Single Binding Event Research Articles

Heterodimer-based analysis of subunit and domain contributions to double-stranded RNA processing by Escherichia coli RNase III in vitro

Members of the RNase III family are the primary cellular agents of dsRNA (double-stranded RNA) processing. Bacterial RNases III function as homodimers and contain two dsRBDs (dsRNA-binding domains) and two catalytic sites. The potential for functional cross-talk between the catalytic sites and the requirement for both dsRBDs for processing activity are not known. It is shown that an Escherichia coli RNase III heterodimer that contains a single functional wt (wild-type) catalytic site and an inactive catalytic site (RNase III[E117A/wt]) cleaves a substrate with a single scissile bond with a k(cat) value that is one-half that of wt RNase III, but exhibits an unaltered K(m). Moreover, RNase III[E117A/wt] cleavage of a substrate containing two scissile bonds generates singly cleaved intermediates that are only slowly cleaved at the remaining phosphodiester linkage, and in a manner that is sensitive to excess unlabelled substrate. These results demonstrate the equal probability, during a single binding event, of placement of a scissile bond in a functional or nonfunctional catalytic site of the heterodimer and reveal a requirement for substrate dissociation and rebinding for cleavage of both phosphodiester linkages by the mutant heterodimer. The rate of phosphodiester hydrolysis by RNase III[E117A/wt] has the same dependence on Mg(2+) ion concentration as that of the wt enzyme, and exhibits a Hill coefficient (h) of 2.0+/-0.1, indicating that the metal ion dependence essentially reflects a single catalytic site that employs a two-Mg(2+)-ion mechanism. Whereas an E. coli RNase III mutant that lacks both dsRBDs is inactive, a heterodimer that contains a single dsRBD exhibits significant catalytic activity. These findings support a reaction pathway involving the largely independent action of the dsRBDs and the catalytic sites in substrate recognition and cleavage respectively.

The bacteriophage ϕ29 DNA polymerase

The bacteriophage ϕ29 DNA polymerase

Stochastic binding of Ca2+ ions in the dyadic cleft; continuous vs random walk description of diffusion

AbstractCa2+ signaling in the dyadic cleft in ventricular myocytes is fundamentally discrete and stochastic. In this paper we study the stochastic binding of single Ca2+ ions to receptors in the cleft using two different models of diffusion; a stochastic and discrete Random walk (RW) model, and a deterministic continuous model. We investigate if the latter model, together with a stochastic receptor model, can reproduce binding events registered in fully stochastic RW simulations. By evaluating the continuous model goodness‐of‐fit, we present evidences that it can. The large fluctuations in binding rate observed at the time level of single time steps are integrated and smoothed at the larger time scale of binding events, explaining the continuous model goodness‐of‐fit. With this we demonstrate that the stochasticity and discreteness of the Ca2+ signaling in the dyadic cleft, determined by single binding events, can be described with a deterministic model of Ca2+ diffusion together with a stochastic model of the binding events. Time consuming RW simulations can thus be avoided. We also present a new analytical model of bi‐molecular binding probabilities that is used in the RW simulations, and in the statistical analysis. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)

A Biochemical Model of Matrix Metalloproteinase 9 Activation and Inhibition

Matrix metalloproteinases (MMPs) are a class of extracellular and membrane-bound proteases involved in an array of physiological processes, including angiogenesis. We present a detailed computational model of MMP9 activation and inhibition. Our model is validated to existing biochemical experimental data. We determine kinetic rate constants for the processes of MMP9 activation by MMP3, MMP10, MMP13, and trypsin; inhibition by the tissue inhibitors of metalloproteinases (TIMPs) 1 and 2; and MMP9 deactivation. This computational approach allows us to investigate discrepancies in our understanding of the interaction of MMP9 with TIMP1. Specifically, we find that inhibition due to a single binding event cannot describe MMP9 inhibition by TIMP1. Temporally accurate biphasic inhibition requires either an additional isomerization step or a second lower affinity isoform of MMP9. We also theoretically characterize the MMP3/TIMP2/pro-MMP9 and MMP3/TIMP1/pro-MMP9 systems. We speculate that these systems differ significantly in their time scales of activation and inhibition such that MMP9 is able to temporarily overshoot its final equilibrium value in the latter. Our numerical simulations suggest that the ability of pro-MMP9 to complex TIMP1 increases this overshoot. In all, our analysis serves as a summary of existing kinetic data for MMP9 and a foundation for future models utilizing MMP9 or other MMPs under physiologically well defined microenvironments.

