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Binding Interactions (binding + interaction)
Selected AbstractsChemInform Abstract: Theoretical Study of Binding Interactions and Vibrational Raman Spectra of Water in Hydrogen-Bonded Anionic Complexes: (H2O)n - (n = 2 and 3), H2O×××X - (X: F, Cl, Br, and I), and H2O×××M - (M: Cu, Ag, and Au).CHEMINFORM, Issue 18 2008De-Yin Wu Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a "Full Text" option. The original article is trackable via the "References" option. [source] Evaluation of relative DNA binding affinities of anthrapyrazoles by electrospray ionization mass spectrometryJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 5 2007Suncerae I. Smith Abstract Binding interactions of a new series of anthrapyrazoles (APs) with DNA were evaluated by electrospray ionization mass spectrometry (ESI-MS). Relative binding affinities were estimated from the ESI-MS data based on the fraction of bound DNA for DNA/anthrapyrazole mixtures, and they show a correlation to the shift in melting point of the DNA measured from a previous study. Minimal sequence specificity was observed for the series of anthrapyrazoles. Upon collisionally activated dissociation of the duplex/anthrapyrazole complexes, typically ejection of the ligand was the dominant pathway for most of the complexes. However, for complexes containing AP2 or mitoxantrone, strand separation with the ligand remaining on one of the single strands was observed, indicative of a different binding mode or stronger binding. Copyright © 2007 John Wiley & Sons, Ltd. [source] Binding interactions between peptides and proteins of the class II Major Histocompatibility ComplexMEDICINAL RESEARCH REVIEWS, Issue 2 2002Benjamin J. McFarland Abstract The activation of helper T cells by peptides bound to proteins of the class II Major Histocompatibility Complex (MHC II) is pivotal to the initiation of an immune response. The primary functional requirement imposed on MHC II proteins is the ability to efficiently bind thousands of different peptides. Structurally, this is reflected in a unique architecture of binding interactions. The peptide is bound in an extended conformation within a groove on the membrane distal surface of the protein that is lined with several pockets that can accommodate peptide side-chains. Conserved MHC II protein residues also form hydrogen bonds along the length of the peptide main-chain. Here we review recent advances in the study of peptide-MHC II protein reactions that have led to an enhanced understanding of binding energetics. These results demonstrate that peptide-MHC II protein complexes achieve high affinity binding from the array of hydrogen bonds that are energetically segregated from the pocket interactions, which can then add to an intrinsic hydrogen bond-mediated affinity. Thus, MHC II proteins are unlike antibodies, which utilize cooperativity among binding interactions to achieve high affinity and specificity. The significance of these observations is discussed within the context of possible mechanisms for the HLA-DM protein that regulates peptide presentation in vivo and the design of non-peptide molecules that can bind MHC II proteins and act as vaccines or immune modulators. © 2002 John Wiley & Sons, Inc. Med Res Rev, 22, No. 2, 168,203, 2002; DOI 10.1002/med.10006 [source] Efficient Increase of DNA Cleavage Activity of a Diiron(III) Complex by a Conjugating Acridine GroupEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 34 2007Xiao-Qiang Chen Abstract A new diferric complex, Fe2Lb, in which a DNA intercalator (acridine) is linked to a precursor diferric complex (Fe2La), has been designed and synthesised as a hydrolytic cleaving agent of DNA. Compared with Fe2La (without the DNA intercalator) (La: 2,6-bis{[(2-hydroxybenzyl)(pyridin-2-yl)methylamino]methyl}-4-methylphenol), Fe2Lb [Lb: 5-(acridin-9-yl)- N -(3,5-bis{[(2-hydroxybenzyl)(pyridin-2-yl)methylamino]methyl}-4-hydroxybenzyl)pentanamide] leads to a 14-fold increase in the cleavage efficiency of plasmid DNA due to the binding interaction between DNA and the acridine moiety. The interaction has been demonstrated by UV/Vis absorption, CD spectroscopy, viscidity experiments and thermal denaturation studies. The hydrolytic mechanism is supported by evidence from T4 DNA ligase assay, reactive oxygen species (ROS) quenching and BNPP [bis(4-nitrophenyl) phosphate, a DNA model] cleavage experiments. The pH dependence of the BNPP cleavage by Fe2La in aqueous buffer media shows a bell-shaped pH,kobs profile with an optimum point around a pH of 7.0 which is in good agreement with the maximum point of the pH-dependent relative concentration curve of active species from the pH titration experiments. The determination of the initial rates at a pH of 7.36 as a function of substrate concentration reveals saturation kinetics with Michaelis,Menten-like behaviour and Fe2La shows a rate acceleration increase of 4.7,×,106 times in the hydrolysis of BNPP. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007) [source] Metabolic GHB precursor succinate binds to ,-hydroxybutyrate receptors: Characterization of human basal ganglia areas nucleus accumbens and globus pallidusJOURNAL OF NEUROSCIENCE RESEARCH, Issue 1 2006Tünde Molnár Abstract Binding of the metabolic ,-hydroxybutyrate (GHB) precursor succinate to NCS-382-sensitive [3H]GHB-labeled sites in crude synaptosomal or purified synaptic membrane fractions prepared from the human nucleus accumbens (NA), globus pallidus (GP) and rat forebrain has been shown. This site can be characterized by binding of ethyl hemisuccinate and gap-junction blockers, including carbenoxolone hemisuccinate and ,-GRA. There was no significant binding interaction between GABAB receptor ligands (CGP 55845, (R)-baclofen) and these [3H]GHB-labeled sites. GHB, NCS-382 and succinate binding profile of [3H]GHB-labeled sites in rat forebrain, human NA or GP synaptic membranes were