Local structural perturbation

In addition to unsaturated fatty acids, several other modified fatty acids are found in nature. Microorganisms, for example, often contain branched-chain fatty acids, such as tuberculostearic acid (Figure 8.2). When these fatty acids are incorporated in membranes, the methyl group constitutes a local structural perturbation in a manner similar to the double bonds in unsaturated fatty acids (see Chapter 9). Some bacteria also synthesize fatty acids containing cyclic structures such as cyclopropane, cyclopropene, and even cyclopentane rings. 

Our interest will go to the second derivative spectrum since in the literature there are many relevant papers describing how we can monitor local structural perturbation within the environment of the three concerned amino acids and mainly phenylalanine and tyrosine. 

More recently, experimental studies have been carried out using a similar device but with an annular external hot coflow of burned gases that allowed one to operate within a much larger velocity range. Chen et al. [26] and more recently Chen and Bilger [27,28] have studied the perturbations that the smallest scales of turbulence can impose to the local flamelet structures. Those studies are of paramount importance, first because they have allowed to get deeper insights into the local structure... 

In summary, 2AP incorporation into an RJMA can be used to map its folding pathway, its kinetics of local and global folding, and its intrinsic dynamics. It is uniquely able to report on RJMA properties since it fits tidily into secondary and tertiary structures without the structural perturbations... 

Coulomb effects dominate liquid structure. The local structure of ions in the neat liquid is controlled primarily by Coulomb interactions. In solution, ion-ion interactions are far larger than ion-dipole interactions, and the presence of a neutral solute represents a local disruption of the neat liquid structure but is otherwise a relatively weak perturbation on the charge distribution of the neat liquid. 

In general, when one wants to determine if global and/or local structural modifications have occurred within a protein, circular dichroism experiments are performed. Also, one can record the fluorescence excitation spectrum of the protein. If perturbations occur within the protein, one should observe excitation spectra that differ from one state to another. One should not forget to correct the recorded spectra for the inner filter effect. 

Figure 4 Cd PAC data—example, (a) Experimentally determined perturbation function that contains the information on the local structure and dynamics at the PAC probe site (data points with error bars and fit (fiiU line)).(b) Fourier transform of the experimental data (red) and of the fit (blue). This dataset was recorded for the cadnumn-substituted blue copper protein azurin. (After Figure 6 in )...

Originally, photoluminescence spectroscopy was applied to characterize the local coordination of metal ions as well as to probe structural perturbations that occur due to alkaline earth and rare earth metal ions in oxides such as silica and alumina. Emphasis has turned to elucidating the mechanisms of catalytic and photocataljTic reactivity, i.e., the characterization, at the molecular level, of the active surface sites as well as the significant role of these sites in catalysis and photocatalysis. 

It is clear that these questions can be answered if information about the local structure and intermolecular interactions in the layers of the perturbed water can be obtained. 

An important step in understanding the local structure around a nonpolar solute in water was made by Jorgensen et al. Using Monte Carlo simulations based on an intermolecular potential, which contained Lennard-Jones and Coulomb contributions, they determined the number of water molecules in the first hydration layer (located between the first maximum and the first minimum of the radial distribution function) around a nonpolar solute in water. This number (20.3 for methane, 23 for ethane, etc.) was surprisingly large compared with the coordination numbers in cold water and ice (4.4 and 4, respectively). These results provided evidence that major changes occur in the water structure around a nonpolar solute and that the perturbed structure is similar to that of the water—methane clathrates, ... 

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