Sequential-dissociation kinetics of non-covalent complexes of DNA with multiple proteins in separation-based approach: General theory and its application

Binding of multiple proteins to DNA is crucial in many regulatory cellular processes. The kinetics of assembly and disassembly of DNA–multiple protein complexes is very difficult to study in detail due to the lack of suitable experimental approaches. A separation-based approach has been recently proposed to resolve disassembly kinetics of such complexes. While conceptually simple, the separation-based approach generates experimental data with very complex patterns. The analysis of these patterns is a challenging problem on its own. Here we report on a mathematical approach that can extract a solution for the experimental data obtained in separation-based analysis of sequential dissociation of a DNA complex with multiple proteins. This case describes the dissociation of proteins one-by-one from the complex. Generally speaking, a mathematical solution of such problems requires calculations of multiple integrals. Our approach reduces this procedure to taking double integrals and constructing their superposition. We tested this approach with the experimental data obtained for three-step sequential dissociation of complexes of DNA with two protein copies.     

Fluorescence polarization detection for affinity capillary electrophoresis

Affinity capillary electrophoresis (ACE) with laser-induced fluorescence polarization (LIFP) detection is described, with examples of affinity interaction studies. Because fluorescence polarization is sensitive to changes in the rotational motion arising from molecular association or dissociation, ACE-LIFP is capable of providing information on the formation of affinity complexes prior to or during CE separation. Unbound, small fluorescent probes generally have little fluorescence polarization because of rapid rotation of the molecule in solution. When the small fluorescent probe is bound to a larger affinity agent, such as an antibody, the fluorescence polarization (and anisotropy) increases due to slower motion of the much larger complex molecule in the solution. Fluorescence polarization results are obtained by simultaneously measuring fluorescence intensities of vertical and horizontal polarization planes. Applications of CE-LIFP to both strong and weak binding systems are discussed with antibody-antigen and DNA-protein binding as examples. For strong affinity binding, such as between cyclosporine and its antibody, complexes are formed prior to CE-LIFP analysis. For weaker binding, such as between single-stranded DNA and its binding protein, the single-stranded DNA binding protein is added to the CE separation buffer to enhance dynamic formation of affinity complexes. Both fluorescence polarization (and anisotropy) and mobility shift results are complementary and are useful for immunoassays and binding studies.     

Direct observation of enhanced translocation of a homeodomain between DNA cognate sites by NMR exchange spectroscopy

A novel approach is presented for studying the kinetics of specific protein-DNA interactions by NMR exchange spectroscopy. The experimental design involves the direct observation of translocation of a homeodomain between cognate sites on two oligonucleotide duplexes, differing by only a single base pair at the edge of the DNA recognition sequence. The single base-pair change perturbs the 1H-15N correlation spectrum of a number of residues, while leaving the affinity for the DNA unchanged. The exchange process has apparent rate constants in the 5-20 s-1 range which are linearly dependent upon the concentration of free DNA. These rates are about 3 orders of magnitude larger than the dissociation rate constant determined by gel shift assays at nanomolar DNA concentrations. The complete NMR exchange data set, comprising auto- and cross-peak intensities as a function of mixing time at five concentrations of free DNA, can be fit simultaneously to a simple model in which protein translocation between DNA duplexes occurs via a second-order process (with rate constants of approximately 6 x 104 M-1 s-1) involving direct collision of a protein-DNA complex with free DNA. This is akin to intersegmental transfer, and a physical model for the process is discussed. Rapid translocation at high concentrations of free DNA observed directly by NMR exchange spectroscopy reconciles the long half-lives of protein-DNA complexes measured by biochemical analysis in vitro with the highly dynamic behavior of such complexes observed in vivo. The relevance of this mechanism to the kinetics of protein-DNA interactions within the cell is discussed.     

