Conformational transition and

Fig. 10. Conformational flooding accelerates conformational transitions and makes them accessible for MD simulations. Top left snapshots of the protein backbone of BPTI during a 500 ps-MD simulation. Bottom left a projection of the conformational coordinates contributing most to the atomic motions shows that, on that MD time scale, the system remains in its initial configuration (CS 1). Top right Conformational flooding forces the system into new conformations after crossing high energy barriers (CS 2, CS 3,. . . ). Bottom right The projection visualizes the new conformations they remain stable, even when the applied flooding potentials (dashed contour lines) is switched off.

For modelling conformational transitions and nonlinear dynamics of NA a phenomenological approach is often used. This allows one not just to describe a phenomenon but also to understand the relationships between the basic physical properties of the system. There is a general algorithm for modelling in the frame of the phenomenological approach determine the dominant motions of the system in the time interval of the process treated and theti write... 

Volkov, S.N. Conformational transitions and the mechanism of transmission of long-range effects in DNA. Preprint ITP-88-12E, Kiev (1988) 22 Krumhansl, J.A., Alexander, D.M. Nonlinear dynamics and conformational exitations in biomolecular materials. In Structure and dynamics nucleic acids and proteins. (Clementi, E., Sarma, R.H., eds) Adenine Press, New York (1983) 61-80... 

I ilman, D.J., et al. Structural factors that control conformational transitions and serotype specificity in type 3 poliovirus. EMBO J. 8 1567-1579, 1989. 

Table 4. Values of pK 0 5, pKc (of conformational transition) and the range of degrees of ionization in which conformational transition (a, — a2) takes place for the carboxylic CP at various ionic strength (CNatl)...

Rousseau, R., Schreiner, E., Kohbneyer, A., and Marx, D., Ternperamre-dependent conformational transitions and hydrogen-bond d3mamics of the elastin-bke octapeptide GVG(VPGVG) A molecular-dynamics study, Biophys. J., 86, 1393-1407, 2004. 

Schafer, L., V. J. Klimkowski, F. A. Momany, H. Chuman, and C. Van Alsenoy. 1984. Conformational Transitions and Geometry Differences Between Low-Energy Conformers of N-Acetyl-N -Methyl Alanineamide An Ab Initio Study at the 4-21G Level with Gradient Relaxed Geometries. Biopolymers 23, 2335-2347. 

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

The reactions of intramolecular cross-linking is a rather poorly investigated area in the field of macro-molecular reactions. However, the problems of regularities of such processes are related to such important problems of polymer chemistry as chemical modification of polymers, networks formation, sorption of low molecular reagents by polymers, intramolecular catalysis, conformational transitions and so on. In spite of the great importance of the study of regularities of cross-linking reactions, the experimental and theoretical analysis of such processes is complicated by many difficulties. ... 

There are substantial difficulties in the interpretation of temperature-dependent shifts of protein spectra because of the thermal lability of proteins and the possibility of temperature-dependent conformational transitions. Low-temperature studies in aqueous solutions revealed that for many of the proteins investigated the observed shifts of the fluorescence spectra within narrow temperature ranges were probably the result of cooperative conformational transitions, and not of relaxational shifts/100 1 Spectral shifts have also been observed for proteins in glass-forming solvents, 01) but here there arise difficulties associated with the possible effects of viscous solvents on the protein dynamics. 

Keywords. Hyperbranched macromolecules. Polymer films. Scanning force microscopy. Conformational transitions and interfacial ordering of single molecules... 

Conformational transitions and electron redistribntion on pressure results in changes of the ion-radical properties and this is essential for optoelectronic devices. Pressure is the thrust distributed over a surface. The most important results of compression are reduction of molecular volumes and conformational changes of organic componnds. Spectral changes of solids are also termed piezo-chromism. Let ns consider several relevant examples of piezochromism. 

The symmetry model is useful even if it does oversimplify the situation, because it provides a conceptual framework for discussing the relationships between conformational transitions and the effects of allosteric activators and inhibitors. In the following sections we consider three oligomeric enzymes that are under metabolic control and see that substrates and allosteric effectors do tend to stabilize each of these enzymes in one or the other of two distinctly different conformations. 

Malnasi-Csizmadia, A., Pearson, D. S., Kovacs, M., Woolley, R. J., Geeves, M. A., and Bagshaw, C. R. (2001). Kinetic resolution of a conformational transition and the ATP hydrolysis step using relaxation methods with a Dictyostelium myosin ii mutant containing a single tryptophan residue. Biochemistry 40, 12727-12737. 

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. 

Abstract. Walter Kauzmann stated in a review of protein thermodynamics that volume and enthalpy changes are equally fundamental properties of the unfolding process, and no model can be considered acceptable unless it accounts for the entire thermodynamic behaviour (Nature 325 763-764, 1987). While the thermodynamic basis for pressure effects has been known for some time, the molecular mechanisms have remained rather mysterious. We, and others in the rather small field of pressure effects on protein structure and stability, have attempted since that time to clarify the molecular and physical basis for the changes in volume that accompany protein conformational transitions, and hence to explain pressure effects on proteins. The combination of many years of work on a model system, staphylococcal nuclease and its large numbers of site-specific mutants, and the rather new pressure perturbation calorimetry approach has provided for the first time a fundamental qualitative understanding of AV of unfolding, the quantitative basis of which remains the goal of current work. 

The physical chemical properties of proteins inform their function and as such have been the object of intense investigation for over 50 years. Indeed, major progress in the understanding of protein structure, dynamics and thermodynamics, as well as their inter-relationships has been made thanks to advances in experimental and computational approaches. Despite this gain in fundamental understanding, a complete description of the factors that control these properties has not been achieved. In particular, the characterization of the role of solvent in controlling protein conformational transitions and stability remains to be accomplished [1]. 

Fig. 8 Conformational transition and pKa values of functional groups of polyCEACPhos in aqueous solution. [polyCEACPhos] = 1.4 x 10 molL T = 303 K [245]...

ET reactions controlled by conformational transitions and solvent viscocity... 

Another useful property of APhe is its strong absorption in the near-UV region (=280 nm). This characteristic has been exploited in several studies to probe peptide conformational transitions and helix screw sense changes of chiral switches (26-28). 

An extreme case that has received attention is that of a cooperative conformational transition examplified by the coil-helix (c h) transition that occurs in poly-a-aminoacids. Whereas the polypeptide chain is quite flexible when it exists as a random coil, the rigid helical form may bring about formation of a liquid crystalline phase, as discussed above, if its concentration is sufficient. The conformational transition and the phase transition may therefore be coupled. The helix-coil transition may then acquire the character of a first-order phase transition, owing to generation of the liquid crystalline phase. 

Passing now to a brief examination of some properties of PMA beyond the conformational transition and going back to the interesting point of how stereoregularity influences the equilibrium physicochemical properties of PMA in solution, some recent results deserve comment. Differences in the electrophoretic mobility of isotactic and syndiotactic PMA have been reported (77) indicating that the isotactic form is the slower moving one. 

Insights into the Role of Conformational Transitions and Metal Ion Binding in RNA Catalysis from Molecular Simulations... 

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