protein-DNA Binding Affinity Research Articles

Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs

p53 binds as a tetramer to DNA targets consisting of two decameric half-sites separated by a variable spacer. Here we present high-resolution crystal structures of complexes between p53 core-domain tetramers and DNA targets consisting of contiguous half-sites. In contrast to previously reported p53-DNA complexes that show standard Watson-Crick base pairs, the newly reported structures show noncanonical Hoogsteen base-pairing geometry at the central A-T doublet of each half-site. Structural and computational analyses show that the Hoogsteen geometry distinctly modulates the B-DNA helix in terms of local shape and electrostatic potential, which, together with the contiguous DNA configuration, results in enhanced protein-DNA and protein-protein interactions compared to noncontiguous half-sites. Our results suggest a mechanism relating spacer length to protein-DNA binding affinity. Our findings also expand the current understanding of protein-DNA recognition and establish the structural and chemical properties of Hoogsteen base pairs as the basis for a novel mode of sequence readout.

Gold-Nanoparticle-Based Assay for Instantaneous Detection of Nuclear Hormone Receptor−Response Elements Interactions

Gold nanoparticles (AuNPs) are widely used as colorimetric probes for biosensing, relying on their unique particle size-dependent and/or interparticle distance-dependent extinction spectrum and solution color. Herein, we describe an AuNP-based colorimetric assay to detect binding interactions between nuclear hormone receptors and their corresponding DNA-binding elements, particularly the human estrogen receptors (ERalpha and ERbeta) and their cognate estrogen response elements (EREs). We found that the protein-DNA (ER-ERE) complexes can stabilize citrate anion-capped AuNPs against salt-induced aggregation to a larger extent than the protein (ER) or the DNA (ERE) alone, due to their unique molecular size and charge properties that provide a strong electrosteric protection. Moreover, our results show that the extent of stabilization is sequence-dependent and can distinguish a single base variation in the ERE associated with minor changes in protein-DNA binding affinity. With this assay, many important parameters of protein-DNA binding events (e.g., sequence selectivity, distinct DNA binding properties of protein subtypes, binding stoichiometry, and sequence-independent transient binding) can be determined instantly without using labels, tedious sample preparations, and sophisticated instrumentation. These benefits, in particular the high-throughput potential, could enable this assay to become the assay of choice to complement conventional techniques for large scale characterization of protein-DNA interactions, a key aspect in biological research.

Prediction of kinetic parameters from DNA-binding site sequences for modeling global transcription dynamics in Escherichia coli

The majority of dynamic gene regulatory network (GRN) models are comprised of only a few genes and do not take multiple transcription regulation into account. The models are conceived in this way in order to minimize the number of kinetic parameters. In this paper, we propose a new approach for predicting kinetic parameters from DNA-binding site sequences by correlating the protein–DNA-binding affinities with nucleotide sequence conservation. We present the dynamic modeling of the cra modulon transcription in Escherichia coli during glucose-limited fed-batch cultivation. The concentration of the Cra regulator protein inhibitor, fructose 1,6-bis(phosphate), decreases sharply, eventually leading to the repression of transcription. Total RNA concentration data indicate a strong regulation of transcription through the availability of RNA polymerase. A critical assessment of the results of the model simulations supports this finding. This new approach for the prediction of transcription dynamics may improve the metabolic engineering of gene regulation processes.

Gamma-Linolenic Acid Inhibits Inflammatory Responses by Regulating NF-κB and AP-1 Activation in Lipopolysaccharide-Induced RAW 264.7 Macrophages