Particulate and soluble Eu(III)-chelates as donor labels in homogeneous fluorescence resonance energy transfer based immunoassay

Many well-established homogeneous separation free immunoassays rely on particulate label technologies. Particles generally contain a high concentration of the embedded label and they have a large surface area, which enables conjugation of a large amount of protein per particle. Eu(III)-chelate dyed nanoparticles have been successfully used as labels in heterogeneous and homogeneous immunoassays. In this study, we compared the characteristics of two homogeneous competitive immunoassays using either soluble Eu(III)-chelates or polystyrene particles containing Eu(III)-chelates as donors in a fluorescence resonance energy transfer based assay. The use of the particulate label significantly increased the obtained sensitized emission, which was generated by a single binding event. This was due to the extremely high specific activity of the nanoparticle label and also in some extent the longer Förster radius between the donor and the acceptor. The amount of the binder protein used in the assay could be decreased by 10-fold without impairing the obtainable sensitized emission, which subsequently led to improved assay sensitivity. The optimized assay using particulate donor had the lowest limit of detection (calculated using 3 × S.D. of the 0 nM standard) 50 pM of estradiol in the assay well, which was approximately 20-fold more sensitive than assays using soluble Eu(III)-chelates.

Crystal Structure of Bacteriophage T4 5′ Nuclease in Complex with a Branched DNA Reveals How Flap Endonuclease-1 Family Nucleases Bind Their Substrates

Bacteriophage T4 RNase H, a flap endonuclease-1 family nuclease, removes RNA primers from lagging strand fragments. It has both 5' nuclease and flap endonuclease activities. Our previous structure of native T4 RNase H (PDB code 1TFR) revealed an active site composed of highly conserved Asp residues and two bound hydrated magnesium ions. Here, we report the crystal structure of T4 RNase H in complex with a fork DNA substrate bound in its active site. This is the first structure of a flap endonuclease-1 family protein with its complete branched substrate. The fork duplex interacts with an extended loop of the helix-hairpin-helix motif class 2. The 5' arm crosses over the active site, extending below the bridge (helical arch) region. Cleavage assays of this DNA substrate identify a primary cut site 7-bases in from the 5' arm. The scissile phosphate, the first bond in the duplex DNA adjacent to the 5' arm, lies above a magnesium binding site. The less ordered 3' arm reaches toward the C and N termini of the enzyme, which are binding sites for T4 32 protein and T4 45 clamp, respectively. In the crystal structure, the scissile bond is located within the double-stranded DNA, between the first two duplex nucleotides next to the 5' arm, and lies above a magnesium binding site. This complex provides important insight into substrate recognition and specificity of the flap endonuclease-1 enzymes.

Tandem Dye Acceptor Used To Enhance Upconversion Fluorescence Resonance Energy Transfer in Homogeneous Assays

In fluorescence resonance energy transfer (FRET)-based assays, spectral separation of acceptor emission from donor emission is a common problem affecting the assay sensitivity. The challenge derives from small Stokes shifts characteristic to conventional fluorescent dyes resulting in leakage of donor emission to the measurement window intended only to collect the acceptor emission. We have studied a FRET-based homogeneous bioaffinity assay utilizing a tandem dye acceptor with a large pseudo-Stokes shift (139 nm). The tandem dye was constructed using B-phycoerythrin as an absorber and multiple Alexa Fluor 680 dyes as emitters. As a donor, we employed upconverting phosphor particles, which uniquely emit at visible wavelengths under low-energy infrared excitation enabling the fluorescence measurements free from autofluorescence even without time-resolved detection. With the tandem dye, it was possible to achieve four times higher signal from a single binding event compared to the conventional Alexa Fluor 680 dye alone. Tandem dyes are widely used in cytometry and other multiplex purposes, but their applications can be expanded to fluorescence-based homogeneous assays. Both the optimal excitation and emission wavelengths of tandem dye can be tuned to a desired region by choosing appropriate fluorophores enabling specifically designed acceptor dyes with large Stokes shift.

