA/DNA hybridization kinetics at surfaces. However, changes in the configuration of the PNA/DNA duplex due to the ionic strength variations influence the fluorescence yield drastically.

The effects of hairpin loops on ligand-DNA interactions

Hairpin nucleic acids are frequently used in physical studies due to their greater thermal stability compared to their equivalent duplex structures. They are also good models for more complex loop-containing structures such as quadruplexes, i-motifs, cruciforms, and molecular beacons. Although a connecting loop can increase stability, there is little information on how the loop influences the interactions of small molecules with attached base-paired nucleic acid regions. In this study, the effects of different hairpin loops on the interactions of A/T specific DNA minor groove binding agents with a common stem sequence have been investigated by spectroscopic and surface plasmon resonance (SPR) biosensor methods. The results indicate that the hairpin loop has little influence on the specific site interactions on the stem but significantly affects nonspecific binding. The use of a non-nucleotide loop (with a reduced negative charge) not only enhances the thermal stability of the hairpin but also reduces the nonspecific binding at the loop without compromising the primary binding affinity on the stem.

The role of mass transport limitation and surface heterogeneity in the biophysical characterization of macromolecular binding processes by SPR biosensing

This chapter presents an introduction to the kinetic analysis of SPR biosensor data for the determination of affinity and kinetic rate constants of biomolecular interactions between an immobilized and a soluble binding partner. The need to be aware of and critically test the assumptions underlying the analysis models is emphasized and the consequences for the experimental design are discussed. The two most common sources of deviation in SPR surface binding kinetics from the ideal pseudo-first-order binding kinetics of bimolecular reactions are mass transport limitations and the heterogeneity of the surface sites. These problems are intrinsic to the use of a biosensor surface for characterizing interactions. The effect of these factors on the observed binding kinetics, and strategies to account for them are reviewed, both in the context of mathematical data analysis, as well as the design of the experiments and controls.

Multifunctional plasmonic sensors on low-cost subwavelength metallic nanoholes arrays

Localized surface plasmon resonance (LSPR) sensing is combined with surface enhanced Raman scattering (SERS) detection on periodic arrays of subwavelength metallic nanoholes for the first time. LSPR sensors provide detection of molecular adsorption in both transmission and reflectivity modes with sensitivity greater that 300 nm/RIU and a spectral shift of 16 nm in the case of binding a monolayer of p-aminothiophenol (p-ATP) molecules. Subsequent SERS analysis enables identification of the adsorbed p-ATP molecule, its structure and orientation on the metal surface. This synergistic LSPR-SERS approach on low-cost metallic films perforated with periodic arrays of subwavelength nanoholes opens a route for molecular dual-modal detection to be integrated in lab-on-chip systems to increase the reliability of biological detection.

Suboptimal engagement of the T-cell receptor by a variety of peptide-MHC ligands triggers T-cell anergy

T cells recognize antigen via the T-cell receptor (TCR) and produce a spectrum of responses that range from activation to anergy or cell death. The variety of outcomes may be dictated by the strength of the signals transmitted upon cognate recognition of the TCR. The physiological outcome of TCR engagement is determined by several factors, including the avidity of the ligand for TCR, the duration of engagement, and the presence and nature of accessory molecules present on antigen-presenting cells (APCs). In this review, we discuss a model of anergy induced by presentation of low densities of peptide-major histocompatibility complex (MHC) ligand in CD4(+) T cells and compare it to anergy induced by altered peptide ligands in an effort to identify a unifying mechanism. We suggest that altered peptide ligand (APL) and low densities of agonist ligands induce anergy by engaging less than optimal numbers of TCRs. The physiological impacts of anergy in memory CD4(+) T cells are discussed.

Single injection microarray-based biosensor kinetics

Binding affinity of biomolecular interactions can be directly extracted from measured surface plasmon resonance biosensor sensorgrams by fitting the data to the appropriate model equations. The conventional method for affinity estimation uses a series of analytes and buffers that are injected serially to a single immobilized ligand on the sensing surface, including a regeneration step between each injection, to generate information about the binding behavior. We present an alternative method to estimate the affinity using a single analyte concentration injected to multiple ligand densities in a microarray format. This parameter estimation method eliminates the need for multiple analyte injections and surface regeneration steps, which can be important for applications where there is limited analyte serum, fragile ligand-surface attachment, or the detection of multiple biomolecule interactions. The single analyte injection approach for binding affinity estimation has been demonstrated for two different interactant pairs, β2 microglobulin/anti-β2 microglobulin (β2M) and human IgG/Fab fragments of anti-human IgG (hIgG), where the ligands are printed in a microarray format. Quantitative comparisons between the estimated binding affinities measured with the conventional method are β2M: KD = 1.48 ± 0.28 nM and hIgG: KD = 12.6 ± 0.2 nM and for the single injection method are β2M: KD = 1.52 ± 0.22 nM and hIgG: KD = 12.5 ± 0.6 nM, which are in good agreement in both cases.

