Conformation species

Using circular dichroism and nuclear magnetic resonance spectrometry, Veatch and coworkers1 established that four conformational species of gramicidin A exist in solution. Two were postulated to be helixes of opposite handedness. 

Analysis of the two average structures obtained from the two unique starting points demonstrated convergence to a similar conformational species. In each, the sum of the NOE restraint energy was less than 4.7 kcal/mol and the RMS deviation from the target distances was below 0.25 A. Similar results were obtained for each simulation when they were repeated without the electrostatic term being included in the total potential-energy function. This important data lends credence to the hypothesis that the final structures are derived from the NOE restraints and not by poorly represented electrostatic interactions. 

When the folding reactions have reached equilibrium, 2 fiL of each sample is loaded into separate lanes of a native 8% polyacrylamide gel that was prepared and prerun as described above (< 10 ° C). It is helpful to use narrow tips that allow the sample to be placed near the bottom of the well. The current should be applied to the gel as soon as possible after the samples are loaded. Gels must be run long enough to resolve the conformational species of interest, but not so long that smaller RNAs run off the bottom of the gel. To resolve the folded and unfolded forms of the Tetrahymena ribozyme, gels are run 4 h at 15 W. 

Isouni-uni pathway Typified by solvent-induced solute unfolding-refolding phenomena in the mobile phase with all conformational species binding to the sorbent with the same distribution coefficient elution is characterized as a single zone with high mass recovery but time-dependent loss of biological activity in the mobile phase. 

Mouse, rat, guinea pig, rabbit, monkey, dog, goat, sheep, pig, cattle (human is a non-conforming species). For each drug, the level of significance is R < 0.001. 

Based on these findings, extinction coefficients for the various conformational species were measured under the following conditions OM urea for native hCAB, 8M urea for the denatured conformer, incubation in 5M urea for 90-120 minutes to estimate the extinction coefficient for X, and incubation in SM urea for an extended period of time (2 3 weeks was used in this study) to determine the extinction coefficient for conformer I. Initial extinction coefficients evaluations at 238 nm and 292 nm for the various human carbonic anhydrase B conformers were determined in O.IM Tris-HCl (pH=7.45) at 23 C. The results are presented in Table 2. It is evident that while there is a substantial (-25-35%) difference in extinction coefficients between the native and denatured states, the intermediate conformations X and I could not be separated spectroscopically, and therefore, UV absorbance cannot be used to determine the concentration of species X and I separately. Instead, the overall concentration of intermediate species, Z where [Z]=[X]+[q, was monitored over the course of a refolding experiment... 

In summary, the concentration of the different conformational species were determined as follows i) [N] from the activity assay, ii) [A] from turbidity measurements, iii) [Z] and [D] were determined using UV absorbance at 238 and 292 nm with the following equations ... 

Standards must also be used for evaluating Av,oh> in the case of conformationally nonhomogeneous molecules in which the free OH and the associated OH belong to different conformational species. 

Joo, C, McKinney, SA, Lilley, DMJ, and Ha, T, Exploring rare conformational species and ionic effects in DNA Holliday junctions using single-molecule spectroscopy. Journal of... 

The conformational landscape of phenylalanine (R=CH2-C6Hs, m.p. = 270-275°C) has been widely investigated [11, 137-147]. Six conformational species were identified using laser induced fluorescence LIF, hole burning UV-UV, and ion dip IR-UV spectroscopy coupled with ab initio calculations [11, 137-141]. Lee et al. [141] carried out a definitive identification of the conformers of phenylalanine, based upon comparisons between the partially resolved ultraviolet band contours and that simulated by ab initio computations. The study of the rotational spectrum of phenylalanine by LA-MB-FTMW [153] showed rather weak spectra of only two conformers, Ila and Ilb (see Fig. 21). Both conformers exhibit a trans configuration in the COOH group, being stabilized by O-H- N and N-H- - -it... 

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