value analysis of binding intermediates

... below Competitive binding of CBC and Cbl, calculation of k+ We have tested the application of the uorescent analogue CBC as a tool for investigation of the binding kinetics of nonuorescent ligands ... uorescence induced by binding of [CBC] ẳ 0.5 lM to [IF20] ẳ 0.5, 0.75, 1.0, 2.5 lM (C) Timedependent binding of [CBC] ẳ 0.5 lM to [IF30] ẳ 1, 10, 20, 40 lM (D) Time-dependent binding of [IF20CBC] ẳ ... Application of a uorescent Cbl analogue S N Fedosov et al A B C D Fig Binding of CBC to the fragments IF20 and IF30 (A) Equilibrium binding of 0.5 lM CBC to IF20, IF30 and IF20 + IF30 The amplitude of...

Ngày tải lên: 19/02/2014, 05:20

... least squares fit of the data The slope of this plot is found to ð3Þ These values are also listed in Table The thermodynamic parameters, enthalpy of binding (DH°) and entropy of binding (DS°) associated ... of MCL, recorded at 20 °C, are shown in Fig 2A Spectrum is that of CuTCPP alone, and spectra 2–14 correspond to CuTCPP in the presence of A binding curve depicting progress of the titration of ... concentration (in subunits) Inset: plot of 1/DA as a function of the reciprocal total protein concentration The reciprocal of the Y-intercept of this plot gave the value of DA1, the change in absorbance...

Ngày tải lên: 19/02/2014, 16:20

... viscosity of the extract as a result of DNA, lL of DNase I (200 units) was added per 100 lL of buffer [30] Following filtration through two layers of miracloth and the addition of four volumes of ice-cold ... ÔStainsAllÕ analysis of Fig and the 1D immunoblotting of Fig As the full-length Dp427 isoform of dystrophin does not enter the second dimension of conventional 2D gels, the expression level of a-dystroglycan ... identification of Ca2+ -binding proteins (data not shown) The analysis of ÔStains-AllÕ labelled spot no 8, using a corresponding Coomassie-labelled gel plug, resulted in the identification of the transcription...

Ngày tải lên: 19/02/2014, 16:20

... Conventional pepscan analysis however, does not allow easy analysis of the contribution of the carbohydrate portion To assess the involvement of carbohydrates in antibody recognition of glycosylated ... fragment of the ligand of the X-ray structure (RCSB PDB entry 1SM3) After small manual corrections, the ligands were docked into the binding site of SM3 using the FLEXIDOCK module of the SYBYL software ... to about 36% of the interaction of the full peptide with the binding cavity of SM3 The sizes of the surfaces were determined using distances between ligand ˚ atoms and protein atoms of less than...

Ngày tải lên: 21/02/2014, 15:20

... DNA -binding sites of Mhr1 Table DNA -binding activity of the Mhr1 variants N, DNA -binding activity is comparable to that of the wild type; +, DNA -binding activity is slightly stronger than that of ... DNA binding (Fig 5A), although their DNA -binding activities were not completely lost We also examined the DNA -binding activity of Mhr1 in the absence of Mg2+, because the DNAbinding activities of ... the binding of Mhr1 to DNA by measuring changes in the fluorescence spectra of Mhr1 after binding To distinguish the fluorescence of Trp from that of Tyr, we selected an excitation wavelength of...

Ngày tải lên: 06/03/2014, 09:22

... comprehensive proteomics analysis of 14-3-3 -binding proteins under physiological conditions as compared with apoptosis stimulation, with the aim of increasing our knowledge of the role of 14-3-3 proteins ... identification of genuine 14-3-3 ligands Detailed analysis of the 14-3-3-asociated proteins found showed that 46 of them were exclusively present in one of the conditions analyzed and 15 of them were ... in 14-3-3 -binding patterns in HeLa cells during C2-ceramideinduced apoptosis With the aim of further analyzing the role of 14-3-3 proteins in apoptosis, an evaluation of the ability of proteins...

