Sidechain motions sidechains

In the case that the macromolecule is nonspherical or sidechain or segmental motions occur, then the anisotropy will decay as a sum of exponential functions. The work of Kinosita etal. deals with the case in which there are restricted motions. The anisotropy decay function becomes... 

Gelin BR, Karplus M. Sidechain torsional potentials and motion of amino acids in proteins bovine pancreatic trypsin inhibitor. Proc Natl Acad Sci USA 1975 72 2002-2006. 

Poly(n-butyl acrylate). A study of the relaxation properties of PBA was initiated for several reasons. There are two backbone carbons with directly bonded protons thus the effect of the side chain on backbone motion might be determined. Also, the CH carbon should more directly reflect the distribution of correlation times necessary to begin analysis of alkyl sidechain motion. Finally, the lack of the additional chain-CH3 groups significantly loosens motional constraints in PBA. The effect of this on the overall dynamics of PBA was of interest. 

In summary, it appears from spectroscopic studies such as neutron scattering or NMR relaxation measurements which probe rotational water motions on a short time scale, 10 -10 s, and thus over a short distance range that, at the highest water contents, water mobility within the pore of an ionomeric membrane is not drastically different than bulk water mobility. However, as the water content of the membrane decreases, its mobility is increasingly hindered. The nanopore liquid in the membrane is essentially a concentrated acid solution and ion-water (as well as ion-ion) interactions will have significant influences on water motion. Intrusions of sidechains... 

The scenario would envisage that the crystal strain increases in the phenylurethane series such that a blue shift, which is essentially that of the LT to HT transition, would result. The loss of detailed structure occurring on the thermochromic transition to the HT spectrum would result from an extreme increase in disorder which could be mainly attributed to dynamic processes, such as sidechain motions, which are intensified at higher temperatures. A theoretical approach not unlike this has been recently advanced by Schweizer (24). Both weak and strong disorder regimes are considered in that treatment. 

Stochastic dynamics has been found to be particularly useful for introducing simplified descriptions of the internal motions of complex systems. When applied to small systems (e.g., a peptide or an amino acid sidechain) it is possible to do simulations that extend into the microsecond range, where many important phenomena occur. Simulation studies using this method have been carried out, for example, to explore solvent effects on the dynamics of internal soft degrees of freedom in small biopolymers, e.g., the dynamics of dihedral angle rotations in the alanine dipeptide (see Chapt. IX.B.l). 

For some problems, such as the motion of heavy particles in aqueous solvent (e.g., conformational transitions of exposed amino acid sidechains, the diffusional encounter of an enzyme-substrate pair), either inertial effects are unimportant or specific details of the dynamics are not of interest e.g., the solvent damping is so large that inertial memory is lost in a very short time. The relevant approximate equation of motion that is applicable to these cases is called the Brownian equation of motion,... 

The fluctuations of atoms and the motions of sidechains in proteins have been examined experimentally and theoretically. In this section we characterize these two types of motions in terms of their amplitudes, time scales, and other properties by describing a series of theoretical studies related to them. Some results on the functional roles of specific atomic and sidechain motions are also presented. Comparisons with experiment are provided, where available a more detailed analysis of the experimental measurements is given in Chapt. XI. 

The motions of sidechains in proteins play an important role in their dynamics. The time scales involved range from picoseconds for local oscillations in a single potential well to milliseconds or longer for some barrier crossings, such as the 180° rotations (ring flips ) of aromatic sidechains. This range of motions makes it necessary to use a variety of theoretical approaches in the analysis of sidechain dynamics they include molecular dynamics, activated dynamics, and stochastic dynamics (see Chapt. IV.). There are a number of well-characterized examples where sidechain motions have been shown to play a specific role in protein function. 

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