Fractal Analysis of Binding and Dissociation Kinetics and Interactions of Cancer Markers on Biosensor Surfaces

A fractal analysis is presented for the binding and dissociation of different cancer markers on biosensor surfaces. The data analyzed include putrescine in solution to PDDA/APTES/MWCNT/Puo-modified GCE (glassy carbon electrode) () and vascular endothelial growth factor (VEGF) in solution to the soluble form of the VEGF receptor (SFlt-1 or VEGF-1) immobilized on a sensor chip (). Single- and dual-fractal models were used to fit the data. Values of the binding and dissociation rate coefficient(s), affinity values, and the fractal dimensions were obtained from the regression analysis provided by Corel Quattro Pro 8.0 (). The binding rate coefficients and the affinity values are sensitive to the degree of heterogeneity on the sensor chip surface. Predictive equations are developed for the binding rate coefficient as a function of the heterogeneity present on the biosensor chip surface. The analysis presented provides physical insights into these cancer biomarker-receptor reactions occurring on the different biosensor surfaces.     

Detection of Glucose and Related Analytes by Biosensors: A Fractal Analysis

A fractal analysis is used to model the binding and dissociation kinetics of connective tissue interstitial glucose, adipose tissue interstitial glucose, insulin, and other related analytes on biosensor surfaces. The analysis provides insights into diffusion-limited analyte-receptor reactions occurring on heterogeneous biosensor surfaces. Numerical values obtained for the binding and the dissociation rate coefficients are linked to the degree of heterogeneity or roughness [fractal dimension (D_f)] present on the biosensor chip surface. The binding and dissociation rate coefficients are sensitive to the degree of heterogeneity on the surface. For example, for the binding of plasma insulin, as the fractal dimension value increases by a factor of 2.47 from D_f1 = 0.6827 to D_f2 = 1.6852, the binding rate coefficient increases by a factor of 4.92 from k₁ = 1.0232 to k₂ = 5.0388. An increase in the degree of heterogeneity on the probe surface leads to an increase in the binding rate coefficient. A dual-fractal analysis is required to fit the binding kinetics in most of the cases presented. A single fractal analysis is adequate to describe the dissociation kinetics. Affinity (ratio of the binding to the dissociation rate coefficient) values are also presented. Interferents for glucose, such as uric acid and ascorbic acid, were also detected by using glucose biosensors based on carbon nanotube (CNT) nanoelectrode ensembles (NEEs) (Lin Y, Lu F, Tu Y, Ren Z. Nano Lett 2004, 4, 191–195).     

A fractal analysis of analyte-estrogen receptor binding and dissociation kinetics using biosensors: environmental and biomedical effects

A fractal analysis is used to model the binding and dissociation kinetics between analytes in solution and estrogen receptors (ERs) immobilized on a sensor chip of a surface plasmon resonance (SPR) biosensor. The influence of different ligands is also analyzed. A better understanding of the kinetics provides physical insights into the interactions, and suggests means by which appropriate interactions (to promote correct signaling) and inappropriate interactions such as with xenoestrogens (to minimize inappropriate and deleterious to health signaling) may be better controlled. The fractal approach is applied to analyte–ER interaction data available in the literature. The units for the different parameters (rate coefficients and affinities) in fractal-type kinetics are different from those obtained in classical kinetics. Numerical values obtained for the binding and the dissociation rate coefficients are linked to the degree of roughness or heterogeneity (fractal dimension, D_f) present on the biosensor chip surface. In general, the binding and the dissociation rate coefficients are very sensitive to the degree of heterogeneity on the surface. A single-fractal analysis is adequate in some cases. In others (that exhibit complexities in the binding or the dissociation curves) a dual-fractal analysis is required to obtain a better fit. This has biomedical and environmental implications in that the dissociation (and the binding) rate coefficient may be used to alleviate (deleterious effects) or enhance (beneficial effects) by selective modulation of the surface. The affinity values obtained in the analysis are consistent with the numbers required to (a) promote signaling between the correct analyte and the estrogen receptor, and (b) minimize the signaling between xenoestrogens and the estrogen receptor.     

