Oscillatory conformational motions

E-fS ES ES. The standard deviation of the distribution, (Atopen ) = 8.3 2ms, reflects the distribution bandwidth. For the individual T4 lysozyme molecules examined under the same enz unatic reaction conditions, we found that the first and second moments of the single-molecule topen distributions are homogeneous, within the error bars. The hinge-bending motion allows sufficient structural flexibility for the enzyme to optimize its domain conformation the donor fluorescence essentially reaches the same intensity in each turnover, reflecting the domain conformation reoccurrence. The distribution with a defined first moment and second moment shows typical oscillatory conformational motions. The nonequilibrium conformational motions in forming the active enzymatic reaction intermediate states intrinsically define a recurrence of the essentially similar potential surface for the enzymatic reaction to occur, which represents a memory effect in the enzymatic reaction conformational dynamics [12,41,42]. 

An earlier suggestion of Fixman of how to mimic flexibility has been discussed with respect to a system with two degrees of freedom. Harmonic stretching and bending of the bonds of butane in liquid CCI4 has subsequently been allowed transition state theory does not exactly apply as many barrier crossings are reflected by solvent collisions. In a modified molecular dynamics examination of conformational isomerizations in butane the effect of solvent was expressed with a stochastic model in which the Newtonian trajectory was modified by random impulses. The frequency of these impulses, which have a frictional effect upon the trajectory, reduced the value of the transmission coefficient by inducing oscillatory motion at the col. At the inner bonds of decane isomerization rates are less than in butane. 

One of the most popular methods of studying such transitions is dynamic mechanical thermal analysis, DMTA.The sample is subjected to some form of oscillatory distortion, as described in Chapter 10, and its response observed as a function of frequency and temperature. In aU cases, the scale of the motion being observed is relatively local, usually limited to the motion of eight to ten units of the polymer. The shape of the response curve conforms to that of a simple relaxation or a Hmited distribution of relaxation processes. It is only when the polymer is in the melt phase that the longer range motions become apparent. 

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