Millisecond enzyme dynamics

The data of Fig. 15.10 are remarkable in showing that there exists a number of fast processes previously unresolved in studies of enzymic dynamics. It is clear that the minimal number of steps shown above is not sufficient to explain the kinetic data. In general, the minimal number of species in a kinetic model of the data is equal to one more than the number of observed relaxation rates. Hence, the data can be fit by four processes involving five species. We believe that none of the transients correspond to the reaction LDH/NADH —> LDH + NADH because we have measured this reaction [49], and none of the events of the binding reaction correspond to any of signals shown in Fig. 15.10. The dissociation of pymvate from LDH/NADH would be observed on the millisecond time scale. Taking a binding constant of 0.27 mM and the bimolecular rate constant of 8.33 x 10 s yields a... 

Pisliakov AV, Cao J, Kamerlin SCL, Warshel A (2009) Enzyme millisecond conformational dynamics do not catalyze the chemical step. Proc Natl Acad Sci USA 106(41) 17359-17364... 

The long lifetime of phosphorescence allows it to be used for processes which are slow—on the millisecond to microsecond time scale. Among these processes are the turnover time of enzymes and diffusion of large aggregates or smaller proteins in a restricted environment, such as, for example, proteins in membranes. Phosphorescence anisotropy is one method to study these processes, giving information on rotational diffusion. Quenching by external molecules is another potentially powerful method in this case it can lead to information on tryptophan location and the structural dynamics of the protein. 

Bph. Enzymes in the Bph QA- state accumulates at 100 K and undergo an irreversible change between 100 K and 200 K. It was shown (Kotel nikov et al., 1983b Likhtenshtein, 1993) that within this temperature range the phosphorence probes detect animation of millisecond dynamics in the RC. 

Recent single-molecule experimental studies of proteins provide more detailed views of protein motions, and confirm that a wide variety of timescales is involved in, e.g., catalytic action of enzymes [7,14,15,19,33], Of course, molecular dynamics simulations have been used to probe motions in single proteins for many years, and advances in both theory and computational science have made simulations a powerful approach to building theoretical understanding of protein dynamics [1], The recent introduction of accelerated molecular dynamics methods is helpful in this context [11]. Although detailed dynamical information is sacrificed to the enhanced sampling of conformational space in these methods, which have been shown to access conformational fluctuations that are revealed by nuclear magnetic resonance experiments on the millisecond... 

Enzyme turnover often occurs on the millisecond timescale, and it is reasonable to assume that turnover should represent the upper limit for the time constants of conformational transitions linked to catalysis [54]. As a consequence, any conventional timescale HX measurement of dynamics in an... 

---