Home About us Contact
|
Home About us Contact | ||
|
|
||
Weak Binding (weak + binding)
Selected AbstractsAn Acyclic Aminonaphthyridine-Based Receptor for Carbohydrate Recognition: Binding Studies in Competitive SolventsEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 22 2007Monika Mazik Abstract 1H NMR spectroscopic and microcalorimetric titrations revealed that receptor 3b, consisting of three protonated 2-amino-1,8-naphthyridine units, binds N -acetylneuraminic acid (Neu5Ac), the most commonly occurring sialic acid, with high affinity in competitive solvents such as water/dimethyl sulfoxide. Receptor 3b is able to form neutral/charge-reinforced hydrogen bonds and ion pairs with Neu5Ac, similar to sialic acid-binding proteins. Furthermore, indications for weak binding of neutral sugars, such as methyl ,- D -glucopyranoside, D -maltose and D -cellobiose were provided by NMR spectroscopy. Molecular modelling calculations, synthesis and binding studies in aqueous media are described. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007) [source] Structural consequences of site-directed mutagenesis in flexible protein domainsFEBS JOURNAL, Issue 8 200156)S mutant of RhoGDI, NMR characterization of the L(5 The guanine dissociation inhibitor RhoGDI consists of a folded C-terminal domain and a highly flexible N-terminal region, both of which are essential for biological activity, that is, inhibition of GDP dissociation from Rho GTPases, and regulation of their partitioning between membrane and cytosol. It was shown previously that the double mutation L55S/L56S in the flexible region of RhoGDI drastically decreases its affinity for Rac1. In the present work we study the effect of this double mutation on the conformational and dynamic properties of RhoGDI, and describe the weak interaction of the mutant with Rac1 using chemical shift mapping. We show that the helical content of the region 45,56 of RhoGDI is greatly reduced upon mutation, thus increasing the entropic penalty for the immobilization of the helix, and contributing to the loss of binding. In contrast to wild-type RhoGDI, no interaction with Rac1 could be identified for amino-acid residues of the flexible domain of the mutant RhoGDI and only very weak binding was observed for the folded domain of the mutant. The origins of the effect of the L55S/L56S mutation on the binding constant (decreased by at least three orders of magnitude relative to wild-type) are discussed with particular reference to the flexibility of this part of the protein. [source] CD247 can bind SHC1, no matter if CD247 is phosphorylatedJOURNAL OF MOLECULAR RECOGNITION, Issue 3 2009Tao Liu Abstract On T cell receptor (TCR) stimulation, src homology 2 domain-containing transforming protein C1 (SHC1) had been found to bind the tyrosine-phosphorylated CD247 chain of the receptor via its src homology 2 (SH2) domain, delivering signals that control T cell development and activation. However, how the phosphorylation of CD247 led to the instant binding has not been characterized clearly. To study the binding process in detail, we simulated and compared the interaction processes of the SH2 domain with CD247 and phosphorylated CD247, respectively. Unexpectedly, the simulation revealed that SHC1 can also bind the nonphosphorylated CD247 peptide, which was further validated to be a weak binding by affinity pull-down experiment. The molecular dynamics (MD) simulation also revealed that the CD247 peptide formed a folding conformation with its Leu209 inserted into the hydrophobic binding pocket in SHC1. And on phosphorylation, it was the electrostatic attraction between the CD247 Tyr(P)206 and the SHC1 Tyr(P)-binding pocket that destroyed the folding conformation of the nonphosphorylated CD247 and, aided by the electrostatic attraction between SHC1 and the Asp203 of CD247, led to the extended conformation of the phosphorylated CD247 binding to SHC1 strongly. The results suggest that nonphosphorylated CD247 can recruit SHC1 in advance to prepare for the instant needs for SHC1 on TCR stimulation. In view of the ubiquity of phosphorylation in protein interaction regulation, we think this study also exemplified the usefulness of MD in more interactome research involving phosphorylation. Copyright © 2009 John Wiley & Sons, Ltd. [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] Novel mode of transcription regulation by SdiA, an Escherichia coli homologue of the quorum-sensing regulatorMOLECULAR MICROBIOLOGY, Issue 5 2001Kaneyoshi Yamamoto SdiA, an Escherichia coli homologue of the quorum-sensing regulator, controls the expression of the ftsQAZ operon for cell division. Transcription of ftsQ is under the control of two promoters, upstream ftsQP2 and downstream ftsQP1, which are separated by 125 bp. SdiA activates transcription from ftsQP2 in vivo. Here, we demonstrate that SdiA facilitates the RNA polymerase binding to ftsQP2 and thereby stimulates transcription from P2. Gel shift and DNase I footprinting assays indicated that SdiA binds to the ftsQP2 promoter region between ,51 and ,25 with respect to the P2 promoter. Activation of ftsQP2 transcription by SdiA was observed with a mutant RNA polymerase containing a C-terminal domain (CTD)-deleted ,-subunit (,235) but not with RNA polymerase containing ,S or a CTD-deleted ,D (,D529). In good agreement with the transcription assay, no protection of P2 was observed with the RNA polymerase holoenzymes, E,S and E,D529. These observations together indicate that: (i) SdiA supports the RNA polymerase binding to ftsQP2; and (ii) this recruitment of RNA polymerase by SdiA depends on the presence of intact ,CTD. This is in contrast to the well-known mechanism of RNA polymerase recruitment by protein,protein contact between class I factors and ,CTD. In addition to the P2 activation, SdiA inhibited RNA polymerase binding to the ftsQP1 promoter and thereby repressed transcription from P1. Gel shift assays indicate weak binding of SdiA to the P1 promoter region downstream from ,13 (or +112 with respect to P2). Neither ,CTD nor ,CTD are required for this inhibition. Thus, the transcription repression of P1 by SdiA may result from its competition with the RNA polymerase in binding to this promoter. [source] Electrochemical deposition of Pt nanoparticles on diamond substratesPHYSICA STATUS SOLIDI (A) APPLICATIONS AND MATERIALS SCIENCE, Issue 9 2009Jingping Hu Abstract Platinum nanoparticles were deposited on polished smooth, as-grown large grain and small grain diamond substrates by a potentiostatic method. The influence of deposition potential and the morphology of BDD substrates were studied. A progressive nucleation along with spherical clusters was observed on smooth BDD electrode, accompanied with a heterogeneous segregation of platinum on diamond facets of higher electrochemical activities and a weak binding to the substrate. In contrast, an instantaneous nucleation was observed on as-grown small grain and large grain BDD electrodes, with a dendritic microstructure and a much larger specific active area. The platinum decorated as-grown smaller grain BDD electrodes show a much better electrochemical stability than the other electrodes investigated. [source] Structure of the X (ADRP) domain of nsp3 from feline coronavirusACTA CRYSTALLOGRAPHICA SECTION D, Issue 12 2009Justyna A. Wojdyla The structure of the X (or ADRP) domain of a pathogenic variant of feline coronavirus (FCoV) has been determined in tetragonal and cubic crystal forms to 3.1 and 2.2,Å resolution, respectively. In the tetragonal crystal form, glycerol-3-phosphate was observed in the ADP-ribose-binding site. Both crystal forms contained large solvent channels and had a solvent content of higher than 70%. Only very weak binding of this domain to ADP-ribose was detected in vitro. However, the structure with ADP-ribose bound was determined in the cubic crystal form at 3.9,Å resolution. The structure of the FCoV X domain had the expected macro-domain fold and is the first structure of this domain from a coronavirus belonging to subgroup 1a. [source] | ||||||||||