Ligands Binding and Molecular Simulation: the Potential Investigation of a Biosensor Based on an Insect Odorant Binding Protein

Based on mimicking biological olfaction, biosensors have been applied for the detection of various ligands in complex environment, which could represent one of the most promising research fields. In this study, the basic characters of one insect odorant binding protein (OBP) as a biosensor were explored. To explore the molecular recognition process, the tertiary structure of the protein was modeled and the protein-ligand interactions with 1,536,550 chemicals were investigated by the molecular docking. The availability of large amount of recombinant SlitOBP1 overcame the difficulty to obtain biological sensing material. After obtained the purified recombinant protein, the result of fluorescence binding assays proved the candidate protein has good affinities with the majority of the tested chemicals. With the aid of simulation docking, the key conserved amino acids within the binding site were identified and then mutated to alanine. After mutation, the protein-ligand binding characteristics were recorded, and the competitive binding assays were carried out to provide experimental verification. The detailed information on its structure and affinities investigated in this study could allow the design of specific mutants with desired characteristics, which provides a solid base for tailoring OBP for biosensor and provides a role model for screening the other elements in olfactory system for different applications.     

Binding kinetics and multi-bond: Finding correlations by synthesizing interactions between ligand-coated bionanoparticles and receptor surfaces

The number of bonds formed between one single bionanoparticle and many surface receptors is an important subject to be studied but is seldom quantitatively investigated. A new evaluation of the correlation between binding kinetics and number of bonds is presented by varying ligand density and receptor density. An experimental system was developed using measurements with surface plasmon resonance spectroscopy. A corresponding multi-site adsorption model elucidated the correlation. The results show that with the increase of the receptor density, the adsorption rate first decreased when the number of bonds was below a maximum value and then increased when the number of bonds stayed at this maximum value. The investigation on ligand density variation suggests that the coating density on top of the bionanoparticle surface may have a particular value below which more ligand will accelerate the adsorption rate. The ratio of ligand amount bound by the receptors to the total ligand amount associated with a single bionanoparticle will remain constant even if one attaches more ligands to a bionanoparticle. We envision that the bionanoparticle desorption will not depend on density changes from either ligand or receptor when the number of bonds reaches a specific efficient value.     

Determination of Partition Coefficients of Labile Compounds Subject to Dissociation Extraction Analysis of Partitioning

A novel method for the determination of partition coefficients in aqueous-organic two-phase systems is described. It is applicable for characterizing the distribution of substances undergoing proton dissociation in the aqueous phase. The method is based on titration by means of the organic phase. A linear form of the respective model is given for parameter estimation by linear regression. This strategy is used for the determination of the partition coefficients of some N-unprotected n-alkyl esters of phenylalanine in various aqueous-organic biphasic systems. These esters are of interest for the optical resolution of phenylalanine with chymotrypsin.     

Binding specificity and the ligand dissociation process in the E. coli biotin holoenzyme synthetase

The binding of the Escherichia coli biotin holoenzyme synthetase to the two ligands, biotin and bio-5'-AMP, is coupled to disorder-to-order transitions in the protein. In the structure of the biotin complex, a "glycine-rich" loop that is disordered in the apo-enzyme is folded over the ligand. Mutations in three residues in this loop result in significant changes in the affinity of the enzyme for both biotin and bio-5'-AMP. The kinetic basis of these losses in the affinity resides primarily in changes in the unimolecular rates of dissociation of the complexes. In this work, isothermal titration calorimetry has been employed to examine the detailed thermodynamics of binding of three loop mutants to biotin and bio-5'-AMP. The energetic features of dissociation of the protein*ligand complexes also have been probed by measuring the temperature dependencies of the unimolecular dissociation rates. Analysis of the data using the Eyring formalism yielded entropic and enthalpic contributions to the energetic barrier to dissociation. The thermodynamic results coupled with the known structures of the apo-enzyme and biotin complex have been used to formulate a model for progression from the ground-state complex to the transition state in biotin dissociation. In this model, the transition-state is characterized by both partial disruption of noncovalent bonds and acquisition of some of the disorder that characterizes the glycine-rich loop in the absence of ligand.     