Comparative Study of Three Methods for Affinity Measurements: Capillary Electrophoresis Coupled with UV Detection and Mass Spectrometry, and Direct Infusion Mass Spectrometry

We present affinity capillary electrophoresis and mass spectrometry (ACE-MS) as a comprehensive separation technique for label-free solution-based affinity analysis. The application of ACE-MS for measuring affinity constants between eight small molecule drugs [ibuprofen, s-flurbiprofen, diclofenac, phenylbutazone, naproxen, folic acid, resveratrol, and 4,4'-(propane-1,3-diyl) dibenzoic acid] and β-cyclodextrin is described. We couple on-line ACE with MS to combine the separation and kinetic capability of ACE together with the molecular weight and structural elucidation of MS in one system. To understand the full potential of ACE-MS, we compare it with two other methods: Direct infusion mass spectrometry (DIMS) and ACE with UV detection (ACE-UV). After the evaluation, DIMS provides less reliable equilibrium dissociation constants than separation-based ACE-UV and ACE-MS, and cannot be used solely for the study of noncovalent interactions. ACE-MS determines apparent dissociation constants for all reacting small molecules in a mixture, even in cases when drugs overlap with each other during separation. The ability of ACE-MS to interact, separate, and rapidly scan through m/z can facilitate the simultaneous affinity analysis of multiple interacting pairs, potentially leading to the high-throughput screening of drug candidates.     

Methods for the determination of binding constants by capillary electrophoresis

Apparent equilibrium constants for molecular association (e.g., association constants, binding constants, dissociation constants, partition coefficients) can be determined with a variety of different capillary electrophoresis (CE) approaches. In many cases, the investigated association behavior is between a smaller molecule or ion (i.e., the solute, drug, or analyte of interest) and a larger entity (e.g., proteins, micelles, polymers, chiral selectors such as cyclodextrins, etc.). Each experimental approach has advantages and disadvantages. Frequently, it is the nature of the system being evaluated that determines the optimal experimental approach. Six different CE-based techniques for evaluating binding constants are reviewed. Examples of each method, and recent references on its use are given.     

Characterization of interaction kinetics between chiral solutes and human serum albumin by using high-performance affinity chromatography and peak profiling

Peak profiling and high-performance columns containing immobilized human serum albumin (HSA) were used to study the interaction kinetics of chiral solutes with this protein. This approach was tested using the phenytoin metabolites 5-(3-hydroxyphenyl)-5-phenylhydantoin (m-HPPH) and 5-(4-hydroxyphenyl)-5-phenylhydantoin (p-HPPH) as model analytes. HSA columns provided some resolution of the enantiomers for each phenytoin metabolite, which made it possible to simultaneously conduct kinetic studies on each chiral form. The dissociation rate constants for these interactions were determined by using both the single flow rate and multiple flow rate peak profiling methods. Corrections for non-specific interactions with the support were also considered. The final estimates obtained at pH 7.4 and 37°C for the dissociation rate constants of these interactions were 8.2-9.6 s(-1) for the two enantiomers of m-HPPH and 3.2-4.1 s(-1) for the enantiomers of p-HPPH. These rate constants agreed with previous values that have been reported for other drugs and solutes that have similar affinities and binding regions on HSA. The approach used in this report was not limited to phenytoin metabolites or HSA but could be applied to a variety of other chiral solutes and proteins. This method could also be adopted for use in the rapid screening of drug-protein interactions.     

Exploiting Complex Fluorophore Interactions to Monitor Virus Capsid Disassembly

Supramolecular protein complexes are the corner stone of biological processes; they are essential for many biological functions. Unraveling the interactions responsible for the (dis)assembly of these complexes is required to understand nature and to exploit such systems in future applications. Virus capsids are well-defined assemblies of hundreds of proteins and form the outer shell of non-enveloped viruses. Due to their potential as a drug carriers or nano-reactors and the need for virus inactivation strategies, assessing the intactness of virus capsids is of great interest. Current methods to evaluate the (dis)assembly of these protein assemblies are experimentally demanding in terms of instrumentation, expertise and time. Here we investigate a new strategy to monitor the disassembly of fluorescently labeled virus capsids. To monitor surfactant-induced capsid disassembly, we exploit the complex photophysical interplay between multiple fluorophores conjugated to capsid proteins. The disassembly of the capsid changes the photophysical interactions between the fluorophores, and this can be spectrally monitored. The presented data show that this low complexity method can be used to study and monitor the disassembly of supramolecular protein complexes like virus capsids. However, the range of labeling densities that is suitable for this assay is surprisingly narrow.     

