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Binding Model (binding + model)
Selected AbstractsAdding magnesium to the silver-gill binding model for rainbow trout (Oncorhynchus mykiss)ENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 3 2001Melissa L. Schwartz Abstract Rainbow trout (Oncorhynchus mykiss; 2,17 g) were exposed to approximately 0.1 ,M silver as AgNO3 for 3 to 4 h in synthetic, ion-poor water (20 ,M Ca, 100 ,M Na, 150 ,M Cl, pH 7) to which was added Mg, Ca, or thiosulfate (S2O3). Gills were extracted and assayed for Ag using graphite furnace atomic absorption spectrophotometry. Up to 210 mM Mg (four fold the concentration of Mg in seawater) did not reduce accumulation of Ag by trout gills. The conditional equilibrium stability constant (K) for Mg at silver-binding sites on the gills was calculated to be log KMg-gillAg = 3.0, or approximately half-as-strong binding as for Ca at these sites. The inclusion of the Mg-gill stability constant into the original Ag-gill binding model increases the flexibility of the model, although the competitive effects of Mg are only important in sodium-poor systems. [source] Structure of the HIV-1 Rev response element alone and in complex with regulator of virion (Rev) studied by atomic force microscopyFEBS JOURNAL, Issue 15 2009Jesper Pallesen The interaction of multiple HIV-1 regulator of virion (Rev) proteins with the viral RNA target, the Rev response element (RRE), is critical for nuclear export of incompletely spliced and unspliced viral RNA, and for the onset of the late phase in the viral replication cycle. The heterogeneity of the Rev,RRE complex has made it difficult to study using conventional structural methods. In the present study, atomic force microscopy is applied to directly visualize the tertiary structure of the RRE RNA alone and in complex with Rev proteins. The appearance of the RRE is compatible with the earlier proposed RRE secondary structure in dimensions and overall shape, including a stalk and a head interpreted as stem I, and stem-loops II,V in the secondary structure model, respectively. Atomic force microscopy imaging of the Rev,RRE complex revealed an increased height of the structure both in the stalk and head regions, which is in accordance with a binding model in which Rev binding to a high affinity site in stem IIB triggers oligomerization of Rev proteins through cooperative binding along stem I in RRE. The present study demonstrates that atomic force microscopy comprises a useful technique to study complex biological structures of nucleic acids at high resolution. [source] Microfibril-associated glycoprotein-1 binding to tropoelastinFEBS JOURNAL, Issue 14 2004Multiple binding sites, the role of divalent cations Microfibrils and elastin are major constituents of elastic fibers, the assembly of which is dictated by multimolecular interactions. Microfibril-associated glycoprotein-1 (MAGP-1) is a microfibrillar component that interacts with the soluble elastin precursor, tropoelastin. We describe here the adaptation of a solid-phase binding assay that defines the effect of divalent cations on the interactions between MAGP-1 and tropoelastin. Using this assay, a strong calcium-dependent interaction was demonstrated, with a dissociation constant of 2.8 ± 0.3 nm, which fits a single-site binding model. Manganese and magnesium bestowed a weaker association, and copper did not facilitate the protein interactions. Three constructs spanning tropoelastin were used to quantify their relative contributions to calcium-dependent MAGP-1 binding. Binding to a construct spanning a region from the N-terminus to domain 18 followed a single-site binding model with a dissociation constant of 12.0 ± 2.2 nm, which contrasted with the complex binding behavior observed for fragments spanning domains 17,27 and domain 27 to the C-terminus. To further elucidate binding sites around the kallikrein cleavage site of domains 25/26, MAGP-1 was presented with constructs containing C-terminal deletions within the region. Construct M1659, which spans a region from the N-terminus of tropoelastin to domain 26, inclusive, bound MAGP-1 with a dissociation constant of 9.7 ± 2.0 nm, which decreased to 4.9 ± 1.0 nm following the removal of domain 26 (M155n), thus displaying only half the total capacity to bind MAGP-1. These results demonstrate that MAGP-1 is capable of cumulative binding to distinct regions on tropoelastin, with different apparent dissociation