Specific Protein Domains Mediate Cooperative Assembly of HuR Oligomers on AU-rich mRNA-destabilizing Sequences

The RNA-binding factor HuR is a ubiquitously expressed member of the Hu protein family that binds and stabilizes mRNAs containing AU-rich elements (AREs). Hu proteins share a common domain organization of two tandemly arrayed RNA recognition motifs (RRMs) near the N terminus, followed by a basic hinge domain and a third RRM near the C terminus. In this study, we engineered recombinant wild-type and mutant HuR proteins lacking affinity tags to characterize their ARE-binding properties. Using combinations of electrophoretic mobility shift and fluorescence anisotropy-based binding assays, we show that HuR can bind ARE substrates as small as 13 nucleotides with low nanomolar affinity, but forms cooperative oligomeric protein complexes on ARE substrates of at least 18 nucleotides in length. Analyses of deletion mutant proteins indicated that RRM3 does not contribute to high affinity recognition of ARE substrates, but is required for cooperative assembly of HuR oligomers on RNA. Finally, the hinge domain between RRM2 and RRM3 contributes significant binding energy to HuR.ARE complex formation in an ARE length-dependent manner. The hinge does not enhance RNA-binding activity by increased ion pair formation despite extensive positive charge within this region, and it does not thermodynamically stabilize protein folding. Together, the results define distinct roles for the HuR hinge and RRM3 domains in formation of cooperative HuR.ARE complexes in solution.

Translesion synthesis in Escherichia coli: Lessons from the NarI mutation hot spot

Duplication of DNA containing damaged bases is a challenge to DNA polymerases that normally replicate with high speed, high accuracy and high processivity undamaged templates only. When a replicative DNA polymerase encounters a chemically altered base that it is unable to copy, a process called translesion synthesis (TLS) takes place during which the replicative polymerase is transiently replaced by a so-called specialized or lesion bypass polymerase. In addition to the central players that are the replicative and translesion DNA polymerases, TLS pathways involve accessory factors such as the general replication processivity factor (i.e. the beta-clamp in prokaryotes and PCNA in eukaryotes). In Escherichia coli, besides the beta-clamp, RecA plays a fundamental role as a co-factor of Pol V the major bypass polymerase in this organism. An integrated view of TLS pathways necessarily requires both genetic and biochemical studies. In this review we will attempt to summarize the insights into TLS gained over the last 25 years by studying a frameshift mutation hot spot, the NarI site. This site was initially discovered by serendipity when establishing a forward mutation spectrum induced by a chemical hepatocarcinogen, N-2-acetylaminofluorene (AAF). Indeed, this chemical carcinogen covalently binds to DNA forming adducts with guanine residues. When bound to G* in the NarI site, 5′-GGCG*CC-, AAF induces the loss of the G*pC dinucleotide at a frequency that is ≈10 7-fold higher than the spontaneous frequency. In vivo studies showed that the NarI mutation hot spot is neither restricted to the NarI sequence itself, nor to the carcinogen AAF. Instead, the hot spot requires a sequence containing at least two GpC repeats and any of a family of aromatic amides and nitro aromatic compounds that form a large class of human carcinogens. Genetic analysis initially revealed that the NarI frameshift pathway is SOS dependent but umuDC (i.e. Pol V) independent. More recently, DNA Pol II was identified as the enzyme responsible of this frameshift pathway. Concurrently the AAF adduct in the NarI site can be bypassed in an error-free way by Pol V. The NarI site thus offers a unique possibility to study the interplay between two specialized DNA polymerases, Pol II and Pol V, that can both extend replication intermediates formed when the replicative Pol III dissociates in the vicinity of the damage. Full reconstitution of the two pathways led us to highlight a key feature for TLS pathways, namely that it is critical the specialized DNA polymerase synthesizes, during the course of a single binding event, a patch of DNA synthesis (TLS patch) that is long enough as to “hide the lesion induced distortion” from the proofreading activity upon reloading of the replicative DNA polymerase (or any exonuclease that may get access to the primer when the specialized DNA polymerase detaches). The beta-clamp, to which all DNA polymerases bind, plays a critical role in allowing the specialized DNA polymerases to synthesize TLS patches that are long enough to resist such “external proofreading” activities.