Non-equilibrium capillary electrophoresis of equilibrium mixtures--appreciation of kinetics in capillary electrophoresis

We describe a new electrophoretic method (patent pending), Non-Equilibrium Capillary Electrophoresis of Equilibrium Mixtures (NECEEM), and demonstrate its application to the study of protein-DNA interactions. A single NECEEM experiment allows for the determination of equilibrium and kinetic parameters of protein-DNA complex formation. The equilibrium mixture is prepared by mixing protein and DNA; it contains three components: free protein, free DNA, and the protein-DNA complex. A small plug of such a mixture is injected onto a capillary and the three components are separated under non-equilibrium conditions using a run buffer that does not contain the components of the equilibrium mixture. The protein-DNA complex decays during the NECEEM separation; the resulting electropherograms contain characteristic peaks and exponential curves. A simple analysis of a single electropherogram reveals two parameters: the equilibrium dissociation constant of the protein-DNA complex and the monomolecular rate constant of complex decay. The bimolecular rate constant of complex formation can then be calculated as the ratio of the two experimentally-determined constants. NECEEM was applied to find the equilibrium and kinetic parameters of interaction between an E. coli single-stranded DNA binding protein and a fluorescently-labeled oligonucleotide. The constants determined by NECEEM are in good agreement with those obtained by other methods. The new method is simple, fast, and accurate. It can be equally applied to other non-covalent molecular complexes.     

Solid-phase extraction for the simultaneous preconcentration of organic (selenocystine) and inorganic [Se(IV), Se(VI)] selenium in natural waters

The recombinantly produced different forms of protein G, namely monofunctional immunoglobulin G (IgG) binding, monofunctional serum albumin (SA) binding and bifunctional IgG/SA binding proteins G, are compared with respect to their specific affinities to blood IgG and SA. The affinity mode of the recently developed high-performance monolithic disk chromatography has been used for fast quantitative investigations. Using single affinity disks as well as two discs stacked into one separation unit, one order of magnitude in adsorption capacities for IgG and SA were found both for monofunctional and bifunctional protein G forms used as specific affinity ligands. However, despite the adsorption difference observed, the measured dissociation constants of the affinity complexes seemed to be very close. The analytical procedure developed can be realized within a couple of minutes. Up-scaling of the developed technology was carried out using another type of monolithic materials, i.e. CIM affinity tubes.     

NMR distinction of single- and multiple-mode binding of small-molecule protein ligands

Identifying and characterizing small-molecule inhibitors of protein-protein interactions is of high interest for drug discovery and for chemical genetics studies of biological pathways. Very often, initial hits or first-generation compounds have low micromolar dissociation constants and cause line broadening in NMR spectra. It is very important for subsequent structure-based compound optimization to know if this line broadening is caused by intermediate exchange of the dissociation kinetics only or in addition by multiple binding modes. Here, we present an approach of how to distinguish these two situations and demonstrate its experimental application. Two very similar small-molecule ligands of Bcl-xL are considered that cause both severe line broadening of interface residues. We show that one compound exhibits single-mode binding, and broadening is just due to dissociation kinetics in the intermediate exchange regime, and the line broadening can be overcome by providing excess ligand. In the other case, line broadening is due to dissociation kinetics and exchange between multiple bound conformations, and broadening cannot be overcome by providing excess ligand. The procedures used are very general and can also be applied to characterizing protein-protein and protein-nucleic acid interactions.     

Protein detection by nanopores equipped with aptamers

Protein nanopores have been used as stochastic sensors for the detection of analytes that range from small molecules to proteins. In this approach, individual analyte molecules modulate the ionic current flowing through a single nanopore. Here, a new type of stochastic sensor based on an αHL pore modified with an aptamer is described. The aptamer is bound to the pore by hybridization to an oligonucleotide that is attached covalently through a disulfide bond to a single cysteine residue near a mouth of the pore. We show that the binding of thrombin to a 15-mer DNA aptamer, which forms a cation-stabilized quadruplex, alters the ionic current through the pore. The approach allows the quantification of nanomolar concentrations of thrombin, and provides association and dissociation rate constants and equilibrium dissociation constants for thrombin·aptamer interactions. Aptamer-based nanopores have the potential to be integrated into arrays for the parallel detection of multiple analytes.     