Ngày tải lên: 06/03/2014, 22:21

... FnBRs of FnBPB A panel of mouse mAbs was produced against the recombinant repetitive region of FnBPB Analysis of mAbs binding to the recombinant FnBR indicated the generation of two categories of ... Time s Fig SPR analysis of NTD binding to FnBRs of FnBPA and FnBPB fused to GST Different concentrations of the NTD were compared for binding to GST–repeats immobilized on the surface of a CM5 sensor ... injection of soluble repeats or 10 of both FnBPA and FnBPB across the sensor chip surface Table reports the kinetic constants of the binding and the calculated KD values The affinities of 15E11...

Ngày tải lên: 06/03/2014, 22:21

... BIAcore analysis of rhIGF1R binding by IGF analogues High af®nity binding of IGF-I, IGF-II and their analogues to rhIGF1R was measured by BIAcore analysis (Figs and 2), and relative binding af®nities ... obtained from BIAcore analysis of binding of IGF-I, IGF-II and mutant IGF analogue to rhIGF1R Data were analysed using BIAevaluation software 3.0 and ®tted to a Langmuir : binding model as outlined ... direct comparison of rhIGF1R binding by IGF-I, IGF-II and 14 analogues using BIAcore analysis IGF1R binding by all of these analogues has not previously been compared in a single binding assay Analogues...

Ngày tải lên: 08/03/2014, 22:20

... the architecture of the aglycone -binding site of Zm-p60.1 differs distinctly from that of Bgl4:1 and its homologs These findings offer exciting prospects for comparative analysis of the molecular ... introducing features of the consensus motif into the Zm-p60.1 scaffold, an analysis of structural and catalytic properties of the mutants, and simulations of the substrate–enzyme interactions of the wild-type ... of enzyme activity, which also excluded investigation of the effects of accumulation of the mutations in a single protein molecule Experimental procedures Structural analysis The structural analysis...

Ngày tải lên: 16/03/2014, 04:20

... functional analysis of the ABD of spinophilin We show that residues 1–154 of spinophilin are both necessary and sufficient to mediate F-actin binding Critically, we also show that residues 1–154 of spinophilin ... spectra of the spinophilin ABD constructs 62 (Fig 2C), which enables rapid analysis of the overall secondary structure content of proteins The CD spectra of residues 1–154, 1–221 and 1–305 of spinophilin ... actin binding domain of spinophilin A B C Fig Recombinant proteins containing N-terminal fragments of rat spinophilin are active in F-actin binding (A) Cosedimentation assays of lM polymers of calf...

Ngày tải lên: 16/03/2014, 06:20

... comparison of the amounts of GST fusion proteins used in each case Some degradation of the GST fusion proteins is evident from the presence of products running at the position of GST itself (E) Binding ... detectable stable binding of raptor to 4E-BP1, but does not tell us whether it is sufficient To assess the contribution of other regions of 4E-BP1 to raptor binding, we created a series of N-terminally ... regions of 4E-BP1 also contribute to stable binding to raptor The first 17 residues of 4E-BP1 contain the RAIP motif To assess whether removal of the RAIP motif accounts for the reduced binding of...

Ngày tải lên: 16/03/2014, 06:20

... cHx cHx cHx A B Fig PAGE analysis of CF-expressed ETB fragments on SDS gels (A) CF expression of ETB fragments in the presence of Brij78; 0.7 lL of supernatant (S) and lL of eluate (E) after Ni–chelate ... coelution approach gives good evidence for a ligand -binding activity of CF-produced ETB 3262 Fig Ligand binding of ETB derivatives Binding of ETB derivatives to bET-1 was analyzed by pull-down ... presence of Brij78 This expression condition was therefore chosen for further sample preparations of ETBcHx and its derivatives Fig Functional conformation of full-length ETBcHx ET-1 binding of ETBcHx...

Ngày tải lên: 16/03/2014, 10:20

... that of the wild-type enzyme (data not shown) On the other hand, the Km value for benzonitrile of the aT109S mutant was similar to that of the wild-type enzyme (Table 2) The binding affinity of ... values for aromatic nitriles than for small aliphatic nitriles n-Butyric acid competitively inhibited P thermophila NHase, which showed a Ki value of 1.3 mM This Ki value is similar to that of ... interpreted (data not shown) Mutagenic analysis of bTyr68 To evaluate the importance of bTyr68, we replaced it with phenylalanine The kcat and Km values of the bY68F mutant are shown in Table...