Gamma linolenic acid (GLA) is a member of the n-6 family of polyunsaturated fatty acids and can be synthesized from linoleic acid (LA) by the enzyme delta-6-desaturase. The therapeutic values of GLA supplementation have been documented, but the molecular mechanism behind the action of GLA in health benefits is not clear. In this study, we assessed the effect of GLA with that of LA on lipopolysaccharide (LPS)-induced inflammatory responses and further explored the molecular mechanism underlying the pharmacological properties of GLA in mouse RAW 264.7 macrophages. GLA significantly inhibited LPS-induced protein expression of inducible nitric oxide synthase, pro-interleukin-1beta, and cyclooxygenase-2 as well as nitric oxide production and the intracellular glutathione level. LA was less potent than GLA in inhibiting LPS-induced inflammatory mediators. Both GLA and LA treatments dramatically inhibited LPS-induced IkappaB-alpha degradation, IkappaB-alpha phosphorylation, and nuclear p65 protein expression. Moreover, LPS-induced nuclear factor-kappaB (NF-kappaB) and activator protein-1 (AP-1) nuclear protein-DNA binding affinity and reporter gene activity were significantly decreased by LA and GLA. Exogenous addition of GLA but not LA significantly reduced LPS-induced expression of phosphorylated extracellular signal-regulated kinase (ERK) 1/2 and c-Jun N-terminal kinase (JNK)-1. Our data suggest that GLA inhibits inflammatory responses through inactivation of NF-kappaB and AP-1 by suppressed oxidative stress and signal transduction pathway of ERK and JNK in LPS-induced RAW 264.7 macrophages.

An all‐atom knowledge‐based energy function for protein‐DNA threading, docking decoy discrimination, and prediction of transcription‐factor binding profiles

How to make an accurate representation of protein-DNA interaction by an energy function is a long-standing unsolved problem in structural biology. Here, we modified a statistical potential based on the distance-scaled, finite ideal-gas reference state so that it is optimized for protein-DNA interactions. The changes include a volume-fraction correction to account for unmixable atom types in proteins and DNA in addition to the usage of a low-count correction, residue/base-specific atom types, and a shorter cutoff distance for protein-DNA interactions. The new statistical energy functions are tested in threading and docking decoy discriminations and prediction of protein-DNA binding affinities and transcription-factor binding profiles. The results indicate that new proposed energy functions are among the best in existing energy functions for protein-DNA interactions. The new energy functions are available as a web-server called DDNA 2.0 at http://sparks.informatics.iupui.edu. The server version was trained by the entire 212 protein-DNA complexes.

Mitogen activated protein kinase‐dependent inhibition of osteocalcin gene expression by transforming growth factor‐β1

TGF-beta (transforming growth factor-beta) plays a key role in osteoblast differentiation and bone development. While the ability of TGF-beta to inhibit the expression of osteoblast differentiation genes has been well documented, the mechanism of this inhibition is not yet completely characterized. Runx2, a transcription factor necessary for expression of osteoblast differentiation genes is a central target of inhibition by TGF-beta. In this study, we found that TGF-beta1 inhibits expression of osteoblast differentiation genes without altering expression of Runx2. Transient transfection experiments determined that TGF-beta1 inhibited osteocalcin promoter activity and this effect is mediated through Runx2. We further identified that there was no change in protein expression, cellular localization, or DNA binding affinity of Runx2 after TGF-beta1-treatment of osteoblasts, suggesting that Runx2 undergoes post-translational modifications following TGF-beta1 treatment. Co-immunoprecipitation experiments identified increased phosphorylation of Runx2 when differentiating osteoblasts were treated with TGF-beta1. Mitogen activated protein kinase (MAPK) inhibitors relieved the TGF-beta1-inhibitory effect of Runx2-mediated osteocalcin expression. Thus, our results suggest that TGF-beta1-inhibition of osteoblast differentiation is dependent on the MAPK pathway and this effect is most likely mediated by post-translational modification of Runx2 such as phosphorylation rather than other regulatory mechanisms.