Fractal analysis of vascular networks: Insights from morphogenesis

Considering their extremely complicated and hierarchical structure, a long standing question in vascular physio-pathology is how to characterize blood vessels patterns, including which parameters to use. Another question is how to define a pertinent taxonomy, with applications to normal development and to diagnosis and/or staging of diseases.To address these issues, fractal analysis has been applied by previous investigators to a large variety of healthy or pathologic vascular networks whose fractal dimensions have been sought. A review of the results obtained on healthy vascular networks first shows that no consensus has emerged about whether normal networks must be considered as fractals or not.Based on a review of previous theoretical work on vascular morphogenesis, we argue that these divergences are the signature of a two-step morphogenesis process, where vascular networks form via progressive penetration of arterial and venous quasi-fractal arborescences into a pre-existing homogeneous capillary mesh. Adopting this perspective, we study the multi-scale behavior of generic patterns (model structures constructed as the superposition of homogeneous meshes and quasi-fractal trees) and of healthy intracortical networks in order to determine the artifactual and true components of their multi-scale behavior. We demonstrate that, at least in the brain, healthy vascular structures are a superposition of two components: at low scale, a mesh-like capillary component which becomes homogeneous and space-filling over a cut-off length of order of its characteristic length; at larger scale, quasi-fractal branched (tree-like) structures. Such complex structures are consistent with all previous studies on the multi-scale behavior of vascular structures at different scales, resolving the apparent contradiction about their fractal nature.Consequences regarding the way fractal analysis of vascular networks should be conducted to provide meaningful results are presented. Finally, consequences for vascular morphogenesis or hemodynamics are discussed, as well as implications in case of pathological conditions, such as cancer.     

Analyte-receptor binding on surface plasmon resonance biosensors: a fractal analysis of Cre-loxP interactions and the influence of Cl, O, and S on drug-liposome interactions

A fractal analysis of the association and dissociation (whereever applicable) of Cre-loxP interactions and drug-liposome interactions on a sensor chip surface is presented. In both of these cases a dual-fractal analysis is required to adequately describe the association kinetics. The dissociation kinetics for Cre-loxP interactions is adequately described by a single-fractal analysis. The dual-fractal analysis used to describe the association kinetics of Cre-loxP interactions is consistent with the original two-step mechanism presented using a surface plasmon resonance biosensor. Our analysis includes both diffusion and surface effects by introducing the fractal dimension which makes quantitative the degree of heterogeneity on the sensor chip surface. Affinities are provided. Only the association kinetics were analysed for drug-liposome interactions since the initial sections of the dissociation curves were too steep to obtain reasonable drug-liposome complex concentration values on the sensor chip with time. Attempts made to relate the association rate coefficients with the molecular weight of the drug were unsuccessful. On using desipramine and imipramine as "arbitrarily selected standards" or "references" (only C, H, and N atoms present), it was noticed from the data analysed that the inclusion of the O and S atoms in the drug leads to a decrease in the association rate coefficients, ka1 (or k1) and ka2 (or k2) (compared with the arbitrarily selected standards or references). Similarly, the addition of the Cl atom in the drug leads to an increase in the association rate coefficient (compared with the arbitrarily selected standards or references). More data needs to be analysed to determine whether this is true for other drugs also.     

Heart and T-Lymphocyte Cell Surfaces Both Exhibit Positive Cooperativity in Binding a Membrane-Lytic Toxin

Cobra venom cytotoxins (CTX) have been shown to disrupt cells as different as immunocytes, skeletal myocytes, erythrocytes and tumor cells. Nevertheless, even subpopulations of tumor cells are differentially susceptible to CTX by an order of magnitude. In the present study, our objective was to compare CTX-specific binding with cytolytic potency for two disparate cell types in vitro. We investigated the lytic activity of cytotoxin-III from Naja naja atra (NNA, fraction D) using heart cells and human leukemic T-cells (CEM cells). For both cell types, 50% cytolysis, assessed by tetrazolium dye conversion, occurred with μm concentrations of toxin (EC₅₀= 2.2 μm). We examined the binding of radiolabeled CTX III to both heart cells and CEM cells and found the apparent dissociation constant (K _Dapp) to be 0.69 μm and 0.75 μm, for CEM and heart cells respectively. The B _max for the CEM cells was 1.0 fmoles/cell and that for heart cells was 5.2 fmoles/cell, both exhibiting positive cooperativity between the sites (Hill coefficients 1.4, T-cells; 1.6, heart). Relatively modest dissociation constants plus high numbers of binding sites per cell are consistent with a model of CTX binding to plasma membranes by interaction with phospholipids in the bilayer. Our results suggest that the lytic activity of this cytotoxin follows its binding to a population of sites on the cells in a cooperative fashion. Received: 8 May 1995/Revised: 17 November 1995     

Binding,unfolding and refolding dynamics of serum albumins

Background

The serum albumins (human and bovine serum albumin) occupy a seminal position among all proteins investigated until today as they are the most abundant circulatory proteins. They play the major role of a transporter of many bio-active substances which include various fatty acids, drug molecules, and amino acids to the target cells. Hence, studying the interaction of these serum albumins with different binding agents has attracted enormous research interests from decades. The nature and magnitude of these bindings have direct consequence on drug delivery, pharmacokinetics, therapeutic efficacy and drug design and control.