Ngày tải lên: 16/03/2014, 16:20

... bands, indicative of covalent binding of the dyes [19] Binding activities of Ag-NPA-1 Binding of fatty acids, retinol and DAUDA were studied by changes in the intrinsic Trp fluorescence of Ag-NPA-1 ... assumed (K2 0.667 [30]) A value of 1.36 was taken for the refractive index n [31] MALDI-TOF analysis MALDI-TOF analysis of the peptides obtained after tryptic digestion of the labeled and nonlabeled ... incorporation of the ligand Binding of DAUDA to Ag-NPA-1 caused  20% quenching of the emission of Trp17 indicating FRET between the single Trp residue and the dansyl group We calculated a value of 3.74...

Ngày tải lên: 16/03/2014, 18:20

... accessed out -of- bounds The details of this analysis are given in Chap 11, which presents the string buffer analysis as a refinement of the basic analysis of C that is described in the first part of the ... While the aspects of soundness and efficiency need to be addressed before an analysis is implemented, the precision of an analysis (or the lack thereof) often manifests itself when the analysis is run ... Value- Range Analysis of C Programs Axel Simon Value- Range Analysis of C Programs Towards Proving the Absence of Buffer Overflow Vulnerabilities 123 Axel...

Ngày tải lên: 19/03/2014, 14:05

... the corresponding Tm values Table Thermodynamic parameters of the heat-induced unfolding of HUTmar-wt and its E34D mutant Values were determined by the simultaneous fitting of 24 DSC curves (recorded ... responsible for the higher stability of the wild-type protein compared to the mutant Thus, the value of 1.8 kJÆmol)1 could be taken as being the maximum cost of the disruption of the K13-E34 salt bridge ... advantages of solvent-exposed salt bridges as the disruption of a salt bridge by the substitution of one of the partners by a neutral amino acid does not always decrease the stability of the original...

Ngày tải lên: 23/03/2014, 12:20

... forms of topo70 Y723F, each of which eliminates the positive charges associated with clusters of basic amino acids within one of the a-helices of the linker region (a18) The changes in one of the ... topoisomerization of bent DNA Nucleic Acids Res 17, 8463–8474 35 Caserta M, Amadei A, Camilloni G & Di Mauro E (1990) Regulation of the function of eukaryotic DNA topoisomerase I: analysis of the binding ... Supercoil binding by topoisomerase I Z Yang et al Fig Alternative modes for topoisomerase I binding to a DNA node (A) Node binding occurs through dimerization of topoisomerase I (B) Node binding...

Ngày tải lên: 29/03/2014, 22:21

... the analysis of their binding activity to the receptor to investigate the role of mutated amino acid residues; (b) the analysis of the influence of the modification of the cysteine residues of mutants ... FEBS Receptor binding ⁄ oligomerization of Cry1Aa mutants F Obata et al Analysis of the binding ability of synthetic peptides To evaluate the binding capability of the loop regions of Cry1Aa toxins ... Quantitative binding analysis of cysteine-substituted mutant toxins First, we performed binding analyses of nonmodified mutant toxins to BtR175 fragments immobilized on the cuvette of an IAsys...

Ngày tải lên: 29/03/2014, 22:21

... motif of cardosin A is located at the surface of the protein [4], as seen in other structures of biologically active proteins [32,33] However, a careful examination of the X-ray structure of cardosin ... the tip of a loop protruding away from the core of the protein This amino-acid motif mimics RGD in terms of charge and is positioned at the tip of a loop and is therefore reminiscent of RGD sequences ... RGD motif located at the surface of the protein [4] The presence of this wellknown integrin -binding motif [11], and the previous purification of a cardosin A -binding protein from pollen, raised...

Ngày tải lên: 30/03/2014, 11:20

... Results and discussion Zn(II) and Cd(II) binding abilities of ckMT and its separate domains Metal binding analysis rationale The metal binding abilities of ckMT were analysed following a two-step ... titrations of Zn–ckMT and Zn4–ackMT with Cd(II) at pH Arrows show the evolution of the spectra when the indicated number of Cd(II) was added (B) CD spectrum of the acidification of the final solution of ... binding abilities of the ckMT peptides deserve explicit comment First, analysis of the Zn ⁄ Cd replacement in bckMT (Fig 2A and 2B, Table S2) further corroborates the peculiar CD fingerprint of...

Ngày tải lên: 30/03/2014, 11:20