Global motions

Elamrani et al. 1996] Elamrani, S., Berry, M.B., Phillips Jr., G.N., McCammon, J.A. Study of Global Motions in Proteins by Weighted Masses Molecular Dynamics Adenylate Kinase as a Test Case. Proteins 25 (1996) 79-88 [Elcock et al. 1997] Elcock, A.H., Potter, M.J., McCammon, J.A. Application of Poisson-Boltzmann Solvation Forces to Macromolecular Simulations. In Computer Simulation of Biomoleeular Systems, Vol. 3, A.J. Wilkinson et al. eds., ESCOM Science Publishers B.V., Leiden... 

Apart from the global motions of the ehains in the film as a whole, one ean eonsider the loeal mobility as a funetion of distanee from the plates. While for e = 0 this mobility is slightly larger near the walls than in the eenter of the film, the opposite is true for large e [16]. This behavior refleets simply the strueture of the density profile for a purely repulsive wall the density is redueed near the wall whereas, for an attraetive wall, a layer of enhaneed density is found elose to the wall. These simulational results are in... 

While the assumption of an isotropic rotational motion is reasonable for low molecular weight chelates, macromolecules have anisotropic rotation involving internal motions. In the Lipari-Szabo approach, two kinds of motion are assumed to affect relaxation a rapid, local motion, which lies in the extreme narrowing limit and a slower, global motion (86,87). Provided they are statistically independent and the global motion is isotropic, the reduced spectral density function can be written as ... 

Although theoretically it would be possible to go from one configuration to another through the global motion of the N system particles, actually the probability that... 

With increasing polymer concentration, we may expect that the polymer global motion changes from the fuzzy cylinder model mechanism to the repta-tion model mechanism. The onset of the crossover should depend on the degree in which the lateral motion of a polymer chain is suppressed by entanglement with its surrounding chains, but it is difficult to estimate this degree. There are some disputes over it in the case of flexible polymers [20]. 

Figure 2.17 Difference between component motion and global motion. Cells found in VI respond to component motion. Cells found in V5 respond to the global motion of objects. (Car image from SmartDraw used by permission from SmartDraw.com.)...

However, during the excited-state lifetime, energy transfer to neighboring molecules and/or local and global motions of the fluorophores can be observed. These two phenomena induce reorientation of the emission dipole, thereby depolarizing the system. Therefore, the value of the measured polarization P will be lower than intrinsic polarization value PQ (Weber, 1952). 

Trylska J, Tozzini V, McCammon JA (2005) Exploring global motions and correlations in the ribosome, Biophys. J. 89 1455-1463... 

In the O-like state the extracellular ends of helices A, B, C, and D are tilted outward, but their cytoplasmic ends are not displaced. Helix E is tilted also, but around a pivot point near its middle, so its extracellular and cytoplasmic ends are displaced outward and inward, respectively. If this structure is indeed like that of the O state, the implication is that the protein undergoes a scissoring motion in the second half of the photocycle. It begins with a splaying of the cytoplasmic side of the seven helical bundle in M, which continues in N but reverses in O and opens the extracellular cavity instead. These suggested large-scale global motions are in sharp contrast with the relatively small (1-2 A) and more local atomic displacements in the first half of the photocycle. The rationale must be that the structure of the protein in the unilluminated state predisposes it to the early reactions in the cycle, but the later reactions require drastically different conformations. 

II. Global Motion in Systems with Many Degrees of Freedom... 

II. GLOBAL MOTION IN SYSTEMS WITH MANY DEGREES OF FREEDOM... 

Figure 1. Schematic description showing that a KAM toms can or cannot block the global motion of a chaotic orbit in low- (left) or high-dimensional (right) phase space.

Up to now we just looked at the topological aspect of the problem and have understood that in systems with many degrees of freedom, KAM tori cannot block the global motion of the system in the entire state space (energy surface). Then how can the system move beyond the KAM tori ... 

Fig. 6.4.5. N powder pattern spectra of [ N ]Trpi3 gramicidin A in a lipid environment as a function of temperature. (A) at 143 K all significant amplitude motions except for methyl and primary amine groups cease. Samples were fast frozen by plunging thin films into liquid propane.

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