similar. The synaptic fraction isolated from the rat forebrain was characterized by GHB binding inhibition constants: Ki,NCS-382 = 1.2 ± 0.2 ,M, Ki,GHB = 1.6 ± 0.3 ,M and Ki,SUCCINATE = 212 ± 66 ,M. In crude membranes containing mainly extrasynaptic membranes, distinct GHB and GABAB receptor sites were found in the NA. By contrast, extrasynaptic GABAB receptor sites of rat forebrain and GP were GHB- and succinate-sensitive, respectively. The heterogeneity of GABAB sites found in native membranes indicates GABAB receptor-dependent differences in GHB action. Based on these findings, we suggest that succinate (and possibly drugs available as succinate salt derivatives) can mimic some of the actions of GHB. © 2006 Wiley-Liss, Inc. [source] The role of segment 32,47 of cholecystokinin receptor type A in CCK8 binding: synthesis, nuclear magnetic resonance, circular dichroism and fluorescence studiesJOURNAL OF PEPTIDE SCIENCE, Issue 3 2003Stefania De Luca Abstract The segment 32,47 of the N -terminal extracellular domain of the type A cholecystokinin receptor, CCKA -R(32,47), was synthesized and structurally characterized in a membrane mimicking environment by CD, NMR and molecular dynamics calculations. The region of CCKA -R(32,47) encompassing residues 39,46 adopted a well-defined secondary structure in the presence of DPC micelles, whereas the conformation of the N -terminal region (segment 32,37) could not be uniquely defined by the NOE derived distance constraints because of local flexibility. The conformation of the binding domain of CCKA -R(32,47) was different from that found for the intact N -terminal receptor tail, CCKA -R(1,47). To assess whether CCKA -R(32,47) was still able to bind the nonsulfated cholecystokinin C -terminal octapeptide, CCK8, a series of titrations was carried out in SDS and DPC micelles, and the binding interaction was followed by fluorescence spectroscopy. These titrations gave no evidence for complex formation, whereas a high binding affinity was found between CCKA -R(1,47) and CCK8. The different affinities for the ligand shown by CCKA -R(32,47) and CCKA -R(1,47) were paralleled by different interaction modes between the receptor segments and the micelles. The interaction of CCKA -R(32,47) with DPC micelles was much weaker than that of CCKA -R(1,47), because the former receptor segment lacks proper stabilizing contacts with the micelle surface. In the case of SDS micelles CCKA -R(32,47) was found to form non-micellar adducts with the detergent that prevented the onset of a functionally significant interaction between the receptor segment and the micelle. It is concluded that tertiary structure interactions brought about by the 1,31 segment play a key role in the stabilization of the membrane bound, biologically active conformation of the N -terminal extracellular tail of the CCKA receptor. Copyright © 2003 European Peptide Society and John Wiley & Sons, Ltd. [source] Perfluorocarbons: Life sciences and biomedical uses Dedicated to the memory of Professor Guy Ourisson, a true RENAISSANCE man.JOURNAL OF POLYMER SCIENCE (IN TWO SECTIONS), Issue 7 2007Marie Pierre Krafft Abstract Perfluorocarbons are primarily characterized by outstanding chemical and biological inertness, and intense hydrophobic and lipophobic effects. The latter effects provide a powerful noncovalent, labile binding interaction that can promote selective self- assembly. Perfluoro compounds do not mimic nature, yet they can offer abiotic building blocks for the de novo design of functional biopolymers and alternative solutions to physiologically vital issues. They offer new tags useful for molecular recognition, selective sorting, and templated binding (e.g., selective peptide and nucleic acid pairing). They also stabilize membranes and provide micro- and nanocompartmented fluorous environments. Perfluorocarbons provide inert, apolar carrier fluids for lab-on-a-chip experiments and assays using microfluidic technologies. Low water solubility, combined with high vapor pressure, allows stabilization of injectable microbubbles that serve as contrast agents for diagnostic ultrasound imaging. High gas solubilities are the basis for an abiotic means for intravascular oxygen delivery. Other biomedical applications of fluorocarbons include lung surfactant replacement and ophthalmologic aids. Diverse colloids with fluorocarbon phases and/or shells are being investigated for molecular imaging using ultrasound or magnetic resonance, and for targeted drug delivery. Highly fluorinated polymers provide a range of inert materials (e.g., fluorosilicons, expanded polytetrafluoroethylene) for contact lenses, reconstructive surgery (e.g., vascular grafts), and other devices. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 1185,1198, 2007. [source] Distribution and binding of novel photosensitizer 2-devinyl-2-(1-methoxyl-ethyl) chlorin f in human breast cancer cells MCF-7LASER PHYSICS LETTERS, Issue 6 2009Y. Liu Abstract The interaction of novel Photosensitizer 2-devinyl-2-(1-methoxyl-ethyl) chlorin f (CPD4) with human breast cancer cells MCF-7 was studied by fluorescence spectrum and laser confocal scan microscopy (LCSM). The experimental results exhibit that fluorescence emission band of CPD4 in MCF-7 cells move to long wavelength about 5 nm compared with that in incubation solution, which suggest that CPD4 could enter into MCF-7 cells and bind them strongly by electrostatic or hydrogen binding interaction. The LCSM images of CPD4 in MCF-7 cells show that the binding of CPD4 in MCF-7 cells takes place in cellular membrane and mitochondria mainly. These results indicate that CPD4 can be of selective subcellular location, but not free ionic status in MCF-7 cells.CPD4 could be a kind of promising photosensitizer for Photodynamic therapy. (© 2009 by Astro Ltd., Published exclusively by WILEY-VCH Verlag GmbH & Co. KGaA) [source] High-resolution crystal structure of human Mapkap kinase 3 in