Abstract
Conformational fluctuation is usually the key characteristic of the bio-molecular system, and many kinds of elements from bio-molecules themselves and surroundings can affect this fluctuation. Flexibility is a typical feature of the bio-molecules, and it can also be easily affected by the surroundings. As flexibility is regarded to connect with the conformational fluctuation, it becomes an important entrance to analyze the behavior of the bio-molecules. It is known that the typical kinetic characteristics of bio-molecules are mainly controlled by the rate constant, and these properties are usually dominated by surrounding conditions and configuration features of bio-molecules. We have studied the migration rate of bio-molecules by using the two-dimensional (2D) free-energy landscape and the 2D model that includes the extension coordinate and conformational variable in this work. The 2D generalized Langevin equation with a fractional Gaussian noise or white noise matrix is adopted to reveal the key qualities of the bio-molecular system. The reaction temperature and its flexibility (∆k‡) have been particularly analyzed, and these factors can affect the mean waiting time significantly. Particular attention is paid to distinguish typical discrepancies between normal diffusion and dynamic disorder situations. Our results show that the important conditions from complex surroundings cannot be neglected, and they can be the important factors that affect the kinetic behavior of bio-molecules seriously.
Highlights
The study of kinetic properties of bio-molecules1–3 in complex surroundings has become more popular
Kramers’ theory4 based on the generalized Langevin equation (GLE)5,6 is a reliable theory, which can be used to obtain the key information from the pulling experiments, and the details of the dynamic behavior of the bio-molecules can be estimated
FGn must be needed in the kernel for calculation if the non-Markovian characteristic and conformational fluctuation can be clearly detected
Summary
The study of kinetic properties of bio-molecules in complex surroundings has become more popular. Kramers’ theory based on the generalized Langevin equation (GLE) is a reliable theory, which can be used to obtain the key information from the pulling experiments, and the details of the dynamic behavior of the bio-molecules can be estimated. Unlike Bell’s model and Zwanzig’s work, this theory can provide more important information to evaluate the influence from surroundings, such as the flexibility (∆k‡) of bio-molecules, which is usually considered to be affected by sharp collision from other molecules in the whole surroundings. As the DD phenomenon and affection from ∆k‡ cannot be neglected, it is important to build a two-dimensional (2D) freeenergy model to study the characteristics of bio-molecules. Motivated by the typical factors (∆k‡ and temperature), we have aimed to use the 2D model to analyze the dynamic characteristics of bio-molecules. IV, and the key nature of the bio-molecular system is described
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