Phase and amplitude sensitivities in surface plasmon resonance bio and chemical sensing

We consider amplitude and phase characteristics of light reflected under the Surface Plasmon Resonance (SPR) conditions and study their sensitivities to refractive index changes associated with biological and chemical sensing. Our analysis shows that phase can provide at least two orders of magnitude better detection limit due to the following reasons: (i) Maximal phase changes occur in the very dip of the SPR curve where the vector of probing electric field is maximal, whereas maximal amplitude changes are observed on the resonance slopes: this provides a one order of magnitude larger sensitivity of phase to refractive index variations; (ii) Under a proper design of a detection scheme, phase noises can be orders of magnitude lower compared to amplitude ones, which results in a much better signal-to-noise ratio; (iii) Phase offers much better possibilities for signal averaging and filtering, as well as for image treatment. Applying a phase-sensitive SPR polarimetry scheme and using gas calibration model, we experimentally demonstrate the detection limit of 10(-8) RIU, which is about two orders of magnitude better compared to amplitude-sensitive schemes. Finally, we show how phase can be employed for filtering and treatment of images in order to improve signal-to-noise ratio even in relatively noisy detection schemes. Combining a much better physical sensitivity and a possibility of imaging and sensing in micro-arrays, phase-sensitive methodologies promise a substantial upgrade of currently available SPR technology.

Biomolecule association rates do not provide a complete description of bond formation

The efficiency of many cell-surface receptors is dependent on the rate of binding soluble or surface-attached ligands. Much effort was exerted to measure association rates between soluble molecules (three-dimensional k(on)) and, more recently, between surface-attached molecules (two-dimensional [2D] k(on)). According to a generally accepted assumption, the probability of bond formation between receptors and ligands is proportional to the first power of encounter duration. Here we provide new experimental evidence and review published data demonstrating that this simple assumption is not always warranted. Using as a model system the (2D) interaction between ICAM-1-coated surfaces and flowing microspheres coated with specific anti-ICAM-1 antibodies, we show that the probability of bond formation may scale as a power of encounter duration that is significantly higher than 1. Further, we show that experimental data may be accounted for by modeling ligand-receptor interaction as a displacement along a single path of a rough energy landscape. Under a wide range of conditions, the probability that an encounter of duration t resulted in bond formation varied as erfc[(t(0)/t)(1/2)], where t(0) was on the order of 10 ms. We conclude that the minimum contact time for bond formation may be a useful parameter to describe a ligand-receptor interaction, in addition to conventional association rates.

Direct observation of the binding process between protein and quantum dots by in situ surface plasmon resonance measurements

A layer-by-layer surface decoration technique has been developed to anchor quantum dots (QDs) onto a gold substrate and an in situ surface plasmon resonance technique has been used to study interactions between the QDs and different proteins. Direct observation of the binding of the protein onto the QDs and the kinetics of the adsorption and dissociation of different proteins on the QDs has been achieved. This would be helpful for the identification of particle-associated proteins and may offer a fundamental prerequisite for nanobiology, nanomedicine and nanotoxicology. The combination of the novel layer-by-layer surface modification method and in situ surface plasmon resonance would be powerful in studying biological systems such as DNA and cells.

Isothermal microcalorimetry to investigate non specific interactions in biophysical chemistry

Isothermal titration microcalorimetry (ITC) is mostly used to investigate the thermodynamics of “specific” host-guest interactions in biology as well as in supramolecular chemistry. The aim of this review is to demonstrate that ITC can also provide useful information about non-specific interactions, like electrostatic or hydrophobic interactions. More attention will be given in the use of ITC to investigate polyelectrolyte-polyelectrolyte (in particular DNA-polycation), polyelectrolyte-protein as well as protein-lipid interactions. We will emphasize that in most cases these “non specific” interactions, as their definition will indicate, are favoured or even driven by an increase in the entropy of the system. The origin of this entropy increase will be discussed for some particular systems. We will also show that in many cases entropy-enthalpy compensation phenomena occur.

