4 - Theoretical methods

Summary

Survey of approaches

Given the structure of a protein or nucleic acid (e.g., from X-ray diffraction analysis) and a potential energy function, there are a variety of methods that can be used to study the dynamics of the molecule. In the present section, we mention a number of these methods and briefly indicate their strengths and weaknesses. More detailed descriptions of the potential functions and of several particularly important dynamics methods are given in the following sections. A useful, brief summary of some of these methods has been presented by van Gunsteren & Berendsen (1985).

The simplest method for studying motion in biopolymers is essentially static in nature and involves the characterization of low energy paths for specific motions. This is the method of adiabatic mapping (section 4.5). In this method, one induces a proposed structural change by forcing the primary atoms involved to move along a given path. The remaining atoms are allowed to move so as to reduce or minimize the potential energy of the whole system at each point on the path. These energies are taken to approximate the change in average potential energy that would occur during a real, spontaneous motion, because the shifts in atomic positions during relaxation correspond roughly to structural fluctuations that would facilitate the motion. The method is easy to use, requires only modest computational power, and has been applied to study both local and large scale structural changes.