Structural and Biochemical Investigation of the Role in Proofreading of a β Hairpin Loop Found in the Exonuclease Domain of a Replicative DNA Polymerase of the B Family

Replicative DNA polymerases, as exemplified by the B family polymerases from bacteriophages T4 and RB69, not only replicate DNA but also have the ability to proofread misincorporated nucleotides. Because the two activities reside in separate protein domains, polymerases must employ a mechanism that allows for efficient switching of the primer strand between the two active sites to achieve fast and accurate replication. Prior mutational and structural studies suggested that a beta hairpin structure located in the exonuclease domain of family B polymerases might play an important role in active site switching in the event of a nucleotide misincorporation. We show that deleting the beta hairpin loop in RB69 gp43 affects neither polymerase nor exonuclease activities. Single binding event studies with mismatched primer termini, however, show that the beta hairpin plays a role in maintaining the stability of the polymerase/DNA interactions during the binding of the primer DNA in the exonuclease active site but not on the return of the corrected primer to the polymerase active site. In addition, the deletion variant showed a more stable incorporation of a nucleotide opposite an abasic site. Moreover, in the 2.4 A crystal structure of the beta hairpin deletion variant incorporating an A opposite a templating furan, all four molecules in the crystal asymmetric unit have DNA in the polymerase active site, despite the presence of DNA distortions because of the misincorporation, confirming that the primer strand is not stably bound within the exonuclease active site in the absence of the beta hairpin loop.

RecFOR proteins are essential for Pol V-mediated translesion synthesis and mutagenesis

When the replication fork moves through the template DNA containing lesions, daughter-strand gaps are formed opposite lesion sites. These gaps are subsequently filled-in either by translesion synthesis (TLS) or by homologous recombination. RecA filaments formed within these gaps are key intermediates for both of the gap-filling pathways. For instance, Pol V, the major lesion bypass polymerase in Escherichia coli, requires a functional interaction with the tip of the RecA filament. Here, we show that all three recombination mediator proteins RecFOR are needed to build a functionally competent RecA filament that supports efficient Pol V-mediated TLS in the presence of ssDNA-binding protein (SSB). A positive contribution of RecF protein to Pol V lesion bypass is demonstrated. When Pol III and Pol V are both present, Pol III imparts a negative effect on Pol V-mediated lesion bypass that is counteracted by the combined action of RecFOR and SSB. Mutations in recF, recO or recR gene abolish induced mutagenesis in E. coli.

Aptamer-Conjugated Nanoparticles for Selective Collection and Detection of Cancer Cells

We have developed a method for the rapid collection and detection of leukemia cells using a novel two-nanoparticle assay with aptamers as the molecular recognition element. An aptamer sequence was selected using a cell-based SELEX strategy in our laboratory for CCRF-CEM acute leukemia cells that, when applied in this method, allows for specific recognition of the cells from complex mixtures including whole blood samples. Aptamer-modified magnetic nanoparticles were used for target cell extraction, while aptamer-modified fluorescent nanoparticles were simultaneously added for sensitive cell detection. Combining two types of nanoparticles allows for rapid, selective, and sensitive detection not possible by using either particle alone. Fluorescent nanoparticles amplify the signal intensity corresponding to a single aptamer binding event, resulting in improved sensitivity over methods using individual dye-labeled probes. In addition, aptamer-modified magnetic nanoparticles allow for rapid extraction of target cells not possible with other separation methods. Fluorescent imaging and flow cytometry were used for cellular detection to demonstrate the potential application of this method for medical diagnostics.

RecJ exonuclease: substrates, products and interaction with SSB

The RecJ exonuclease from Escherichia coli degrades single-stranded DNA (ssDNA) in the 5′–3′ direction and participates in homologous recombination and mismatch repair. The experiments described here address RecJ's substrate requirements and reaction products. RecJ complexes on a variety of 5′ single-strand tailed substrates were analyzed by electrophoretic mobility shift in the absence of Mg2+ ion required for substrate degradation. RecJ required single-stranded tails of 7 nt or greater for robust binding; addition of Mg2+ confirmed that substrates with 5′ tails of 6 nt or less were poor substrates for RecJ exonuclease. RecJ is a processive exonuclease, degrading ∼1000 nt after a single binding event to single-strand DNA, and releases mononucleotide products. RecJ is capable of degrading a single-stranded tail up to a double-stranded junction, although products in such reactions were heterogeneous and RecJ showed a limited ability to penetrate the duplex region. RecJ exonuclease was equally potent on 5′ phosphorylated and unphosphorylated ends. Finally, DNA binding and nuclease activity of RecJ was specifically enhanced by the pre-addition of ssDNA-binding protein and we propose that this specific interaction may aid recruitment of RecJ.