Binding of cationic porphyrin to human serum albumin studied using comprehensive spectroscopic methods

The interaction between cationic porphyrin, a potential valuable anti-tumor and antibiotic drug, and human serum albumin (HSA) was investigated using spectroscopy methods. The binding constants were obtained using fluorescence quenching method (K(SV) = (3.24 +/- 0.29) x 10(4) M(-1)) and surface plasmon resonance (SPR) spectroscopy (K(A) = (6.287 +/- 0.407) x 10(4) M(-1)). The association rate constant (k(a) = 1622 +/- 72.9 M(-1) s(-1)) and dissociation rate constant (K(d) = 0.02589 +/- 0.0024 s(-1)) of the binding process were also calculated. Compared with the two results, it was known that one of the binding sites was near the tryptophan residue and also there existed other binding sites. The Fourier transform infrared (FT-IR) spectroscopy and circular dichroism (CD) spectroscopy indicated that the confirmation of HSA was nearly not affected with the addition of porphyrin.

Autoantibodies to glucose‐6‐phosphate isomerase are elevated in the synovial fluid of rheumatoid arthritis patients

OBJECTIVE

This study investigated whether anti-glucose-6-phosphate isomerase (GPI) antibody in the synovial fluid is specifically related to human rheumatoid arthritis (RA).

METHODS

Synovial fluid was collected from patients with RA, osteoarthritis (OA), gout, Behcet's disease, or ankylosing spondylitis. GPI-binding activity was measured in the synovial fluid using a surface plasmon resonance (SPR) biosensor.

RESULTS

The mean level of anti-GPI signal in the synovial fluid of RA patients was significantly elevated compared with that of OA patients (2.84 +/- 1.41 AU versus 1.19 +/- 0.42 AU, respectively; p < 0.0001). Anti-GPI signals in the synovial fluids of patients with non-rheumatoid arthritis, such as gout, Behcet's disease, or ankylosing spondylitis were significantly lower than in the synovial fluid of RA patients (p < 0.005), and were similar to those of OA patients.

CONCLUSION

Our study indicates that anti-GPI antibody in the synovial fluid is specifically related to RA, and suggests that GPI and its autoantibody might be important in the pathogenesis of human RA.

Association kinetics from single molecule force spectroscopy measurements

Single molecule force spectroscopy is often used to study the dissociation of single molecules by applying mechanical force to the intermolecular bond. These measurements provide the kinetic parameters of dissociation. We present what to our knowledge is a new atomic force microscopy-based approach to obtain the activation energy of the association reaction and approximate grafting density of reactive receptors using the dependence of the probability to form molecular bonds on probe velocity when one of the interacting molecules is tethered by a flexible polymeric linker to the atomic force microscopy probe. Possible errors in the activation energy measured with this approach are considered and resulting corrections are included in the data analysis. This new approach uses the same experimental setup as traditional force spectroscopy measurements that quantify dissociation kinetics. We apply the developed methodology to measure the activation energy of biotin-streptavidin association (including a contribution from the steric factor) and obtain a value of 8 +/- 1 kT. This value is consistent with the association rate measured previously in solution. Comparison with the solution-derived activation energy indicates that kinetics of biotin-streptavidin binding is mainly controlled by the reaction step.

Detection and Identification of Bioanalytes with High Resolution LSPR Spectroscopy and MALDI Mass Spectrometry

High resolution localized surface plasmon resonance (HR-LSPR) sensors were combined with matrix assisted laser desorption ionization mass spectrometry (MALDI-MS) for the first time. LSPR sensors provide real-time label-free detection of molecular adsorption. Subsequent MALDI-MS analysis enables identification of the adsorbed molecules. This synergistic LSPR-MS approach was applied to the detection and identification of amyloid beta oligomers which play an important role in the molecular pathogenesis of Alzheimer's Disease.

Designing efficient zero calibration point for phase-sensitive surface plasmon resonance biosensing

This work is related to the development of phase-sensitive methodologies in Surface Plasmon Resonance (SPR) biosensing. We take advantage of a specific angular dependence of phase of light, reflected under SPR geometry, on parameters of the SPR-supporting metal, and propose a polarimetry-based methodology to easily determine the optimal calibration zero point, corresponding to the maximal phase sensitivity. The proposed methodology can significantly facilitate the calibration of the system in field and multi-channel sensing, broaden the dynamic range, as well as contribute to the development of feedback loops.