complex with a high affinity ligandPROTEIN SCIENCE, Issue 1 2010Robert Cheng Abstract The Mapkap kinases 2 and 3 (MK2 and MK3) have been implicated in intracellular signaling pathways leading to the production of the pro-inflammatory cytokine tumor necrosis factor alpha. MK2 has been pursued by the biopharmaceutical industry for many years for the development of a small molecule anti-inflammatory treatment and drug-like inhibitors have been described. The development of some of these compounds, however, has been slowed by the absence of a high-resolution crystal structure of MK2. Herein we present a high-resolution (1.9 Å) crystal structure of the highly homologous MK3 in complex with a pharmaceutical lead compound. While all of the canonical features of Ser/Thr kinases in general and MK2 in particular are recapitulated in MK3, the detailed analysis of the binding interaction of the drug-like ligand within the adenine binding pocket allows relevant conclusions to be drawn for the further design of potent and selective drug candidates. [source] Tuberous Sclerosis: from Tubers to mTORANNALS OF HUMAN GENETICS, Issue 1 2003D. J. Kwiatkowski Summary Tuberous sclerosis (TSC) is an autosomal dominant hamartoma syndrome whose causative genes (TSC1 and TSC2) were identified 5 and 9 years ago respectively. Their encoded proteins are large, and apart from a strong binding interaction with each other, relatively little was known about their biochemical function. Recent studies in Drosophila have pinpointed a critical function for the DrosophilaTSC1/TSC2 homologues in the regulation of cell size. Epistasis experiments and a variety of biochemical studies that followed have indicated a critical function for these proteins in the highly conserved PI-3-kinase-Akt-mTOR signalling pathway. [source] Behavior of interacting species in vacancy affinity capillary electrophoresis described by mass balance equationELECTROPHORESIS, Issue 16 2008Ying Sun Abstract Vacancy ACE (VACE) is one of the ACE methods, and has been used to study binding interactions between different biomolecules. Thermodynamic binding constants can be estimated with nonlinear regression methods. With a highly efficient computer simulation program (SimDCCE), it is possible to demonstrate the detailed behaviors of each species during the interaction process under different conditions. In this work, thirteen scenarios in four different combinations of migration orders of the free protein, free drug, and complex formed are studied. The detailed interaction process between protein and ligand is discussed and illustrated based on the mass balance equation, also called mass transfer equation. By properly setting the parameters in the simulation model, the influence of different factors during the interaction process can be well understood. [source] Developmental and Therapeutic Pharmacology of Antiepileptic DrugsEPILEPSIA, Issue 2000Hisao Miura Summary: We investigated the clinical effects and plasma levels of zonisamide (ZNS) in children with cryptogenic localization-related epilepsies. ZNS is absorbed slowly from the gastrointestinal tract, and its biological half-life is long as compared with that of other common antiepileptic drugs. The peak-to-trough plasma level ratios during a day were as small as 1.28 ± 0.15 in children taking a daily dose of 8 mg/kg of ZNS once a day as a single drug. The plasma level (,g/ml) to dose (mg/kg/day) ratios estimated by the trough and peak plasma levels both increased with advancing age, but the peak-to-trough plasma level ratios were maintained almost uniformly throughout the pediatric age period. A wide range of the plasma levels was associated with complete freedom from seizures. The range of the plasma levels in patients who did not respond to ZNS was higher than that in the controlled group. However, the clinical effects of ZNS were in agreement with the range of generally accepted therapeutic plasma levels of ZNS, 15,40 ,g/ml. Any patient who receives polytherapy is at risk to develop 1 or more drug interactions. Concurrent administration of carbamazepine (CBZ) decreases plasma concentrations of ZNS. However, ZNS does not alter plasma concentrations of CBZ or its primary metabolite, carbamazepine-10,11-epoxide (CBZ-E). It is evident that the concurrent administration of lamotrigine (LTG) affects plasma concentrations of CBZ-E, while plasma CBZ levels remain unaltered. However, the effect of LTG on plasma concentrations of CBZ-E is small, and none of the study patients showed toxic plasma concentrations of CBZ-E or associated clinical toxicity. Drug-protein binding interactions are another source of side effects. A simultaneous administration of valproic acid increases the total plasma CBZ-E levels relative to the CBZ dose associated with the raised free fractions of CBZ and CBZ-E. The high free plasma concentrations of CBZ-E above 1.5 ,g/ml may be responsible for the side effects. [source] Efficient Removal of Anionic Surfactants Using Mesoporous Functionalised Hybrid MaterialsEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 25 2009Carmen Coll Abstract A new hybrid system for surfactant removal from water has been developed using mesoporous material (MCM-41) functionalised with suitable binding groups. Solid S1, S2 and S3 were prepared by reaction of the mesoporous material with N -methyl- N, -(propyltrimethoxysilyl)imidazolium chloride, (3-aminopropyl)trimethoxysilane or 4-[(triethoxysilylpropylthio)methyl]pyridine, respectively. The functionalised materials were characterised following standard solid-state techniques. The final prepared solids consist of a siliceous MCM-41-type mesoporous support with the surface decorated by imidazolium, amine and pyridine binding groups suitable for anion coordination. Equilibrium adsorption studies of linear alkylbenzenesulfonate (LAS) using S1, S2 and S3 in water have been carried out. The obtained adsorption data were correlated with