Structural models of protein-DNA complexes based on interface prediction and docking

Protein-DNA interactions are the physical basis of gene expression and DNA modification. Structural models that reveal these interactions are essential for their understanding. As only a limited number of structures for protein-DNA complexes have been determined by experimental methods, computation methods provide a potential way to fill the need. We have developed the DISPLAR method to predict DNA binding sites on proteins. Predicted binding sites have been used to assist the building of structural models by docking, either by guiding the docking or by selecting near-native candidates from the docked poses. Here we applied the DISPLAR method to predict the DNA binding sites for 20 DNA-binding proteins, which have had their DNA binding sites characterized by NMR chemical shift perturbation. For two of these proteins, the structures of their complexes with DNA have also been determined. With the help of the DISPLAR predictions, we built structural models for these two complexes. Evaluations of both the DNA binding sites for 20 proteins and the structural models of the two protein-DNA complexes against experimental results demonstrate the significant promise of our model-building approach.     

Binding constant determination of high-affinity protein-ligand complexes by electrospray ionization mass spectrometry and ligand competition

We describe an approach for the determination of binding constants for protein-ligand complexes with electrospray ionization mass spectrometry, based on the observation of unbound ligands competing for binding to a protein target. For the first time, dissociation constants lower than picomolar could be determined with good accuracy by electrospray ionization mass spectrometry. The presented methodology relies only on the determination of signal intensity ratios for free ligands in the low mass region. Therefore, all the advantages of measuring low masses with mass spectrometry, such as high resolution are preserved. By using a reference ligand with known binding affinity, the affinity of a second ligand can be determined. Since no noncovalently bound species are observed, assumptions about response factors are not necessary. The method is validated with ligands binding to avidin and applied to ligands binding to p38 mitogen-activated protein kinase.     

Using DNA-binding proteins as an analytical tool

We propose that DNA-binding proteins can be used as highly efficient and versatile tools in analyses of DNA, RNA, and proteins. This work reports assays applying specific affinity probes: hybridization probes for analyses of DNA and RNA, and aptamer probes for analyses of proteins. Both types of probes are single-stranded DNA. In affinity analyses, in general, the probe (P) binds to a target molecule (T), and the amounts of the probe-target complex (P.T) and unbound P are determined. Distinguishing between P and P.T can be achieved by electrophoretic separation. If the electrophoretic mobilities of P and P.T are close in gel-free media, which is always the case for hybridization analyses, separation typically requires the use of a sieving matrix. Here we utilized a single-stranded DNA binding protein (SSB) to facilitate highly efficient gel-free separation of P and P.T in capillary electrophoresis (CE) for three types of targets: DNA, RNA, and proteins. When present in the CE run buffer, SSB binds differently to P and P.T. Due to this selective binding, SSB induces difference in electrophoretic mobilities of P and P.T in an SSB concentration-dependent fashion. The difference in the electrophoretic mobilities allows for affinity analyses of DNA, RNA, and proteins in gel-free CE. The large number of well-characterized DNA- and RNA-binding proteins and the diversity of their properties will allow researchers to design a comprehensive tool set for quantitative analyses of DNA, RNA, and proteins. Such analyses will facilitate identification of genomic DNA in ultra-small samples without error-prone and time-consuming PCR. They can also be used for monitoring gene expression at both mRNA and protein levels.     