Chapter 4. Interactions of chemokines with glycosaminoglycans

Many proteins require interactions with cell surface glycosaminoglycans (GAGs) to exert their biologic activity. The effect of GAG binding on protein function ranges from essential roles in development, organogenesis, cell growth, cell adhesion, inflammation, tumorigenesis, and interactions with pathogens. A classic example is the role of GAGs in the interaction of fibroblast growth factors with their receptors, where GAGs play a role in specificity determination and control of receptor-ligand engagement. The other well-studied example involves the binding of antithrombin to heparin/heparan sulfate, which results in the inactivation of the coagulation cascade. In view of their specialized activity in cellular recruitment, chemokines interact with GAGs, minimally as a mechanism for localization of chemokines to specific anatomical spaces enabling them to act as directional signals for migrating cells. The biological relevance of these interactions has been recently demonstrated by functional characterization of mutants that are deficient in GAG binding. These mutants bind receptor normally in vitro but are unable to recruit cells in vivo. Observations like this have motivated investigations to identify GAG-binding epitopes on chemokines, the specificity and affinity of chemokines for different GAGs, the oligomerization of chemokines on GAGs, and the efficacy of GAG-binding mutants in the context of in vivo cell recruitment and animal models of disease. To this end, several techniques have been developed to measure the interactions of chemokines with GAGs. In this chapter we describe these various assays with particular reference to those that have been used to assess the binding of chemokines to GAGs and to define their epitopes. In the end, we believe both in vitro and in vivo characterization are absolutely necessary for understanding these interactions and their biologic relevance in the context of the whole organism.

Surface plasmon resonance (SPR) analysis of binding interactions of proteins in inner-ear sensory epithelia

Surface plasmon resonance is an optical technique utilized for detecting molecular interactions. Binding of a mobile molecule (analyte) to a molecule immobilized on a thin metal film (ligand) changes the refractive index of the film. The angle of extinction of light, reflected after polarized light impinges upon the film, is altered, monitored as a change in detector position for the dip in reflected intensity (the surface plasmon resonance phenomenon). Because the method strictly detects mass, there is no need to label the interacting components, thus eliminating possible changes of their molecular properties. We have utilized surface plasmon resonance to study the interaction of proteins of hair cells.

Nanoscale growth factor patterns by immobilization on a heparin-mimicking polymer

In this study, electrostatic interactions between sulfonate groups of an immobilized polymer and the heparin binding domains of growth factors important in cell signaling were exploited to nanopattern the proteins. Poly(sodium 4-styrenesulfonate-co-poly(ethylene glycol) methacrylate) (pSS-co-pPEGMA) was synthesized by reversible addition-fragmentation chain transfer (RAFT) polymerization using ethyl S-thiobenzoyl-2-thiopropionate as a chain transfer agent and 2,2'-azoisobutyronitrile (AIBN) as the initiator. The resulting polymer (1) was characterized by 1H NMR, GPC, FT-IR, and UV-vis and had a number average molecular weight (Mn) of 24,000 and a polydispersity index (PDI) of 1.17. The dithioester end group of 1 was reduced to the thiol, and the polymer was subsequently immobilized on a gold substrate. Binding of basic fibroblast growth factor (bFGF) and vascular endothelial growth factor (VEGF) to the polymer via the heparin binding domains was then confirmed by surface plasmon resonance (SPR). The interactions were stable at physiological salt concentrations. Polymer 1 was cross-linked onto silicon wafers using an electron beam writer forming micro- and nanopatterns. Resolutions of 100 nm and arbitrary nanoscale features such as concentric circles and contiguous squares and triangles were achieved. Fluorescence microscopy confirmed that bFGF and VEGF were subsequently immobilized to the polymer micro- and nanopatterns.