a Langmuir isotherm model that gives an acceptable description of the experimental data. The maximum surfactant uptake/binding site (mol,mol,1) and the surfactant adsorption capacity (mmol,g,1) for materials S1, S2 and S3 were calculated. S1 shows a positive-charged functionalised surface that is independent of the pH of the solution, whereas S2 and S3 are functionalised with neutral groups that need to be protonated in order to display electrostatic binding interactions with the anionic surfactants. Therefore, whereas the adsorption capacity of S1 is pH-independent, S2 and S3 display larger LAS adsorption at acidic pH. The adsorption ability at a certain pH follows the order S1 >> S3 > S2. A remarkable maximum surfactant adsorption of 1.5 mmol per gram of material was observed for S1 at neutral pH. S2 and S3 behave as poorer adsorbents and show maximum surfactant adsorption of 0.197 and 0.335 mmol per gram of material, respectively, at pH 2.(© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009) [source] Hexaazamacrocycle Containing Pyridine and Its Dicopper Complex as Receptors for Dicarboxylate AnionsEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 22 2005Feng Li Abstract The host,guest binding interactions of the hexaazamacrocycle [26]py2N4, in its tetraprotonated form H4[26]py2N44+ as well as in its dicopper(II) complex [Cu2([26]py2N4)(H2O)4]4+, with dicarboxylate anions of different stereoelectronicrequirements, such as oxalate (ox2,), malonate (mal2,), succinate (suc2,), fumarate (fu2,) and maleate (ma2,), were evaluated. The association constants were determined using potentiometric methods in aqueous solution, at 298.0 K and 0.10 mol·dm,3 KCl. These values for the tetraprotonated ditopic receptor with the dicarboxylate anions revealed that the main species in solution corresponds to the formation of {H4[26]py2N4(A)}2+ (pH , 4,9), A being the substrate anion. The values determined are not especially high, but the receptor exhibits selectivity for the malonate anion. The study of the cascade complexes revealed several species in solution, involving mononuclear and dinuclear complexes, mainly protonated and hydrolysed species, as well as the expected complexes [Cu2([26]py2N4)(A)(H2O)x]2+ or [Cu2([26]py2N4)(A)2(H2O)y]. Ox2, and mal2, form cascade complexes with only one anion, which will necessarily bridge the two copper atoms because of the symmetrical arrangement of the dinuclear complex. The two other studied anions, suc2, and ma2,, form species involving two substrate anions, although species with only one suc2, anion were also found. UV/Vis and EPR spectroscopy have shown that the dicopper complex can operate as a sensor to detect and quantitatively determine oxalate spectrophotometrically because of the red shift of the maximum of the visible band observed by addition of ox2, to an aqueous solution of the dinuclear copper complex. However the selectivity of [Cu2([26]py2N4)(H2O)4]4+ as a receptor for ox2, in the studied series is not sufficiently high to detect ox2, spectrophotometrically in the presence of the other anions. Molecular dynamics simulations indicated that the H4[26]py2N44+ receptor provides a large and flexible cavity to accommodate the studied anions. Molecular recognition is based in electrostatic interactions rather than in multiple hydrogen-bonding interactions acting cooperatively. By contrast, the [Cu2([26]py2N4)]4+ receptor has a well-shaped cavity with adequate size to uptake these anions as bridging ligands with formation of four Cu,O bonds. The ox2, anion is encapsulated within the cascade complex while the remaining anions are located above the N6 macrocyclic plane, suggesting a selective coordination behaviour of this receptor. In spite of our molecular simulation being carried out in gas phase, the modelling results are consistent with the solution studies. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005) [source] Evolutionary divergence of valosin-containing protein/cell division cycle protein 48 binding interactions among endoplasmic reticulum-associated degradation proteinsFEBS JOURNAL, Issue 5 2009Giacomo Morreale Endoplasmic reticulum (ER)-associated degradation (ERAD) is a cell-autonomous process that eliminates large quantities of misfolded, newly synthesized protein, and is thus essential for the survival of any basic eukaryotic cell. Accordingly, the proteins involved and their interaction partners are well conserved from yeast to mammals, and Saccharomyces cerevisiae is widely used as a model system with which to investigate this fundamental cellular process. For example, valosin-containing protein (VCP) and its yeast homologue cell division cycle protein 48 (Cdc48p), which help to direct polyubiquitinated proteins for proteasome-mediated degradation, interact with an equivalent group of ubiquitin ligases in mouse and in S. cerevisiae. A conserved structural motif for cofactor binding would therefore be expected. We report a VCP-binding motif (VBM) shared by mammalian ubiquitin ligase E4b (Ube4b),ubiquitin fusion degradation protein 2a (Ufd2a), hydroxymethylglutaryl reductase degradation protein 1 (Hrd1),synoviolin and ataxin 3, and a related sequence in Mr 78 000 glycoprotein,Amfr with slightly different binding properties, and show that Ube4b and Hrd1 compete for binding to the N-terminal domain of VCP. Each of these proteins is involved in ERAD, but none has an S. cerevisiae homologue containing the VBM. Some other invertebrate model organisms also lack the VBM in one or more of these proteins, in contrast to vertebrates, where the VBM is widely conserved. Thus, consistent with their importance in ERAD, evolution has developed at least two ways to bring these proteins together with VCP,Cdc48p. However, the differing molecular architecture of VCP,Cdc48p complexes indicates a key point of divergence in the molecular details of ERAD mechanisms. [source] Transgalactosylation by thermostable ,-glycosidases