Internal conformation fluctuations

Dynamic light scattering allows the determination of the self-diffusion coefficient and the mutual-diffusion coefficient. In addition, internal conformational fluctuations can be observed for large-chain molecules. 

Note that large density fluctuations are suppressed by construction in a random lattice model. In order to include them, one could simply simulate a mixture of hard disks with internal conformational degrees of freedom. Very simple models of this kind, where the conformational degrees of freedom affect only the size or the shape of the disks, have been studied by Fraser et al. [206]. They are found to exhibit a broad spectrum of possible phase transitions. 

To describe correlated peptide conformation fluctuations in internal coordinates, the multivariate Gaussian distribution fiG used for characteristic packets and integration kernels in Cartesian space must be adapted to the periodic and multiply connected torsion angle space. Although the Carte-... 

Bolton, P. H., James, T. L. (1980). Fast and slow conformational fluctuations of RNAand DNA. Subnanosecond internal motion correlation times determined by P NMR, J. Am. Chem. Soc., 102 25. 

Subpicosecond and picosecond motions are related to localized vibrations. According to [23], it appears that the main contribution to absorption in the spectral interval from 1 to 200 cm is caused by the hydrogen bond kinetics of the protein structural elements and of the bound water rather than by the excitation of the protein structure. Although this kind of motion primarily includes the solvent, it probably provides a viscous damping for the fast conformational fluctuations, and thus can play a certain role in the relaxation process. As noted by the authors, the most important time scales are the nanosecond and the microsecond ones. Corresponding motions determine the internal mobility in proteins, as well as in an enzyme action. Otherwise, Carreri and Gratton are sure that the motions in the millisecond-second time scale are not important for the determination of the catalytic properties of an enzyme. The authors discussed mainly the conformational fluctuations which take place near the conformationally equilibrium state of a protein globule. 

Several experimental techniques have have been used to study conformational flexibility in protein molecules. Spectroscopic methods such as NMR, ESR, Mossbauer, and fluorescence techniques provide direct and detailed studies of internal motions in proteins. Hydrogen-deuterium (or tritium) exchange methods are particularly convenient for kinetic studies. Immuno-chemistry may be also a very helpful method to study conformational fluctuations. These results are discussed in the second part of this volume. 

The simplest MD procedure is to keep the total energy constant and allow the molecule to drift through various conformations as the kinetic energy (temperature) fluctuates. This routine, also known as microcanonical MD is useful for simulating internal motion in a molecule. 

Linker positive crossing provided an attractive explanation to the linking number paradox. Positive crossing would indeed partially or totally compensate for the internal negative crossing, so that the (ALkn) value associated with such closed positive nucleosomes would be close to zero. This explanation further required nucleosomes to spontaneously fluctuate to that conformation, rather than being... 

Entropic factors are a major problem for relatively large molecules. For organic macromolecules, the simulation of the probability W(S=k-In (W)) by molecular dynamics calculations or Monte Carlo simulations, has been used to calculate the entropy from fluctuations of the internal coordinates189"921. For simple coordination compounds the corrections based on calculated entropy differences are often negligible in comparison with the accuracy of the calculated enthalpies116,63,881. Therefore, the relatively easily available statistical term (Sstat) is usually the only one that is included in the computation of conformational equilibria (see Chapters 7 and 8). 

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