Surface Plasmon Resonance Monitoring of Cell Monolayer Integrity: Implication of Signaling Pathways Involved in Actin-Driven Morphological Remodeling

Morphological changes occurring in individual cells largely influence the physiological functions of various cell layers. The control of barrier function of epithelia and endothelia is a prime example of processes highly dependent on cellular morphology and cell layer integrity. Here, we applied the surface plasmon resonance (SPR) technique to the quantification of cellular activity of an epithelial cell monolayer stimulated by angiotensin II. The analysis of the SPR signal shows reproducible concentration-dependent biphasic responses after cell activation with angiotensin II. Phase-contrast and confocal microscopy imaging was performed to link the SPR signal to molecular and global morphological remodeling. The SPR signal was observed to be in relation with the rapid cell contraction and the subsequent cell spreading observed by phase-contrast microscopy. Additionally, the temporal redistribution of actin, observed by confocal microscopy after angiotensin II stimulation, was also found to be consistent with the SPR signal variation. The modulation of signaling pathways involved in actin-myosin driven cell contraction confirms the direct implication of actin structures in the SPR response. Additionally, we show that the intracellular calcium mobilization associated with angiotensin II stimulation did not produce any significant SPR signal variation. Altogether, our results demonstrate that SPR is a rapid label-free method to study cellular activity and molecular mechanisms implicated in the modulation of the integrity of a cell monolayer in relation to cytoskeleton remodeling with associated cell morphological changes.

Bayesian analysis of heterogeneity in the distribution of binding properties of immobilized surface sites

Once a homogeneous ensemble of a protein ligand is taken from solution and immobilized to a surface, for many reasons the resulting ensemble of surface binding sites to soluble analytes may be heterogeneous. For example, this can be due to the intrinsic surface roughness causing variations in the local microenvironment, nonuniform density distribution of polymeric linkers, or nonuniform chemical attachment producing different protein orientations and conformations. We previously described a computational method for determining the distribution of affinity and rate constants of surface sites from analysis of experimental surface binding data. It fully exploits the high signal/noise ratio and reproducibility provided by optical biosensor technology, such as surface plasmon resonance. Since the computational analysis is ill conditioned, the previous approach used a regularization strategy assuming a priori all binding parameters to be equally likely, resulting in the broadest possible parameter distribution consistent with the experimental data. We now extended this method in a Bayesian approach to incorporate the opposite assumption, i.e., that the surface sites a priori are expected to be uniform (as one would expect in free solution). This results in a distribution of binding parameters as close to monodispersity as possible given the experimental data. Using several model protein systems immobilized on a carboxymethyl dextran surface and probed with surface plasmon resonance, we show microheterogeneity of the surface sites in addition to broad populations of significantly altered affinity. The distributions obtained are highly reproducible. Immobilization conditions and the total surface density of immobilized sites can have a substantial impact on the functional distribution of the binding sites.

Stability and kinetics of G-quadruplex structures

In this review, we give an overview of recent literature on the structure and stability of unimolecular G-rich quadruplex structures that are relevant to drug design and for in vivo function. The unifying theme in this review is energetics. The thermodynamic stability of quadruplexes has not been studied in the same detail as DNA and RNA duplexes, and there are important differences in the balance of forces between these classes of folded oligonucleotides. We provide an overview of the principles of stability and where available the experimental data that report on these principles. Significant gaps in the literature have been identified, that should be filled by a systematic study of well-defined quadruplexes not only to provide the basic understanding of stability both for design purposes, but also as it relates to in vivo occurrence of quadruplexes. Techniques that are commonly applied to the determination of the structure, stability and folding are discussed in terms of information content and limitations. Quadruplex structures fold and unfold comparatively slowly, and DNA unwinding events associated with transcription and replication may be operating far from equilibrium. The kinetics of formation and resolution of quadruplexes, and methodologies are discussed in the context of stability and their possible biological occurrence.

Deciphering the key residues in Plasmodium falciparum beta-ketoacyl acyl carrier protein reductase responsible for interactions with Plasmodium falciparum acyl carrier protein