from Pyrococcus furiosus and Sulfolobus solfataricusFEBS JOURNAL, Issue 16 2000-glycosides during lactose conversion, Binding interactions of nucleophiles with the galactosylated enzyme intermediate make major contributions to the formation of new The hyperthermostable ,-glycosidases from the Archaea Sulfolobus solfataricus (Ss,Gly) and Pyrococcus furiosus (CelB) hydrolyse ,-glycosides of d -glucose or d -galactose with relaxed specificities pertaining to the nature of the leaving group and the glycosidic linkage. To determine how specificity is manifested under conditions of kinetically controlled transgalactosylation, the major transfer products formed during the hydrolysis of lactose by these enzymes have been identified, and their appearance and degradation have been determined in dependence of the degree of substrate conversion. CelB and Ss,Gly show a marked preference for making new ,(1,3) and ,(1,6) glycosidic bonds by intermolecular as well as intramolecular transfer reactions. The intramolecular galactosyl transfer of CelB, relative to glycosidic-bond cleavage and release of glucose, is about 2.2 times that of Ss,Gly and yields ,- d -Galp- (1,6)- d -Glc and ,- d -Galp- (1,3)- d -Glc in a molar ratio of ,,1 : 2. The partitioning of galactosylated Ss,Gly between reaction with sugars [kNu (m,1·s,1)] and reaction with water [kwater (s,1)] is about twice that of CelB. It gives a mixture of linear ,- d -glycosides, chiefly trisaccharides at early reaction times, in which the prevailing new glycosidic bonds are ,(1,6) and ,(1,3) for the reactions catalysed by Ss,Gly and CelB, respectively. The accumulation of ,- d -Galp- (1,6)- d -Glc at the end of lactose hydrolysis reflects a 3,10-fold specificity of both enzymes for the hydrolysis of ,(1,3) over ,(1,6) linked glucosides. Galactosyl transfer from Ss,Gly or CelB to d -glucose occurs with partitioning ratios, kNu/kwater, which are seven and >,170 times those for the reactions of the galactosylated enzymes with 1-propanol and 2-propanol, respectively. Therefore, the binding interactions with nucleophiles contribute chiefly to formation of new ,-glycosides during lactose conversion. Likewise, noncovalent interactions with the glucose leaving group govern the catalytic efficiencies for the hydrolysis of lactose by both enzymes. They are almost fully expressed in the rate-limiting first-order rate constant for the galactosyl transfer from the substrate to the enzyme and lead to a positive deviation by ,,2.5 log10 units from structure,reactivity correlations based on the pKa of the leaving group. [source] ONIOM quantum chemistry study of cyclic nucleotide recognition in phosphodiesterase 5INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 12 2007Kerrie A. O'Brien Abstract Cyclic nucleotide phosphodiesterases (PDEs) are enzymes that contribute to the regulation of cyclic nucleotides in the cell by catalyzing the hydrolysis reaction of the O3,-phosphorous bond, yielding the noncyclic nucleotide as the product. The principal substrates are cyclic 3,,5,-adenosine and -guanosine monophosphate (cAMP and cGMP). PDE5, an important target of drug inhibition, is known to be highly selective for hydrolysis of cGMP. We use all-quantum hybrid calculations to accurately describe the binding interactions between PDE5 and cAMP/cGMP for the first time. The main reasons for cGMP preference in PDE5 are found to be to the fixed orientation of a conserved glutamine residue (Gln 817) together with the fixed orientation of a nonconserved glutamine residue (Gln 775). We report ONIOM(B3LYP/6-31g(d):PM3MM) binding energies, which reflect favorable guanine alignment with Gln 817 and steric crowding of adenine by Gln 775. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007 [source] Carrier proteins determine local pharmacokinetics and arterial distribution of paclitaxelJOURNAL OF PHARMACEUTICAL SCIENCES, Issue 9 2001Mark A. Lovich Abstract The growing use of local drug delivery to vascular tissues has increased interest in hydrophobic compounds. The binding of these drugs to serum proteins raises their levels in solution, but hinders their distribution through tissues. Inside the arterial interstitium, viscous and steric forces and binding interactions impede drug motion. As such, this might be the ideal scenario for increasing the amount of drug delivered to, and residence time within, arterial tissues. We quantified carrier-mediated transport for paclitaxel, a model hydrophobic agent with potential use in proliferative vascular diseases, by determining, in the presence or absence of carrier proteins, the maximum concentration of drug in aqueous solution, the diffusivity in free solution, and the diffusivity in arterial tissues. Whereas solubility of paclitaxel was raised 8.1-, 21-, and 57-fold by physiologic levels of ,1 -acid glycoproteins, bovine serum albumin, and calf serum over that in protein-free solution, diffusivity of paclitaxel in free solution was reduced by 41, 49, and 74%, respectively. When paclitaxel mixed in these solutions was applied to arteries both in vitro and in vivo, drug was more abundant at the tissue interface, but protein carriers tended to retain drug in the lumen. Once within the tissue, these proteins did not affect the rate at which drug traverses the tissue because this hydrophobic drug interacted with the abundant fixed proteins and binding sites. The protein binding properties of hydrophobic compounds allow for beneficial effects on transvascular transport, deposition, and distribution, and may enable prolonged effect and rationally guide local and systemic strategies for their administration. © 2001 Wiley-Liss, Inc. and the American Pharmaceutical Association J Pharm Sci 90:1324,1335, 2001 [source] Substituent effects of phthalimide-based nucleoside analogs on binding a CG Watson,Crick base pairJOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 10 2007Z. Xiao Abstract Five differently substituted phthalimide nucleosides were studied by NMR spectroscopic techniques for their ability to recognize and bind a cytosine,guanosine (CG) Watson,Crick base pair in CD2Cl2. Whereas only rather weak binding was observed for analogs with an amino, acetamido, or benzamido substituent, strong binding was observed with the analogs carrying an ureido and n -butyl ureido residue. 