Electrophoretic behavior of DNA‐methyl‐CpG‐binding domain protein complexes revealed by capillary electrophoreses laser‐induced fluorescence

The free solution electrophoretic behavior of DNA‐protein complexes depends on their charge and mass in a certain experimental condition, which are two fundamental properties of DNA‐protein complexes in free solution. Here, we used CE LIF to study the free solution behavior of DNA‐methyl‐CpG‐binding domain protein (MBD2b) complexes through exploring the relationship between the mobilities, charge, and mass of DNA‐protein complexes. This method is based on the effective separation of free DNA and DNA‐protein complexes because of their different electrophoretic mobility in a certain electric field. In order to avoid protein adsorption, a polyacrylamide‐coated capillary was used. Based on the evaluation of the electrophoretic behavior of formed DNA‐MBD2b complexes, we found that the values of (μ₀/μ)‐1 were directly proportional to the charge‐to‐mass ratios of formed complexes, where the μ₀ and μ are the mobility of free DNA probe and DNA‐protein complex, respectively. The models were further validated by the complex mobilities of protein with various lengths of DNA probes. The deviation of experimental and calculated charge‐to‐mass ratios of formed complexes from the theoretical data was less than 10%, suggesting that our models are useful to analyze the DNA‐binding properties of the purified MBD2b protein and help to analyze other DNA‐protein complexes. Additionally, this study enhances the understanding of the influence of the charge‐to‐mass ratios of formed DNA‐protein complexes on their separation and electrophoretic behaviors.     

Blackbody infrared radiative dissociation of nonspecific protein-carbohydrate complexes produced by nanoelectrospray ionization: The nature of the noncovalent interactions

Gas-phase thermal dissociation experiments, implemented with blackbody infrared radiative dissociation (BIRD) and Fourier transform ion cyclotron resonance mass spectrometry, have been performed on a series of protonated and deprotonated 1:1 and protonated 1:2 protein-carbohydrate complexes formed by nonspecific interactions during the nanoflow electrospray (nanoES) ionization process. Nonspecific interactions between the proteins bovine carbonic anhydrase II (CA), bovine ubiquitin (Ubq), and bovine pancreatic trypsin inhibitor and several carbohydrates, ranging in size from mono- to tetrasaccharides, have been investigated. Over the range of temperatures studied (60-190 degrees C), BIRD of the protonated and deprotonated complexes proceeds exclusively by the loss of the carbohydrate in its neutral form. The rates of dissociation of the 1:1 complexes containing a mono- or disaccharide decrease with reaction time, suggesting the presence of two or more kinetically distinct structures produced during nanoES or by gas-phase processes. In contrast, the 1:1 complexes of the tri- and tetrasaccharides exhibit simple first-order dissociation kinetics, a result that, on its own, is suggestive of a single preferred carbohydrate binding site or multiple equivalent sites in the gas phase. A comparative analysis of the dissociation kinetics measured for protonated 1:1 and 1:2 complexes of Ubq with alphaTal[alphaAbe]alphaMan further supports the presence of a single preferred binding site. However, a similar analysis performed on the complexes of CA and alphaTal[alphaAbe]alphaMan suggests that equivalent but dependent carbohydrate binding sites exist in the gas phase. Analysis of the Arrhenius activation parameters (E(a) and A) determined for the dissociation of 1:1 complexes of CA with structurally related trisaccharides provides evidence that neutral intermolecular hydrogen bonds contribute, at least in part, to the stability of the gaseous complexes. Surprisingly, the E(a) values for the complexes of the same charge state are not sensitive to the structure (primary or higher order) of the protein, suggesting that the carbohydrates are able to form energetically equivalent interactions with the various functional groups presented by the protein. For a given protein-carbohydrate complex, the dissociation E(a) is sensitive to charge state, initially increasing and then decreasing with increasing charge. It is proposed that both ionic and neutral hydrogen bonds stabilize the nonspecific protein-carbohydrate complexes in the gas phase and that the relative contribution of the neutral and ionic interactions is strongly influenced by the charge state of the complex, with neutral interactions dominating at low charge states and ionic interactions dominating at high charge states.     

