Conformer fluctuations, rate

It is interesting to compare the fluctuation rate vn for mobile conformations characterized by two or more positions with the molecular dislocations taking place in the... 

Of the mechanistic issues dealt with in the full study (including kinetic trade-off s between different Co-+ spin states in the reaction product and the role of solvent and conformational fluctuations of the DBA system), we focus here on the activation parameters and related nuclear tunneling and entropy effects which are crucial for establishing meaningful contact with the Arrhenius parameters obtained from the experimental rate data [158]. The theoretical analysis also led to new insights... 

This equilibrium conformational fluctuation is again a general phenomenon that occurs in every system that we have studied, taking place at the same time scales at which we observed the enzymatic rate fluctuations. Such... 

Forming loops and tails - these monomeric units have the freedom of a random rotation. Conformational fluctuations are restricted by fixed points on the filler s surface. The relaxation rate of these units, O[, is reduced according to the equation =o /< > where is the mean number of skeletal bonds in one loop. With this relationship the relaxation rate decreases with the number of units in the loop. These units behave in a manner similar to polymer gels. 

Let us assume that a variable A(t) is coupled to the reaction coordinate and that (A) is its mean value. If a measurement of some property P depends on (A), but not on the particular details of the time dependence of A(t), then we will call it a statistical dependence. If the property P depends on particular details of the dynamics of A(t) we will call it a dynamical dependence. Note that in this definition it is not the mode A(t) alone that causes dynamical effects, but it also depends on the timescale of the measured property P. Promoting vibrations (to be discussed in Sections 2-4) are a dynamic effect in this sense, since their dynamics is coupled to the reaction coordinate and have similar timescales. Conformation fluctuations that enhance tunneling (to be discussed in Section 5) are a statistical effect the reaction rate is the sum of transition state theory (TST) rates for barriers corresponding to some configuration, weighted by the probability that the system reaches that configuration. This distinction between dynamic and statistical phenomena in proteins was first made in the classic paper of Agmon and Hopfield.4 We will discuss three kinds of motions ... 

Section 7.3.1 describes the experimental apparatus for collecting and analyzing fluorescence lifetime data vs temperature. Section 7.3.2 presents the results of lifetime measurements of polyproline peptides and MD simulations to (a) relate fluorescence quenching rates to specific conformational fluctuations, and (b) calculate the implications of intramolecular electrostatic interactions for the quenching mechanism. 

Slow conformational fluctuation was characterized by the difference decay rates (Rcc) ofDQC and ZQC selected by CPMG experiments [98,99]. The relaxation rates, DQC = (>2)(N H + N H ) and ZQC =(>2) (N H + N H ), depend on the pulse repetition rate if there are local motions on slow timescale (ps—ms). This dispersion effect occurs when the two nuclei experience slow correlated modulations of the isotropic chemical shifts. The difference of the decay rates, Rcc, is the sum of chemical shift anisotropy cross-correlation (CSA/CSA) and isotropic chemical shift modulation (CSM/CSM) as well as additional dipole/dipole crosscorrelation (DD/DD) contributions due to coupftngs to neighbouring nuclei ... 

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