The app Kd values for Cyr61/VTNC or Cyr61/SMTB 1–44 interactions were calculated by nonlinear regression analysis of the binding data according to the Langmuir isotherm equation using GraphPad Prism 5.0 (GraphPad Software, Inc., San Diego, CA, USA).
Analysis of the binding data according to the linear lattice model [33] revealed additional information regarding the association of TM isoforms with actin.
Analysis of the binding data according to a Hill model yields a Kapp of (9.2 ± 0.4) × 10 M–1 and a Hill coefficient n of 3 ± 1. Virtually identical results were obtained with [ I2-R3-I1], a 75 bp duplex that contains both I2 and I1 elements located at the ends of the duplex rather than the center.
The concentration of Cu2+ (expressed as log [Cu]) was calculated from the total dissolved copper concentrations determined initially within the dome system (t = 0) and the copper-binding ligand data according to Moffett and Dupont (2007).
The process aligns miRNA sequences against potential target sequences, filters the output data according to observed miRNA target binding characteristics, assigns gene functional descriptions, determines the binding locations, and prunes by phylogenetic homology with C. savignyi.
Data analysis according to a multiple stepwise equilibrium model using six constants reveals the presence of three high affinity binding sites with Kd values from 22-28 nM at 37°C (11), whereas analysis of the same data according to a single site equilibrium binding constant gives a Kd of 1.63 μM (12).
In agreement with these data, according to UniProtKB, membrane proteins with a high aggregation propensity are preferentially involved in "electron transport" and "sugar transport" whereas proteins with low Na4vSS are associated to processes like "protein binding" and "ATP binding".
Titration binding data were fit according to the equation where Pt is the total S100B protein concentration, Lt is the total IC3 ligand peptide concentration, Kd is the dissociation constant, and N is the maximum chemical shift change upon ligand binding.
To shed light on the molecular features underlying the remarkable selectivity of quinalizarin, a multiple alignment of the human kinome has been performed), highlighting the amino acids involved in the quinalizarin binding motif, according to the crystallographic data available (PDB codes: 3FL5 [ 10], 3Q9Z, and 3Q9Y [ 29]).
The positive data sets are constructed from 226 known binding sites in our test data set by splitting the known binding sites into single- and double-strand binding sets according to the binding preference of each TF.
Specifically, for each studied transcription factor we obtained the set of genes with detected promoter region-transcription factor binding according to the primary study that generated binding data.