constants and different amounts of bound protein. [source] Cyclin-dependent kinase inhibitors for treating cancerMEDICINAL RESEARCH REVIEWS, Issue 6 2001Peter L. Toogood Abstract Cyclin dependent kinases (Cdks) are essential enzymes for the control of cell cycle progression. Inhibitors of cyclin-dependent kinases are anticipated to possess therapeutic utility against a wide variety of proliferative diseases, especially cancer. The field of published small molecule Cdk inhibitors is briefly reviewed here as background to a summary of work on a class of pyrido[2,3- d]pyrimidine Cdk inhibitors. Compounds from this class are described that display potency against cyclin D/Cdk4 up to IC50,=,0.004 ,M. Good to moderate selectivity for cyclin D/Cdk4 is also reported for compounds in this structural class. Structure-activity relationship data are presented for substitution at the C2 and N8 positions and these data are interpreted in the context of a binding model that is based on the Cdk2 crystal structure. A representative cyclin D/Cdk4 inhibitor (compound 56) is demonstrated to selectively inhibit the proliferation of an Rb+ cell line vs. a matched Rb, cell line and to produce a distinct G1 block consistent with cyclin D/Cdk4 inhibition in cells. © 2001 John Wiley & Sons, Inc. Med Res Rev, 21, No. 6, 487,498, 2001 [source] Sequence-dependent Interactions of Cationic Naphthalimides and PolynucleotidesPHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 4 2007Sun McMasters The binding interactions of three naphthalimide derivatives with heteropoly nucleic acids have been evaluated using fluorescence, absorption and circular dichroism spectroscopies. Mono- and bifunctionalized naphthalimides exhibit sequence-dependent variations in their affinity toward DNA. The heteropoly nucleic acids, [Poly(dA-dT)]2 and [Poly(dG-dC)]2, as well as calf thymus (CT) DNA, were used to understand the factors that govern binding strength and selectivity. Sequence selectivity was addressed by determining the binding constants as a function of polynucleotide composition according to the noncooperative McGhee,von Hippel binding model. Binding affinities toward [poly(dA-dT)]2 were the largest for spermine-substituted naphthalimides (Kb = 2,6 × 106 m,1). The association constants for complex formation between the cationic naphthalmides and [poly(dG-dC)]2 or CT DNA (58% A-T content) were 2,500 times smaller, depending on the naphthalmide,polynucleotide pair. The binding modes were also assessed using a combination of induced circular dichroism and salt effects to determine whether the naphthalimides associate with DNA through intercalative, electrostatic or groove-binding. The results show that the monofunctionalized spermine and pyridinium-substituted naphthalimides associate with DNA through electrostatic interactions. In contrast, intercalative interactions are predominant in the complex formed between the bifunctionalized spermine compound and all of the polynucleotides. [source] Tight binding modelling of electronic band structure in conventional InGaN/GaN and dilute GaAsN/GaAs nitride heterostructuresPHYSICA STATUS SOLIDI (C) - CURRENT TOPICS IN SOLID STATE PHYSICS, Issue 2 2007H. Hakan Gürel Abstract We utilize a semi-empirical sp3s * tight binding model to investigate the strain and composition effects on electronic structure of conventional InGaN/GaN and dilute GaAsN/GaAs cubic nitride heterostructures. The model includes the second nearest neighbor (2NN) atomic interactions, spin-orbit splitting and nonlinear composition variation of atomic energies and bond lengths of ternaries. Results show that band gaps of conventional InGaN increase with composition for 0 < x < 1. However, the , band gap of dilute GaAsN decreases with composition for x < 0.25 and then starts to increase for 0.26 < x < 1. (© 2007 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Single run measurements of drug-protein binding by high-performance frontal analysis capillary electrophoresis and mass spectrometryRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 12 2005Hong Wan A novel drug-protein binding measurement method based on high-performance frontal analysis and capillary electrophoresis (HPFA/CE) is presented. A single run measurement approach is proposed to circumvent utilization of a calibration curve that is often performed with HPFA. A sensitive mass spectrometer is applied as a detector enabling the measurement of in vitro protein binding at