Conformationally gated rate processes in biological macromolecules

The concept of gating has been applied to the theoretical description of ra te processes coupled to conformational rearrangements of biological macromo lecules both out of equilibrium and near equilibrium The out-of-equilibrium rearrangements are discussed in terms of requirements imposed by the compl exity of biomolecules. These include (i) a variety of relaxation time scale s for different degrees of freedom, (ii) constraints arising from their int eractions, and (iii) the hierarchy of conformational substates. The simples t possible model that satisfies the requirements i-iii is developed. The mo del suggests that the motion along the reaction,coordinate is gated by slow er degrees of freedom. We show that under this assumption dynamics of the r eaction coordinate resembles anomalous (non-Gaussian) diffusion. Expression s for observables derived within our model predict (i) a suppression of rea ction coordinate dynamics in biomolecules imbedded in rigid matrixes, (ii) a transition from the familiar Debye exponential relaxation to the Kohlraus ch-Williams-Watts relaxation described by a stretched exponential, and (iii ) distinct temperature dependencies of relaxation:rates for these relaxatio n processes; The experimental data on Ligand binding to myoglobin support p redictions i and ii. Coupling of rate processes to local conformational rea rrangements near equilibrium has also been studied. As a particular example of such processes, we consider hole injection and transport in DNA molecul ar wires. Our treatment suggests that fluctuations in the mutual arrangemen t of base pairs in the stack can serves as a gate for both processes. This explains the unusual temperature dependence of the voltage gay found experi mentally for poly(guanine)-poly(cytosine):molecular wires. The diffusion co efficient of holes and their mobility as a function of temperature are esti mated for base pair stacks of varying structure.