APC's order of business

The anaphase-promoting complex (APC) has a hectic schedule. From mitosis through the G1/S transition, the APC is busily targeting cell cycle regulators for degradation. Yet it must keep an ordered degradation schedule for proper cell cycle progression. Now, results from Michael Rape, Sashank Reddy, and Marc Kirschner (Harvard Medical School, Boston, MA) suggest that the APC lets its substrates determine their own death order. The degradation order of cell cycle regulators correlates with the kinetics of their ubiquitination by the APC. In vitro, securin—one of the first of the APC's substrates to be degraded—rapidly obtained full-length polyubiquitin chains, which are required for proteasome recognition. The late-degraded substrates took much longer for multiubiquitination. The kinetics reflects differences in substrate processivity—that is, how many ubiquitins are added in a single APC binding event. The most processive substrate outcompeted the rest in vitro for polyubiquitination and thus degradation. “Why do we need so many ubiquitins in the first place?” asks Kirschner. “Isn't it overboard?” Not according to the group's new results. “We argue that by having multiple steps, chances for things to come off, you could accentuate very small differences in kinetic processes.” Differences are probably further compounded by deubiquitinating enzymes. Nonprocessive substrates easily lost ubiquitin moieties upon dissociation from the APC. Reference: Rape, M., et al. 2006. Cell. 124:89–103. [PubMed]

The Processivity of Multiubiquitination by the APC Determines the Order of Substrate Degradation

The anaphase-promoting complex (APC) coordinates mitosis and G1 by sequentially promoting the degradation of key cell-cycle regulators. Following the degradation of its substrates in G1, the APC catalyzes the autoubiquitination of its E2 UbcH10. This stabilizes cyclin A and allows it to inactivate APC(Cdh1). How the APC establishes this complex temporal sequence of ubiquitinations, referred to as substrate ordering, is not understood. Here we show that substrate ordering depends on the relative processivity of substrate multiubiquitination by the APC. Processive substrates obtain ubiquitin chains in a single APC binding event. The multiubiquitination of distributive substrates requires multiple rounds of APC binding, which render it sensitive to lower APC concentrations, competition by processive substrates, and deubiquitination. Consequently, more processive substrates are preferentially multiubiquitinated in vitro and degraded earlier in vivo. The processivity of multiubiquitination is strongly influenced by the D box within the substrate, suggesting that substrate ordering is established by a mechanism intrinsic to APC and its substrates and similar to kinetic proofreading.

Interaction of the Ty3 Reverse Transcriptase Thumb Subdomain with Template-Primer

Amino acid sequence alignment was used to identify the putative thumb subdomain of reverse transcriptase (RT) from the Saccharomyces cerevisiae long terminal repeat-containing retrotransposon Ty3. The counterpart to helix alphaH of human immunodeficiency virus type 1 (HIV-1) RT, which mediates important interactions with a duplex nucleic acid approximately 3-6 bp behind the DNA polymerase catalytic center, was identified between amino acids 290 and 298 of the Ty3 enzyme. The consequences of substituting Ty3 RT Gln290, Phe292, Gly294, Asn297, and Tyr298 (the counterparts of HIV-1 RT Gln258, Leu260, Gly262, Asn265, and Trp266, respectively) for both DNA polymerase and RNase H activities were examined. DNA-dependent DNA synthesis was evaluated on unmodified substrates and on duplexes containing targeted insertion of locked nucleic acid analogs and abasic lesions in either the template or primer. Based on this combined strategy, our data suggest an interaction of Ty3 RT Tyr298 with primer nucleotide -3, Gly294 with primer nucleotide -4, and Asn297 with template nucleotide -6. Substitution of Ala for Gln290 was well tolerated, despite the high degree of conservation at this position. Mutations in the thumb subdomain of Ty3 also affected RNase H activity, suggesting a closer spatial relationship between its N- and C-terminal catalytic centers compared with HIV-1 RT.