Genome-wide identification ofin vivoprotein-DNA binding sites from ChIP-Seq data

ChIP-Seq, which combines chromatin immunoprecipitation (ChIP) with ultra high-throughput massively parallel sequencing, is increasingly being used for mapping protein–DNA interactions in-vivo on a genome scale. Typically, short sequence reads from ChIP-Seq are mapped to a reference genome for further analysis. Although genomic regions enriched with mapped reads could be inferred as approximate binding regions, short read lengths (∼25–50 nt) pose challenges for determining the exact binding sites within these regions. Here, we present SISSRs (Site Identification from Short Sequence Reads), a novel algorithm for precise identification of binding sites from short reads generated from ChIP-Seq experiments. The sensitivity and specificity of SISSRs are demonstrated by applying it on ChIP-Seq data for three widely studied and well-characterized human transcription factors: CTCF (CCCTC-binding factor), NRSF (neuron-restrictive silencer factor) and STAT1 (signal transducer and activator of transcription protein 1). We identified 26 814, 5813 and 73 956 binding sites for CTCF, NRSF and STAT1 proteins, respectively, which is 32, 299 and 78% more than that inferred previously for the respective proteins. Motif analysis revealed that an overwhelming majority of the identified binding sites contained the previously established consensus binding sequence for the respective proteins, thus attesting for SISSRs’ accuracy. SISSRs’ sensitivity and precision facilitated further analyses of ChIP-Seq data revealing interesting insights, which we believe will serve as guidance for designing ChIP-Seq experiments to map in vivo protein–DNA interactions. We also show that tag densities at the binding sites are a good indicator of protein–DNA binding affinity, which could be used to distinguish and characterize strong and weak binding sites. Using tag density as an indicator of DNA-binding affinity, we have identified core residues within the NRSF and CTCF binding sites that are critical for a stronger DNA binding.

Regulation of Cardiac Specific nkx2.5 Gene Activity by Small Ubiquitin-like Modifier

The cardiac specific homeobox gene nkx2.5, a member of the nk-2 class family, plays a central role in cardiogenesis and is a target of the small ubiquitin-like modifier (SUMO). Nkx2.5 was modified by SUMO on its 51st amino acid, a lysine residue conserved across species but absent in other nk-2 members. Conversion of this lysine to an arginine (K51R) substantially reduced Nkx2.5 DNA binding and also its transcriptional activity. Unexpectedly, mutant K51R was targeted by ubiquitin. E3 ligase PIAS proteins PIAS1, PIASx, and PIASy, but not PIAS3, enhanced SUMO-1 attachment to Nkx2.5 on the primary SUMO acceptor site. SUMO-2 linkage to Nkx2.5 was catalyzed only by PIASx and not by other PIAS proteins. SUMO conjugation stabilized the formation of Nkx2.5-containing complexes that led to robust transcriptional activation. Thus, SUMO modification serves as a positive regulator for Nkx2.5 transcriptional activity.

Transcription Factor SIX5 Is Mutated in Patients with Branchio-Oto-Renal Syndrome

Branchio-oto-renal syndrome (BOR) is an autosomal dominant developmental disorder characterized by the association of branchial arch defects, hearing loss, and renal anomalies. Mutations in EYA1 are known to cause BOR. More recently, mutations in SIX1, which interacts with EYA1, were identified as an additional cause of BOR. A second member of the SIX family of proteins, unc-39 (SIX5), has also been reported to directly interact with eya-1 in Caenorhabditis elegans. We hypothesized that this interaction would be conserved in humans and that interactors of EYA1 represent good candidate genes for BOR. We therefore screened a cohort of 95 patients with BOR for mutations in SIX5. Four different heterozygous missense mutations were identified in five individuals. Functional analyses of these mutations demonstrated that two mutations affect EYA1-SIX5 binding and the ability of SIX5 or the EYA1-SIX5 complex to activate gene transcription. We thereby identified heterozygous mutations in SIX5 as a novel cause of BOR.