2D NOE measurements at low temperatures confirm the proposed binding mode for the high-affinity ligands but indicate binding interactions for the weakly bound analogs different from the expected geometry. Copyright © 2007 John Wiley & Sons, Ltd. [source] A genome-inspired DNA ligand for the affinity capture of insulin and insulin-like growth factor-2JOURNAL OF SEPARATION SCIENCE, JSS, Issue 10 2009Junfeng Xiao Abstract The insulin-linked polymorphic region (ILPR) of the human insulin gene contains tandem repeats of similar G-rich sequences, some of which form intramolecular G-quadruplex structures in vitro. Previous work showed affinity binding of insulin to an intramolecular G-quadruplex formed by ILPR variant a. Here, we report on interactions of insulin and the highly homologous insulin-like growth factor-2 (IGF-2) with ILPR variants a, h, and i. Circular dichroism indicated intramolecular G-quadruplex formation for variants a and h. Affinity MALDI MS and surface plasmon resonance were used to compare protein capture and binding strengths. Insulin and IGF-2 exhibited high binding affinity for variants a and h but not i, indicating the involvement of intramolecular G-quadruplexes. Interaction between insulin and variant a was unique in the appearance of two binding interactions with KD , 10,13 M and KD , 10,7 M, which was not observed for insulin with variant h (KD , 10,8 M) or IGF-2 with either variant (KDs , 10,9 M). The results provide a basis for the design of DNA binding ligands for insulin and IGF-2 and support a new approach to discovery of DNA affinity binding ligands based on genome-inspired sequences rather than the traditional combinatorial selection route to aptamer discovery. [source] Binding interactions between peptides and proteins of the class II Major Histocompatibility ComplexMEDICINAL RESEARCH REVIEWS, Issue 2 2002Benjamin J. McFarland Abstract The activation of helper T cells by peptides bound to proteins of the class II Major Histocompatibility Complex (MHC II) is pivotal to the initiation of an immune response. The primary functional requirement imposed on MHC II proteins is the ability to efficiently bind thousands of different peptides. Structurally, this is reflected in a unique architecture of binding interactions. The peptide is bound in an extended conformation within a groove on the membrane distal surface of the protein that is lined with several pockets that can accommodate peptide side-chains. Conserved MHC II protein residues also form hydrogen bonds along the length of the peptide main-chain. Here we review recent advances in the study of peptide-MHC II protein reactions that have led to an enhanced understanding of binding energetics. These results demonstrate that peptide-MHC II protein complexes achieve high affinity binding from the array of hydrogen bonds that are energetically segregated from the pocket interactions, which can then add to an intrinsic hydrogen bond-mediated affinity. Thus, MHC II proteins are unlike antibodies, which utilize cooperativity among binding interactions to achieve high affinity and specificity. The significance of these observations is discussed within the context of possible mechanisms for the HLA-DM protein that regulates peptide presentation in vivo and the design of non-peptide molecules that can bind MHC II proteins and act as vaccines or immune modulators. © 2002 John Wiley & Sons, Inc. Med Res Rev, 22, No. 2, 168,203, 2002; DOI 10.1002/med.10006 [source] Theoretical Prediction of the Phenoxyl Radical Formation Capacity and Cyclooxygenase Inhibition Relationships by Phenolic CompoundsMOLECULAR INFORMATICS, Issue 6 2002Juan Ruiz Abstract Due to the importance of the O-H bond dissociation in the antioxidant mechanism of anti-inflammatory phenols, we studied the biradical process Ph-OH,PhO.+H. for 25 phenolic compounds using ab initio calculations. Enthalpies of reaction (,Hr), changes in the electron density at the O-H bond critical point (,OH) and total atomic charges of ortho and para carbon atoms strongly correlate with the in vitro inhibition of cyclooxygenase activity by phenols. The most active compounds have large values of the electron density at the O-H bond (,OH), thus favouring the O-H bond dissociation. In contrast, inactive compounds have small values of the electron density at the O-H bond (,OH), thus reducing the hydrogen donation ability. These results are also supported by the representation of the molecular electrostatic potentials maps. The prediction of the cyclooxygenase inhibitory activity of the proposed QSAR equations is analysed using the multilineal (MLR) method. Finally, the differences in biological activity are examined by analysing the binding interactions of active compounds in the pocket site of human COX-2 enzyme structure derived from crystallographic X -ray data. [source] Surface plasmon resonance study on binding interactions of multivalent cyclophane hosts with immobilized guestsPOLYMERS FOR ADVANCED TECHNOLOGIES, Issue 2 2010Osamu Hayashida Abstract Guest-binding affinities of water-soluble cyclophane heptadecamer (1) and pentamer (2) with immobilized guests such as 1-pyrenylmethylamine (PMA) and 2-(1- naphthyl)ethylamine (NEA) were investigated by surface plasmon resonance (SPR) measurements. As a typical example, the binding constants (K) for 1 and 2 with the immobilized PMA as a guest were evaluated to be 2.5,×,107 and 2.7,×,106,M,1, respectively, and were much larger than that of a monocyclic reference cyclophane (K, 2.5,×,104,M,1). Interestingly, in the complexation of 1 and 2 