Kinetic Stabilization of an Oligomeric Protein by a Single Ligand Binding Event

Protein native state stabilization imposed by small molecule binding is an attractive strategy to prevent the misfolding and misassembly processes associated with amyloid diseases. Transthyretin (TTR) amyloidogenesis requires rate-limiting tetramer dissociation before misassembly of a partially denatured monomer ensues. Selective stabilization of the native TTR tetramer over the dissociative transition state by small molecule binding to both thyroxine binding sites raises the kinetic barrier of tetramer dissociation, preventing amyloidogenesis. Assessing the amyloidogenicity of a TTR tetramer having only one amyloidogenesis inhibitor (I) bound is challenging because the two small molecule binding constants are generally not distinct enough to allow for the exclusive formation of TTR.I in solution to the exclusion of TTR.I(2) and unliganded TTR. Herein, we report a method to tether one fibril formation inhibitor to TTR by disulfide bond formation. Occupancy of only one of the two thyroxine binding sites is sufficient to inhibit tetramer dissociation in 6.0 M urea and amyloidogenesis under acidic conditions by imposing kinetic stabilization on the entire tetramer. The sufficiency of single occupancy for stabilizing the native state of TTR provides the incentive to search for compounds displaying striking negative binding cooperativity (e.g., K(d1) in nanomolar range and K(d2) in the micromolar to millimolar range), enabling lower doses of inhibitor to be employed in the clinic, mitigating potential side effects.

Detection of HSP60 on the membrane surface of stressed human endothelial cells by atomic force and confocal microscopy

The highly conserved and ubiquitous heat shock proteins (HSP) are essential for the cellular homeostasis and efficiently trigger cellular responses to stress conditions. Both microbial and human HSP act as dominant antigens in numerous infectious and autoimmune diseases such as atherosclerosis, inducing a strong immune-inflammatory response. In the present study, the surface localization of HSP60 on stressed and unstressed human umbilical venous endothelial cells (HUVECs) was investigated using sensitive high resolution microscopy methods and flow cytometry. Confocal laser scanning microscopy (CLSM) revealed an increase of HSP60 in the mitochondria and on the surface of heat-stressed living and fixed HUVECs compared to unstressed cells. Atomic force microscopy (AFM), which has developed as sensitive surface-probe technique in biology, confirmed the presence of HSP60 on the membrane of stressed cells at an even higher lateral resolution by detecting specific single molecule binding events between the monoclonal antibody AbII-13 tethered to AFM tips and HSP60 molecules on cells. The interaction force (force required to break a single AbII-13/HSP60 bond) was 59+/-2 pN, which correlated nicely to the 51+/-1 pN measured with isolated HSP60 attached to mica surfaces. Overall, we found clear evidence for the occurrence of HSP60 on the surface of stressed HUVECs in a very similar patchy distribution pattern in living and fixed cells. The relevance of our findings with respect to the role of HSP60 in atherogenesis is discussed.

2P258 リアノジン-リアノジン受容体チャネル結合の電気・光学的1分子同時測定(生体膜・人工膜 A) 構造・物性))

2P258 リアノジン-リアノジン受容体チャネル結合の電気・光学的1分子同時測定(生体膜・人工膜 A) 構造・物性))

Novel assay format permitting the prolonged use of regeneration-based sensor chip technology

A polyclonal antibody raised against morphine-3-glucuronide (M3G, the main metabolite of heroin and morphine) was used in the development of a novel assay format using a surface plasmon resonance (SPR)-based biosensor. Previously developed assays have generated calibration curves based on differences in the quantity of response units binding to the surface of a chip coated with the analyte. The novel assay described here was based on the development of a standard curve using the slope of a series of consecutive binding interactions. Using this format, regeneration between each assay cycle was no longer required. This increased the useable life span of the chip surface and, as a result, decreased the cost associated with the assay. Thus, at least 15 binding interactions could be carried out before the saturation of antibody on the surface of the chip caused the response to deviate significantly from linearity. After 15 nonregenerated binding interactions, the slope still remained within 1.5% of the slope after a single binding event. Analysis time, and the sample volumes required were also markedly decreased while sensitivity was enhanced. The inhibition assay developed had a detection range of 270 to 17,500 pg ml −1.