The type II fatty acid synthase (FAS) pathway of Plasmodium falciparum is a validated unique target for developing novel antimalarials, due to its intrinsic differences from the typeI pathway operating in humans. beta-Ketoacyl acyl carrier protein (ACP) reductase (FabG) performs the NADPH-dependent reduction of beta-ketoacyl-ACP to beta-hydroxyacyl-ACP, the first reductive step in the elongation cycle of fatty acid biosynthesis. In this article, we report intensive studies on the direct interactions of Plasmodium FabG and Plasmodium ACP in solution, in the presence and absence of its cofactor, NADPH, by monitoring the change in intrinsic fluorescence of P.falciparum FabG (PfFabG) and by surface plasmon resonance. To address the issue of the importance of the residues involved in strong, specific and stoichiometric binding of PfFabG to P.falciparum ACP (PfACP), we mutated Arg187, Arg190 and Arg230 of PfFabG. The activities of the mutants were assessed using both an ACP-dependent and an ACP-independent assay. The affinities of all the PfFabG mutants for acetoacetyl-ACP (the physiological substrate) were reduced to different extents as compared to wild-type PfFabG, but were equally active in biochemical assays with the substrate analog acetoacetyl-CoA. Kinetic analysis and studies of direct binding between PfFabG and PfACP confirmed the identification of Arg187 and Arg230 as critical residues for the PfFabG-PfACP interactions. Our studies thus reveal the significance of the positively charged/hydrophobic patch located adjacent to the active site cavities of PfFabG for interactions with PfACP.

Structural transitions of the RING1B C-terminal region upon binding the polycomb cbox domain

Polycomb group (PcG) proteins are required for maintaining cell identity and stem cell self-renewal. RING1B and Polycomb (Pc) are two components of a multiprotein complex called polycomb repression complex 1 (PRC1) that is essential for establishing and maintaining long-term repressed gene states. Here we characterize the interaction between the C-terminal region of RING1B (C-RING1B) and the Pc cbox domain. The C-RING1B-cbox interaction displays a 1:1 stoichiometry with dissociation constants ranging from 9.2 to 180 nM for the different Pc orthologues. NMR analysis of C-RING1B alone reveals line broadening. However, when it is in complex with the cbox domain, there is a striking change to the NMR spectrum indicative of conformational tightening. This conformational change may arise from the organization of the C-RING1B subdomains. The C-terminal regions of all PcG RING1 proteins are composed of two stretches of conserved sequences separated by a variable linker sequence. While the entire C-RING1B region is required for cbox binding, the N- and C-terminal halves of C-RING1B can be separated and are able to interact, suggesting the presence of an intramolecular interaction within C-RING1B. The flexibility within the C-RING1B structure allowing transitions between the intramolecular bound and unbound states may cause the broadened peaks of the C-RING1B NMR spectrum. Binding the cbox domain stabilizes C-RING1B, whereby broadening is eliminated. The presence of flexible regions could allow C-RING1B to bind a variety of different factors, ultimately recruiting RING1B and its associated PcG proteins to different genomic loci.

Humanized monoclonal antibodies derived from chimpanzee Fabs protect against Japanese encephalitis virus in vitro and in vivo

Japanese encephalitis virus (JEV)-specific Fab antibodies were recovered by repertoire cloning from chimpanzees initially immunized with inactivated JE-VAX and then boosted with attenuated JEV SA14-14-2. From a panel of 11 Fabs recovered by different panning strategies, three highly potent neutralizing antibodies, termed Fabs A3, B2, and E3, which recognized spatially separated regions on the virion, were identified. These antibodies reacted with epitopes in different domains: the major determinant for Fab A3 was Lys(179) (domain I), that for Fab B2 was Ile(126) (domain II), and that for Fab E3 was Gly(302) (domain III) in the envelope protein, suggesting that these antibodies neutralize the virus by different mechanisms. Potent neutralizing antibodies reacted with a low number of binding sites available on the virion. These three Fabs and derived humanized monoclonal antibodies (MAbs) exhibited high neutralizing activities against a broad spectrum of JEV genotype strains. Demonstration of antibody-mediated protection of JEV infection in vivo is provided using the mouse encephalitis model. MAb B2 was most potent, with a 50% protective dose (ED(50)) of 0.84 microg, followed by MAb A3 (ED(50) of 5.8 microg) and then MAb E3 (ED(50) of 24.7 microg) for a 4-week-old mouse. Administration of 200 microg/mouse of MAb B2 1 day after otherwise lethal JEV infection protected 50% of mice and significantly prolonged the average survival time compared to that of mice in the unprotected group, suggesting a therapeutic potential for use of MAb B2 in humans.

What is the biological relevance of the specific bond properties revealed by single-molecule studies?