with the immobilized guests, more favorable association and dissociation rate constant values (ka and kd, respectively) were observed in comparison with those for the monocyclic cyclophane, reflecting multivalent effects in macrocycles. The multivalent effects in macrocycles as well as molecular recognition abilities of the cyclophane oligomers were confirmed even when the guest molecules were immobilized on SPR sensor chip surfaces. Copyright © 2009 John Wiley & Sons, Ltd. [source] Bioactive polyurethanes in clinical applications,POLYMERS FOR ADVANCED TECHNOLOGIES, Issue 9-10 2006G. Ciardelli Abstract Biomaterials play an important role in most tissue engineering strategies. They can serve as substrates on which cell populations can attach and migrate, can be used as cell delivery vehicles and as bioactive factor carriers to activate specific cellular functions. A series of biodegradable polyurethanes (PUs) with tunable chemical, physical and degradation properties, showing an adequate response to in vitro tests was proposed for applications in soft tissue engineering. Three-dimensional scaffolds of superimposed square meshed grids were prepared by using a rapid prototyping technique (pressure activated microsyringe, PAM) and tested in vivo. Functionalization of PU systems was performed in order to control the chemistry of the materials for the promotion of highly specific binding interactions between materials and biological environments. Two different approaches were used for the coupling of bioactive molecules such as gelatin. The first involved the modification of the polymer chain through a novel monomer and the second one consisted in a surface modification by plasma-induced graft copolymerization of acrylic acid. Copyright © 2006 John Wiley & Sons, Ltd. [source] Unusual binding interactions in PDZ domain crystal structures help explain binding mechanismsPROTEIN SCIENCE, Issue 4 2010Jonathan M. Elkins Abstract PDZ domains most commonly bind the C-terminus of their protein targets. Typically the C-terminal four residues of the protein target are considered as the binding motif, particularly the C-terminal residue (P0) and third-last residue (P-2) that form the major contacts with the PDZ domain's "binding groove". We solved crystal structures of seven human PDZ domains, including five of the seven PDLIM family members. The structures of GRASP, PDLIM2, PDLIM5, and PDLIM7 show a binding mode with only the C-terminal P0 residue bound in the binding groove. Importantly, in some cases, the P-2 residue formed interactions outside of the binding groove, providing insight into the influence of residues remote from the binding groove on selectivity. In the GRASP structure, we observed both canonical and noncanonical binding in the two molecules present in the asymmetric unit making a direct comparison of these binding modes possible. In addition, structures of the PDZ domains from PDLIM1 and PDLIM4 also presented here allow comparison with canonical binding for the PDLIM PDZ domain family. Although influenced by crystal packing arrangements, the structures nevertheless show that changes in the positions of PDZ domain side-chains and the ,B helix allow noncanonical binding interactions. These interactions may be indicative of intermediate states between unbound and fully bound PDZ domain and target protein. The noncanonical "perpendicular" binding observed potentially represents the general form of a kinetic intermediate. Comparison with canonical binding suggests that the rearrangement during binding involves both the PDZ domain and its ligand. [source] Effects of molecular crowding by saccharides on ,-chymotrypsin dimerizationPROTEIN SCIENCE, Issue 5 2002Chetan N. Patel Abstract Given the importance of protein complexes as therapeutic targets, it is necessary to understand the physical chemistry of these interactions under the crowded conditions that exist in cells. We have used sedimentation equilibrium to quantify the enhancement of the reversible homodimerization of ,-chymotrypsin by high concentrations of the osmolytes glucose, sucrose, and raffinose. In an attempt to rationalize the osmolyte-mediated stabilization of the ,-chymotrypsin homodimer, we have used models based on binding interactions (transfer-free energy analysis) and steric interactions (excluded volume theory) to predict the stabilization. Although transfer-free energy analysis predicts reasonably well the relatively small stabilization observed for complex formation between cytochrome c and cytochrome c peroxidase, as well as that between bobtail quail lysozyme and a monoclonal Fab fragment, it underestimates the sugar-mediated stabilization of the ,-chymotrypsin dimer. Although predictions based on excluded volume theory overestimate the stabilization, it would seem that a major determinant in the observed stabilization of the ,-chymotrypsin homodimer is the thermodynamic nonideality arising from molecular crowding by the three small sugars. [source] New insight on ,-lactoglobulin binding sites by 1-anilinonaphthalene-8-sulfonate fluorescence decayPROTEIN SCIENCE, Issue 10 2000Maddalena Collini Abstract The fluorescence time decay parameters of the ,-lactoglobulin-1-anilinonaphthalene-8-sulfonate complex have been investigated under physical and chemical perturbations (2 < pH < 8 and added electrolyte 0 < NaCl < 0.5 M) to obtain new insight on the nature of the protein binding interactions. A double exponential decay of the bound probe lifetime has been confirmed by the presence of a longer component, 11 to 14.5 ns, and a shorter component, 2.5 to 3.5 ns. The two lifetimes are ascribed to different binding modes associated also with different exposure to the solvent; in particular, the longer component is attributed to binding inside the hydrophobic beta barrel, while a "surface" site is suggested for the shorter component. A detailed analysis of the lifetime fractional intensities correlates the