Using reverse electrophoretic mobility shift assay to measure and compare protein–DNA binding affinities

Using reverse electrophoretic mobility shift assay to measure and compare protein–DNA binding affinities

Evaluating the Binding Affinities of NF-<I>κ</I>B Protein to the Single-Nucleotide Mismatch DNA Binding Sites by Using Double-Stranded DNA Microarray

Protein-DNA sequence-specific interaction plays an essential role in many biological processes. Here we immobilized a series of double-stranded DNA probes on an agarose coated slide to investigate the binding affinity of NF-kappaB p50 homodimer to the single-nucleotide mismatches (G<-->A or T<-->C) of the 10 base pair (bp) protein binding sites. The results demonstrated that the nucleotides at different positions contribute differently to the p50p50/DNA binding interaction. Within the 10 bp binding sites, the 5tG or 6cA mismatch has less effect on the protein-DNA binding affinity. Even the 5tG mismatch may have the ability to enhance the protein-DNA interaction (5t/w = 1.07). On the other hand, the 7cA or 10tG mismatch blocked the protein-DNA interaction more significantly than other six single-nucleotide mismatches. (7c/W = 0.37, 10t/W = 0.35). It also indicated that the duplex DNA probes immobilized on the agarose-coated surface were apt to be recognized by DNA-binding proteins, and this method would provide a reliable method for exploring the binding affinities of DNA-binding proteins with a larger number of DNA targets.

Protein-DNA binding specificity predictions with structural models

Protein–DNA interactions play a central role in transcriptional regulation and other biological processes. Investigating the mechanism of binding affinity and specificity in protein–DNA complexes is thus an important goal. Here we develop a simple physical energy function, which uses electrostatics, solvation, hydrogen bonds and atom-packing terms to model direct readout and sequence-specific DNA conformational energy to model indirect readout of DNA sequence by the bound protein. The predictive capability of the model is tested against another model based only on the knowledge of the consensus sequence and the number of contacts between amino acids and DNA bases. Both models are used to carry out predictions of protein–DNA binding affinities which are then compared with experimental measurements. The nearly additive nature of protein–DNA interaction energies in our model allows us to construct position-specific weight matrices by computing base pair probabilities independently for each position in the binding site. Our approach is less data intensive than knowledge-based models of protein–DNA interactions, and is not limited to any specific family of transcription factors. However, native structures of protein–DNA complexes or their close homologs are required as input to the model. Use of homology modeling can significantly increase the extent of our approach, making it a useful tool for studying regulatory pathways in many organisms and cell types.

Evaluation of protein-DNA binding affinity by electrospray ionization mass spectrometry

Binding affinity of complexes between a DNA-binding domain (DBD) of a transcription factor, c-Myb, and several double-stranded DNA (dsDNA) were evaluated by collision-induced dissociation (CID) of the multiply protonated molecules generated by electrospray ionization mass spectrometry (ESI-MS). Complexes of the c-Myb DBD and dsDNA were prepared in solution and analyzed by ESI-MS. Multiply protonated molecules of a high-affinity complex, the c-Myb DBD and dsDNA with a specific sequence, were clearly observed in ESI mass spectrum. Protonated molecules of the complex were quite stable in the gas-phase, and not easily dissociated even if high cone voltage was applied in the first vacuum chamber source when the sample was prepared in 10 mM ammonium acetate. As for the sample prepared in buffer with higher concentration of ammonium acetate, such as 500 mM ammonium acetate, protein-dsDNA complexes could easily be dissociated with an increase in the cone voltage, giving multiply protonated molecules of free c-Myb DBD and some DNA fragments. Systematic CID experiments were carried out on seven complexes between the c-Myb DBD and 22-mer dsDNA with different solution-Kd values in the range of 10(-9) M to 10(-7) M. For each complex dissociation curve as a function of cone voltage was plotted, and the cone voltage where 50% of the complex was dissociated (V(50%)) was calculated. Consequently, positive correlation was obtained between V(50%) and relative binding free energy change (DeltaDeltaG) in complex formation in solution. This suggests that ESI-CID experiments can provide quantitative evaluation of the stability of protein-DNA complexes based on proper calibration.

Contribution of conjugated linoleic acid to the suppression of inflammatory responses through the regulation of the NF-kappaB pathway.