During the last decade, many authors took advantage of new methodologies based on atomic force microscopy (AFM), biomembrane force probes (BFPs), laminar flow chambers or optical traps to study at the single-molecule level the formation and dissociation of bonds between receptors and ligands attached to surfaces. Experiments provided a wealth of data revealing the complexity of bond response to mechanical forces and the dependence of bond rupture on bond history. These results supported the existence of multiple binding states and/or reaction pathways. Also, single bond studies allowed us to monitor attachments mediated by a few bonds. The aim of this review is to discuss the impact of this new information on our understanding of biological molecules and phenomena. The following points are discussed: (i) which parameters do we need to know in order to predict the behaviour of an encounter between receptors and ligands, (ii) which information is actually yielded by single-molecule studies and (iii) is it possible to relate this information to molecular structure?

Characterizing protein-protein interactions by sedimentation velocity analytical ultracentrifugation

This unit introduces the basic principles and practice of sedimentation velocity analytical ultracentrifugation for the study of reversible protein interactions, such as the characterization of self-association, heterogeneous association, multi-protein complexes, binding stoichiometry, and the determination of association constants. The analytical tools described include sedimentation coefficient and molar mass distributions, multi-signal sedimentation coefficient distributions, Gilbert-Jenkins theory, different forms of isotherms, and global Lamm equation modeling. Concepts for the experimental design are discussed, and a detailed step-by-step protocol guiding the reader through the experiment and the data analysis is available as an Internet resource.

A lectin recognizes differential arrangements of O-glycans on mucin repeats

Interaction of Vicia villosa agglutinin-B4 (VVA-B4) to glycopeptides with O-linked GalNAc residues was investigated by surface plasmon resonance. The affinity was shown to be influenced by the arrangement of O-glycosylation sites on a peptide, PTTTPITTTTK, representing the tandem repeat of MUC2. The association rate constant was relatively high with a particular category of GalNAc-peptides in which more than three amino acid residues were placed between GalNAc-Thr residues. PTT( *)T( *)PITT( *)T( *)TK (T( *) indicates GalNAc-Thr) had the highest association rate constant among the glycopeptides tested. The dissociation rate constant was low in the peptides containing consecutive GalNAc residues and PT( *)TTPIT( *)T( *)T( *)TK was the lowest of the glycopeptides tested. Dissociation constant (K(D)), calculated as k(d)/k(a) was the lowest with PTT( *)T( *)PITT( *)T( *)TK. Therefore, the arrangement but not the quantity of GalNAc residues apparently determines the affinity between VVA-B4 and peptides with attached GalNAc residues.

Molecular and cellular approaches for the detection of protein-protein interactions: latest techniques and current limitations

Homotypic and heterotypic protein interactions are crucial for all levels of cellular function, including architecture, regulation, metabolism, and signaling. Therefore, protein interaction maps represent essential components of post-genomic toolkits needed for understanding biological processes at a systems level. Over the past decade, a wide variety of methods have been developed to detect, analyze, and quantify protein interactions, including surface plasmon resonance spectroscopy, NMR, yeast two-hybrid screens, peptide tagging combined with mass spectrometry and fluorescence-based technologies. Fluorescence techniques range from co-localization of tags, which may be limited by the optical resolution of the microscope, to fluorescence resonance energy transfer-based methods that have molecular resolution and can also report on the dynamics and localization of the interactions within a cell. Proteins interact via highly evolved complementary surfaces with affinities that can vary over many orders of magnitude. Some of the techniques described in this review, such as surface plasmon resonance, provide detailed information on physical properties of these interactions, while others, such as two-hybrid techniques and mass spectrometry, are amenable to high-throughput analysis using robotics. In addition to providing an overview of these methods, this review emphasizes techniques that can be applied to determine interactions involving membrane proteins, including the split ubiquitin system and fluorescence-based technologies for characterizing hits obtained with high-throughput approaches. Mass spectrometry-based methods are covered by a review by Miernyk and Thelen (2008; this issue, pp. 597-609). In addition, we discuss the use of interaction data to construct interaction networks and as the basis for the exciting possibility of using to predict interaction surfaces.

Quantitative FRAP in analysis of molecular binding dynamics in vivo

Fluorescence recovery after photobleaching (FRAP) reveals the dynamics of fluorescently tagged molecules within live cells. These molecular dynamics are governed by diffusion of the molecule and its in vivo binding interactions. As a result, quantitative estimates of the association and dissociation rates of binding can be extracted from the FRAP. This chapter describes a systematic procedure to acquire the FRAP data, and then fit it with appropriate mathematical models to estimate in vivo association and dissociation rates of binding. Also discussed are the applicability and limitations of the models, the utility of the estimated parameters, and the prospects for increased accuracy and confidence in the estimates.