Scope of the review

In the present review, we summarize the binding characteristics of both the serum albumins with surfactants, lipids and vesicles, polymers and dendrimers, nanomaterials and drugs. Finally we have reviewed the effect of various chemical and physical denaturants on these albumins with a special emphasis on protein unfolding and refolding dynamics.

Major conclusions

The topic of binding and dynamics of protein unfolding and refolding spans across all areas of inter-disciplinary sciences and will benefit clinical toxicology and medicines. The extensive data from several contemporary research based on albumins will help us to understand protein dynamics in a more illustrious manner.

General significance

These data have immense significance in understanding and unravelling the mechanisms of protein unfolding/refolding and thus can pave the way to prevent protein mis-folding/aggregation which sometimes leads to severe consequences like Parkinson's and Alzheimer's diseases. This article is a part of a Special Issue entitled Serum Albumin. This article is part of a Special Issue entitled Serum Albumin.     

Binding of nitrite-N on polyphenols during nitrification

Summary The conversion of substantial amounts of ammonia nitrogen into organic nitrogen as a direct result of nitrification at neutral pH-values, was monitored in soil suspensions amended with ammonium nitrogen. The influence of the chemolithotrophic nitrifying bacteria was verified by applying nitrapyrin as a selective inhibitor in control experiments. In addition, the role of phenolic compounds was examined by adding α naphthol. The factors influencing the nitrification processi.e. pH, NH ₄ ⁺ −N, NO ₂ ⁻ −N, NO ₃ ⁻ −N were measured during a 60 days incubation period. Nitrification started to be active after 5 and 10 days in the normal and the naphthol spiked soil suspensions respectively; it was inhibited in the nitrapyrin controls. Parallel with nitrification, formation of organic nitrogen was observed. The humic matter fractions were extracted and analyzed by I.R. spectroscopy which revealed the valence vibration ranges of nitro and nitroso groups fixed in different positions on aromatic compounds, both for normal and naphthol spiked samples. High resolution gas chromatography combined with mass spectroscopic analysis indicated the formation of nitrosonaphtholes. In addition a novel organic nitro compound was identifiedi.e. an azido nitro benzene. No nitrogen was fixed in the samples treated with nitrification inhibitor. A mechanism for the fixation of nitrite nitrogen during nitrification is proposed.     

Effects of Ceramics Irradiation on Dissociation State of L-Amino Acids

Non-thermal effects of ceramics irradiation on dissociation state of twenty L-amino acids have been investigated. Dissociation constants of the amino acids other than His and Glu varied by a 3-h irradiation under cooling. pK’s of α-carboxyl group of amino acids having longer side chains on the α-carbon were decreased by the irradiation. Although pK’s of α-amino group of Arg, Lys, Asp, and CySH were decreased by the irradiation and pK of Tyr was increased, pK’s of the other fifteen amino acids were not affected. Although the isoelectric points of Lys, Arg, Trp, Asp, and CySH were decreased by the irradiation, those of the other fifteen amino acids were not affected. It was suggested that various changes in pH of amino acids in aqueous solution and dissociation state of the functional groups will be caused from stimulation by the irradiation and stabilization of the hydration layer around amino acids.     

Electron Capture Dissociation Mass Spectrometry in Characterization of Peptides and Proteins

Electron capture dissociation (ECD) represents one of the most recent and significant advancements in tandem mass spectrometry (MS/MS) for the identification and characterization of polypeptides. In comparison with the conventional fragmentation techniques, such as collisionally activated dissociation (CAD), ECD provides more extensive sequence fragments, while allowing the labile modifications to remain intact during backbone fragmentation—an important attribute for characterizing post-translational modifications. Herein, we present a brief overview of the ECD technique as well as selected applications in characterization of peptides and proteins. Case studies including characterization and localization of amino acid glycosylation, methionine oxidation, acylation, and “top–down” protein mass spectrometry using ECD will be presented. A recent technique, coined as electron transfer dissociation (ETD), will be also discussed briefly.     