Data from a number of researchers have shown that conjugated linoleic acid (CLA) has some beneficial health activities in animal models. Because inflammatory responses are associated with pathophysiology of many diseases, the aim of this study is to explore the effect and mechanism of CLA in the regulation of lipopolysaccharide (LPS)-induced inflammatory responses in RAW 264.7 macrophages. The addition of increasing levels of CLA proportionally augmented the incorporation of CLA in cultures. CLA diminished LPS-induced mRNA and protein expression of inducible nitric oxide synthase (iNOS) and cyclooxygenase 2 (COX2) as well as subsequent production of nitric oxide and prostaglandin E(2), respectively. We further examined the effect of CLA on LPS-induced NF-kappaB activation by Western blot and the electrophoretic mobility shift assay. The addition of CLA at 200 microM significantly diminished LPS-induced protein expression of the cytoplasmic phosphorylated inhibitor kappaBalpha and nuclear p65 as well as NF-kappaB nuclear protein-DNA binding affinity. In conclusion, our data suggest that CLA may inhibit LPS-induced inflammatory events in RAW 264.7 macrophages and this inhibitory activity of CLA, at least in part, occurs through CLA modulating the NF-kappaB activation and therefore negatively regulating expression of inflammatory mediators.

High-resolution assessment of protein DNA binding affinity and selectivity utilizing a fluorescent intercalator displacement (FID) assay.

Protein titration displacement of ethidium bromide bound to hairpin deoxyoligonucleotides containing any sequence of interest provides a well-defined titration curve (measuring the loss of fluorescence derived from the DNA bound ethidium bromide) that provides both absolute binding constants (K(a)) and stoichiometry of binding. This use of a fluorescent intercalator displacement (FID) assay for establishing protein DNA binding affinity and selectivity is demonstrated with the examination of the LEF-1 HMG domain binding to hairpin deoxyoligonucleotides containing its commonly accepted consensus sequence 5'-CTTTGWW (W=A or T) and those modified (5'-CTNTGWW) to examine sequences implicated in early studies (5'-CTNTG). The effectiveness of the FID assay coupled with its technically non-demanding experimental use makes it an attractive alternative or complement to selection screening, footprinting or affinity cleavage, and electrophoretic mobility shift assays for detecting, characterizing, and quantitating protein DNA binding affinity and selectivity.

HMGB1 interacts differentially with members of the Rel family of transcription factors

HMGB1 is an architectural factor that enhances the DNA binding affinity of several proteins. We have investigated the influence of HMGB1 on DNA binding by members of the Rel family. HMGB1 enhances DNA binding by p65/p50 and p50/p50, but reduces binding by p65/p65, c-Rel/c-Rel, p65/c-Rel, and p50/c-Rel. In pull-down assays, HMGB1 interacts directly with the p50 subunit via its HMG boxes and this interaction is weakened by the presence of the acidic tail. Functionally, HMGB1 is required for the NF-κB-dependent expression of the adhesion molecule VCAM-1.

Protein-DNA binding affinities by capillary electrophoresis.

Described in this chapter is a capillary electrophoresis (CE) method for the accurate determination of protein-DNA binding constants (). The advantages of the method include the fast separation and quantitation of protein-DNA complex and free DNA, in uncoated capillaries without sieving matrices, coupled with LIF detection of fluorescently-labeled DNA at nM to πM concentrations.

