Conformational transition localized

Figure 8 shows a one-dimensional sketch of a small fraction of that energy landscape (bold line) including one conformational substate (minimum) as well as, to the right, one out of the typically huge number of barriers separating this local minimum from other ones. Keeping this picture in mind the conformational dynamics of a protein can be characterized as jumps between these local minima. At the MD time scale below nanoseconds only very low barriers can be overcome, so that the studied protein remains in or close to its initial conformational substate and no predictions of slower conformational transitions can be made. 

The result of such a series of steps is depicted in Figure 9. This method has proved effective in isolating reaction pathways for conformational transitions involving localized torsional transitions including those involving a subtle isomerization mechanism [56]. 

Klimkowski, V. J., L. Schafer, F. A. Momany, and C. Van Alsenoy. 1985. Local Geometry Maps and Conformational Transitions Between Low-Energy Conformers of N-Acetyl-N -Methyl Glycine Amide An Ab Initio Study at the 4-21G Lever with Gradient Relaxed Geometries, J. Mol. Struct. (Theochem) 124, 143-153. 

In summary, the dynamics of the hierarchical interaction between silk proteins in solution suggest that spiders and insects are trading long range crystallinity for local conformational transitions, thus allowing the... 

The divergence between the rate of conformational transitions and the decay of the torsional autocorrelation functions (and hence local relaxations)... 

The dynamic RIS model, which was proposed before to investigate the dynamics of local conformational transitions in polymers, is elaborated to formulate the increase in the number of excimer-forming sites through rotational sampling. Application of the model to the meso and racemic diads in PS confirms the fact that conformational mobility of the chain plays a major role in intramolecular exclmer formation. Comparison with experiments demonstrates that the decay of the monomer fluorescence in styrene dimers is predominantly governed by the process of conformational transitions. 

The conformational transitions observed in the simulations [97] resemble in some aspects the so-called zipping transitions [211], the process in which two strongly attracting strands composing the polymer come in contact in such a way as to form a bound double structure, which remains swollen and does not assume compact configurations. The cylindrical-shaped conformations in which the hydrophobic backbone is in a locally collapsed state (Figs. 41e and f) look a lot like three-dimensional zipped structures. 

Like other macromolecules, RNA is dynamic. The process of folding into a structured RNA involves dynamic rearrangement of RNA helices, and many RNAs function via a series of conformational transitions. Thus, measurement of the dynamics of individual helices will be required to fully understand RNA folding and function. Additionally, dynamic information can also be used to provide information about local structural features. 

Andersen, J.P., Vilsen, B Collins, Jit., Jorgensen, P.L. (1986). Localization of ErE2 conformational transitions of sarcoplasmic reticulum Ca-ATPase by tryptic cleavage and hydrophobic labeling. J. Membr. Biol. 93, 85-92. 

Biomolecular recognition is mediated by water motions, and the dynamics of associated water directly determine local structural fluctuation of interacting partners [4, 9, 91]. The time scales of these interactions reflect their flexibility and adaptability. For water at protein surfaces, the studies of melittin and other proteins [45, 46] show water motions on tens of picoseconds. For trapped water in protein crevices or cavities, the dynamics becomes much slower and could extend to nanoseconds [40, 71, 92], These rigid water molecules are often hydrogen bonded to interior residues and become part of the structural integrity of many enzymes [92]. Here, we study local water motions in various environments, from a buried crevice to an exposed surface using site-selected tryptophan but with different protein conformations, to understand the correlation between hydration dynamics and conformational transitions and then relate them to biological function. 

Experimental results from studies of Arrhenius dependence of different characteristics of lysozyme are presented in Fig 4.1. (Alfimova and Likhtenshtein, 1979 Likhtenshtein, 1993 Likhtenshtein et al., 2000). The discontinuities on the curves indicate local conformational transitions and are apparently due to the appearance of a more open conformation of the protein. As can be seen from Fig. 4.1., these methods reveal conformational transitions at a temperature of about 30°C, whereas the temperature dependence of the partial heat capacity decreases monotonically in this temperature region. Recently, the presence of the conformational transition in lysozyme was confirmed independently. It was shown that the segmental motion of Trp 108 is hindered by the local cage structure at T < 30°C, although relieved from restricted motion by thermal agitation or by the formation of a ligand complex. 

Later studies by Poliszko et al.m documented that, in freeze-dried starch gels, several complex conformational transitions take place that increase the rigidity of starch chains nearly 105 times. The free energy of mechanical relaxations due to the reorientation of hydroxymethyl groups reaches 38 kJ/mol the activation energy due to the local conformational mobility of polymeric chain is reported at 48.7 kJ/mol. 

An extension of the original RIS theory deals with how the RIS theory may be extended to deal with dynamic processes in single chains. Rapid relaxation processes in polymers are related to local conformational transitions of... 

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