影响纳豆激酶酶促反应速度因素的研究

利用分光光度法对由纳豆菌发酵产生的纳豆激酶 (NK)进行了动力学性质的研究。以双倒数作图法 (L -B作图法 )求取Km。采用单因素试验法和正交试验法研究了底物浓度、酶浓度、温度、pH值对酶促反应速度的影响。结果表明该纳豆激酶的Km值为 3.4 98× 1 0 -6g·mL-1 ,当水解时间为 1 0min时 ,最适底物浓度为 1 6mg·mL-1 ,最适温度为 6 0℃ ,最适 pH为 8.0。     

Effects of Guanyl Nucleotides on [3H]Flunitrazepam Binding to Rat Hippocampal Synaptic Membranes: Equilibrium Binding and Dissociation Kinetics

The effects of guanyl nucleotides on the binding of [3H]flunitrazepam to rat hippocampal synaptic membranes were studied. In equilibrium binding studies, gamma-amino-n-butyric acid (GABA) increased and GTP decreased the binding affinity of [3H]flunitrazepam; GTP also caused a decrease in binding capacity. The effect, however, is variable. In studies of the dissociation kinetics of [3H]flunitrazepam using diazepam and the antagonist Ro 15-1788 as the displacers, there was evidence of two dissociation rate constants. GTP increased both the fast- and slow-dissociation rate constants and increased the ratio of the slow-dissociation binding state. The effect of GTP was mimicked by its nonhydrolyzable analogue 5'-guanylylimidodiphosphate but not by ATP and occurred when diazepam, but not when Ro 15-1788, was used as the displacer. GABA antagonized the effect of GTP on the dissociation of [3H]flunitrazepam. The nature of the benzodiazepine receptor, its actions, and the possible role of cyclic AMP as a second messenger are discussed.     

Ontogeny of Calcium Antagonist Binding Sites in Chick Brain and Heart

The ontogeny of chick brain and heart ventricle calcium antagonist binding sites was determined, using [3H]nitrendipine ([3H]NDP), as the ligand. The binding of [3H]NDP to adult heart and brain was kinetically very similar, with the former displaying a KD of 0.28 +/- 0.02 nM and a Bmax of 138 +/- 17 fmol/mg protein, and the latter a KD of 0.30 +/- 0.02 nM and a Bmax of 160 +/- 12 fmol/mg protein. The binding site in both brain and heart was highly specific for dihydropyridine calcium antagonists, such as nifedipine, nimodipine, and nisoldipine, since these drugs were several orders of magnitude more potent as inhibitors of [3H]NDP binding than verapamil, methoxyverapamil, or diltiazem. The developmental appearance of [3H]NDP binding sites in brain was rather gradual, with adult levels being attained just prior to birth. This was in contrast to the profile in heart ventricle which showed essentially adult levels at seven days gestation. The acquisition of [3H]NDP binding sites in chick brain roughly paralleled the onset of neuronal maturation and functional activity. In both chick brain and heart, verapamil and methoxyverapamil were weak inhibitors of [3H]NDP binding. However, the inhibition of binding in both tissues was markedly biphasic, with only 50% of the binding sites being susceptible to inhibition by each agent, suggesting that multiple calcium antagonist binding sites may exist in both tissues.     

The Neurophysiology of Dissociation and Chronic Disease

Dissociation as a clinical psychiatric condition has been defined primarily in terms of the fragmentation and splitting of the mind, and perception of the self and the body. Its clinical manifestations include altered perceptions and behavior, including derealization, depersonalization, distortions of perception of time, space, and body, and conversion hysteria. Using examples of animal models, and the clinical features of the whiplash syndrome, we have developed a model of dissociation linked to the phenomenon of freeze/immobility. Also employing current concepts of the psychobiology of posttraumatic stress disorder (PTSD), we propose a model of PTSD linked to cyclical autonomic dysfunction, triggered and maintained by the laboratory model of kindling, and perpetuated by increasingly profound dorsal vagal tone and endorphinergic reward systems. These physiologic events in turn contribute to the clinical state of dissociation. The resulting autonomic dysregulation is presented as the substrate for a diverse group of chronic diseases of unknown origin.