Molecular dynamics simulations
نویسنده
چکیده
Large biological molecules are frequently represented by a single three-dimensional structure, but in reality, under physiological conditions, they are dynamic entities in constant motion. One important theoretical technique for analyzing both motions and energetics and the roles they play in macromolecular structure and function is a form of simulation termed molecular dynamics. The field of organic chemistry has been extraordinarily successful in using the structures of small organic molecules to rationalize their stability, reactivity, and product distributions. But in biology, the situation for proteins, nucleic acids and other large biomolecules is complicated by two issues. Firstly, there are so many interactions contributing to the stability of a macromolecule that it is usually impractical to attempt to assess the relative favorability of a structure by inspection. Secondly, in addition to structure, motion is important for biological function; methods to examine the important motions accessible at room temperature are needed. Molecular dynamics addresses both of these issues through use of detailed physical models that describe the energy of any molecular conformation, coupled with methods to integrate the appropriate equations of motion (such as Newton’s equations) to produce a movie showing the molecule in motion (see Fig. 1). The resulting computer models respond appropriately when manipulated — pushing on a deformable portion of the molecule causes it to change shape more, whereas pushing with equal force on stiff portions results in less motion. These models for large biological molecules have been under continuous development, testing and application since the 1970s and are now standard tools in a number of research areas.
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عنوان ژورنال:
- Current Biology
دوره 7 شماره
صفحات -
تاریخ انتشار 1997