binding constants with ionic strength and supports the presence of electrostatic effects at both sites. A Debye,Hückel approach, applied to extrapolate the electrostatic free energy contribution vs. pH at vanishing ionic strength, gives interesting clues on the effective charge felt by the ANS ligands in the proximity of each site. In particular, binding is found to parallel the aspartate and glutamate titrations between pH 3 and pH 4.5; the "surface" site mainly responds to the presence of these local titrating charges while the "internal" site more closely follows the overall protein net charge. [source] Structure of the nucleotide-binding domain of Plasmodium falciparum Rab6 in the GDP-bound formACTA CRYSTALLOGRAPHICA SECTION D, Issue 8 2000Debasish Chattopadhyay Rab proteins are small Ras-like GTPases which play important roles in regulating intracellular vesicle trafficking. The nucleotide-binding domain of Rab6 from the malaria parasite Plasmodium falciparum was crystallized with GDP bound to the active site. The MAD phasing technique was used to determine the crystal structure to 2.3,Å resolution. Comparisons of the structure of GDP-bound PfRab6 with the recently determined structures of Rab3A in complex with either a GTP analog or with GTP and Rabphillin present structural evidence supporting the traditional model for the molecular GTP/GDP switch in Rab proteins. PfRab6 residues homologous to those distinguishing human Rab6 isoforms, which differ in binding to Rabkinesin-6 in human cells, are located next to the recognized complementarity-determining region (CDR) and constitute a conceptual broadening of that domain. Despite significant observable differences in Golgi ultrastructure, the Rab6 core structure and switch mechanism appear highly conserved when compared with murine Rab3a structures. A significant difference between the PfRab6 and higher eukaryotic Rabs may be the lack of CDR features that allow binding interactions with Rabkinesin-type effectors. [source] Production and Molecular Characterization of Clinical Phase I Anti-Melanoma Mouse IgG3 Monoclonal Antibody R24BIOTECHNOLOGY PROGRESS, Issue 5 2001Sven E. Kemminer R24 is a mouse IgG3 monoclonal antibody (mab) that reacts with the ganglioside GD3 expressed by cells of neuroectodermal origin. The anti-tumor activity of R24 has been demonstrated in initial phase I and pilot trials in patients suffering from metastatic melanoma. The purpose of this study was to investigate the biotechnological production and particularly the glycosylation of this clinically important antibody. Growth, metabolism, and IgG production of R24 secreting hybridoma cells were analyzed on 1 L bioreactor bench scale using repeated-batch mode. The amount of 57 mg of pure mab was obtained from 1.6 L crude supernatant by protein A chromatography. Western blot binding assays with sugar-specific lectins revealed glycosylation of the heavy chains, whereas no carbohydrates were detectable on the light chains. Because glycosylation is essential for antibody effector functions in vivo (such as complement fixation or binding to macrophage Fc receptors), mab R24 was subjected to both enzymatic deglycosylation using PNGase F and chemical deglycosylation by hydrazinolysis. Released glycans were structurally characterized by high pH anion exchange chromatography with pulsed amperometric detection (HPAEC-PAD), matrix assisted laser desorption ionization time-of-flight (MALDI-TOF), and electrospray ionization quadrupole time-of-flight (ESI-QTOF) mass spectrometry. Six major biantennary chains of the complex glycosylation phenotype were found with variations in galactosylation and core fucosylation. The predominant N-linked structure, indicating the high degree of agalactosyl glycoforms, was the agalacto biantennary chain with a relative percentage of 57% (51% core-fucosylated, 6% nonfucosylated). The second most abundant oligosaccharide was the monogalacto biantennary chain amounting to 30% (26% core- and 4% nonfucosylated). The antibody contained 0.46 ,g sialic acid per mg protein, which splits into 0.243 ,g Neu5Gc and 0.217 ,g Neu5Ac, corresponding to a Neu5Ac:Neu5Gc ratio of 1:1.06. Furthermore, the antigen specificity of R24 was determined by immunodetection of GD3 on thin-layer chromatograms, and real time GD3-antibody binding interactions were measured with an optical biosensor (BIAcore). From the structural data obtained in this study it is concluded that glycosylation of the antibody may be important in the clinical outcome of targeted anti-cancer immunotherapy. [source] One-Armed Artificial Receptors for the Binding of Polar Tetrapeptides in Water: Probing the Substrate Selectivity of a Combinatorial Receptor LibraryCHEMISTRY - A EUROPEAN JOURNAL, Issue 5 2006Carsten Schmuck Prof. Dr. Abstract We have recently developed a new class of one-armed artificial receptors 1 for the binding of the polar tetrapeptide N -Ac- D -Glu- L -Lys- D -Ala- D -Ala-OH (EKAA) 2 in water using a combined combinatorial and statistical approach. We have now further probed the substrate selectivity of this receptor library 1 by screening a second tetrapeptide substrate (3) with the inverse sequence N -Ac- D -Ala- D -Ala- L -Lys- D -Glu-OH (AAKE). This "inverse" substrate is also efficiently bound by our receptors, with Kass ,6000,m,1 for the best receptors, as determined both by a quantitative on-bead binding assay and by UV and fluorescence titration studies in free solution. Hence, the inverse tetrapeptide 3 is in general bound two to three times less efficiently than the "normal" peptide 2 (Kass ,17,000,m,1), even though the complexation mainly involves long-range electrostatic interactions and both the receptor and substrate are rather flexible. Molecular modeling and ab initio calculations have been used to rationalize the observed substrate selectivity and to analyze the various binding interactions within the complex. [source] | |||||||||||||||||||