Probe hydrophobic

Solvent-laden air (SLA), 70 95 Solvent mixtures flash point of, 23 116 viscosity of, 23 99 Solvent Orange 107, 60, 63, 7 colorant for plastics, 7 374t Solvent polarity/hydrophobicity probing, polymethine dyes in, 20 517 Solvent polarity/temperature, in initiating systems, 74 268 Solvent power, 23 89 Solvent preparation, for Grignard reactions, 72 823 Solvent properties... 

ANS (see Basic Protocol 1) has been the most popular hydrophobic probe for the determination of surface hydrophobicity of proteins. Its dimeric form bis-ANS, which has a greater quantum yield in nonpolar environments by binding more strongly with proteins than the ANS monomer, is occasionally used for the same purpose (Das and Surewicz, 1995). These effects permit the observation of depolarization by energy transfer among the bound fluoropho-res, which can be used to estimate the distribution of the ligands among the protein molecules (Farris et al., 1978). 

Soo, P. L., L. Luo, D. Maysinger, andA. Eisenberg. 2002. Incorporation and release of hydrophobic probes in biocompatible polycaprolactone-block-poly(ethylene oxide) micelles implications for drug delivery. Langmuir18 996-10004. 

The hydrophobic probe highlights an area of the binding pocket where the bi-and tricyclic inhibitors are actually accommodated with their non-polar ring system (Fig. 8.5 d). 

Hydrophobicity Measurement. A conventional method (25) of using l-anilinonaphthalene-8-sulfonate (ANS) as a semiquantitative hydrophobic probe was applied. To 8 X 10 5Af ANS in 0.1M Tris-HCl (pH 8.5) was added the sample at a concentration of 0.05% (w/w) and the resulting solution measured for the intensity of its emission spectrum... 

PHB/polyP complexes were first discovered in the plasma membranes of bacteria by Reusch and Sadoff22-25,85 during spectrofluorometric studies of membrane structure, using the hydrophobic probe, /V-pheny 1-1 -naphthylamine (NPN). When NPN is added to cell suspensions, it partitions into the hydrocarbon region of the cell membranes and... 

Figure 9. A. Thermotropic fluorescence spectra of E. coli DH1 cells using the hydrophobic probe, N-phenyl-1 -naphthylamine (NPN). (a) Mid-log phase cells (b) stationary phase cells (c) cells made genetically transformable by the method of Hanahan.146 NPN was added to 4 mL of cell culture to a final concentration of 1 pM and the thermotropic fluorescence spectra were recorded.24 Measurements were made at increasing temperature (ca. 2 °C per min). Excitation 360 nm emission 410 nm. Measurements were made at increasing temperature (ca. 2 °C per min). B. Effects of physical treatments on the thermotropic transitions in genetically competent E. coli DH1. (a) Thermotropic transitions at descending temperature (b) cells pelleted at low speed and suspended in supernatant (c) as in b but suspended in equal volume of distilled water (d) as in (b) but suspended in 10 mM phosphate buffer, pH 7.4. Excitation 360 nm emission 410 nm. Fluorescent probe was NPN. Measurement (a) was made at decreasing temperature and (b), (c), (d) at increasing temperatures (ca. 2 °C per min).

Fluorescent probe for protein conformation considered a hydrophobic probe study of molten globules. 

There is now a hydrophobic probe which detects hydrophobic regions on the surface of the target, and this probe must also take account of entropy. 

Figure 1.9. A molecule of leucine with GRID maps for a hydrophobic probe (A, yellow) a multiatom cis-amide probe (B, red) and an sp3 NHj probe (C, blue). See text.

When a probe binds a target molecule, it may displace ordered water molecules and it may result in ordering of a flexible part of the protein. Both these events have entropic effects. To account for these, an entropy term has been included in more recent versions of GRID and takes different forms according to the type of calculation. It is computed when parts of the target are treated as flexible, when the probe interactions are compared to that of water, and for the hydrophobic probe, known as the DRY probe. 

Our studies also suggested that H-bond acceptors play an important role for compounds that bind the HERG channel (GRIND descriptors 13 and 34 in both the pharmacophoric models, as shown in Fig. 9.8). The statistical relevance of the MIFs generated by the hydrophobic probe confirmed the assumptions that were made in a previous CoMSiA model [17] regarding the presence of a hydrophobic feature. 

---