Protolytic dissociation mechanisms and comparative acid stabilities of palladium(II), zinc(II), copper(II), and nickel(II) complexes of alkylated dipyrrins

Complexes of Pd(II), Cu(II), Ni(II), and Zn(II) with alkylated dipyrrins (Hdpm) were synthesized and characterized by physicochemical and spectroscopic methods. Protolytic dissociation kinetics of these complexes in benzene in the presence of acetic and trichloroacetic acid was studied. A protonated dipyrrin is the reaction product of protolytic dissociation of the complexes in acid solutions. The observed and true dissociation rate constants, as well as activation reaction parameters, were calculated. Kinetic models of the processes are proposed, and the patterns of influence of the ligand nature on dissociation kinetics were determined. The Pd(II) complexes proved to be much more stable than other those of the other metals, according to the results of the kinetic studies. The lability of the complexes strongly depends on the length and position of the alkyl substituent of the ligand. The dissociation of the Ni(II) complex gives a heteroligand complex at low concentrations of acid, but the complex undergoes full protolytic dissociation at higher concentrations of acid. The dissociation of the complex of Cu(II) is an equilibrium process, involving formation of the protonated form of the ligand.     

Development of a Surface Plasmon Resonance-Based DNA Sensor and Its Application for Screening DNA-Targeted Anticancer Drugs

In this paper, we present a surface plasmon resonance (SPR)-based sensor for measuring DNA hybridization and DNA/small-molecule interactions. A mixed self-assembled monolayer (SAM) was used to optimize the biosensor sensitivity. It was observed that the mixed SAM formed by mixing 10 mM of 16-mercapto-1-hexadecanoic acid (16-MHA) and 6-mercapto-1-hexanol (6-MCH) at a 1:10 molar ratio showed the best results. Subsequently, avidin was attached to the carboxyl groups on the SAM to serve as a binding element for biotinylated single-stranded (ss)DNA. The ssDNA-coated sensor was first evaluated as a nucleic acid biosensor through a DNA-DNA hybridization assay for synthetic 28-mer ssDNA. A linear calibration curve was observed in the range of 0.25–2.5 µg/mL. Non-complementary DNA induced no significant SPR angle shift, which demonstrated the specificity of the assay. Secondly, the sensor was used to monitor the binding kinetics of DNA/small-molecule interactions in real time. The dissociation constant between immobilized DNA and sanguinarine was determined to be 8.0 × 10^?6 M. This complies with most data from the literature. In addition, the sensor could be regenerated with 0.01 M HCl and would be feasible for multiple testing. In conclusion, the experimental approach described in this study allows analysis of molecular interactions between DNA-binding drugs and selected targeted DNA sequences.     

Electrochemical Investigation of Heterogeneous Affinity Behaviour of Methylene Blue and G-quadruplex

The heterogeneous binding behaviour between methylene blue (MB) and G-quadruplex, one kind of single-stranded (ss) DNA with specific guanine tetrads, has been thoroughly studied via electrochemical techniques. Positively charged MB interacted electrostatically with both G-quadruplex and normal ssDNA but the binding and dissociation kinetics between them were significantly different. Compared with ssDNA, G-quadruplex had a slower binding rate constant and dissociation rate constant with MB since there existed other different binding mechanisms between G-quadruplex and MB besides electrostatic interaction. This work might provide valuable information in the design and development of DNA sensors.     

Photoreactive DNA as a Tool to Study Replication Protein A Functioning in DNA Replication and Repair

Replication protein A (RPA), eukaryotic single-stranded DNA-binding protein, is a key player in multiple processes of DNA metabolism including DNA replication, recombination and DNA repair. Human RPA composed of subunits of 70-, 32- and 14-kDa binds ssDNA with high affinity and interacts specifically with multiple proteins. The RPA heterotrimer binds ssDNA in several modes, with occlusion lengths of 8–10, 13–22 and 30 nucleotides corresponding to global, transitional and elongated conformations of protein. Varying the structure of photoreactive DNA, the intermediates of different stages of DNA replication or DNA repair were designed and applied to identify positioning of the RPA subunits on the specific DNA structures. Using this approach, RPA interactions with various types of DNA structures attributed to replication and DNA repair intermediates were examined. This review is dedicated to blessed memory of Prof. Alain Favre who contributed to the development of photoreactive nucleotide derivatives and their application for the study of protein–nucleic acids interactions.