lower drug concentrations. Unbound free fraction and binding constants can be determined by a single run measurement by consecutive injections of an internal drug standard, a buffer plug and a drug-protein mixture. Effects of injection volumes on peak height and plateau profile were investigated in two different separation systems, non-volatile buffer and volatile buffer, with UV and mass spectrometry detection, respectively. A simplified one-to-one binding model is employed to evaluate the proposed method by using both single and multiple drug concentrations to measure the unbound free fraction and calculate the binding constants of some selected compounds. The method is suitable for rapid and direct screening of the binding of a drug to a specific protein or drug-plasma protein binding. Copyright © 2005 John Wiley & Sons, Ltd. [source] Single-molecule pair studies of the interactions of the ,-GalNAc (Tn-antigen) form of porcine submaxillary mucin with soybean agglutininBIOPOLYMERS, Issue 9 2009Marit Sletmoen Abstract Mucins form a group of heavily O -glycosylated biologically important glycoproteins that are involved in a variety of biological functions, including modulating immune response, inflammation, and adhesion. Mucins are also involved in cancer and metastasis and often express diagnostic cancer antigens. Recently, a modified porcine submaxillary mucin (Tn-PSM) containing GalNAc,1- O -Ser/Thr residues was shown to bind to soybean agglutinin (SBA) with ,106 -fold enhanced affinity relative to GalNAc,1- O -Ser, the pancarcinoma carbohydrate antigen. In this study, dynamic force spectroscopy is used to investigate molecular pairs of SBA and Tn-PSM. A number of force jumps that demonstrate unbinding or rebinding events were observed up to a distance equal to 2.0 ,m, consistent with the length of the mucin chain. The unbinding force increased from 103 to 402 pN with increasing force loading rate. The position of the activation barrier in the energy landscape of the interaction was 0.1 nm. The lifetime of the SBA,TnPSM complex in the absence of applied force was determined to be in the range 1.3,1.9 s. Kinetic parameters describing the rate of dissociation of other sugar lectin interactions are in the range 3.3 × 10,3,2.5 × 10,3 s. The long lifetime of the SBA-TnPSM complex is compatible with a binding model in which lectin molecules "bind and jump" from ,-GalNAc residue to ,-GalNAc residue along the polypeptide chain of Tn-PSM before dissociating. These findings have important implications for the molecular recognition properties of mucins. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 719,728, 2009. This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] A Novel Methodological Approach for the Analysis of Host,Ligand Interactions,CHEMPHYSCHEM, Issue 2 2007Daniela Strat Dr. Abstract Traditional analysis of drug-binding data relies upon the Scatchard formalism. These methods rely upon the fitting of a linear equation providing intercept and gradient data that relate to physical properties, such as the binding constant, cooperativity coefficients and number of binding sites. However, the existence of different binding modes with different binding constants makes the implementation of these models difficult. This article describes a novel approach to the binding model of host,ligand interactions by using a derived analytical function describing the observed signal. The benefit of this method is that physically significant parameters, that is, binding constants and number of binding sites, are automatically derived by the use of a minimisation routine. This methodology was utilised to analyse the interactions between a novel antitumour agent and DNA. An optical spectroscopy study confirms that the pentacyclic acridine derivative (DH208) binds to nucleic acids. Two binding modes can be identified: a stronger one that involves intercalation and a weaker one that involves oriented outer-sphere binding. In both cases the plane of the bound acridine ring is parallel to the nucleic acid bases, orthogonal to the phosphate backbone. Ultraviolet (UV) and circular dichroism (CD) data were fitted using the proposed model. The binding constants and the number of binding sites derived from the model remained consistent across the different techniques used. The different wavelengths at which the measurements were made maintained the coherence of the results. 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