Global Strategies for Disease Detection and Treatment: Proteomics

The field of proteomics holds great promise for identifying nontargeted, global molecular profiles “signatures” of normal and diseased cells. While genomics offers a wide array of tools for identifying mutated or dysregulated genes, proteomics offers the ability to measure post-translational modifications, protein stability, phosphorylation state, protein-protein interactions, and protein DNA-binding affinities. These biological events play major roles in the pathogenesis of disease and cannot be studied by DNA and mRNA efforts alone. Recent studies have shown that there is no specific correlation between mRNA abundance and protein expression levels in a cell at a given time. The discrepancy could arise from the control of mRNA translation, and the stability of mRNAs and proteins. Because almost all therapeutic intervention strategies or early detection technologies target expressed proteins, proteomic-based studies can provide fundamental information to characterize disease progression at the molecular level. Therefore, proteomics has particular relevance to diagnostics and to the identification of disease markers, as proteins can be assayed in serum and other biological fluids. Since the completion of human genome sequence, the discipline of proteomics has taken a center stage in defining the future of molecular diagnostics. This is due, to some extent, to the fact that the sequencing of the human genome and other important genomes has opened the door for proteomics by providing a sequence-based framework for mining the proteome. The growth in proteomic tools and proteomics is in an extraordinary growth phase. As a consequence, proteomics is witnessing an extraordinary growth in the number of new investigators and biotechnology companies that are taking an active interest in the field. Proteomics is evolving at a fast pace, as is evident from this special issue. Strategies for protein fractionation prior to analysis are increasingly being relied upon. Selective enrichment for a subset of proteins of interest can be achieved using a variety of techniques from centrifugation procedures to affinity capture. In addition to reducing sample complexity and increasing sensitivity, strategies based on the separate analysis of subcellular compartments provide the means to determine protein location in a cell. There is clearly interest in developing robust “industrial strength” proteomic platforms to achieve high-throughput and high sensitivity. During the lean years of proteomics, the field was largely dominated by a single approach, namely twodimensional (2-D) gels, backed up by an assortment of related tools, ranging from software for image analysis to mass spectrometry. Several technologies for protein profiling are emerging that are not 2-D gel based, including direct profiling by mass spectrometry and the use of protein microarrays. High throughput technologies, such as Surface-Enhanced Laser Desorption/Ionization Time-of-Flight (SELDI-TOF) and Matrix-Assisted Laser Desorption/Ionization Time-ofFlight (MALDI-TOF) technologies, are providing us with a non-biased, global discovery approach using patient serum, plasma, urine or other sources of secretions, to identify – in a single run – the expression patterns in thousands of small molecular mass proteins (< 20 kDa) based on their molecular mass and charge, offering a tool to determine which proteins are secreted from tumor cells or are measurable in the bodily fluids of patients. However, it is likely that no one technology platform will meet the needs of the wide spectrum of applications encompassed by proteomics. Diagnosing disease through proteomics may well require all the tools at our disposal to identify and validate the most promising markers.

Schnurri interacts with Mad in a Dpp-dependent manner.

Decapentaplegic (Dpp) is a member of the transforming growth factor-beta superfamily. Dpp governs various developmental processes in Drosophila through the transcriptional regulation of a variety of genes. Signals of Dpp are transmitted from the cell membrane to the nucleus by Medea and Mad, both belonging to the Smad protein family. Mad was shown to bind to the Dpp-responsive element in genes such as vestigial, labial, and Ultrabithorax. The DNA binding affinity of Smad proteins is relatively low, and requires other nuclear factor(s) to form stable DNA binding complexes. schnurri (shn) was identified as a candidate gene acting downstream of Dpp receptors, but its relevance to Mad has remained unknown. We characterized the biochemical functions of Shn. Shn forms homo-oligomers. Shn is localized in the nucleus, and is likely to have multiple nuclear localizing signals. Finally, we found that Shn interacts with Mad in a Dpp-dependent manner. The present results argue that Shn may act as a nuclear component of the Dpp signalling pathway through direct interaction with Mad.

A capillary electrophoresis mobility shift assay for protein-DNA binding affinities free in solution.

Quantitative determination of dissociation constants for DNA-protein complexes will help clarify the molecular mechanisms of transcription, replication and DNA repair. A practical capillary electrophoresis mobility shift assay (CEMSA) for protein-DNA affinities free in solution is presented. The method is fast and simple, precise and general. The speed (<2 min separations) and simplicity derive from the use of an uncoated capillary with no gel matrix. The dissociation constant for GCNK58, a DNA-binding-region construct of the yeast transcription factor GCN4, binding to the AP1 DNA site was measured ( K d = 35 +/- 4 nM) to demonstrate the utility of the method.