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Stronger Binding (stronger + binding)
Selected AbstractsEvaluation of the role of black carbon in attenuating bioaccumulation of polycyclic aromatic hydrocarbons from field-contaminated sediments,ENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 11 2004Brita Sundelin Abstract The significance of black carbon (BC) for the bioavailability of polycyclic aromatic hydrocarbons (PAHs) was examined by using historically contaminated intact sediment cores in laboratory exposure experiments with the deposit-feeding amphipod Monoporeia affinis. Log values of amphipod biota,sediment accumulation factors (BSAFs) were significantly related to log BC, whereas log BSAFs were related to log octanol,water partition coefficients only in background sediments containing less BC. In the background sediments, the BSAF for polycyclic aromatic hydrocarbons (PAHs) was 1 to 2 for phenanthrene, with lower values for more hydrophobic PAHs, indicating an increase in nonequilibrium conditions with increasing PAH molecular size. For the near-equilibrated phenanthrene and fluoranthene, higher BSAFs were measured during exposure to background sediments, with BSAF decreasing to <0.1 in contaminated sediments in the Stockholm waterways. In situ caged mussels (Dreissena polymorpha) exhibited field BSAF values (relative to sediment-trap,collected suspended matter) for polychlorinated biphenyls (PCBs) of 0.1 to 0.4, but for PAHs of similar hydrophobicity and molecular size, the field BSAFs were much lower and in the range 0.002 to 0.05. This PAH,PCB dichotomy is consistent with recently reported much stronger binding to diesel soot (a form of BC) for PAHs than for PCBs of equal hydrophobicities. Lower BSAFs for the near-equilibrated PAHs (phenanthrene and fluoranthene) in the urban sediments relative to the background sediments were consistent with the larger presence of BC in the urban sediments. This study provides the first linked BSAF,BC field data that supports a causal relationship between strong soot sorption and reduced bioavailability for PAHs. [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] Elucidation of spermidine interaction with nucleotide ATP by multiple NMR techniquesMAGNETIC RESONANCE IN CHEMISTRY, Issue 2 2010Zhiyan Song Abstract Interaction of polyamines with nucleotides plays a key role in many biological processes. Here we use multiple NMR techniques to characterize interaction of spermidine with adenosine 5,-triphosphate (ATP). Two-dimensional 1H- 15N spectra obtained from gs-HMBC experiments at varied pH show significant shift of N-1 peak around pH 2.0,7.0 range, suggesting that spermidine binds to N-1 site of ATP base. The binding facilitates N-1 deprotonation, shifting its pKa from 4.3 to 3.4. By correlating 15N and 31P chemical shift data, it is clear that spermidine is capable of concurrently binding to ATP base and phosphate sites around pH 4.0,7.0. The self-diffusion constants derived from 1H PFG-diffusion measurements provide evidence that binding of spermidine to ATP is in 1:1 ratio, and pH variations do not induce significant nucleotide self-association in our samples. 31P spectral analysis suggests that at neutral pH, Mg2+ ion competes with spermidine and shows stronger binding to ATP phosphates. From 31P kinetic measurements of myosin-catalyzed ATP hydrolysis, it is found that binding of spermidine affects the stability and reactivity of ATP. These NMR results are important for advancing the studies on nucleotide,polyamine interaction and its impact on nucleotide structures and activities under varied conditions. Copyright © 2009 John Wiley & Sons, Ltd. [source] Solution structures and characterization of human immunodeficiency virus Rev responsive element IIB RNA targeting zinc finger proteins,BIOPOLYMERS, Issue 4 2006Subrata H. Mishra Abstract The Rev responsive element (RRE), a part of unspliced human immunodeficiency virus (HIV) RNA, serves a crucial role in the production of infectious HIV virions. The viral protein Rev binds to RRE and facilitates transport of mRNA to the cytoplasm. Inhibition of the Rev,RRE interaction disrupts the viral life cycle. Using a phage display protocol, dual zinc finger proteins (ZNFs) were generated that bind specifically to RREIIB at the high affinity Rev binding site. These proteins were further shortened and simplified, and they still retained their RNA binding affinity. The solution structures of ZNF29 and a mutant, ZNF29G29R, have been determined by nuclear magnetic resonance (NMR) spectroscopy. Both proteins form C2H2 -type zinc fingers with essentially identical structures. RNA protein interactions were evaluated quantitatively by isothermal titration calorimetry, which revealed dissociation constants (Kd's) in the nanomolar range. The interaction with the RNA is dependent upon the zinc finger structure; in the presence of EDTA, RNA binding is abolished. For both proteins, RNA binding is mediated by the ,-helical portion of the zinc fingers and target the bulge region of RREIIB-TR. However, ZNF29G29R exhibits significantly stronger binding to the RNA target than ZNF29; this illustrates that the binding of the zinc finger scaffold is amenable to further improvements. © 2006 Wiley Periodicals, Inc. Biopoly 83:352,364, 2006 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] | ||||||||||